BIOL 1403                     Test #2                                     _____________
FALL 1998                    100 points                               Essay Numeral
DR. DINI                         FORM

Part I (60 points): Choose the letter representing the BEST response to each test item. There should only be one BEST response for each (2 points each). Ace it!

1. Which lipids are important components of eukaryotic membranes?
             1. Triglycerides
             2. Prostaglandins
             3. Cholesterol molecules
             4. Phospholipids
(a) 4 only     (b) 1&3     (c) 2&4     (d) 3&4     (e) 2,3&4

2. Polymers of glucose can vary from one another in all of the following, EXCEPT:
(a) the arrangement of the -H and -OH groups that are attached to carbon #1 on individual glucose molecules.
(b) the degree of branching exhibited by each type of polymer.
(c) the side groups that are attached to carbon #2 on individual glucose molecules.
(d) whether individual glucose molecules are in their linear or ring configuration.

3. What is true of steroid hormones? They:
(a) have a C-terminus and an N-terminus.
(b) are able to pass through membrane bilayers by diffusing through them.
(c) are composed of amino acids.
(d) are based on modified prostaglandin molecules.
(e) are effective only locally, i.e. in the neighborhood where they are synthesized.

4. Which pair should NOT be found together in the same living cell?
(a) glycogen granules:chloroplasts     (d) glycogen granules:mitochondria
(b) starch granules:chloroplasts          (e) starch granules:central vacuole
(c) starch granules:mitochondria

5. DNA polymerase molecules are to DNA replication as _____ are to translation.
(a) RNA polymerase molecules    
(b) chromosomes                       
(c) ribosomes
(d) molecules of the transforming principle
(e) spliceosomes

6. Which of these is/are NOT generally performed by prokaryotes?
             1. DNA replication
             2. Mitosis
             3. RNA processing
             4. Transcription
             5. Translation
(a) 2 only     (b) 1&3     (c) 2&3     (d) 3&5     (e) 1,4&5

7. In eukaryotes, spliceosomes act on mRNA transcripts by removing _____, and by adding _____ to the ends of the transcript.
(a) exons, GTP cap & Poly-A tail     (d) introns, GTP cap & Poly-A tail
(b) exons, termination sequences    (e) introns, exons
(c) thymines, uracils

8. DNA "proofreading" is performed by _____, with the result that the number of _____ mutations is reduced.
(a) DNA polymerases, spontaneous     (d) DNA ligases, spontaneous
(b) DNA ligases, induced                       (e) DNA polymerases, induced
(c) RNA polymerases, induced

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The next five questions are based on the drawing and description below:

The following drawing represents an enzyme that is embedded in a plasma membrane. The arrow labeled "Y" is pointing at the enzyme’s active site.

Formatting problems prevent this figure from appearing here.

9. What should be true of portions of the protein that are located in areas V & X?
(a) Most amino acids there have R groups that are either polar or charged.
(b) Hydrophobic R groups predominate in these areas of the protein.
(c) Secondary structures should be especially common there.
(d) all three of these are true
(e) only b & c are true

10. If a hypothetical chemical undergoes reversible bonding to the area labeled "Z" and causes the enzyme to operate more effectively when bonded there, then this chemical is most properly identified as:
(a) the substrate.         (d) an allosteric inhibitor.
(b) a cofactor.              (e) an allosteric stimulator.
(c) an allosteric site.

11. Assume that this protein cannot undergo conformational changes. What other feature of this protein should prevent it from permitting the facilitated diffusion of a particular chemical through it?
(a) It is not a transmembrane protein. 
(b) lack of ATP.
(c) its attachment to intracellular microfilaments.
(d) its interior is completely hydrophobic.

12. This protein has a single N-terminus and a single C-terminus. From this what is the highest level of structure that can be assigned to this protein?
(a) primary (b) secondary (c) tertiary (d) quaternary (e) quintenary

13. What type of bond/interaction should be abundant in the portion of the protein that is within area W?
(a) disulfide bonds                                                     (d) electrical interactions
(b) hydrogen bonds involving backbone elements (e) phosphodiester bonds
(c) hydrogen bonds between R groups

~~~~~~

14. Both replication and transcription involve the breaking of _____ bonds in DNA. In replication, this is catalyzed by _____, whereas in transcription it is catalyzed by _____.
(a) phosphodiester. DNA ligase, RNA polymerase
(b) hydrogen. helicase, heat
(c) phosphodiester. DNA polymerase, RNA polymerase
(d) hydrogen. DNA polymerase, RNA polymerase
(e) hydrogen. helicase, RNA polymerase

15. What is true about enzymes?
(a) They eliminate the activation energy needed to initiate chemical reactions.
(b) They all work optimally at temperatures around 36 °C.
(c) "Induced fit" is a term that describes an enzyme’s response to substrate in its active site.
(d) A mutation in the gene that codes for an enzyme will always reduce that enzyme’s effectiveness.
(e) The true substrate molecule normally bonds to the allosteric site.

16. An RNA primer must be in place within DNA polymerase III’s active site before DNA pol III can catalyze the polymerization of DNA. Accordingly, the RNA primer best fits the description of:
(a) the substrate.             (d) a competitive inhibitor.
(b) a cofactor.                  (e) an allosteric inhibitor.
(c) an allosteric enzyme.

17. In trying to determine whether DNA or protein was the genetic material, Hershey and Chase made use of which of the following facts?
(a) DNA does not contain sulfur, whereas protein does.
(b) DNA does contain phosphorus, whereas protein does not.
(c) DNA contains greater amounts of phosphorus than does protein.
(d) Protein contains greater amounts of sulfur than does DNA.
(e) Both a & b                                                         [submitted by RL]

18. In prokaryotes and eukaryotes, the primary structure of a polypeptide is ultimately determined by the _____, and is directly held together by _____ bonds.
(a) sequence of nucleotides in DNA, peptide
(b) sequence of nucleotides in DNA, phosphodiester
(c) sequence of nucleotides in RNA, ionic
(d) rules of protein folding overriding the chaperone proteins, disulfide
(e) rules of protein folding in concert with chaperone proteins, hydrogen

19. The product of primase activity is most similar to the product of _____ activity.
(a) DNA polymerase     (c) DNA ligase
(b) RNA polymerase     (d) helicase

20. What can be true of a mRNA transcript that lacks a Poly-A tail?
             1. It may not be able to exit the nucleus.
             2. If it enters the cytoplasm, it may quickly be degraded.
             3. It may be prokaryotic mRNA.
             4. It has fewer ribonucleotides than if it had a Poly-A tail.
(a) 1 only     (b) 1&2     (c) 2&3     (d) 1,3&4     (e) all of these

21. Linus Pauling believed that protein, not DNA, would be found to be the genetic material because:
(a) DNA is not found in the nucleus.
(b) proteins have great functional diversity.
(c) proteins have great structural diversity, being composed of 20 different monomers, compared to the 4 monomers found in DNA.
(d) both b & c are true.
(e) On the contrary, Linus Pauling initially believed that DNA was the genetic material.                                                                                                                                                                                         [submitted by BD, modified]

22. During prokaryotic DNA replication, all of these should be more active/prevalent on the lagging strand than they are on the leading strand, EXCEPT:
(a) helicase.                         (d) DNA polymerase I.
(b) Okazaki fragments.       (e) RNA primers.
(c) DNA ligase.

23. What is NOT true of mRNA?
(a) It is the only type of RNA that is translated into an amino acid sequence.
(b) It is known to act as a ribozyme.
(c) It features a ribosome binding sequence at its 5’ end.
(d) In eukaryotes, it undergoes processing between its transcription and its passage out of the nucleus.
(e) It is constructed upon a DNA template.

24. In both prokaryotes and eukaryotes, what is true of the polymerization of ALL nucleic acids? It:
(a) proceeds with 5’ to 3’ directionality.     (d) produces double helices.
(b) occurs in the nucleus.                             (e) produces Okazaki fragments.
(c) requires deoxyribonucleotides.

25. Translation directly involves all of these, EXCEPT:
(a) initiation factors.     (d) rRNAs.
(b) mRNA.                     (e) snRNAs.
(c) tRNAs.

26. Which feature explains the spatial and temporal separation between transcription and translation in eukaryotes?
(a) histone proteins         (d) the large number of ori’s on each chromosome
(b) introns                         (e) the existence of 3 different types of RNA polymerase
(c) nuclear envelope

27. Which is NOT included in the "Central Dogma of Molecular Biology"?
(a) RNA-directed* synthesis of DNA (d) polypeptide-directed synthesis of RNA
(b) DNA-directed synthesis of RNA (e) DNA-directed synthesis of DNA
(c) RNA-directed synthesis of polypeptides
(* i.e. RNA acts as the template)

28. Upon chemical analysis, a particular protein was found to contain 400 amino acids. Exons were found to comprise 10% of the corresponding gene. How many peptide bonds would be found in this protein, and how many base pairs would have been found in the complete original gene?
(a) 399, 120,000             (d) 400, 120,000
(b) 399, 12,000               (e) 400, 12,000
(c) 399, 1,200                                                                                                          [submitted by RL, modified]

From the Textbook........

29. Chaperone proteins assist in:
(a) guiding mature mRNA transcripts to waiting ribosomes.
(b) catalyzing the linkage of amino acids to the proper tRNA molecules.
(c) guiding amino acids to the site of protein synthesis.
(d) helping certain proteins into their final conformation.
(e) removing histone proteins from eukaryotic chromosomes in advance of the arrival of the replisome.

30. To practicing biologists, the significance of the (near) universality of the genetic code is:
(a) a miraculous coincidence, about which they are at a loss for words.
(b) that it provides evidence that God(s) was/were very proud of this creation.
(c) that it evolved very early in the history of life and Earth and has been highly conserved throughout evolutionary history.
(d) the finding that most amino acids are coded by more than one codons.
(e) that all organisms on Earth share the same proteins.

Proceed to Part II and read the directions.

PART II (40 points). Write the numeral stamped on these pages in the essay numeral space on the cover of your test booklet. Using ink, answer both of these essay questions neatly, logically, completely, concisely and in well-organized paragraph format. You may use both sides of the paper (20 points each).

1a. Given the sequence of the non-sense strand of DNA found below and a copy of the genetic code, show all of the intervening sequences needed to finally determine the sequence of amino acids in the corresponding polypeptide, and be sure to give the sequence of amino acids too.

Non-Sense DNA: C G C C A T A C C A A G T T T

Sense DNA: G C G G T A T G G T T C A A A

mRNA: C G C |C A U |A C C |A A G| U U U

amino acid: Arg - His - Thr - Lys - Phe

1b. If (1a) was answered correctly, you created three separate sequences in 3 steps. In life, each of these steps is catalyzed by something. For each step, describe the chief catalytic agent, being sure to include what materials are needed by each agent to successfully catalyze the polymerization of the particular polymer.

2. How do ribozymes affect the ability of eukaryotic cells to synthesize the correct polypeptides, i.e. those with the proper sequence of amino acids?

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                            Test #2                                               _____________
FALL 1999                                          100 points                                          Essay Numeral
DR. DINI                                               FORM 1

Part I.  Choose the letter representing the BEST response to each item.  There should be only one BEST response to each (2 points each, except where indicated).  Kick arse!

1. The various polymers of glucose can differ from each other in the:
                                                     1.         type of glucose involved.
                                                     2.         degree of branching involved.
                                                     3.         number of glucose molecules involved.
                                                     4.         type of glycosidic linkage that bonds them together.
(a) 1 & 2            (b) 1 & 4            (c) 2 & 3            (d) 2, 3 & 4        (e) All of these can differ

2. Which of these is primarily used as a structural carbohydrate?
            (a) sucrose                    (d) chitin
            (b) amylose                   (e) glycogen
            (c) amylopectin

3. An individual performs strenuous physical activity for 6 hours on an empty stomach, depleting his/her entire glycogen store, and losing 4 gm of body mass in the process.  Working without eating for another 6 hours, only fat is burnt for energy.  Assuming that an equal number of calories were used during the second 6-h period as during the first, about how much body mass was lost during the second 6-h period?
            (a) 1/2 gm         (b) 2 gm            (c) 4 gm            (d) 6 gm            (e) 8 gm

4. All of these are generally true of lipids, EXCEPT the statement that they:
            (a) are hydrophobic or amphipathic, but not hydrophilic.
            (b) contain less oxygen than does the same mass of carbohydrate.
            (c) can be used to provide energy for the synthesis of ATP.
            (d) have less structural diversity than carbohydrates.

5. R-groups are to polypeptides as _____ are to nucleic acids.
            (a) nucleotides               (d) nitrogenous bases
            (b) amino acids              (e) phosphate groups
            (c) pentose sugars

6. Which of these are NOT bonds that directly involve R-groups?
            (a) peptide bonds                       (d) disulfide bonds
            (b) ionic bonds                           (e) hydrogen bonds
            (c) hydrophobic interactions

7. All of these are true of regions of proteins that are rich in a-helices, EXCEPT:
            (a) in aqueous environments, these regions should be found on the protein’s exterior.
            (b) the same regions should be rich in hydrogen bonds between backbone elements.
   
         (c) the amino acids in this region should mostly be non-polar and/or electrically neutral.
            (d) they may also be the general locations of pleated sheets.

8. A polypeptide is to a quaternary-level protein as a _____ is to a DNA double helix.
            (a) mRNA polynucleotide            (d) deoxyribonucletide
            (b) DNA polynucleotide               (e) polysaccharide
            (c) ribonucleotide

9. Helicobacter pylori is a bacterium that can infect human stomachs, and which has been found to be the cause of most cases of gastric (stomach) ulcers.  Which graph of enzyme activity provides the closest match with the activity levels of this bacterial species’ enzymes?

Formatting problems prevent this figure from appearing here.

~~~~~~~~~~~                   

10. What is true of the primary level of protein structure?
            (a) In retroviruses, it is ultimately determined by the sequence of ribonucleotides.
   
         (b) It is maintained by hydrogen bonds that link the amine group of one amino acid to the acid group of another amino acid.
            (c) It can be changed by mutations that occur well inside of introns.
            (d) By disrupting it, one kills the protein.
            (e) It requires secondary structures in order to remain intact.

11. The substrates of reverse transcriptase enzymes are free:
            (a) ribonucleotides.                     (d) retronucleotides.
            (b) amino acids.                          (e) fatty acids.
            (c) deoxyribonucleotides.

12. A hypothetical enzyme is prevented from catalyzing its reaction when chemical X bonds to, and removes from solution, all of the enzyme’s cofactor molecules by a potentially reversible reaction.  Chemical X is best described as a(n):
            (a) substrate.                             (d) non-competitive inhibitor.
            (b) poison.                                 (e) allosteric inhibitor.
            (c) allosteric activator.

13. An enzyme requires a re-usable cofactor in order to catalyze a reaction.  By what means could one determine whether this particular enzyme-catalyzed reaction is running to completion?  Over time, one could measure the amount of:
                                                            1.         enzyme present
                                                            2.         substrate present
                                                            3.         product present
                                                            4.         cofactor present
            (a) 1 only           (b) 2 only           (c) 4 only           (d) 1 or 4           (e) 2 or 3

14. To which feature of DNA structure are Chargaff’s rules most closely associated?
            (a) consistent diameter of the molecule
            (b) anti-parallel nature of the molecule
            (c) type of covalent bond that links the nucleotides
            (d) whether or not an –OH group is present on the pentose’s #2 carbon
            (e) number of base pairs in each complete turn of the double helix

15. Avery, MacLeod and McCarty performed many repetitions of their experiments; repetitions which, in hindsight, turned out to be unnecessary.  These unnecessary repetitions were actually the result of:
            (a) using DNA that was contaminated by protein.
            (b) using proteins that were contaminated by DNA.
            (c) authoritarianism affecting the conduct of scientists.
            (d) Both a & b are true.
            (e) Both b & c are true.

16. If prokaryotic DNA were parallel, rather than anti-parallel, then what other change would be necessary (assuming that the 5’ to 3’ rule still applies) in order to replicate all of the chromosome’s DNA? (HINT: Draw a picture.)
            (a) The order in which DNA polymerase III and DNA polymerase I work on a given stretch of DNA would have to be reversed.
            (b) Replication would have to proceed unidirectionally, instead of bidirectionally.
            (c) More than one origin of replication would be required.
            (d) Telomeres would have to be temporarily removed.
            (e) Several replisomes would be required, one following the other, like trucks in a convoy.

17. Which does NOT belong?
(a) lagging strand                                    (d) intense DNA ligase activity
(b) Okazaki fragments                            (e) continuous DNA replication
(c) intense use of RNA primers

18. Which of these play prominent roles during eukaryotic, but NOT during prokaryotic, transcription?
            (a) RNA polymerases                  (d) transcription factors
            (b) free ribonucleotides               (e) spliceosomes
            (c) ribosomes

Match the four descriptions on the left with the type of bond listed on the right (1 point each).  All should be used.

19. Bonds broken by helicase.                                                        (a) peptide bonds
                                                                                                            (b) disulfide bonds
20. Bonds whose formation is catalyzed by DNA ligase.             (c) hydrogen bonds
                                                                                                             (d) phosphodiester bonds
21. Covalent bonds between amino acid R groups.

22. Bonds whose formation is catalyzed by rRNA.

~~~~~~~~

23. If an exon within the gene coding for the enzyme that catalyzes the addition of the Poly-A tail were to experience an uncorrected proofreading error, then which of these would most likely result first?
            (a) Ribosomes would be unable to attach to mRNA.
            (b) Replisomes would be unable to attach to origins of replication.
            (c) mRNA molecules would be hydrolyzed within the nucleus.
            (d) The nucleolus would immediately cease the synthesis of rRNA.
            (e) Mature mRNA transcripts would be just as long as the corresponding pre-mRNA transcripts.

24. What is true of prokaryotic mRNA, but untrue of eukaryotic mRNA?  Prokaryotic mRNA:
            (a) has little protection against degradation by ribonucleases.
            (b) has introns, but they are not removed.
            (c) can participate in polyribosomes.
            (d) translation must be delayed until its transcription is complete.
            (e) undergoes intensive processing before it is translated.

25. During the initiation phase of translation, which of these bonds to mRNA’s ribosome binding sequence first?
            (a) the initiator tRNA                                (d) proteins located in the small subunit
            (b) rRNA located in the small subunit    (e) proteins located in the large subunit
            (c) rRNA located in the large subunit

26. Which of these is directly and crucially involved in DNA replication, RNA transcription, ribosome-to-mRNA bonding and amino-acyl tRNA-to-mRNA bonding?
            (a) complementary base pairing               (d) synthesis of phosphodiester bonds
            (b) proofreading                                          (e) transcription factors
            (c) the 5’ to 3’ rule

27. Which of these enzymes are used in both mismatch and excision repair of DNA?
                                                            1.         Primases
                                                            2.         DNA polymerases
                                                            3.         DNA ligases
                                                            4.         RNA polymerases
            (a) 1 only           (b) 2 only           (c) 1 & 3            (d) 2 & 4            (e) 2, 3 & 4
                                                                                                         [submitted by AS, modified]

28. What is the correct sequence in which amino-acyl tRNAs, other than the initiator tRNA, encounter these sites on the large ribosomal subunit?
                                                            1.         E site
                                                            2.         P site
                                                            3.         A site
            (a) 1,2,3            (b) 3,2,1            (c) 1,3,2            (d) 3,1,2            (e) 2,3,1

29. A substitution mutation involving an exonic DNA base that corresponds to the third base of a mRNA codon often has no affect on the corresponding polypeptide.  This observation is most easily accounted for by the:
            (a) observation that exons are removed from eukaryotic RNA.
            (b) unimportance of that particular polypeptide.
            (c) redundancy of the genetic code.
            (d) high likelihood of a reverse mutation at that same location.
            (e) ribosome changing its reading frame so as to skip over the incorrect nucleotide.

30. Telomeres are an adaptation that helps cells cope with the:
(a) circular nature of prokaryotic genomes, which requires that some site be identified as the place where replication should end.
            (b) need to balance the density differential created by the centromeres.
            (c) inability of DNA polymerases to catalyze the synthesis of new DNA without a DNA template.
            (d) inability of DNA polymerases to catalyze the synthesis of new DNA without a RNA template.
   
         (e) inability of DNA polymerases to catalyze the synthesis of new DNA without a previously    existing piece of nucleic acid that they can extend.

31. Theoretically, which of these cells should have NO need of functional telomerases?
                                             1.         prokaryotic cells
                                             2.         eukaryotic cells permanently in a non-dividing (G0) state
                                             3.         eukaryotic cells progressing rapidly through cell cycles
                                             4.         eukaryotic cells with defective DNA polymerases
            (a) 1 only           (b) 1 & 2            (c) 1, 2 & 4        (d) 1, 3 & 4        (e) 2, 3 & 4

32. If release factor were to become permanently bonded to its correct site on the ribosome, then it would be to the ribosome as a _____ is to an enzyme.
            (a) cofactor                    (d) competitive inhibitor
            (b) substrate                  (e) non-competitive inhibitor
            (c) poison

Proceed to Part II and read the directions.

Part II.  Using ink, and writing in paragraph format, answer both essay questions neatly, logically, completely, concisely and in well-organized fashion (20 points each).

1a. Using a copy of the genetic code and the sequence of amino acids below, present and label all of the sequences needed by one who wishes to determine the corresponding nucleotide sequence of the non-transcribed DNA strand.  If done correctly, you ought to perform three steps.

 

Amino Acid Sequence:            Trp – Trp --  Met – Met – Trp

 

1b. Regarding each of these three steps in the order in which they were performed by you, explain (for Step 1) why this step cannot occur in nature, (for Step 2) which biological entity can perform this process, what accounts for its unique ability to do so, and the significance of this ability for human health, and (for Step 3) the time during the cell cycle when this process occurs, and the significance of this activity for the cell(s) that perform(s) it.

2. Explain the importance of controlling metabolic pathways in living organisms, and explain how allosteric enzymes act to achieve this control.

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                         Test #2                                         _____________
FALL 2000                                         100 points                                   Essay Numeral
DR. DINI                                             FORM 1

Part I. (60 points) Choose the letter representing the BEST response to each item. There should be only one BEST response to each (2 points each, except where indicated). Dominate!

1. All are true of prostaglandins, EXCEPT:
(a) Their primary source is the prostate gland.
(b) They have two fatty acid tails extending from a 5-carbon ring.
(c) They generally act as local, or tissue, hormones.
(d) Their intracellular site of synthesis should be the sER.

2. To catalyze the hydrolysis of triglyceride into glycerol and fatty acids, lipase, will require _____ molecules of _____.
(a) 2, ATP     (b) 3, ATP     (c) 2, H2O     (d) 3, H2O     (e) 2, AMP

3. Many animals can hydrolyze starch; none can hydrolyze cellulose. The best explanation for this observation is:
(a) starch is composed of a hexose, whereas cellulose is composed of a pentose, and animal enzymes are adapted only for polymers of hexose.
(b) animals don’t have enzymes that can hydrolyze glycosidic bonds between alpha-glucose molecules.
(c) the geometry or chemistry of glycosidic bonds between beta-glucose molecules does not match the active site of enzymes found in animals.
(d) cellulose is made of a sugar that has more double bonds than has the sugar found in starch.
(e) cellulose has a lower energy of activation than has starch.

4. It is harder to lose weight by hydrolyzing fats than it is by hydrolyzing carbohydrates because:
(a) fats have twice as many calories per unit mass as have carbohydrates.
(b) carbohydrates have twice as many calories per unit mass as have fats.
(c) carbohydrates have 1/2 as many calories per unit mass as have fats.
(d) fats have 1/4 as many calories per unit mass as have carbohydrates.
(e) Two of these are true.

5. During translation, polypeptides are built as _____ reactions are catalyzed by _____ creating _____ bonds.
(a) dehydration synthesis, rRNA, peptide   (d) dehydration synthesis, ribozymes, disulfide
(b) condensation,rRNA, hydrogen                (e) hydrolysis, peptidyl transferase, disulfide
(c) hydrolysis, peptidyl transferase, peptide

6. Which of these enzymes can use an RNA template to direct the synthesis of DNA?
1. RNA polymerase
2. Telomerase
3. DNA polymerase I
4. Primase
5. Reverse transcriptase
(a) 1 only     (b) 3 only     (c) 1 & 5     (d) 2 & 5     (e) 2, 4 & 5

7. Proteins are:
(a) synonymous with polypeptides.
(b) encoded by sequences of nucleotides in the genome.
(c) composed of long chains of fatty acids.
(d) synthesized at the nucleolus.
(e) More than one is true.

8. Which chemical group participates in the covalent bonds that are directly involved in maintaining tertiary and quaternary levels of protein structure, but NOT primary or secondary levels of structure?
(a) –H+         (b) –OH-         (c) –SH         (d) –COOH         (e) –NH2

9. All are true statements about ribozymes, EXCEPT that they:
(a) can catalyze reactions in biological systems.
(b) are composed of amino acids.
(c) have monomers that are linked by phosphodiester bonds.
(d) some function inside the nucleus; others in the cytoplasm.
(e) contain uracil.

10. A hypothetical hydrolysis reaction requires 2.7 kcal of activation energy to bring the reactants to their transition states when no enzymes are involved. When the same reaction is enzyme-catalyzed, the amount of energy required might well be:
(a) 0 kcal         (b) 1.0 kcal         (c) 2.7 kcal         (d) 3.0 kcal         (e) 5.4 kcal

11. Enzymes that catalyze dehydration synthesis reactions can do so by:
1. stressing covalent bonds in the substrate.
2. introducing the substrate to a chemical environment that favors reaction.
3. bringing substrate molecules into close proximity for reaction.
4. bringing substrate molecules together in correct orientation for reaction.
(a) 1 only         (b) 1 & 2         (c) 2 & 3         (d) 3 & 4         (e) 2, 3 & 4

12. What is the correct sequence in which these proteins become involved in prokaryotic DNA replication?
1. DNA pol I
2. SSBs
3. DnaA
4. Helicase
5. DNA pol III
6. DNA ligase
7. Primase
(a) 4,3,2,7,5,1,6                     (d) 3,4,5,2,7,1,6
(b) 4,3,2,7,1,5,6                     (e) 3,4,2,7,1,5,6
(c) 3,4,2,7,5,1,6

The next four questions are based on the description below:

Prokaryotic DNA polymerase III is a protein that consists of 7 different polypeptides, each known as a subunit, and each seemingly with its own particular function. The epsilon subunit, for example, bears the active site that removes mismatched nucleotides. The alpha subunit bears the active site that polymerizes the daughter strand. The tau subunit covalently attaches the whole enzyme to its "partner" DNA polymerase III. The functions of the other four subunits have not yet been fully resolved.

13. Referring to a single DNA polymerase III protein, its highest level of structure is the _____ level, but when referring to the DNA polymerase III and its covalently bound partner, the highest level of structure is the _____ level.
(a) tertiary, quaternary             (c) quaternary, quintenary
(b) quaternary, tertiary             (d) quintenary, quaternary

14. The substrate of the alpha subunit’s active site is/are most properly identified as:
(a) free deoxyribonucleotides.               (d) the primer.
(b) free ribonucleotides.                         (e) both c & d
(c) the parental template.

15. The hydrolysis of phosphodiester bonds is catalyzed by the _____ subunit, which therefore performs the _____.
(a) alpha, DNA synthesizing function            (d) tau, Okazaki fragmentation function
(b) alpha, excision repair function                 (e) epsilon, proofreading function
(c) epsilon, DNA synthesizing function

16. If the correct bonding of one DNA polymerase III protein to its substrate facilitates the bonding of the other DNA polymerase III to its substrate, then this is an example of:
(a) cooperativity.             (d) allosteric activation.
(b) Chargaff’s rules.       (e) complementary base pairing.
(c) hypercatalysis.

~~~~~~~~~~~~~~~~~

17. Considered together, both strands of a eukaryotic gene (from start sequence to terminator) have a mass of 1,000,000 daltons and are 90% intronic. What should be the mass of the corresponding mature mRNA transcript, excluding its cap and tail?
(a) 50,000 daltons                 (d) 500,000 daltons
(b) 100,000 daltons               (e) 900,000 daltons
(c) 450,000 daltons

18. If 15% of the deoxyribonucleotides in a hypothetical species’ genome are thymines, then approximately what proportion should be guanines?
(a) 15%         (b) 25%         (c) 35%         (d) 45%         (e) impossible to say

19. Eukaryotes’ partial solution to the end-replication problem is the _____, whereas a complete solution is provided by _____.
(a) 5’ to 3’ rule, reverse transcription                   (d) DNA polymerase a , DNA polymerase
(b) telomere, telomerase                                       (e) telomerase, the Central Dogma
(c) reverse transcription, the Central Dogma

20. Which of these is/are known to be ribozymes?
1. rRNA
2. tRNA
3. mRNA
4. snRNA
5. reverse transcriptase
(a) 1 only         (b) 4 only         (c) 1 & 4         (d) 1,2 & 4         (e) 2,3 & 5

Match the names with the accomplishments listed below (1 point each). Responses may be used more than once, or not at all. 
(a) Watson & Crick
(b) Avery, et al.
(c) Chargaff
(d) Hershey & Chase
(e) Griffith 

21. Proposed the existence of a "transforming principle."     

22. Used radioisotopes to demonstrate that DNA is the genetic material of bacteria and bacteriophage.

23. Exposed bacteria to purified samples of DNA and protein for a period of about 14 years.

24. Determined that the proportion of A:T:G:C is species-specific.

~~~~~~

Match the cellular structure with the descriptions listed below (1 point each). Responses may be used more than once, or not at all.
(a) Chromosome
(b) Replisome
(c) Ribosome
(d) Spliceosome
(e) More than one of these

25. Includes a ribozyme. 

26. Includes DNA polymerases. 

27. Most eukaryotic versions get shorter over time. 

28. Performs translation.

~~~~~

Match the process with the descriptions listed below (1 point each). Responses may be used more than once, or not at all.
(a) Replication
(b) Translation
(c) Reverse transcription
(d) RNA processing
(e) More than one of these

29. Is accomplished only by eukaryotes.

30. Can synthesize (a) DNA polynucleotide(s). 

31. Is catalyzed by a molecule of RNA. 

32. In eukaryotes, this typical process occurs only during S phase.

~~~~~

33. All are true of eukaryotic transcription, EXCEPT:
(a) it is performed solely by spliceosomes.
(b) its transcription units are individual genes.
(c) it is catalyzed by RNA polymerase II.
(d) proteins, besides the RNA polymerase molecule, are required for initiation.
(e) it occurs within the nucleus.

34. In a cell with linear DNA, which of the following occur(s) before a given mRNA transcript gets translated?
1. transcription factors bind to the promoter
2. the Poly(A) tail is attached to the 3’ end
3. telomeres lengthen.
4. snRNPs join together with proteins
5. the GTP cap attaches to the 3’ end
(a) 1 only         (b) 1 & 2         (c) 3 & 4         (d) 1, 2 & 4         (e) 2, 3 & 4

from the textbook......

35. Using bacteria grown separately on 15N and on 14N, Meselson & Stahl experimentally demonstrated that DNA is:
(a) replicated semi-conservatively.
(b) anti-parallel.                                
(c) synthesized in its 5’ to 3’ direction.
(d) the genetic material of bacteria and bacteriophage.
(e) bonded to histone proteins in eukaryotic chromosomes.

36. The sort of point mutation most likely to change a ribosome’s reading frame is a:
(a) 3-base deletion.                 (d) 1-base deletion.
(b) 6-base addition.                 (e) Two of these are equally likely.
(c) 1-base substitution.

Proceed to Part 2 and read the directions.

Part II. Enter the essay numeral into the space on the front page of your test booklet. Using ink and writing in paragraph format, answer both essay questions neatly, logically, completely, concisely and in well-organized fashion. You may write on both sides of the paper (20 points each).

1. Write an essay about the levels of protein structure which includes (a) a description of each level, (b) the kind(s) of bond(s) that maintain each of the first four levels, (c) actual examples of each level, where appropriate, and (d) specific factors than can affect the first three levels of structure.

2. The sequence of tRNA anticodons below corresponds to exonic DNA that codes for a region of a polypeptide that is far from the C and N terminals. Using this sequence of tRNA anticodons, determine and show (a) the corresponding amino acid sequence, and (b) the corresponding nucleotide sequence of the non-transcribed strand of DNA. Be sure to show all of the intermediate steps needed to determine both answers.

(c) Notice the underlined tRNA ribonucleotide in the sequence below. Should the corresponding deoxyribonucleotide in the transcribed DNA undergo a mutation that substitutes a T for the original deoxyribonucleotide, then describe the probable effect of this mutation on the structure and function of the corresponding polypeptide.

tRNA: A G A G C G A U G C A C U C C

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                                     Test #2                                   _____________  
FALL 2001                                                    100 points                              Essay Numeral  
DR. DINI                                                         Form 1

Part 1 (60 points).  Choose the letter representing the BEST response for each test item.  There should be only one BEST response for each (2 points each, except where indicated).  Your textbook and notes may be used throughout the test.  Thrash it!

The next 6 questions are based on the description that follows:

Each of the two DNA Pol III proteins of prokaryotic replisomes consists of seven different polypeptides, all seven of which must be present for normal activity.  One of these polypeptides, known as the a subunit, has the active site that catalyzes DNA polymerization.  Another polypeptide, the e subunit*, has the active site that catalyzes the removal of mismatched deoxyribonucleotides.  One or more of the remaining polypeptides bind an ATP molecule needed for DNA Pol III to commence synthesis at the end of an RNA primer.

1. What is the highest level of protein structure represented by a single DNA Pol III enzyme?  
(a) 1
°   (b) 3°   (c) 4°   (d) 5°   (e) 7°

2. What is the highest level of protein structure represented by both DNA Pol III enzymes, considered together?  
(a) 1
°   (b) 3°   (c) 4°   (d) 5°   (e) 7°

3. The eukaryotic version of DNA Pol III is active during which portion of the eukaryotic cell cycle?  
(a) G1 phase                (d) Nuclear division  
(b) G2 phase               (e) More than one of these  
(c) S phase                

4. Which function is performed by the e subunit?  
(a) ligation                               (d) excision repair  
(b) denaturation                       (e) dehydration synthesis  
(c) proofreading

5. All of the following are directly relevant to the function of the a subunit, EXCEPT:  
(a) Chargaff’s Rule.                            (d) the existence of RNA primers.  
(b) the 5’ -> 3’ Rule.                            (e) transcription factors.  
(c) DNA’s antiparallel nature. 

6. All of the following are plausible functions of the remaining subunits of the DNA Pol III enzyme, EXCEPT:  
(a) removing SSBs.  
(b) removing histones from the chromosomes.  
(c) attaching DNA Pol III to other parts of the replisome.  
(d) the occasional advance of the looped portion of the lagging strand.  
(e) the occasional ejection of the lagging strand from the
a subunit’s active site.

* e is the Greek letter epsilon

The next 5 questions are based on the description and figure that follow:

The molecule depicted here in bold is but one of two identical polypeptides that comprise a transmembrane protein called glycophorin A, which is permanently embedded in the plasma membranes of red blood corpuscles (RBCs).  Each polypeptide is 131 amino acids in length, and each features a single secondary structure.  The amino acids at positions 2-4, 5-10, 22, 25, 37, 44, 47, and 50 are each attached to carbohydrate chains consisting of four simple sugars, whereas the amino acid at position 26 has a branched carbohydrate chain of 9 simple sugars attached to it.  The numbered arrows represent the approximate positions of selected amino acids among the total of 131.

7. What is true of the amino acids between positions 73 and 95?  
(a) Most should have hydrophilic R groups.  
(b) They are part of a pleated (
b) sheet.  
(c) They are linked to each other  by covalent phosphodiester bonds.  
(d) The backbone elements of every 4th amino acids are involved in hydrogen bonding.  
(e) Most should have polar R groups.

8. Glycophorin A’s association with _____ best characterizes it as a(n) _____.  
(a) oligosaccharides, glycoprotein                  (c) phosphate heads, peripheral protein  
(b) phospholipids, glycolipid                            (d) polysaccharides, complex carbohydrate  
 

9. If the carbohydrates (and only the carbohydrates) attached to these amino acids were to be disassembled, then an enzyme that catalyzes the _____ of _____ would be most appropriate.  
(a) dehydration synthesis, polypeptides         (d) hydrolysis, glycosidic linkages  
(b) hydrolysis, disulfide bonds                        (e) dehydration synthesis, glycosidic linkages
 (c) hydrolysis, peptide bonds  
 

10. All of the following could be true of the portion of the polypeptide near the C-terminal end, EXCEPT it:  
(a) is part of a secondary structure.  
(b) might be associated with the sub-membrane microfilament layer.  
(c) might be associated with hemoglobin molecules.  
(d) might help convey a signal from the outside of the cell to the inside of the cell.  
(e) is mostly hydrophilic.  
 

11. Glycophorin A is LEAST likely to function as a:  
(a) receptor protein.                            (d) cell-cell adhesion protein.  
(b) transport protein.                           (e) peptide hormone.  
(c) cell-cell recognition protein.

The next 4 questions are based on the description below:

Ribozymes are catalytic RNA molecules that first came to light in the early 1980s.  Since then, our understanding of their significance hasexpanded substantially.  Small nuclear RNA (snRNA), found in spliceosomes, is the catalyst in intron removal from pre-mRNA.  Ribosomal RNA (rRNA) catalyzes peptide bond formation at ribosomes.  Some rRNAs and transfer RNAs (tRNAs) are auto-catalytic, removing their own introns soon after transcription!  
 

12. Arrange the following terms, from most inclusive to least inclusive:  
                                                            1. Spliceosomes  
                                                            2. Ribozymes  
                                                            3. snRNAs  
                                                            4. snRNPs  
                                                            5. Biological catalysts  
(a) 5,2,1,4,3     (b) 2,5,1,4,3     (c) 2,5,4,1,3     (d) 5,1,4,2,3     (e) 5,3,2,1,4  
 

13. The kind of bond that is attacked by the ribozymes that catalyze intron removal is a _____ bond.  
(a) phosphodiester         (b) hydrogen             (c) peptide          (d) ester         (e) disulfide  
 

14. The ribozyme that is normally found within a ribosome should:  
(a) be complementary to the ribosome-binding sequences of mRNA molecules.  
(b) be found at the ribosome’s P site.  
(c) be the catalyst that charges tRNA molecules.  
(d) be synthesized by free ribosomes.  
(e) have monomers that are linked together by peptide bonds.  
 

15. The products released by the catalytic activity of snRNA and auto-catalytic tRNA are made of:  
(a) deoxyribonucleotides.                    (d) amino acids.  
(b) polypeptides.                                 (e) fatty acids.  
(c) ribonucleotides.

The next 5 questions are based on the description below:

RNA viruses have genomes composed of RNA, rather than DNA.  A subset of RNA viruses is the retroviruses.  Retroviruses are unique in possessing an enzyme, reverse transcriptase, which can synthesize DNA using an RNA template.  Following its synthesis, the retroviral DNA can integrate itself into the chromosomal DNA of the eukaryotic host, where it lays dormant during what is known as the “latent period.”  The latent period ends when retroviral DNA undergoes transcription.  Some of the new RNA molecules serve as genomes for daughter viruses, others serve as mRNA transcripts, which the host’s ribosomes then use to synthesize new retroviral proteins.  
 

16. A retroviral enzyme, called integrase, cuts the host DNA, and when the retroviral DNA is in the proper alignment within the host DNA, seals that gap by mimicking _____ and catalyzing the formation of a _____ bond between host DNA and retroviral DNA.  
(a) helicase, ester                                           (d) ligase, phosphodiester  
(b) telomerase, peptide                                   (e) telomerase, polypeptide  
(c) RNA polymerase, phosphodiester  
 

17. Reverse transcriptase is most similar in its use of template and in its product to:  
(a) telomerase.           (b) RNA Pol.       (c) DNA Pol.             (d) snRNA.        (e) primase.  
 

18. All of the following should be involved in the synthesis of new retroviral genomes and mRNAs after the latent period ends, EXCEPT:  
(a) RNA Pol.                            (d) promoter regions.  
(b) DNA Pol.                            (e) ribonucleotides.  
(c) transcription factors.  
 

19. People who suspect that they have been very recently exposed to HIV may receive injections of anti-HIV antibodies.  These defensive proteins circulate throughout the bloodstream, attach to any HIV particles they might encounter, and ultimately remove the viruses from circulation.  Antibody molecules cannot cross plasma membranes.  What should be true?  
(a) The more time that has passed since exposure, the bigger the dose of anti-HIV antibodies is required.  Only very large doses are effective during the latent period.  
(b) During dormancy, the viruses are inside of the nuclei, so it shouldn’t matter that anti-HIV antibodies cannot cross the plasma membrane, as long as they can cross the nuclear envelope.  
(c) Unless the anti-HIV antibody is administered before the retroviruses infect any host cells, it will probably be ineffective.  
(d) Antibodies have the same ability to cross plasma membranes as do steroid hormones.

20. Reverse transcriptase has no proofreading capability.  What should be true?  
(a) It is identical to prokaryotic DNA polymerases in this regard.  
(b) Replication of its genome is less faithful than is replication in other organisms.  
(c) Retroviral genomes undergo adaptation more quickly than should those of other organisms.  
(d) all three of these should be true.  
(e) only b & c should be true.

The next 5 questions are based on the description below:

In a sense, a human female has all of her egg cells by the time she is born, though they are not yet mature eggs.  Each of her ovaries contains about 1 million tiny eggs-to-be, each of which has already begun the process of meiosis.  By the time of puberty’s onset, about 200,000 remain in each ovary, and they are all arrested in Metaphase I.  Every month thereafter until menopause, 6-7 follicles proceed to Metaphase II.  It is the act of fertilization that signals an egg to complete the process of meiosis.  Once meiosis is fully complete, the sperm’s nucleus fuses with one of the egg’s daughter nuclei.  The egg’s other daughter nucleus is expelled from the egg as a polar body and subsequently degenerates.  
 

21. If a mother cell nucleus in G1 phase contains 12000 nanograms (ng) of DNA on 46 chromosomes, then at the end of meiosis (but before nuclear fusion occurs), how many ng of DNA and how many chromosomes should be present in a single daughter nucleus?  
(a) 12000, 46               (b) 6000, 46        (c) 12000, 23            (d) 6000, 23      (e) 12000, 92  
 

22. Until fertilization occurs, what process(es) has an egg cell NOT yet fully undergone?  
                                                            1. Meiosis I  
                                                            2. Meiosis II  
                                                            3. Equational division  
                                                            4. Reductional division  
(a) 1 only         (b) 2 only         (c) 2 & 3          (d) 2 & 4          (e) 1, 2, 3 & 4  
 

23. All of the following should have occurred in developing egg cells by the time of puberty’s onset, EXCEPT:  
(a) synapsis                                                    (d) attainment of the haploid condition.  
(b) crossing over.                                            (e) appearance of tetrads.  
(c) independent assortment of homologs.

24. Which statement is true?  
(a) A single mother cell will ultimately give rise to four functional human egg cells at the completion of meiosis II.  
(b) The fusion of sperm and egg nuclei restores the diploid condition.  
(c) An egg cell at the end of meiosis (but before nuclear fusion) is genetically identical to the mother cell from which it originated.  
(d) By the time of interkinesis, each mother cell has already given rise to four daughter nuclei.  
(e) More than one of these is true.  
 

25. Before fertilization, the sperm’s nucleus should contain _____ chromosomes that comprise a _____ set.  
(a) replicated, diploid               (c) diploid, unreplicated  
(b) unreplicated, haploid         (d) haploid, replicated

The next 6 questions are based on the figure below (1 point each):  


 

If the RNA Pol enzyme traveled from left to right, then which labeled part of the figure is:  


26. closest to the promoter?

27. Closest to the terminator?

28. the transcribed (i.e. template) DNA strand?

29. composed of ribonucleotides?

30. composed of introns?

31. composed of monomers that are linked together by phosphodiester bonds?

 

32. Strands of human DNA consistently have the following percentages of nitrogenous bases during S phase: A=31%, G=20%, T=29%, C=20%.  This is not what one should expect, based on Chargaff’s Rule.  What would be the most likely cause of this discrepancy?  
(a) The presence of RNA primers.  
(b) The decondensed nature of chromatin.  
(c) The semi-conservative nature in which DNA replicates.  
(d) There are only two hydrogen bonds that link adenine with thymine, as opposed to the three that link guanine to cytosine.                                                                      [submitted anonymously]

33. A conformational change occurs when O2 bonds to an iron atom in one polypeptide chain of a hemoglobin molecule.  As a result, the other polypeptides in that same hemoglobin molecule are more likely to bond O2.  What feature of enzyme function is illustrated by this example, and what level of protein structure is necessary for this to occur?  
(a) cofactors, quaternary                    (c) allosteric regulation, tertiary  
(b) cooperativity, quaternary               (d) cofactors, quintenary                         [submitted by SR]  
 

Proceed to Part 2 and read the directions.

Part 2 (40 points).  Be sure that you have entered your essay numeral in the blank on the cover page of your test booklet.  Using ink and writing in paragraph format, answer both essay questions legibly, logically, completely, concisely and in well-organized fashion (20 points each).  You can write on both sides of your paper, but do NOT continue answers on any other sheets besides that provided for a given essay.

1. Below is a sequence of tRNA anticodons that corresponds to an exon that is far from both the GTP-cap and the Poly-A tail.  Using this sequence (plus dictionary of the genetic code, where needed), and working from left to right, determine the following sequences:

 

tRNA anticodon sequence:                         U C C A G A A G G U A G U A C G U A

 

a) mRNA codon sequence:

 

b) transcribed-DNA sequence:

 

c) non-transcribed-DNA sequence:

 

d) amino acid sequence:

            (abbreviations OK)

 

e) On the back of this sheet, name and describe the phenomenon that explains the observation that two of the amino acids (in the correct amino acid sequence) have the same identity, despite having different codons.

 

Dictionary of the Genetic Code

 

 2. Describe the means by which normal cells actively regulate their metabolic pathways.

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                                      Test #2                                   _____________
FALL 2002                                                    100 points                              Essay Numeral
DR. DINI                                                         Form 1

Part 1 (60 points).  Choose the letter representing the BEST response for each test item.  There should be only one BEST response for each (2 points each).  Dominate!!!

The following 4 questions refer to the description below:

The defensive proteins that we call antibodies, or immunoglobulins (Ig), are divided among five different classes (see Fig. 43.15 in Campbell).  Three of these classes (IgD, IgE, and IgG) consist of Y-shaped chemicals that are composed of four polypeptide chains: two identical heavy chains, and two identical light chains.  At the tips of both “arms” of a Y-shaped antibody are the sites where the (usually) foreign chemicals, or antigens, bond.  Only one particular kind of antigen is able to bond to the antigen-bonding sites of a particular antibody, and the antigen’s elimination from the body is dependent upon this bonding (the antibody is eliminated at the same time; no products are produced).  Two other classes of antibodies, IgA and IgM, consist of two and five Y-shaped molecules, respectively, connected together into functional units.

1. What is the highest level of protein structure attainable by members of Ig classes A and M?
a) primary        (b) secondary              (c) tertiary        (d) quaternary             (e) quintenary

2. What is the identity of the amino acid that is directly involved in the attachment of the four polypeptide chains to each other to form an antibody molecule?
a) cysteine      (b) proline        (c) histidine     (d) valine         (e) glutamine

3. Which characteristic(s) of enzymes seem(s) to be shared by antibodies, as determined solely from the description above?                                      1. Catalytic
                                                                        2. Specific
                                                                        3. Re-usable
a) 1 only          (b) 2 only         (c) 3 only         (d) 1 & 3          (e) all of these

4. Concerning bonding, antigen is to antibody as _____ is to enzyme.
a) substrate                 (c) competitive inhibitor
b) cofactor                   (d) non-competitive inhibitor

5. Information flow from DNA to protein is faster in _____ because _____ can begin _____ before mRNA is completely _____.
a) prokaryotes, ribosomes, translation, transcribed
b) eukaryotes, replisomes, recognizing ori’s, translated
c) eukaryotes, spliceosomes, mRNA processing, transcription
d) prokaryotes, ribosomes, transcription, translated                 [submitted by SC, modified]

6. In prokaryotes, which of these enzymes should be much more active in discontinuous DNA replication than in continuous DNA replication?
1. helicase           2. primase          3. DNA pol I          4. DNA pol III           5. DNA ligase
a) 2 only          (b) 2 & 3          (c) 1, 3, & 4          (d) 2, 3, & 5            (e) all of these

The following 6 questions are based on the description below:

Reading the tRNA anticodon sequence below from left to right, answer the questions that follow.  Note that a copy of the dictionary of the genetic code can be found on pg. 308 of your textbook.

tRNA:              U A G  G C A  A A A  C U C  G U U

 

7. What is the corresponding sequence of mRNA codons?
a) A T C  C G T  T T T  G A G  C A A         (d) T A G  G C A  A A A  C T C  G T T
b) U T C  C G T  T T T  G U G  C U U            (e) U A C  G C A  A A A  C U C  C U U
c) A U C  C G U  U U U  G A G  C A A

8. What is the corresponding sequence of amino acids?
a) Pro – Gly – Cys – Ser – Val            (d) Ile – Arg – Lys – Phe – Stop
b) Ile – Arg – Phe – Glu – Gln             (e) Tyr – Ala – Lys – Leu – Leu
c)  Ile – Arg – Lys – Glu – Gln

9. What is the corresponding sequence of template strand (transcribed) DNA nucleotides?
a) T A G G C A A A A C T C G T T                 (d) U T C C G T T T T G U G C U U
b) U A G G C A A A A C U C G U U                (e) A U G C C T A A A C C C G A A
c) A T C C G T T T T G A G C A A

10. What is true of every 3rd base in an anticodon sequence?
a) Its identity can differ, yet the same amino acid may be carried by the modified tRNA.
b) Each is only loosely attached to the rest of the tRNA molecule.
c) It is part of the tRNA molecule’s backbone.
d) It helps hold the tRNA molecule in its typical cloverleaf shape.
e) It is the most important part of each anticodon for determining which amino acid should be attached.

11. What is true of tRNA molecules?
a) In prokaryotes, they have introns that require removal before functionality is attained.
b) They fit into the active site of aminoacyl tRNA synthetases.
c) They are composed of mRNA.
d) Activated amino acids are attached to their 5’ ends.
e) More than one of these is true.

12. What is true of the RNA molecules to which anticodons bond via hydrogen bonding?
a) In prokaryotes, they have introns that require removal before functionality is attained.
b) They fit into the active site of aminoacyl tRNA synthetases.
c) They are composed of mRNA.
d) Activated amino acids are attached to their 5’ ends.
e) More than one of these is true.

The following 6 questions refer to the description below:

In living cells, DNA replication involves dozens of different proteins acting in a coordinated fashion.  In the mid-1980s, however, a technology was invented that permitted the rapid replication of short pieces of DNA with far fewer reagants, a technology called the Polymerase Chain ReactionÔ (PCR).  The basis of the process is the observation that DNA, like proteins, can be reversibly denatured by high heat.  The process also relies on DNA polymerases from prokaryotes that are adapted to alkaline hotsprings where temperatures are about twice that of the human body.   Once a DNA molecule is denatured, the temperature of the reaction mixture is cooled, and the DNA polymerases use the separated DNA strands as templates.  With a few hours’ worth of cycling between hot and cold, and with the proper reagents provided in abundance, thousands of copies of the original DNA molecule can be produced by PCR.

13. The reversible denaturation of one molecule of double-stranded DNA should result in:
a) two polypeptide chains.                              (d) multiple oligonucleotides.
b) two polyribonucleotide chains.                   (e) multiple oligopeptides.
c) two polydeoxyribonucleotide chains.

14. What type of bond is broken during the denaturation of DNA?
a) glycosidic bond                   (d) ester bond
b) phosphodiester bond          (e) hydrogen bond
c) peptide bond

15. Besides the original parental DNA molecule, and the prokaryotic DNA polymerase, all other reagents listed below should be provided for DNA replication to occur by PCR, EXCEPT:
                                                            1. free deoxyribonucleotides
                                                            2. helicase
                                                            3. primers
 a) 1                 (b) 2                 (c) 1 & 2          (d) 2 & 3          (e) 1 & 3         

16. Which of the following is NOT needed for the accurate and efficient operation of the prokaryotic DNA polymerase?
a) proofreading                                    (d) removal of introns
b) the 5’ to 3’ rule                                (e) semiconservative replication
c) complementary base-pairing

17. What are the two types of bond that must NOT be broken by high heat in PCR; otherwise, the reaction would be irreversibly disrupted?
a) hydrogen and van der Waals                     (d) glycosidic and ester
b) ester and phosphodiester                           (e) dipeptide and oligopeptide
c) peptide and phosphodiester

18. Which of these graphs comes closest to accurately depicting the optimal temperature and pH of the prokaryotes from which the DNA polymerase was isolated?

Formatting problems prevent the graphs from appearing here.

The following 4 questions are based on the description below:

Cellulose is the primary structural ingredient of plant cell walls.  Its polymerization is catalyzed by the enzyme, cellulose synthase, which is thought to be composed of many identical proteins, each of which produces its own chain of monosaccharides.  Each monosaccharide chain then becomes cross-linked with the chains of neighboring proteins to produce cellulose microfibrils.  Many such identical proteins form structures called rosettes that are embedded in plasma membranes of plant cells (see figure).  Cellulose de-polymerization is catalyzed by the enzyme, cellulase, which is synthesized only by certain prokaryotes and fungi.

19. What is probably true of the portions of cellulose synthase molecules that are in direct contact with the fatty acids of membrane phospholipids?
a) They are hydrophilic.
b) They are composed of cholesterol.
c)  Peptide bonds here link fatty acids together.
d) They feature amino acids whose side groups are polar or charged.
e) They are the location of secondary structures, such as
a-helices.

20. What ought to prevent the cellulase that is secreted by fungi from digesting the very cell walls that surround fungal cells?  The active site of cellulase:
a) can only recognize polymers of
a-glucose.
b) can only recognize polymers of
b-glucose.
c) cannot recognize polymers made of glucose with a nitrogenous side group at carbon #2.
d) cannot recognize the type of cellulose that comprises fungal cell walls.
e) cannot recognize phospholipids.

21. What ought to prevent cellulase from digesting starch?  The active site of cellulase:
a) can only recognize polymers of
a-glucose.
b) can only recognize polymers of
b-glucose.
c) cannot recognize polymers made of glucose with a nitrogenous side group at carbon #2.
d) cannot recognize the type of cellulose that comprises fungal cell walls.
e) cannot recognize phospholipids.

22. What ought to be true of the triglycerides that plant cells produce?
a) Plant cells do not produce triglycerides; only animal cells do.
b) Their fatty acids are unsaturated.
c) They are stored in the form of cholesterol.
d) They are produced by plants in response to periods marked by locomotion.
e) They are the primary means used by plants to store extra glucose.

The following 4 questions are based on the description below:

In eukaryotes, DNA replication, transcription, mRNA processing, and translation are each carried out by a different, relatively large aggregation of proteins and, sometimes, of proteins and RNA.  Each of these structures has the ability to recognize a particular nucleotide sequence, or sequences.  Each also performs complementary base-pairing during some portion of its activity.

23. All of the following are directly involved in at least one of the processes listed above, EXCEPT:
a) spliceosomes.                    (d) transcription initiation complexes.
b) ribosomes.                          (e) proteasomes.
c) replisomes.

24. Which of the following processes does NOT involve RNA in any way?
a) DNA replication                   (d) translation
b) transcription                        (e) all involve RNA in some way
c) mRNA processing

25. Which of the following include(s) temporary hydrogen bonding between two different kinds of RNA?                                 1. DNA replication
                                                          2. transcription
                                                          3. mRNA processing
                                                          4. translation
a) 2 only          (b) 3 only         (c) 2 & 3          (d) 3 & 4          (e) 1, 3, & 4

26. Which of the following nucleotide sequences must be recognized by a replisome in order for it to function correctly?      1. Promoter
                                                            2. Ribosome Binding Sequence
                                                            3. ori’s
                                                            4. sequences complementary to primers
                                                            5. terminator
                                                            6. splice sites
a) 1 & 2           (b) 3 & 4          (c) 1, 2, & 5     (d) 3, 4, & 6     (e) all of these

The following two questions refer to the description below:

A hypothetical gene is composed of 3,000 base pairs, has a mass of 2 million daltons, and is 90% intronic (i.e. 90% of it is composed of introns).  Hint: Draw pictures!

27. How many bases, and how many daltons of RNA, should the primary transcript possess?
a) 3,000 bases and 1 million daltons              (c) 3,000 bases and 2 million daltons
b) 300 bases and 200,000 daltons                 (d) 300 bases and 100,000 daltons

28. About how many bases, and how many daltons of RNA, should the mature mRNA transcript possess, excluding the cap and tail?
a) 3,000 bases and 1 million daltons              (c) 3,000 bases and 2 million daltons
b) 300 bases and 200,000 daltons                (d) 300 bases and 100,000 daltons

29. Which of the following statements about polynucleotides is/are accurate?
                        1. By adding a nitrogenous base to a nucleotide, chitin can be formed.
                        2. Each polynucleotide has a sugar-phosphate backbone.
                        3. Because pyrimidines have two rings, twice as many single-ring purines are required to make a nucleotide
                        4. The only difference between DNA and RNA is that the former is double-stranded, whereas the latter is single-stranded.
                        5. Phosphodiester bonds maintain the backbone of a polynucleotide.
a) 5 only            (b) 2 & 5           (c) 1, 2, & 4            (d) 1, 3, & 4          (e) 2, 3, & 5
                                                                                                         submitted by GR, modified]

30. The existence of Okazaki fragments is due to the:
a) 5’ to 3’ rule.
b) observation that a replisome can move only in the direction of the opening replication fork.
c) antiparallel nature of DNA.
d) both a & b

Proceed to Part 2 and read the directions.

Part 2 (40 points).  Be sure that you have entered your essay numeral in the blank on the cover page of your test booklet.  Using ink and writing in paragraph format, answer both essay questions legibly, logically, completely, concisely, and in well-organized fashion (20 points each).  You can write on both sides of your paper, but do NOT continue answers on any other sheets besides that provided for a given essay.

1. Excluding the auto-catalytic ones, describe two different ribozymes, including in your description what each is composed of, the specific function of each, and the significance of each for the survival of the cell to which it belongs.

2. In terms of flow of genetic information, discuss the relationship between proteins and nucleic acids.  Describe what, if any, affect the proofreading capability of prokaryotic and eukaryotic DNA polymerases has on protein function.

 Answer Key?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                                      Re-Test #2                              _____________
FALL 2003                                                     100 points                              Essay Numeral
DR. DINI                                                         Form 1

Part 1 (60 points).  Choose the letter representing the BEST response for each test item.  There should be only one BEST response for each (2 points each, except where indicated).  Kick gluteus maximus!!!

 The next 8 questions are based on the series of four drawings below (1 point each).  Note that there is a fifth option (e) more than one of these.  The five responses may be used once, more than once, or not at all.

Formatting problems prevent the appearance of the figure here.

1. Which process(es) prepare(s) a genome for binary fission?

2. In which process(es) is a ribozyme the primary catalyst in the formation of covalent bonds?

3. Which process(es) add(s) new, non-coding sequences to eukaryotic DNA only?

4. Which situation(s) involves RNA synthesis (oligoribonucleotides or polyribonucleotides?

5. In which situation(s) does RNA-directed DNA synthesis occur?

6. In prokaryotes, process (b) could happen in essentially the same time and place as which other process?

7. The effectiveness of which process would be improved by a polysome?

8. Which process must be preceded by RNA processing in eukaryotic cells?

9. Triglycerides can differ from each other in all of the following ways, EXCEPT the:
a)
      lengths of their fatty acid tails.
b)
      degree of unsaturation of their fatty acid tails.
c)
      number of fatty acid tails.
d)
      number of kinks in their fatty acid tails.
e)
      number of double bonds in the backbones of their fatty acid tails.

10. Which of these features do lipids and carbohydrates have in common?
1.
      They can be structural materials.
2.
      The number of calories contained per unit mass.
3.
      The type of covalent bonds that link monomers.
4.
      They can be metabolized for energy.
5.
      They can be used to store energy.
(a) 1 & 4          (b) 2 & 4          (c) 1, 4, & 5                 (d) 2, 3, & 5                 (e) all except #3

11. All are true of the polymers of a glucose, EXCEPT:
a)
      They include the polymer known as chitin.
b)
      They can be used to store energy.
c)
      They are held together by glycosidic linkages.
d)
      They may be branched.
e)
      They cannot be hydrolyzed by the same enzymes that hydrolyze polymers of b glucose.

The next three questions are based on the sequence of tRNA anticodons below.  Use the copy of the genetic code below (or that found on p. 308 of your textbook) as needed to determine the corresponding sequences.

tRNA anticodons:     U U U  A G G  C U G  G A G  U C U

 See genetic code in previous test.

12. What is the corresponding sequence of mRNA codons?
a) AAA TCC GAC CUC AGA              (c) AAA UCC GAC CUC AGA
b) TTT AGG GTC CTC TCT                 (d) UUU ACC CUC CAC UCU

13. What is the correct sequence of the corresponding template DNA strand?
a) AAA TCC GAC CUC AGA              (c) AAA UCC GAC CUC AGA
b) TTT AGG GTC CTC TCT                 (d) UUU ACC CUC CAC UCU
                                                                 (e) TTT AGG CTG GAG TCT

14. What is the corresponding amino acid sequence?
a) Val-His-His-Ser-Ile              (c) Trp-Tyr-Val-Pro-Asn
b) Tyr-Ala-Ala-Ala                    (d) Lys-Ser-Asp-Leu-Arg
~~~~~~~~

15. Twelve successive base pairs are removed from an exon as a unit, rotated 180° end-to-end, replaced into the DNA at the same location, and sealed in place by DNA ligase.  No new stop codons are introduced as a result.  Which two terms are most applicable to this situation?
1.
      point mutation
2.
      frameshift mutation
3.
      mis-sense mutation
4.
      inversion mutation
5.
      deletion mutation
a) 1 & 2           (b) 2 & 3          (c) 2 & 5          (d) 3 & 4          (e) 4 & 5

16. Peptide bonds are to the primary level of protein structure as hydrogen bonds are to the _____ level of protein structure.
a) 2
°                (b) 3°               (c) 4°               (d) 5°               (e) more than one can be true

17. A reaction vessel contains constant amounts of enzyme and of an enzyme inhibitor.  If, in response to increasing substrate concencentration, the enzyme activity increases, then this means that the:
a)
      enzyme is an allosteric enzyme.
b)
      inhibitor is an allosteric inhibitor.
c)
      inhibitor is a competitive inhibitor.
d)
      inhibitor is a poison.
e)
      inhibitor and enzyme are one and the same thing.

18. Which process(es) can change the primary structure of a eukaryotic polypeptide?
1.
      mutation of exonic portions of its gene
2.
      failure of intron removal from its mRNA
3.
      hydrolysis of its peptide bonds
4.
      breaking its backbone
a) 1 only          (b) 1 & 3          (c) 2 & 4          (d) 1, 3, & 4     (e) all of these

19. Watson and Crick knew, before they determined DNA’s structure, that its structure would have to account for:
a)
      the existence of introns.                                  (d) all three of these
b)
      faithful replication.                                           (e) only (b) and (c)
c)
      the storage of genetic information.

The following 15 questions are based on the description below:

When fully assembled, a single prokaryotic RNA polymerase enzyme consists of six polypeptide chains, two of which are identical to each other.  The five different kinds of polypeptides carry out their own functions, but not unless most of the other polypeptides are also present.  These six polypeptides are NOT attached to each other by covalent bonds but, rather, by weaker bonds.  The two identical polypeptide chains are referred to as the b subunits and, together, they form the active site of the enzyme.  Another polypeptide, the s subunit, detaches from the rest of the enzyme immediately following initiation, and is necessary for initiation, but not for subsequent elongation.  Lacking this subunit, the rest of the enzyme cannot even properly attach to the promoter!  The RNA pol enzyme keeps a 12-base-pair section (and no more!) of the DNA molecule open at the site of catalysis.  Prokaryotic RNA pols are inhibited by the antibiotic, rifampin, which interferes with the b subunits.

20. What should be true of the five genes that carry the code for these five polypeptides?  They:
a) are parts of operons.                      (d) have telomeres.
b) have signal sequences.                  (e) are part of a linear DNA molecule.
c) possess 5’ caps and 3’ tails.         

21. The s subunit has a function most similar to that of _____ in eukaryotic transcription.
a) transcription factors            (d) promoter
b) substrate                             (e) template
c) product

22. If rifampin bonds covalently to the b subunits, then it most probably acts as a(n):
a) allosteric inhibitor.               (d) poison.
b) allosteric activator.              (e) coenzyme.
c) competitive inhibitor.

23. The substrates of RNA pol are free _____, whereas the product is a _____.
a)
      ribonucleotides, polydeoxyribonucleotide
b)
      ribonucleotides, polyribonucleotide
c)
      deoxyribonucleotides, polydeoxyribonucleotide
d)
      deoxyribonucleotides, polyribonucleotide
e)
      oligonucleotides, polynucleotides

24. Which of these features are involved in the catalytic activity of RNA pols?
1.
      the 5’ to 3’ rule
2.
      the antiparallel nature of double-stranded polynucleotides
3.
      complementary base pairing
4.
      hydrogen bonding
5.
      dehydration synthesis reactions that create phosphodiester bonds
a) 1 & 2 only              (b) 1 & 3          (c) 1, 2, & 3         (d) 1, 2, 3, & 4       (e) all five of these

25. Which of these bonds is most probably involved in maintaining the structure of the assembled RNA pol enzyme, i.e. of keeping the six polypeptides together as an enzyme?
a) peptide             (b) phosphodiester             (c) ester          (d) hydrogen           (e) disulfide

26. What is the highest level of protein structure that prokaryotic RNA polymerase has?
a) 1
°                (b) 2°               (c) 3°               (d) 4°               (e) 5°

27. Which of the following should NOT be found in the direct products of RNA pol?
1.
      T ribonucleotides
2.
      A deoxyribonucleotides
3.
      C deoxyribonucleotides
4.
      G deoxyribonucletides
5.
      U deoxyribonucleotides
a) 1 only          (b) 2 only         (c) 3 only         (d) 5 only         (e) none should be found

28. Which of the following would normally be made by the catalytic activity of prokaryotic RNA pols?
a) tRNA                 (b) mRNA              (c) rRNA             (d) snRNA                (e) all except (d)

29. What is generally true of prokaryotic mRNAs, compared to eukaryotic mRNAs?  Prokaryotic mRNAs:
a)
      lack introns.
b)
      are more likely to be degraded by nucleases before they can be used.
c)
      will all later become substrates for amino-acyl tRNA synthetases.
d)
      Only (a) and (b)
e)
      Only (b) and (c)

30. Which of the following can get physically close to (close enough to touch!) active prokaryotic RNA pols, but NOT physically close to active eukaryotic RNA pols?
a) functional ribosomes                      (d) transcription factors
b) ribosomal subunits                         (e) spliceosomes
c) newly synthesized tRNAs

31. Various antibiotics target different features of bacteria.  For example, penicillins inhibit the enzymes that catalyze the construction of bacterial cell walls, streptomycin inhibits the catalytic agent of prokaryotic ribosomes, as does tetracycline.  Which antibiotic(s) inhibit(s) a ribozyme?
(a)
   rifampin                       (d) tetracycline
(b)
   penicillin                      (e) both (c) and (d)
(c)   streptomycin  

32. What is the largest number of nucleotides that a mRNA molecule could contain until it is forced to detach from its DNA template as the template re-winds, and how many codons could theoretically be contained in this section of mRNA?
a) 6,3               (b) 12,8            (c) 12,4            (d) 24,8            (e) 24,4

33. Which processes(es) is/are directly catalyzed by RNA pol?
a) DNA-directed DNA synthesis                     (d) RNA-directed RNA synthesis
b) DNA-directed RNA synthesis                     (e) two of these
c) RNA-directed DNA synthesis

34. What normally occurs to prokaryotic mRNAs as soon as their Ribosome Binding Sequences detach from the templates?
a)
      Intron removal                         (d) GTP cap addition
b)
      Translation                              (e) both (a) and (d)
c)
      Reverse transcription

Proceed to Part 2 and read the directions.

Part 2 (40 points).  Be sure that you have entered your essay numeral in the blank on the cover page of your test booklet.  Using ink and writing in paragraph format, answer both essay questions legibly, logically, completely, concisely, and in well-organized fashion (20 points each).  You can write on both sides of your paper, but do NOT continue answers on any other sheets besides that provided for a given essay.

  1. What is the relationship between protein structure and the typical, minute-to-minute regulation of metabolic pathways in cells?

2. Describe three structural differences between prokaryotic genophores and eukaryotic chromosomes, and then separately describe how each difference affects the flow of genetic information (the path that includes DNA --> RNA --> protein) in eukaryotes.

 ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                          Test #2                                               _____________
FALL 2004                                          100 points                                        Essay Numeral
DR. DINI                                               Form 1

Part 1 (60 points).  Choose the letter representing the BEST response for each test item.  There should be only one BEST response (2 points each, except where indicated).  Dominate!

1. A stretch of exonic DNA undergoes a 2-base insertion mutation.  This mutation will definitely be a _____ mutation, and most probably will be a _____ mutation.
(a) deletion, deleterious                       (d) frameshift, deleterious
(b) substitution, frameshift                  (e) substitution, advantageous
(c) nonsense, missense

2. As the result of the process of DNA replication, a mutation occurs in a coding sequence and is still in place when the next round of DNA replication occurs.  Which cellular machinery must have failed to perform properly?
1.      DNA ligase
2.      DNA polymerases
3.      RNA polymerase
4.      DNA-repair enzymes
5.      telomerase
(a) 1 & 2          (b) 2 & 3          (c) 2 & 4          (d) 2, 4, & 5                 (e) 3, 4, & 5

3. The genetic code’s degeneracy (i.e. redundancy) is a direct result of the code’s _____ nature.
(a) universal                            (d) non-ambiguous
(b) nearly universal                 (e) triplet
(c) perverted

4. The result of a 1-base deletion mutation deep within an intron that is always intronic should be
(a) frameshift.                         (d) negligible.
(b) always deleterious.            (e) more than one of these.
(c) a shorter polypeptide.

5. The P site of a functional ribosome
(a)   contains a ribozymal rRNA.
(b)   is the site from which tRNAs usually leave the ribosome.
(c)   is the site from which tRNAs generally depart from the ribosome.
(d)   can contain a codon, or an anticodon, but not both simultaneously.
(e)   is a site where phosphodiester bonds are catalyzed.

6. In eukaryotic cells, the same sequence of nucleotides on template DNA could, at different times, give rise to different polypeptides (i.e. having different 1° structures), depending upon
(a) the reading frame of the ribosome.
(b)   which splice sites are recognized, and which are ignored, by spliceosomes.
(c)   whether post-translational protein processing occurs, or not.
(d)   All three of these
(e)   Both a & c

7. In eukaryotic cells, the affect that polysomes have on rate of protein synthesis is similar to that produced by
(a)   multiple RNA pol II’s reading the same transcription unit simultaneously.
(b)   circularization of mature mRNA in the cytoplasm.
(c)   multiple replication bubbles.
(d)   Both a & b
(e)   Both a & c

8. The “trombone model” is used to account for
(a) RNA processing.               (d) leading strand synthesis.
(b) transcription.                      (e) lagging strand synthesis.
(c) translation.

9. Functionally, snRNA is to RNA processing as rRNA is to _____.
(a) telomerase activity                                    (d) reverse transcriptase activity
(b) transcription                                               (e) translation
(c) post-translational protein processing

10. Which statement concerning biological catalysts is most correct?
(a)   The term “biological catalyst” is equivalent (synonymous) with the term “enzyme.”
(b)   Poisons usually bond to biological catalysts using hydrogen bonds.
(c)   Enzymes eliminate activation energy.
(d)   Allosteric inhibition usually involves feedback inhibition.
(e)   Biological catalysts are necessary to catalyze dehydration synthesis reactions, but not hydrolysis reactions.

11. Structurally, ribonucleotides are to ribozymes as _____ are to enzymes.
(a) deoxyribonucleotides                    (d) nucleic acids
(b) amino acids                                   (e) R groups
(c) nucleotides

12. RNA processing is
(a)   an alternative term for DNA-directed RNA synthesis.
(b)   performed, in part, by spliceosomes within eukaryotic nuclei.
(c)   an alternative term for RNA-directed protein synthesis.
(d)   performed by ribosomes in both prokaryotic and eukaryotic cytoplasm.
(e)   two of these are correct.

13. A hypothetical eukaryotic gene is 100,000 base pairs long, and is 80% intronic.  About how many free ribonucleotides will be required to make the corresponding pre-mRNA; about how many ribonucleotides should be found in the mature transcript (not including cap and tail); and about how many amino acids should there be in the corresponding polypeptide?
(a) 100,000; 20,000; 6,666                  (d) 200,000; 100,000; 33,333
(b) 100,000; 80,000; 26,666                (e) 200,000; 160,000; 53,333
(c) 200,000; 40,000; 120,000

14. A hypothetical prokaryotic operon’s coding sequence (does NOT include promoter or terminator) contains 300,000 base pairs.  About how many free nucleotides will be required to replicate this stretch of DNA; and about how many free nucleotides will be required to transcribe this same stretch?
(a) 300,000; 300,000               (d) 600,000; 600,000
(b) 300,000; 600,000               (e) 1,200,000; 600,000
(c) 600,000; 300,000

15. The role played by helicase in prokaryotic DNA-directed DNA synthesis is played by _____ in prokaryotic DNA-directed RNA synthesis.
(a) RNA pol                 (d) helicase
(b) DNA pol I               (e) ligase
(c) DNA pol III

16. All are important for the proper functioning of cellular DNA polymerases, EXCEPT the
(a)   location of the promoter relative to the DNA sequence.
(b)   anti-parallel structure of DNA.
(c)   type of nucleotide (ribo- or deoxyribo-) that are to be linked.
(d)   nature of the template (whether DNA or RNA).
(e)   presence of primers.

17. All are important for the proper functioning of RNA polymerase II, EXCEPT the
(a)   location of the promoter relative to the DNA sequence.
(b)   availability of transcription factors.
(c)   type of nucleotide (ribo- or deoxyribo-) that are to be linked.
(d)   nature of the template (DNA or RNA).
(e)   presence of primers.

Match the letters in the figure to the appropriate description below.  Dashed lines indicate newly synthesized nucleic acids.  Letters may be used once, more than once, or not at all (1 point each).  NOTE: there is a fifth option (E).

  Figure unavailable

(E) None of these

18. Which labeled structure is performing DNA-directed DNA synthesis?

19. Which labeled structure contains thymine, and has 5’ to 3’ orientation going from right to left on this page?

20. Which labeled structure has a proteinaceous active site?

21. Which labeled structure is a polypeptide that may be destined for this cell’s mitochondria?

~~~~~

22. The mRNA transcript produced by a prokaryote may be equally long as the pre-mRNA transcript produced by a eukaryote, despite the fact that the prokaryotic transcript contains coding sequences for more than one gene.  What best accounts for this equality?
(a)   Eukaryotic transcripts also commonly contain coding sequences for multiple genes.
(b)   The presence of introns in immature eukaryotic transcripts, and their absence from prokaryotic transcripts.
(c)   Prokaryotic polypeptides are much shorter than are eukaryotic polypeptides.
(d)   The absence of cap and tail from prokaryotic transcripts, and their presence on eukaryotic transcripts.

Match the letters in this figure of a portion of a replication bubble to the appropriate description below.  Dashed lines indicate newly synthesized nucleic acids.  Letters may be used once, more than once, or not at all (1 point each).

    [Drawing could not be reproduced in this format]

23. A location closest to the place where DNA polymerization occurred most recently.

24. A location where helicase has, apparently, not yet catalyzed a reaction.

25. Daughter DNA synthesized by discontinuous DNA replication.

26. A location where DNA ligase has, apparently, not yet catalyzed a reaction

~~~~~~

27. Which of these could change the 1° level of protein structure without breaking any existing bonds?
(a) genetic mutation                (c) irreversible denaturation
(b) chaperone proteins            (d) reversible denaturation

28. Which bonds help maintain both 3° and 4° levels of protein structure (but not lower levels) AND, if broken, can lead to irreversible denaturation?
(a) ionic           (b) disulfide     (c) hydrogen   (d) peptide       (e) hydrophobic/hydrophilic

29. Which bonds must be left intact in order to maintain the 1° level of protein structure?
(a) ionic           (b) disulfide     (c) hydrogen   (d) peptide       (e) hydrophobic/hydrophilic

30. It is harder to lose weight by burning _____ than by burning _____ because the former contains about _____ as many calories per unit mass as does the latter.
(a) fats, carbohydrates, 1/2                (c) carbohydrates, fats, 1/2
(b) fats, carbohydrates, twice             (d) carbohydrates, fats, twice

31. Consider an oligosaccharide consisting of six identical monosaccharides.  At the very least, which of these will be needed to break the covalent bonds linking these monosaccharides to each other effectively in living cells?
1.      one enzyme molecule
2.      five enzyme molecules
3.      five water molecules
4.      increased temperatures, well above basal body temp.
(a) 1 only         (b) 1 & 3          (c) 2 & 3          (d) 1, 3, & 4                 (e) 2, 3, & 4

32. The equator is located at 0° latitude, whereas the poles are located at 90° (N or S) latitude.  Which graph best depicts the relationship between latitude and proportion of body weight that exists as fat in animals adapted to life at various latitudes?

  [Figure could not be reproduced in this format]

33. Which feature of animals is most important in making it advantageous for animals to store excess food energy as fat, rather than as carbohydrate?
(a) locomotion                         (d) inability to synthesize polymers of glucose
(b) irritability                            (e) inability to digest polymers of glucose
(c) reproduction

34. Oils are a type of _____ whose _____ are _____.
(a) steroid, cholesterols, amphipathic             (d) cholesterol, fatty acids, aminated
(b) phospholipid, fatty acids, saturated           (e) carbohydrate, polymers, branched
(c) triglyceride, fatty acids, unsaturated

 Part 2. (40 points).  Be sure that you have entered the essay numeral in the blank on the cover of your test booklet.  Make NO identifying marks on the essay pages.  Using ink and writing in paragraph format (except for 1a-c), write answers for both essays.  You may write on the back of the page, but do NOT continue you answer on another sheet of paper.  To receive full credit, essays must be legible, complete, concise, and well organized (20 points each).

  1. A hypothetical eukaryotic cell contains a molecule of exonic, double-stranded DNA (dsDNA) that includes the base-pair sequence below.  The promoter for this sequence is located (off the page) somewhere to the left.

5’ --- G G G G T T A T C G C A G G C --- 3’

3’ --- C C C C A A T A G C G T C C G --- 5’

Using, where necessary, the dictionary of the genetic code below (or on p. 308 of your textbook), determine:
a)
      the corresponding mRNA sequence,
b)
      the corresponding amino acid sequence,
c)
      the corresponding tRNA anticodon sequence,
d)
      and, using Fig. 5.15 in your textbook, comment about the protein structures in which these amino acids might be involved, and what causes you to say so.

  [Figure could not be reproduced in this format.]

2. Compare and contrast the enzymes telomerase and reverse transcriptase concerning the reactions they catalyze (i.e. Substrate? Product? Type of reaction? Specific type of bond?), and the significance of their activities for the biological entities that possess these enzymes.

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                              Test #2                                   ___________________
FALL 2005                              100 points                                   Essay Numeral
DR. DINI                                 Form 1

DIRECTIONS FOR PART 1: Fill-in the SS# bubbles and the Form bubble on your scantron.  Choose the one BEST response for each test item (2 raw points each, except where indicated).  Trounce it!!

Match the questions below with the appropriate lettered process on the diagram below.  All responses will be used at least once (1 point each).

 Figure unavailable

1. In eukaryotes, which process occurs only during S phase?

2. Which step is always necessary in cases where proteins have 4° structure, but not always necessary in cases where proteins lack 4° structure?

3. Which process requires a template that contains uracil to build a daughter polynucleotide that lacks uracil?

4. Which process is catalyzed by a ribozyme?

5. In prokaryotes, which process uses units called “operons” as templates?

6. Which process involves the “trombone model”?

7. All are true of steroid hormones, except
(a)   they are built from a cholesterol precursor.
(b)   their structure is maintained by phosphodiester bonds.
(c)   they are distributed to target organs via the bloodstreams of vertebrates.
(d)   they contain twice as many calories per unit mass as do the oligosaccharide portions of certain peptide hormones.
(e)   they are lipids.

8. What is true of polymers of alpha-glucose?
(a)   They are polymerized by the same enzymes that catalyze polymerization of beta-glucose chains.
(b)   They are primarily used by cells to build structures.
(c)   They can differ from each other in their degree of branching.
(d)   The relative orientations of the –H and –OH groups on carbon #1 are of little consequence to their functions.(e)   The hydrolytic enzymes of animals cannot digest them.

9. Which of these do triglycerides and phospholipids have in common?
1.      a phosphate head
2.      glycerol
3.      three fatty acid chains
4.      variable degrees of saturation
5.      phosphodiester bonds
(a) 2 only        (b) 1 & 2         (c) 2 & 4         (d) 3 & 4         (e) 3, 4, & 5

10. Phospholipids are to biological membranes as _____ is to fungal cell walls.
(a) cellulose               (b) cellulase       (c) amylopectin        (d) glycogen             (e) chitin

The next two questions are topically related.

11. Evidence of proofreading capability in RNA pols is minimal.  If the capability does exist, then where and when would it be most likely to occur in a eukaryotic cell?
(a) at functional ribosomes, mitosis                        (d) in the nucleus, G1 and/or G2
(b) at functional replisomes, S phase                     (e) in the cytoplasm, interphase
(c) at functional spliceosomes, binary fission

12. If a uracil ribonucleotide were to be expelled from the active site of RNA pol as the result of proofreading, then the complementary nucleotide on the template strand would be LEAST likely to be a(n)
(a) guanine.                (b) thymine.                (c) cytosine.               (d) adenine.

~~~~~

13. What is true of eukaryotic RNA pols?
(a)   They detach from the DNA template immediately upon reaching the terminator.
(b)   They do not require primers.
(c)   They build a daughter polynucleotide in the daughter’s 3’ to 5’ direction.
(d)   A given molecule of RNA pol can catalyze the synthesis of all types of RNA.
(e)   They are able to recognize the promoter without assistance.

14. If increasing temperatures break all of the hydrogen bonds in a protein that is composed of > 1 polypeptide, then all of the following levels of protein structure should undergo denaturation, except
(a) primary.                (b) secondary.           (c) tertiary.                  (d) quaternary.

 15. When cellular stores of ATP are low, but stores of ADP are high, ADP molecules can attach reversibly to enzymes at sites far from the active sites and cause the enzymes to accept more substrate molecules per unit time.  The result is increased ATP-synthesis rates.  In this example, ADP is acting as a(n)
(a) cofactor.                           (d) allosteric activator.
(b) allosteric inhibitor.           (e) non-competitive inhibitor.
(c) substrate.

16. Which feature of RNA processing helps to account for the existence of more types of polypeptides in eukaryotes than there are genes to code for them?
(a) addition of 5’ cap                                    (d) sometimes, introns are treated as exons
(b) addition of a poly- tail                              (e) the involvement of a ribozyme
(c) its occurrence within the nucleus

17. Consider a eukaryotic gene that consists of 10,000 base pairs and is 80% intronic. About how many amino acids should be found in the corresponding polypeptide?
(a) 333            (b) 666            (c) 1,000         (d) 2,000        (e) 26,000

The following 6 questions refer to the paragraph below:

Reverse transcriptase (rt) is an enzyme of retroviruses that catalyzes reverse transcription.   The genome of a retrovirus consists of RNA.  Once the retroviral genome and a molecule of rt enter a host cell, the enzyme uses the RNA genome as a template to build a single-stranded DNA complement.  Then, rt works in the opposite direction, catalyzing both the degradation of the RNA genome, and using the newly synthesized DNA as a template to build another strand of DNA.  The result is double-stranded DNA, which is then moved into the nucleus and inserted into a chromosome of the host cell.  The rt molecule has no proofreading capability.

18. In its synthesis of the 2nd strand of DNA, rt has capabilities most like those of
(a) RNA pol II (b) DNA pol I              (c) DNA pol III   (d) primase       (e) telomerase

19. During the synthesis of the 1st DNA strand, rt catalyzes _____-directed _____ synthesis; whereas in the synthesis of the 2nd DNA strand, it catalyzes _____-directed _____ synthesis.
(a) DNA, DNA; RNA, RNA               (d) DNA, RNA; DNA, DNA
(b) DNA, RNA; RNA, DNA               (e) RNA, DNA; DNA, DNA
(c) RNA, DNA; RNA, DNA

20. The depolymerization reaction that is catalyzed by rt uses up a molecule of _____ for each covalent bond broken, and produces free _____.
(a) ATP, amino acids                                   (d) water, ribonucleotides
(b) water, deoxyribonucleotides                  (e) ATP, deoxyribonucleotides
(c) deoxyribonucleotide, ribonucleotides

21. Some drugs used against retroviruses (such as HIV) are called nucleoside analogs.  They fit into rt’s active site and bond covalently there.  These nucleoside analogs are properly described as _____ of rt.
(a) poisons                                         (d) cofactors
(b) competitive inhibitors                  (e) non-competitive inhibitors
(c) substrates

22. If rt follows the 5’ to 3’ rule then, as a consequence, which of these should occur during rt activity?
1.      The 1st DNA strand is initiated at its own 5’ end.
2.      The 1st DNA strand is initiated at its own 3’ end.
3.      The 2nd DNA strand is initiated at its own 5’ end.
4.      The 2nd DNA strand is initiated at its own 3’ end.
5.      The degradation of the RNA molecule is initiated at its own 5’ end.
(a) 1 & 4         (b) 2 & 3         (c) 1, 3, & 5                (d) 1, 4, & 5                (e) 2, 3, & 5

23. In a constant (i.e. unchanging) environment, rt’s lack of proofreading capability would probably be a drawback for the retroviral population.  But in a rapidly changing environment (such as within the body of an HIV patient who is taking anti-viral meds), the lack of proofreading capability can lead to enhanced retroviral              (a) metabolism.         (b) growth.      (c) irritability.     (d) locomotion.       (e) adaptability.

~~~~~~~~~~

24. All are true of allosteric enzymes, except
(b) they have at least one active site.
(b) they have a site to which an allosteric regulator binds.
(c) are positioned near the ends of metabolic pathways.
(d) they usually have quaternary-level structure.
(e) are, if normally in their active conformation, subject to feedback inhibition.

The following nucleotide sequence is part of a polynucleotide whose ends will, ultimately, receive a 5’ cap and a 3’ tail.  Answer the following 10 questions regarding this sequence.  Use the dictionary on p. 314 of your textbook) as needed.

5’ --- C A U U G U G A U A G U C U C --- 3’

 

25. What is the corresponding sequence of anticodons?
(a) G U A-A C A-C U A-U C A-G A G         (c) G T A-A C A-C T A-T C A-G A G
(b) G A T-T C T-C A T-A C T-G T G            (d) C A U-U G U-G A U-A G U-C U C

26. What is the corresponding sequence of bases in the template DNA strand?
(a) G U A A C A C U A U C A G A G          (c) G T A A C A C T A T C A G A G
(b) G A T T C T C A T A C T G T G (d) C A U U G U G A U A G U C U C

27. What is the corresponding sequence of amino acids?
(a) Val – Thr – Leu – Ser – Glu                    (c) Met – Lys – Arg – Gly – Stop
(b) His – Cys – Asp – Ser – Leu                 (d) Met – Thr – Leu – Ser – Stop

Concerning the correct sequence of amino acids in the previous question, use the figure on p. 79 of your textbook to answer the following questions.  The right-most amino acid in the list will be referred to as the “fifth amino acid,” whereas the left-most amino acid will be referred to as the “first amino acid” (answers will be used only once; 1 point each).
(a) first amino acid                            (d) fourth amino acid
(b) second amino acid                     (e) fifth amino acid
(c) third amino acid

28. Which amino acid is most likely to be found lining an acidic active site?
29. Which amino acid is most likely to be found in a hydrophobic microenvironment?
30. Which amino acid has an R group that is most likely to help stabilize the 3
° and/or 4° structure of the polypeptide by participating in a covalent bond?
31. Which amino acid has an R group that is most similar in structure to part of a purine?

~~~~~~~~

32. If the sequence (underneath the bold paragraph on the previous page) is always located inside of, but near the ends of introns, then it would most likely be part of a
(a) spliceosome.                               (d) splice site.
(b) signal sequence.                         (e) polypeptide-coding sequence.
(c) ribosome-binding sequence.

33. If this sequence is part of an exon, and if either the cap or tail does not get attached, then this sequence would be quickly converted into free _____ by the catalytic action of _____.
(a) amino acids, proteases                          (d) ribonucleotides, ribozymes
(b) ribonucleotides, exonucleases              (e) deoxyribonucleotides, DNA pols
(c) deoxyribonucleotides, spliceosomes

34. At the time when the polynucleotide to which the sequence belongs is being synthesized, all of the following can be occurring simultaneously, except
(a)   a separate RNA pol can be transcribing the same gene.
(b)   another transcription initiation complex can be undergoing assembly at the promoter.
(c)   the polynucleotide can start to detach from its template.
(d)   the 5’ cap can be attached.
(e)   the translation of this same polynucleotide.

~~~~~~~

35. The graph below is most likely to show the activity of an enzyme that is found in
(a) the lysosomes of deep-water fishes.                (d) the human stomach.
(b) bacteria growing in an alkaline hot spring.       (e) healthy human saliva.
(c) bacteria growing in an acidic, tropical bog.

 Sorry. The graph did not translate from Word. 

Proceed to Part 2 and read the directions.

Part 2. (40 points).  Be sure that you have entered the essay numeral in the blank on the cover of your test booklet.  Make NO identifying marks on the essay pages.  Using indelible ink and writing in paragraph format, write answers for both essays.  You may write on the back of the page, but do NOT continue your answer on another sheet of paper.  To receive full credit, essays must be legible, complete, concise, and well organized (20 points each).

  1. How do the anti-parallel condition of DNA and the covalently bonded condition of the dimers that comprise replisomes contribute to making the “trombone model” of lagging-strand synthesis necessary?

 2. Structurally (i.e. chemically) what do telomerases, spliceosomes, and ribosomes have in common?  Distinguish between the functions of the nucleic acid component of each.

 ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                              Test #2                                   ___________________
FALL 2006                              100 points                                   Essay Numeral
DR. DINI                                 Form 1

DIRECTIONS FOR PART 1: Fill in the SS# Bubbles and the Form Bubble on your scantron.  Choose the one BEST response for each test item (2 raw points each, except where indicated).  Sparkle!

1. If all peptide bonds of a protein get broken, what are the smallest units that would continue to exist, without attachment to anything else?
(a) atoms     (b) amino acids     (c) alpha helices     (d) polypeptides     (e) proteins

2. The specificity of single polypeptides’ active sites, receptor sites, channels, or allosteric sites is most directly the result of which level of protein structure?
(a) primary                  (d) quaternary
(b) secondary              (e) none; it’s the DNA sequence that directly codes for the polypeptide
(c) tertiary

The next two questions use the key below:
1.
      primary                  3. tertiary
2.
      secondary             4. quaternary

3. If all of the hydrogen bonds of a protein get broken, what level(s) of protein structure should remain intact?
(a) 1 only         (b) 3 only         (c) 1 & 2          (d) 1 & 3          (e) 3 & 4

4. Disulfide bonds are involved in maintaining the _____ level(s) of protein structure.
(a) 1 only         (b) 3 only         (c) 1 & 2          (d) 1 & 3          (e) 3 & 4
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Match the description on the left with the correct chemical bond on the right.  All responses will be used. (1 point each).

5. Form between R groups of only 1 kind of amino acid                    (a) Glycosidic
6. Formation involves the 5’ to 3’ rule                                               (b) Ester
7. More abundant in polysaccharides than in oligosaccharides         (c) Peptide
8. Formation is catalyzed at P sites                                                   (d) Phosphodiester
9. Found in fats and oils                                                                      (e) Disulfide
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

10. Among animals, only a few species (mostly mollusks) can synthesize cellulase.  If it were possible to transfer the gene for cellulase into the human genome, then we humans might be able to derive calories from _____ polymers, such as those that comprise _____.
(a) alpha glucose, amylopectin                       (d) beta glucose, glycogen
(b) beta glucose, wood                                   (e) alpha glucose, cellulose
(c) alpha glucose, chitin

11. Which of these molecules is most likely to be found in the interior of a protein that is suspended in an aqueous environment?
(a) alanine, a non-polar amino acid                (c) amylose, an unbranched starch
(b) thymine, a nitrogenous base                     (d) lysine, a basic amino acid
                                                                                                [submitted by KA, modified]

12. All are true statements about RNA Processing, except
(a)
   it occurs in the nucleus.
(b)
   it can remove introns from mRNA.
(c)
   it is catalyzed by a ribozyme.
(d)
   it immediately follows transcription in eukaryotes.
(e)
   It is performed by RNA pol and, in eukaryotes, by transcription factors as well.

13. A hypothetical eukaryotic chromosome has 500 ori’s.  For replication to occur with maximum efficiency, how many replisomes can be working on this chromosome simultaneously?
(a) 50               (b) 250             (c) 500             (d) 1000           (e) 2000

14. Which amino acids permitted Hershey and Chase to detect radioactivity in viral proteins (refer to chart on back of Essay 1, if necessary)?
(a)
   those with phosphates in their R groups        (d) cysteine and methionine
(b)
   those with potassium in their R groups          (e) glutamine, lysine, and arginine
(c)
   all those with non-polar R groups

15. R-group interactions are to proteins as _____ bonds are to double-stranded DNA (dsDNA).
(a) hydrogen          (b) phosphodiester            (c) ester           (d) ionic          (e) covalent

16. Assuming that each has the same number of base pairs, which double-stranded DNA molecule should require the LEAST amount of energy to completely separate into two strands?  One that has the greatest proportion of
(a)
    A-T pairs.        (c) purine-purine pairs            .                       (e) A-U pairs.
(b)
    G-C pairs.       (d) pyrimidine-pyrimidine pairs.

17. If the nucleotide sequence for an amino acid is GTA on the non-transcribed strand of DNA, what is the nucleotide sequence of the corresponding anticodon?
(a) CTA     (b) CAU     (c) GUA      (d) CAT     (e) GTA             [submitted by NC, modified]

18. Without the trombone model, it would be difficult to account for
(a) simultaneous transcription and translation in prokaryotes.
(b) lagging-strand synthesis.
(c) how replisomes determine where to begin the process of replication.
(d) leading-strand synthesis.
(e) the existence of circular chromosomes.

19. In a prokaryotic cell, Okazaki fragments cease to exist as the direct result of the action of
(a) primase.                (c) DNA pol III.             (e) helicase.
(b) DNA pol I.               (d) DNA ligase.

20. All are true statements about a stretch of DNA whose newly constructed daughter DNA consists of Okazaki fragments, except
(a) it is the site of discontinuous DNA replication.
(b) primase is more active along this stretch than along the same stretch on the complementary template.
(c) it is the leading strand.
(d) its synthesis involves the trombone model.
(e) the daughter DNA is constructed in its own 5’ to 3’ direction.

21. All are observed in prokaryotes, except
(a) segregation of daughter chromosomes.               (d) proofreading by DNA pols.
(b) the end-replication problem.                                  (e) the 5’ to 3’ rule.
(c) involvement of primers in DNA replication.

Partly from the textbook……

22. A eukaryotic gene includes:
                        1. introns
                        2. DNA transcribed into RNA, which is then not translated
                        3. promoters and other regulatory sequences
                        4. exons
(a) 1 only         (b) 4 only         (c) 1, 2, & 4          (d) 1, 3, & 4            (e) all four of these
                                                                                                [submitted by TB, modified]

23. Cellular DNA pols directly require all of the following to catalyze DNA-directed DNA synthesis, except
(a)
   an RNA template strand.
(b)
   pieces of previously existing nucleic acid with free 3’ ends that can be extended.
(c)
   a supply of free nucleoside triphosphates.
(d)
   single-stranded DNA (ssDNA) template strands.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

24. Which drawing best depicts a single-stranded RNA (ssRNA) molecule that can be accurately described as mostly “anti-parallel”?

 

 25. DNA replication is 10X slower in eukaryotes than in prokaryotes.  It would be even slower in eukaryotes, except that eukaryotes have
(a) linear chromosomes.                    (d) condensed chromosomes throughout nuclear division.
(b) multiple ori’s/chromosome.           (e) telomerase activity.
(c) histones on the DNA.

26. Which of these does NOT consist of both protein and nucleic acid?
(a) a ribosomal subunit, by itself     (c) a primer, by itself      (e) a complete bacteriophage
(b) telomerase, by itself                   (d) snRNP

27. All are true of functional ribosomes, except
(a)
   their activity requires at least three different types of RNA.
(b)
   their chief activity is catalyzed by a ribozyme.
(c)
   their chief activity involves complementary base-pairing.
(d)
   they read a triplet code.
(e)
   they perform DNA-directed polypeptide synthesis.

The following three matching-type questions (1 point each) refer to the information below.  If used at all, responses will be used only once.

A hypothetical eukaryotic polypeptide is 1000 amino acids in length, and the gene that codes for this polypeptide is 90% intronic. 

28. About how many base pairs should this gene consist of?                                   (a) 3,000
                                                                                                                                          (b) 6,000
29. About how many nucleotides should be removed by spliceosomes?                (c) 27,000
30. Minus cap and tail, about how many nucleotides should                                      (d) 30,000
  comprise the mature mRNA molecule?                                                                      (e) 100,000

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

31. RNA-directed DNA synthesis is carried out by
1.
      RNA polymerases.
2.
      telomeres.
3.
      telomerases.
4.
      replisomes.
5.
      retroviruses.

(a) 2 only         (b) 1 & 2          (c) 3 & 4          (d) 3 & 5          (e) 1, 3, & 5

32. Irreversible, but not reversible, denaturation of proteins commonly involves breaking
(a) hydrogen bonds.                (c) ionic bonds.                                  (e) R-group interactions.
(b) peptide bonds.                   (d) hydrophobic interactions.

33. The ways to determine the rate of enzyme-catalyzed dehydration synthesis reactions include measuring the
                        1. disappearance of water molecules from the reaction vessel.
                        2. generation of new ATP molecules in the reaction vessel.
                        3. disappearance of enzyme molecules from the reaction vessel.
                        4. appearance of dimers, trimers, oligomers, or polymers in the reaction vessel.
                        5. disappearance of monomers from the reaction vessel.
(a) 1 & 2             (b) 1 & 5           (c) 1, 4 & 5       (d) 3, 4, & 5            (e) all five of these

34. Enzymes _____ reactions by _____ activation energy.
(a) stop, removing                   (c) cause, maintaining                            (e) speed, lowering
(b) cause, providing                (d) catalyze, increasing

Part 2. (40 points).  Enter your essay numeral in the blank on the cover of your test booklet.  Make NO identifying marks on these essay pages.  Using indelible ink, write answers for both questions on these colored sheets.  You may write on the back of the page, but do NOT continue your answer on the other sheet.  To receive full credit, essays must be correct, legible, complete, concise, and well organized (20 points each).

1. Use the dictionary of the genetic code below and the table on the reverse side to answer the following questions about this portion of the non-transcribed (nt) strand of exonic DNA:

                          

ntDNA:            A  T  T  G  A  A  G  T  G  C  C  C  G  C  T  A  A  A  C  T  A
                                      ^

(a) What is the complementary nucleotide sequence of the DNA strand that is to be transcribed?

(b) What is the corresponding nucleotide sequence of the mRNA transcript?

(c) Assuming that the left-most nucleotide in the correct mRNA sequence in (b) above is the first base of a codon, what is the corresponding sequence of amino acids (abbreviations are OK)?

 

            _________ - ________ - ________ - _________ - _________ - _________ - ________

                     1                  2                   3                  4                  5                    6                 7

(d) The 2nd amino acid’s R group interacts with the 6th amino acid’s R group.   What type of R-group interaction should this be, and what affect should this interaction have on the shape of this stretch of amino acids?

(e) If the 4th nucleotide in the non-transcribed DNA strand (the nucleotide indicated by the ^) undergoes a point substitution mutation to Adenine (A), what affect should this mutation ultimately have on the shape of the stretch of amino acids described in (d) above, if the mutation is not repaired?

 2. Assume that the amino acid sequence you determined in Essay 1 is part of an enzyme.  The mutated version of the enzyme has a new binding site that the original enzyme lacked.  The mutated enzyme’s substrate cannot fit into the new binding site, but other chemicals can do so.  Use proper terminology to describe two different ways that these other chemicals can harm the enzyme’s effectiveness by associating with the new binding site.

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                          Test #2                                                          Form 1
FALL 2007                                          100 points                                                   DR. DINI                                

DIRECTIONS: Fill in the SS# bubbles and the Form bubble on your scantron.  Choose the one BEST response for each test item (2 raw points each).  Amaze!

1. Which organelle has an enzyme that is poisoned by hydrogen cyanide?
A) ribosome                (C) lysosome                  (E) mitochondrion
B) nucleus                   (D) rER

2. What type of reaction is catalyzed when an enzyme stresses the covalent bonds of a substrate?
A) coupled                   (C) hydrolysis              (E) dehydration synthesis
B) endergonic              (D) denaturation

3. Experiments performed by which of these researchers most directly and strongly supported the X-ray diffraction evidence that DNA’s diameter is constant?
A) Chargaff      (B) Griffith          (C) Hershey & Chase              (D) Avery, McLeod & McCarty

4. Which bonds of DNA molecules are broken by helicase?
A) hydrogen                 (C) phosphodiester                 (E) Van der Waals forces
B) peptide                    (D) ester

5. Substrate and enzyme molecules are present in a reaction vessel, along with a “mystery chemical.”  As more substrate is added, the reaction proceeds.  Thus, the “mystery chemical” is probably a
            1. poison.    2. competitive inhibitor.    3. non-competitive inhibitor.
A) 1 only                      (C) 1 or 2                     (E) 1, 2, or 3
B) 2 only                      (D) 1 or 3        

6. If a 4° protein’s polypeptides are linked to each other by non-covalent bonds, these will be _____ bonds.
A) peptide        (C) hydrogen                (E) ester
B) disulfide      (D) phosphodiester

7. Which statement is false?
A) Enzymes speed reactions by lowering activation energy.
B) Allosteric enzymes permit regulation of metabolic pathways.
C) Active site conformation changes once the substrate is in place.
D) “Biological catalysts” are limited to proteins called “enzymes.”
E) Enzyme poisons generally form covalent bonds with the enzyme.

8. The observation that the 5’ and 3’ ends on DNA molecules differ from one strand to the other is most closely associated with which feature of DNA?
A) DNA is helical.                    (C) DNA’s nucleotide sequence carries genetic information.
B) DNA is anti-parallel.            (D) A = T and G = C. 

9. Which of the following can be used by humans as energy sources?
    1. fatty acids    2. cellulose    3. starch    4. glycogen    5. chitin
A) 1 only          (B) 1 & 2          (C) 1 & 3         (D) 1, 3, & 4    (E) all five
                                                                                                            [submitted by MR, modified]

10. Considering ALL of its functions, which of the following can a replisome perform?
            1. breaking of hydrogen bonds
            2. breaking of phosphodiester bonds
            3. formation of phosphodiester bonds
A) 1 only          (B) 2 only         (C) 1 & 2                     (D) 2 & 3         (E) 1, 2, & 3

11. A monomer has the following attached to its central carbon: a carboxylic acid group, an amine group, a simple hydrogen, and an R group.  Which of these is a potential function of this monomer's polymers?
A) Contraction                                                 (D) Lubrication

B) Catalyst of peptide bond formation            (E) Insect exoskeleton material
C) Insulation                                                                                        [submitted by ED, modified]


12.
An enzyme that has an optimal pH of 1.5 is placed in alkaline conditions, which of these bonds should be LEAST affected?
A) Electrical interactions         (C) Peptide bonds
B) Ionic bonds                         (D) Hydrogen Bonds                           [submitted by ED, modified]


13.
What is true of lagging strand replication?
A) It involves synthesis of Okazaki fragments.
B) It involves synthesis of a single primer.
C) It violates the 5’ to 3’ rule.
D) It requires frequent but temporary disassembly of the replisome.
E) It involves continuous DNA replication.

14. What is true of prokaryotic chromosomes?
            1. They are circular.
            2. They contain non-coding DNA.
            3. They have lots of histones.
            4. Their replication involves proofreading.
            5. They have telomeres.
A) 1 & 4           (B) 1, 3, & 5          (C) 1, 4, & 5           (D) 2, 3, & 5          (E) 3, 4, & 5

15. Compared to the mature mRNA transcript, the pre-mRNA of eukaryotes
            1. is shorter.    2. is longer.    3. has cap and tail.    4. lacks cap and tail.
A) 1 & 3           (B) 1 & 4          (C) 2 & 3         (D) 2 & 4

16. If a protein is reversibly denatured in a test tube, but attempts to renature it by returning it to its normal functioning conditions are unsuccessful, then the reason for failure to renature is probably
A) a chaperonin was required to get the protein into its final conformation.
B) the solute concentration of the surroundings is not optimal.
C) the number of ribosomal subunits is too low.
D) the pH of the surroundings is not optimal.
E) the temperature of the surroundings is not optimal.                      [submitted by CI, modified]

17. What is true of mature eukaryotic mRNA transcripts?
A) Ribosomes may be observed to attach to them within the nucleus.
B) They contain non-coding nucleotide sequences called introns.
C) They are synthesized by ribosomes.
D) They are composed of amino acids.
E) They are ready for use once they are outside of the nucleus.

18. In translation, which of these is last to associate with the mRNA strand?
A) elongation factor                 (D) large ribosomal subunit
B) release factor                     (E) small ribosomal subunit
C) initiator tRNA

19. Both polypeptides and polynucleotides have “backbones.”  Which of these groups do NOT belong to such backbones?
            1. R groups
            2. amino group attached to alpha carbon
            3. carboxylic acid group attached to alpha carbon
            4. nitrogenous bases
            5. pentoses
A) 1 only          (B) 1 & 4          (C) 1 & 5         (D) 2, 3, & 4        (E) 2, 3, & 5
                                                                                                                        [inspired by CH]

20. In “alternative RNA splicing”
A) prokaryotic mRNA can be translated by more than one ribosome simultaneously.
B) RNA pols select different genes to transcribe from one moment to the next.
C) the length of the cap and tail must vary.
D) enzymes, rather than ribozymes, do the splicing.
E) introns can sometimes be treated as exons.

21. Which is the part of a mRNA molecule that interacts directly with the tRNA molecule?
A) 3’ end          (B) 5’ end        (C) codon        (D) P site         (E) anticodon

22. Which of these can potentially have carbon-containing rings in their structures?
            1. lipids    2. simple sugars    3. cholesterol    4. steroid hormones
A) 1 & 3           (B) 1, 2, & 3         (C) 1, 2, & 4                        (D) 2, 3, & 4           (E) all four
                                                                                                            [submitted by SH, modified]

23. What is true of leading strand replication in prokaryotes?
A) Primase functions only once.
B) Daughter DNA is made in the daughter’s 3’ to 5’ direction.
C) No single strand binding proteins (SSB’s) are involved.
D) It is discontinuous.
E) Only DNA polymerase I is active, not DNA pol III.

24. To catalyze the synthesis of daughter DNA, the DNA pols require
A) a supply of rRNA molecules.          (D) a previously existing nucleotide to start work from.
B) a supply of free amino acids.         (E) spliceosomes
C) a supply of tRNA molecules.

25. The “permanent” solution to the end-replication problem of eukaryotes is
A) telomeres.                          (C) telomerase.                           (E) telophase.
B) centromeres.                      (D) circular DNA molecules.

26. Which of these catalyzes the synthesis of a product that is most similar to the product made by RNA pol?
A) DNA pol III      (B) retroviruses        (C) primase          (D) telomerase          (E) DNA ligase

27. Before eukaryotic RNA pols can attach to DNA templates, ____ must associate with the promoter.
A) ori’s.                        (C) activators.                         (E) transcription factors
B) Dna A.                    (D) enhancers.

28. Which of the following can be found in/on a functioning ribosome during protein synthesis?
              1. pre-mRNA binding site
              2. tRNA molecule
              3. A,P, and E sites
              4. a growing polypeptide
              5. elongation factors
  A) 1 & 2 only      (B) 4 & 5 only      (C) 1, 2, & 3        (D) 2, 3, 4, & 5        (E) All five
                                                                                                            [submitted by SG, modified]


29. Which of the following are characteristics of telomeres?
             1. permanent solution to the end-replication problem of eukaryotes
             2. contain “junk” DNA that acts as a “buffer”
             3. found in both prokaryotes and eukaryotes
             4. rejuvenated by telomerase in normal somatic cells
             5. rejuvenated by telomerase in non-somatic (germ line) cells
 A) 1 & 2 only               (B) 2 & 5 only             (C) 2, 3, & 4                (D) 3, 4, & 5
                                                                                                            [submitted by SG, modified]

       

30. Which is a proper function of both the cap and tail of mature mRNA?
A) to permit ribosomes to associate with mRNA more efficiently.
B) to act as a signal peptide to allow mRNA access to the rER.
C) to attract spliceosomes to the mRNA.
D) to bore new pores in the nuclear envelope.
E) to stimulate RNA pols to work more effectively.

The following six questions refer to the information below:

During G1 in a normal somatic cell, a single eukaryotic chromosome has 600 pg of DNA, is 1,000,000 base pairs long, and 20% of its nitrogenous bases are cytosines.

31. During the subsequent G2, what should be true of this chromosome?
            1. It should be condensed.
            2. It should be decondensed.
            3. It should consist of sister chromatids.
            4. It should have two centromeres.
            5. It should be in the unreplicated condition.
            6. It should be circular.
A) 1 & 3           (B) 2 & 3          (C) 1, 3, & 6       (D) 3, 4, & 5             (E) 2, 3, 4, & 5

32. How much DNA should be present during G2 on this eukaryotic chromosome?
A) exactly 300 pg                                (D) slightly less than 1200 pg
B) exactly 600 pg                                (E) exactly 1200 pg
C) slightly more than 1200 pg

33. Roughly how many free deoxyribonucleotides were required to duplicate this chromosome during S phase?
A) 500,000                   (C) 1,500,000              (E) 4,000,000
B) 1,000,000               (D) 2,000,000

34. What percentage of the nitrogenous bases in the DNA should be adenines?
A) 20%            (B) 30%           (C) 40%           (D) 50%           (E) 60%

35. If 90% of this chromosome is intronic, and if all of the exonic DNA codes for polypeptide sequences, then about how many amino acids should the exonic portions of this chromosome code for?
A) 33,333         (B) 66,666       (C) 1,000,000        (D) 1,666,666        (E) 3,000,000

36. Roughly how many ribonucleotides should be required to build the corresponding mature mRNA for this chromosome, excluding caps and tails?
 A) 10,000        (B) 33,333       (C) 100,000           (D) 200,000           (E) 333,333

~~~~~~~~~~~~~~~~~~~~~~~~~~~

37. Two ways a prokaryotic cell can increase its production of a particular polypeptide are to
            1. increase number of replisomes.
            2. permit more than one RNA pol to transcribe the operon simultaneously.
            3. increase speed of spliceosomes.
            4. use polyribosomes.
A) 1 & 3           (B) 1 & 4          (C) 2 & 3         (D) 2 & 4

38. In translation, a sequence of ___ is used as a template for the synthesis of a sequence of ___.
            1. ribonucleotides    2. riboses    3. deoxyribonucleotides    4. amino acids    5. fatty acids
A) 3, 1              (B) 1, 3                       (C) 1, 4                        (D) 3, 4                   (E) 2, 5

The following three questions are based on the information provided, and the copy of the dictionary of the genetic code below:

A sequence of anticodons bonds to a ribosome in the following sequence (from left to right):

                        Anticodons:               UGU  UUC  UCA  ACA  CUA

39. What is the corresponding DNA sequence of the DNA template strand?
A) A C A A A G A G T T G T C A T                 (C) T G T T T C T C A A C A C T A
B) A C A A A G A G U U G U G A U                (D) T G T T T T T C A A C A G T A

40. What is the corresponding amino acid sequence?
A) Thr – Lys – Ser – Cys – Asp                      (C) Cys – Phe – Ser – Thr – Leu
B) Thr – His – Cys – Leu – Asp                      (D) Cys – Lys – Ser – Cys – Leu

41. According to Table 1 below, the correct sequence of amino acids from the question immediately preceding this one is most likely to occur
A) on the exterior of a membrane protein, next to fatty acid tails.
B) in the interior of a cytosolic protein.
C) on the exterior of a membrane protein, next to cholesterol’s 5-sided ring.
D) in the interior of a membrane protein, lining a channel used to transport a specific material.

Table 1.  Characteristics of Amino Acid R groups

Non-polar

Polar

Charged

Gly

Ser

Asp

Ala

Thr

Glu

Val

Cys

Lys

Leu

Tyr

Arg

Ile

Asn

His

Met

Gln

 

Phe

 

 

Trp

 

 

Pro

 

 

~~~~~~~~~~~~~~~~~~~~~~~~~

42. A student analyzes a sample of cow chromosomes for a professor’s research.  It is determined that the sample contains 5.1% uracil, 5.3% thymine, 10.0% adenine, 39.2% guanine and 40.4% cytosine.  What can be determined about the sample from these data?
            1. The sample is composed of pure DNA.
            2. The sample is composed of a mixture of DNA and RNA.
            3. The sample must be from Chargaff’s lab, for these data are Chargaff’s rules.
            4. The sample is composed of pure RNA.
            5. At least some of the chromosomes may have been collected from cells in S phase.
A) 1 only          (B) 2 & 5          (C) 3 & 4         (D) 1, 3, & 5         (E) 2, 3 & 5
                                                                                                            [submitted by AW, modified]

43. A woman starts her car in the garage while talking on her cell phone.  She forgets to open the garage door and the garage fills with carbon monoxide (CO) gas from her exhaust.  The CO binds to her hemoglobin (Hb), and she starts to lose consciousness.  Her daughter finds her and phones 911.  When the ambulance arrives, the crew places her on 100% O2 as they check her vitals, and rush her to the hospital, where she is placed in a hyperbaric chamber and administered O2 under high pressure.  Which of these best describes CO’s affect on her hemoglobin molecules, and the affect of the hospital treatment?  (NOTE: The answer presumes that CO is not a true poison of Hb.)
A) The CO acted as a competitive inhibitor and the cure was to displace the CO from the Hb with pressurized O2.
B) The CO acted as a non-competitive inhibitor and the cure was to displace the CO from the Hb with pressurized O2.
C) The CO acted as a competitive inhibitor and the cure was to use O2 as a cofactor in releasing the CO from the Hb.
D) The CO acted as a competitive inhibitor and the cure was to use O2 as an allosteric activator to rejuvenate the Hb.                                                                               [submitted by AW, modified]

44. Which of these is a codon for the amino acid whose R group can form a covalent bond that helps maintain the tertiary (and sometimes quaternary) structures of proteins?
A) AUG            (B) UGU          (C) UAG          (D) GCA          (E) GAA

The next two questions refer to the information below:

Glycogen is actually not pure carbohydrate.  It has a small protein at its core, and is more properly called glycogenin.  Unlike starch, which is often stored within organelles (chloroplasts, amyloplasts), glycogenin accumulates in the cytosol where it can form granules.

45. The protein portion of glycogenin
A) should have a signal peptide attached to it.
B) should be synthesized by free ribosomes.
C) should be synthesized by enzymes of the sER.
D) should consist of fatty acids.
E) is properly called an oligosaccharide.

46. The carbohydrate portion of glycogenin should
            1. be composed entirely of beta-glucoses.
            2. be highly branched.
            3. contain many glycosidic linkages.
            4. be an oligosaccharide.
            5. contain ½ as many calories as an equal mass of lipid.
A) 1 & 2           (B) 2 & 3          (C) 1 & 5         (D) 2, 3, & 5                (E) all five

~~~~~~~~~~~~~~~~~~~~~

47. All are true of ribozymes, except
A) telomerase is a good example of a ribozyme.      (C) they play an important role in translation.
B) they are composed of ribonucleotides.                  (D) spliceosomes contain some.

48. With the exception of the initiator tRNA, what is the correct sequence in which these sites are encountered by tRNAs involved in translation?
            1. P site    2. E site    3. A site
A) 1, 2, 3          (B) 3, 2, 1        (C) 1, 3, 2        (D) 2, 3, 1        (E) 3, 1, 2

49. In a healthy cell, when the ultimate product of gene expression is a polypeptide, which of these must be involved in gene expression?
            1. transcription                        3. translation
            2. reverse transcription           4. replication
A) 1 only          (B) 1 & 2          (C) 1 & 3         (D) 2 & 3         (E) 2 & 4

From the textbook…

50. The induced fit model is the current model for understanding how
A) continuous DNA replication occurs.
B) active sites of enzymes process their substrates.
C) leading strand synthesis occurs.
D) Okazaki fragment synthesis occurs.
E) prokaryotic (NOT eukaryotic) DNA replication occurs.

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                          Test #2                                           _____________
FALL 2008                                         100 points                                      Essay Numeral
DR. DINI                                             Form 1

Directions for Part 1 (60 points).  Choose the letter representing the BEST response for each test item.  Each item is worth 2 raw points each, except where indicated.  Shine!

The first six questions are indicated by the BOLD question numbers in the cells of the table below.  Use the common answer key below to provide the appropriate choice for each BOLD numbered cell in the table.  The same cell during G1 has 600 pg of DNA, distributed among 24 chromosomes. All responses will be used at least once (1 point each).           A. 12        B. 24        C. 48        D. 300        E. 1200

Feature

single daughter cell at completion of mitosis

single daughter cell during mid-Prophase I

single daughter cell at completion of meiosis

# of centromeres

1

2

5

# of sister chromatids

0

3

0

mass of DNA (pg)

600

4

6

7. All are true statements concerning prophase I, except
A) Tetrads are present, and each tetrad consists of two sister chromatids.
B) Replicated chromosomes condense at this time.
C) Larger chromosomes have the potential to exhibit greater numbers of chiasmata.
D) Synaptonemal complexes are present at this time.
E) Genes from one parent may be placed on the same chromosome with genes from the other parent.

8. Mitosis and meiosis are similar in that
A) two daughter cells are produced at the final conclusion of each.
B) each includes an equational division.
C) centromeres divide during all of the prophases in each.
D) in each, the final daughter cells contain chromosomes in the replicated condition.
E) introduction of genetic variation is a feature of each.

 9. Textbook question.  Alpha glucose differs from beta glucose in
                                                1. the relative positions of the –H and –OH at carbon #1.
                                                2. the identity of the enzymes that use it as a substrate.
                                                3. the identity of the polymers that it is involved in.
                                                4. its chemical formula i.e. (CH2O)n.
                                                5. its cellular functions.
A) 1, 2, & 3     (B) 1, 3, & 5     (C) 1, 2, 3, & 4     (D) 1, 2, 3, & 5     (E) all 5 of the above

10. Textbook question.  If one gram of carbohydrate contains X number of calories, then one gram of lipid should contain a number of calories equal to about
A) √X              (B) 1/2X          (C) X               (D) 2X             (E) X2

The next two questions refer to the description below:
As they mature, human RBCs lose their nuclei, ribosomes, and all of their organelles, except for their cytoskeletons.  As RBCs lose their organelles, their overall shape changes from spheroids to biconcave discs, a change that makes them more flexible and that makes gas exchange more effective.  At maturity, RBCs are among the smallest cells in the body.

11. Which of these functions should mature human RBCs be able to perform?
A) RNA processing               (C) transcription        (E) none of the above
B) DNA replication                (D) translation

12. What is the functional significance of their small size and change in shape?
A) These give the RBCs a more effective surface area to volume ratio.
B) RBCs are able to grow larger and larger without danger of self-poisoning.
C) RBCs are able to live longer than most cells of the human body.
D) This makes it easier for RBCs to manufacture new ribosomes.
E) There is less cytosol for RBCs’ secretory vesicles to have to move through.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

13. Which statement concerning enzymes is true?
A) Enzymes cause reactions to occur that would otherwise never occur.
B) Enzymes cause reactions to occur more easily by eliminating the activation energy barrier.
C) Ribozymes are enzymes that consist of catalytic RNA.
D) If an enzyme requires a cofactor, then the cofactor will bond to the enzyme’s allosteric site.
E) Allosteric regulation involves competitive inhibitors.

The next four questions are based on the labeled drawing below of a dipeptide.   Responses that are used will be used only once (1 point each).

                                Figure could not be presented in this format.  See test at back of lab manual.   

14. Which arrow is indicating a group that could, potentially, participate in the formation of a new peptide bond?

15. Which arrow is pointing at an atom that is participating in an existing peptide bond?

16. Which arrow is pointing at a group that could help maintain the 3° or 4° structure (but NOT 1° structure) of a protein by participating in the formation of a covalent bond?

17. Which arrow is pointing at an atom that could participate in the type of bond that helps maintain the 2° level of protein structure?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

18. Which of the following is NOT true of the active site of a cytosolic enzyme that catalyzes a hydrolysis reaction by providing the proper acidic environment?
A) there should be negatively charged R groups in the active site.
B) more than one product should be released from the active site per catalysis.
C) products released from the active site have lower free energies than the reactants.
D) the active site should engage in the phenomenon known as “induced fit.”
E) the active site’s pocket should be hydrophobic.

19. Textbook question.  Which statement is NOT true of chaperone proteins?
A) A chaperonin consists of more than one protein that, together, assist in the proper folding of other proteins.
B) Chaperonins direct the final stages of protein folding inside a hydrophobic chamber, changing polypeptides’ primary structures as they do so.
C) Chaperonins isolate unfinished proteins from “bad influences” in the environment, influences that might otherwise interfere with proper folding.
D) Polypeptides enter and exit the chaperonin via the same opening.
E) Within chaperonins, proteins made of a single polypeptide achieve their 3° structure.                                                                                                       [submitted by LA, modified]

20. In a hypothetical situation, two substrate molecules enter an enzyme’s active site.  Subsequently, H is removed from one substrate and OH is removed from the other substrate.  What is true regarding this reaction?
A) The same exact reaction could also occur in this enzyme’s allosteric site.
B) This enzyme catalyzes a hydrolysis reaction.
C) This reaction may link two monomers with a covalent bond.
D) A higher number of substrate molecules, relative to product molecules, will inhibit the forward reaction.
E) Product may be obtained from this reaction without the reactants reaching the transition state.                                                               [submitted by JM, modified]

21. All are true of DNA replication, except
A) it is semi-conservative.        (D) it consists of continuous and discontinuous replication.
B) it occurs during mitosis.     (E) it is usually faithful.
C) it is bidirectional.

22. The “Waring Blender experiment” of Hershey & Chase definitively showed that
A) the nucleus contains a cell’s genetic information.
B) A = T and G = C.
C) eukaryotic chromosomes consist of both DNA and histone proteins.
D) a chemical – the transforming principle – can convert R strain pneumococci into S stain pneumococci.
E) DNA, not protein, is the genetic material of viruses and prokaryotes.

The next two questions refer to the drawing below of a functional cytosolic enzyme consisting of a single polypeptide of 111 amino acids (numbered in intervals of 10 amino acids).  The bold straight lines indicate disulfide bonds.

 Figure could not reproduced in this format.  See test at back of lab manual.

23. What is the minimum number of cysteines that can be present in this enzyme and still allow the enzyme to maintain all of the disulfide bonds shown above?
A) 0                 (B) 2                (C) 4               (D) 8               (E) 16

24. A mutation occurs in the exon that codes for amino acids 40-50, resulting in the loss of all cysteines from this part of the polypeptide.  If no other interactions are created, this mutation will probably cause a change in which level(s) of protein structure?
A) 1° only        (B) 2° only      (C) 3° only      (D) both 1° & 2°         (E) both 1° & 3°

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

25. Even with all of their nitrogen atoms, DNA’s nitrogenous bases are relatively more hydrophobic than are DNA’s phosphate groups.  Watson & Crick, being top-notch biochemists, realized this.  This realization would have allowed them to propose that
A) phosphodiester bonds link neighboring nucleotides together to form a polynucleotide.
B) there are four different types of nitrogenous bases in DNA.
C) In aqueous environments, DNA’s backbones are on the outside of the double helix, whereas the nitrogenous base pairs are on the inside.
D) double-stranded DNA molecules are anti-parallel.
E) deoxyribose, rather than ribose, is the sugar of DNA polynucleotides.

26. If DNA replication were to be done in vitro with all necessary raw materials and proteins present, and if the reaction vessel contained radioactive thymine (T), then what should be true after primase works, but before DNA polymerase I works?
A) There should be no radioactivity in any strand because there is no thymine in DNA.
B) There should be no radioactivity in any strand because there is no uracil in DNA.
C) The leading strand should be more radioactive.
D) The lagging strand should be more radioactive.

27. The existence of primers during DNA replication is required because
A) DNA is anti-parallel.
B) DNA pols can only extend a previously existing oligo- (or poly-) nucleotide.
C) DNA pols follow the 5’ to 3’ rule.
D) of the end-replication problem.
E) DNA replication is bidirectional.

28. Because DNA is anti-parallel, and because a replisome’s dimers are covalently (i.e. permanently) bonded to each other,
A) replication begins at ori’s.
B) RNA primers are required.
C) the lagging strand template as to be looped.
D) SSBs are required to stabilize single-stranded DNA templates.
E) helicase must break hydrogen bonds and unwind the double helix.

29. What is crucial in eukaryotic transcription, that is NOT involved in bacterial transcription?
A) transcription factors                     (C) RNA polymerases                  (E) promoters
B) a ss-DNA template                      (D) uracil ribonucleotides

30. Which of these should be indirectly attached to each other (in the same place and at the same time) during prokaryotic transcription?
     1. ss-DNA    2. pre-mRNA    3. mRNA    4. polypeptides
A) 1 & 3          (B) 2 & 4         (C) 1, 2 & 3         (D) 1, 2 & 4           (E) 1, 3 & 4

31. A hypothetical eukaryotic polypeptide “hot off the ribosome” consists of 500 amino acids.  If the gene that coded for this polypeptide is 90% intronic, then a total of about how many ribonucleotides should have been found in the newly synthesized pre-mRNA molecule (before any RNA processing occurs)?
A) 500                        (B) 1,500          (C) 5,000     (D) 15,000              (E) 150,000

32. What is a consequence of prokaryotic mRNAs lacking a cap and tail?
A) These mRNAs cannot get out of the nucleoid.
B) Ribosomes can attach to prokaryotic mRNAs more readily than to eukaryotic ones.
C) The mRNAs easily (and often) re-attach to the ss-DNA template.
D) Transcription and translation sometimes occur simultaneously.
E) These mRNAs quickly become subject to degradation by exonucleases.

Given the following sequence of exonic non-template DNA located in the interior of a gene, and given a copy of the dictionary of the genetic code, carry out the steps necessary to answer the next two questions.

Non-template DNA:              T A C C G G G T A C A A A T C

33. What is the corresponding amino acid sequence?
A) Tyr – Arg – Val – Gln - Ile            (C) Met – Ala – His – Val – STOP
B) Pro – Arg – Ser – Thr – Tyr         (D) Tyr – Arg – Cys – Val – STOP

34. What is the proper sequence of tRNA anticodons?
A) ATC-CGG-CAU-CAA-ATC        (D) AUG-GCC-CAU-GUU-UAG
B) ATG-GCC-CAT-GTT-TAG          (E) CAU-GGC-AUG-AAC-CUA
C) UAC-CGG-GUA-CAA-AUC

35. Which of these is a ribozyme that carries out one of its catalytic activities in eukaryotic cytoplasm?
A) mRNA                    (B) rRNA                    (C) snRNA                 (D) tRNA

Proceed to Part 2 and read the directions.

PART 2 DIRECTIONS: (40 points) Using indelible ink and writing in paragraphs, answer the 2 essay questions on the page provided for each.  You may continue an answer on the reverse side, but NOT on another sheet.  Do NOT add your name or any identifying marks to these pages.  Enter your essay numeral in the blank on the front page of your test booklet.  Besides being correct, answers must be legible, complete, concise, and well organized to receive full credit (20 points each).

1. Describe the problem posed to the survival of eukaryotic cells because their linear chromosomes have ends.  Then, discuss how certain eukaryotic cells permanently solve this problem.

2. Describe the roles of hydrogen bonds in proteins and in double-stranded DNA.  Then, discuss the significance of hydrogen bond breakage for each of these two polymers.

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                         Test #2                                  _____________
Fall 2009                                           Form 1                                   Essay Numeral
Dr. Dini

Part 1 Directions (60 points).  Be sure your R# grid and Form Bubble are correctly bubbled in on the scantron.  Enter essay numeral above.  For each test item, choose the letter that represents the BEST response (2 points each).   Kick gluteus maximus!

1. Which of these statements is true of starch, but NOT of cellulose?
            1. Its glucose monomers are in the alpha configuration.
            2. It serves as plants’ primary energy-storage material.
            3. It serves as plants’ primary structural material.
            4. It is used to build the cell plate during plant cell cytokinesis.
            5. Its glucose monomers are joined by glycosidic linkages.
A) 1 & 2          (B) 2 & 5         (C) 1, 2, & 4      (D) 1, 3, & 4            (E) 2, 4, & 5                             [Submitted by EH, modified]

2. What is true of both lipids and carbohydrates?
A) Ester bonds link their monomers.
B) They contain roughly equal numbers of calories per unit mass.
C) They contain carbon, hydrogen, and oxygen in a 1:2:1 ratio.
D) Complex versions are built by dehydration synthesis reactions.
E) Double bonds increase the likelihood that they will be fluids, rather than solids.

3. Plants generally store excess calories as carbohydrates, whereas animals generally store excess calories as fats.  What difference between plants and animals is the ultimate reason that this energy-storage difference exists?
A) Plants don’t move from place to place.      (C) Animals don’t photosynthesize.
B) Animals do not have cell walls.                    (D) Plants cannot synthesize lipids.

4. The enzymes that catalyze the synthesis of triglycerides
A) accept portions of glycogen and amino acids into their active sites.
B) add a molecule of water to each bond they catalyze.
C) provide animals with insulation and padding.
D) do not have to lower an activation energy barrier.
E) have active sites that are poisoned by (carboxyl) acid groups.

5. A particular protein consists of four polypeptide chains.  Which of the following levels of protein structure might this particular protein lack?
A) 1
°               (B) 2°              (C) 3°              (D) 4°                         [Submitted by JC]

6. Which of these is the most accurate statement of the induced fit hypothesis?
A) The binding of substrate depends on an immediately perfect fit between the shape of the active site and of the substrate.
B) Some enzymes change their shape when activators attach to allosteric sites.
C) Competitive inhibitors compete with the substrate for access to the active site.
D) The active site provides a chemical microenvironment ideal for the reaction.
E) The binding of substrate changes the shape of the enzyme’s active site, leading to better bonding between substrate and enzyme.
                                                                                    [Submitted by MR, modified]

The next six questions refer to the description below:

In humans, a polypeptide called preproinsulin is produced by bound ribosomes in certain pancreatic cells.
In the rER, the signal peptide is removed, producing
proinsulin.  Within secretory vesicles that have departed
from the Golgi bodies, various proteinases process the
proinsulin further.  A 37-amino-acid section,
known as the C-peptide, is removed from the middle of proinsulin.  After the C-peptide is removed,
mature insulin consists of an alpha chain and a beta chain, linked to each other by 2 disulfide bonds.  A
third disulfide bond attaches different parts of the beta chain to each other.  Once in the bloodstream, insulin
can reach many body cells, and affects their metabolisms by bonding to membrane receptor proteins.

7. About how many exonic DNA base pairs should code for the C-peptide?
A) 12               (B) 37             (C) 111           (D) 222           (E) 370

8. At the very least, how many cysteine (cys) amino acids are present in mature insulin?  HINT: Cysteine has a sulfhydryl group at the end of its R group.
A) 2                 (B) 3                (C) 4               (D) 6               (E) 8

9. Within secretory vesicles, the C-peptide is further processed by an enzyme that, one at a time, cuts 2 amino acids off of its C-terminus.  Such an enzyme should be called a(n)
A) endonuclease.                (C) aminopeptidase.                  (E) endopeptidase.
B) exonuclease.                   (D) carboxypeptidase.

10. What is the highest level of protein structure that mature insulin has?
A) 1
°               (B) 2°              (C) 3°              (D) 4°

11. The signal peptide tells the cell that insulin should ultimately be
A) exported.                                                               (D) moved into the nucleus.
B) inserted permanently into membrane.               (E) packaged within lysosomes.
C) kept in the cytosol.

12. One effect of insulin on cells throughout the body (though it never enters these cells) is to cause these cells to add more glucose transport proteins (GLUTs) to their plasma membranes.  If these cells have no existing stockpiles of GLUTs or of the corresponding mRNAs, then what is insulin’s probable effect on these cells, and what role does insulin seem to play?
A) stimulates DNA replication, 2nd messenger
B) stimulates translation, 2nd messenger
C) stimulates translation, signal transduction pathway protein
D) stimulates transcription, steroid hormone
E) stimulates transcription, peptide hormone
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

13. Unwinding of DNA during formation of replication forks results in
A) continuous synthesis of DNA on the lagging strand.
B) tension in the dsDNA downstream of the fork, relieved by topoisomerase.
C) formation of new 3’ –OH groups on the template DNA.
D) binding of SSB proteins on the double-stranded parental DNA.
E) replisomes breaking apart to construct daughter DNA in opposite directions.
                                                                                                                                                       [Submitted by VM, modified]

14. RNA processing directly involves which of these?
            1. ribosomes             2. spliceosomes       3. nucleosomes       4. replisomes
A) #2 only      (B) 1 & 2         (C) 2 & 3        (D) 2, 3, & 4               (E) all four of these

15. In what way is the RNA of telomerase similar to the RNA of spliceosomes?
A) Both RNAs are ribozymes.
B) Both RNAs act as templates.
C) Both RNAs act directly on eukaryotic chromosomes.
D) Both RNAs catalyze reverse transcription.
E) Both RNAs temporarily bond to another polynucleotide via hydrogen bonds.

16. In eukaryotes, the hypothesis that one gene codes for a single polypeptide is falsified by the phenomenon of
A) cap & tail addition.                      (C) telomere extension.          (E) > 1 of these
B) alternative RNA splicing.            (D) the trombone model.

17. The trombone model helps to explain
A) how both leading and lagging DNA strands can be synthesized in their 5’ to 3’ directions by a replisome moving in only one direction.
B) why cellular DNA pols must extend previously existing oligonucleotides.
C) why primers are needed.
D) how single-stranded DNA remains stable during DNA replication.
E) how RNA lasso structures are created in eukaryotes.

18. RNA-directed DNA synthesis can be catalyzed by
1. spliceosomes.   2. replisomes.   3. telomerase.   4. telomeres.   5. retroviruses.
A) #1 only      (B) 2 & 3         (C) 3 & 4        (D) 3 & 5        (E) 4 & 5

19. A researcher discovers a drug that turns off the human telomerase gene, but has no way of targeting the drug to specific cells.  This drug should be most helpful, and least harmful, in a
A) post-menopausal woman with cancer.         (C) post-pubertal boy with cancer.
B) 55-year-old man with cancer.                        (D) female fetus with cancer.

20. Which of these is/are significant difference(s) between RNA polymerase and DNA pol III of prokaryotes?  Unlike DNA pol III, RNA polymerase
    1. can perform transcription in the 3’ to 5’ direction of the daughter RNA.
    2. attaches amino acids to the growing mRNA strand.
    3. does not require a primer.
    4. can catalyze the formation of phosphodiester bonds between T nucleotides and the other three kinds of nucleotides.
    5. is not part of prokaryotic replisomes.
A) 1 & 3          (B) 2 & 3         (C) 3 & 5        (D) 4 & 5        (E) 3, 4, & 5                      [Submitted by IAE, modified]

21. Most types of RNA that are produced in eukaryotic and prokaryotic cells are directly involved in
A) DNA replication.    (B) translation.        (C) reverse transcription                                [Inspired by AD]

22. In eukaryotes, replication and transcription cannot occur simultaneously.  Further, condensed chromosomes cannot undergo transcription.  Consequently, eukaryotic transcription should be able to occur during
                                                1. G1               3. G2
                                                2. S                 4. M
A) #1 only           (B) #2 only            (C) #3 only        (D) 1 & 3          (E) 2 & 4

23. If a eukaryotic primary transcript receives a cap and tail, but undergoes NO spliceosome activity, then it should be
A) the same length as the mature mRNA molecule.
B) much shorter than the mature mRNA molecule.
C) about 51-251 nucleotides longer than the primary transcript.
D) thousands of nucleotides longer than the primary transcript.

24. Which should be more active on the lagging strand than on the leading strand during DNA replication?
                        1. SSBs                      3. DNA pol I               5. DNA ligase
                        2. primase                 4. DNA pol III
A) 1 & 2          (B) 3 & 4         (C) 2, 3, & 5        (D) 3, 4, & 5          (E) all five of these

25. Which feature(s) of tRNA molecules allow(s) them to act as “interpreters”?
A) tRNAs consist of about 80 nucleotides.         (D) both A & C
B) tRNAs have an amino acid binding site.        (E) both B & C
C) tRNAs have an anticodon.

26. Francis Crick coined the unfortunate term “Central Dogma of Molecular Biology.”  He also
A) determined that the amount of A
» T, and the amount of G » C.
B) experimentally demonstrated that DNA, not protein, is the genetic material.
C) proposed in 1939 that proteins would be found to be the genetic material.
D) discovered that retroviruses can perform reverse transcription.
E) helped determine the structure of DNA.

27. Hershey & Chase’s experimental design in the “Waring Blender experiment” relied on the fact that
A) in mice, S strain pneumococcus is lethal; R strain is harmless.
B) DNA contains phosphorus (P), but not sulfur (S); protein contains S, but not P.
C) in cells, the amount of A
» T, and the amount of G » C.
D) DNA is a double helix with constant diameter.
E) DNA replication is semi-conservative.

28. Textbook question: To say that DNA replication is semiconservative means that
A) it is bidirectional.
B) half of each double-stranded DNA molecule is daughter DNA, synthesized on a parental template.
C) Okazaki fragments are made only on the lagging strand.
D) it occurs on an anti-parallel molecule of DNA.
E) the DNA-proofreading and DNA-repair capabilities of cells are sometimes imperfect, resulting in non-faithful replication.

29. Which of these features of transcription is shared by prokaryotes and eukaryotes?
A) the type of transcription unit
B) the termination process
C) the number of transcription factors
D) the number of different types of RNA pols
E) RNA pols attach to DNA at promoters

30. During the initiation and termination phases of translation, it is possible that neither the E site nor the A site will have tRNAs in them.  Which two of these can help determine if such a ribosome is in the initiation phase or in the termination phase?
            1. if there is a release factor in the E site
            2. if there is a release factor in the A site
            3. if the initiator tRNA is in the P site
            4. if the initiator tRNA is in the A site
A) 1 or 3         (B) 1 or 4        (C) 2 or 3        (D) 2 or 4

Part 2 directions: (40 points). Use indelible ink and paragraphs to write answers for the 2 essay questions on the pages provided here.  You may continue an answer on the reverse side, but NOT on another sheet.  Do NOT add your name or any identifying marks to these pages.  Enter your essay numeral in the blank on the front page of your test booklet.  Besides being correct, answers must be legible, complete, concise, and well organized to receive full credit (20 points each).

1. Compare and contrast (i.e. discuss differences and similarities between) the reactions catalyzed by the enzymes primase and DNA polymerase I in prokaryotes.  Discuss the significance of each reaction for DNA replication.

2.  Given a dictionary of the genetic code and the pentapeptide sequence below, and always working from left to right, determine the corresponding (a) mRNA sequence, (b) template DNA sequence, (c) non-template DNA sequence, and (d) tRNA sequence (2 points/sequence), entering them in the labeled spaces below.

pentapeptide sequence:              trp – met – met – trp – trp

a) mRNA:

b) template DNA:

c) non-template DNA:

d) tRNA:

 Characteristics of Amino Acid R groups

Non-polar, non-charged

Polar

Glycine (gly)

Serine (ser)

Alanine (ala)

threonine (thr)

Valline (val)

Cysteine (cys)

Leucine (leu)

Tyrosine (tyr)

Isoleucine (ile)

Asparagine (asn)

Methionine (met)

Glutamine (glu)

Phenylalanine (phe)

Charged

Tryptophan (trp)

Aspartic acid (asp)

Proline (pro)

Glutamic acid (glu)

 

Lysine (lys)

 

Arginine (arg)

 

Histidine (his)

2e) Given the table of R-group characteristics above, discuss whether or not the original pentapeptide sequence would be likely to participate in secondary (2°) protein structures, and provide a brief rationale (6 pts)

2f) If the T that is the 4th nucleotide from the left end of the correct template DNA sequence of part (b) above undergoes a point deletion, then what specific affect will this have on the ribosomes that read the corresponding mRNA, i.e. what two kinds of mutations will the ribosomes produce?  HINT: Work it all the way out to the mutant amino acid sequence, showing your work (6 pts).

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 

BIOL 1403                                          Test #2                                   _____________
Fall 2010
                                             100 points                              Essay Numeral
Dr. Dini
                                               Form 1

Part 1 Directions (60 points).  Be sure your R# grid and form bubble are correctly bubbled in on the scantron.  Enter essay numeral above.  For each test item, choose the letter that represents the BEST response (2 points each).  Dominate!

1. It’s easier to lose weight by burning carbs than by burning fats because
A) carbs are polymers, and fats are not.
B) triglycerides can exist in many forms, but glucose in only two forms.
C) fats usually contain double bonds, whereas carbs rarely do.
D) a given mass of fat has about twice as many calories as the same mass of carbs.
E) complex sugars are held together by glycosoidic bonds, whereas fats are held together by ester bonds.

2. Which of these solutions, if drunk, should provide cells with NO calories?  A solution of
A) sucrose.
      (B) maltose.    (C)
a-glucose.      (D) b-glucose.        (E) fructose.

3. What is true of a protein that has more than one N-terminus?
A) It is an abnormal protein.
B) It has 4
° level structure.
C) It has multiple, nitrogen-containing R-groups.
D) It has more than one alpha helix.
E) It was made by a bound ribosome, NOT a free ribosome.

4. To break the backbone of a polypeptide requires breaking
A) hydrogen bonds between backbone elements.
    (D) disulfide bonds.
B) hydrogen bonds between R groups.
                     (E) peptide bonds.
C) ionic bonds.

5. Ultimately, the 1° level of protein structure is determined by
A) spliceosomes.
                    (C) genes.                   (E) replisomes.
B) ribosomes.
                          (D) chaperonins.

6. The 1° level of protein structure is most directly the result of _____ activity.
A) spliceosome
                       (C) gene                      (E) replisome
B) ribosome
                            (D) chaperonin

7. R-group interactions can help maintain which levels of protein structure?
A) primary and tertiary
                        (D) secondary and quaternary
B) primary and quaternary
                 (E) tertiary and quaternary
C) secondary and tertiary

8. What is true of an allosteric inhibitor?
A) It binds to an active site.
                                         (D) It alters the optimal temperature.
B) It stabilizes the inactive form of the enzyme.
        (E) It alters the optimal pH.
C) Once bound, it is irreversible.
                                            [submitted by PW, modified]

9. Besides enzyme, substrate, and, possibly, cofactor, which of the following is/are required for a hydrolysis reaction to proceed speedily?                                                1. water
                                               
2. some form of activation energy
                                               
3. ATP
A) #1 only
        (B) #2 only      (C) #3 only      (D) 1 & 2         (E) 2 & 3

10. Within the body, a cell has larger amounts of the amino acid, isoleucine, than is necessary.  Subsequently, isoleucine acts to slow down its own synthesis.  It does so by
                       
1. allosteric inhibition.              4. allosteric activation.
                       
2. negative feedback.             5. enzyme poisoning.
                       
3. competitive inhibition.
A) #1 only
        (B) 1 & 2          (C) 2 & 3         (D) 2 & 5         (E) 4 & 5                                [submitted by AC, modified]

11. An enzyme may lower activation energy in a hydrolysis reaction it catalyzes by
                                   
1. adding heat.
                                   
2. bring substrates together in the correct position to react.
                                   
3. stressing bonds within the substrate.
                                   
4. providing a favorable chemical environment.
A) 1 or 3
          (B) 1 or 4         (C) 2 or 3         (D) 2 or 4         (E) 3 or 4

12. Chargaff’s rules ultimately helped to explain the
A) constant diameter of double-stranded DNA (dsDNA) molecules.
B) anti-parallel nature of dsDNA.
C) structure of DNA’s backbone.
D) number of base-pairs per unit length of DNA.

13. A hypothetical polynucleotide contains thymine (T), but NO hydrogen bonds.  It is most likely to be a short polynucleotide of
A) mRNA.
       (B) tRNA.        (C) rRNA.        (D) ssDNA.     (E) dsDNA.

14. What is true of exonucleases, DNA pols during proofreading, and snRNAs during intron removal?
A) They are proteinaceous (i.e.made of protein) catalysts.
B) They can break phosphodiester bonds.
C) They are directly involved in alternative RNA splicing.
D) They help comprise replisomes.
E) They can perform reverse transcription.

15. Which part of a DNA template must necessarily occupy the active site of a DNA or RNA polymerase?
A) phosphodiester bond
                      (C) nitrogenous base
B) phosphate group
                            (D) deoxyribose

16. Primase catalyzes the synthesis of a product that is most similar to the product of
A) DNA pol I.
               (C) reverse transcriptase.                   (E) RNA pol.
B) DNA pol III.
             (D) telomerase.

17. Which does NOT belong?
A) leading strand
                                 (C) trombone model                            (E) multiple primers
B) Okazaki fragments
                        (D) discontinuous DNA replication

18. RNA polymerase molecules attach to DNA at the
A) start codon.
                          (D) 5’ end of the transcribed strand.
B) origin of replication.
            (E) 3’ end of the first exon.
C) promoter.
                                                                           [submitted by RR, modified]

19. The transcription factors of eukaryotic transcription are most similar in function to which component of prokaryotic DNA replication?
A) single-strand binding proteins
         (C) topoisomerase      (E) primase
B) helicase
                                             (D) Dna A

20. What is the precise function of the RNA molecule of telomerase?
A) It serves as a template for DNA synthesis.
B) It acts as a ribozyme.
C) It catalyzes the formation of phosphodiester bonds.
D) It directly extends the 5’ underhang.
E) It removes introns from telomeres.

21. If prokaryotic DNA polymerase I failed to perform any of its functions, and if DNA ligase subsequently sealed all of the nicks, then what should be true of the resulting product?
                       
1. It should contain two types of pentose.
                       
2. It should contain extra oxygen atoms than if DNA pol I worked properly.
                       
3. It should contain less thymine (T) than if DNA pol I worked properly.
A) #2 only
        (B) 1 & 2          (C) 1 & 3         (D) 2 & 3         (E) all three of these

22. How many of these statements concerning prokaryotic transcription are true?
           
I. The same RNA polymerase synthesizes all types of RNA.
           
II. Typically, the mRNA transcript codes for multiple polypeptides.
           
III. The same transcript can be translated and transcribed simultaneously.
           
IV. The mRNA transcript can be read by only one ribosome at a time.
           
V. The mRNA transcript can undergo circularization.
A) only one statement
    (B) two        (C) three          (D) four           (E) all five statements

23. In eukaryotes, what is true of snRNA and rRNA, but NOT mRNA?
A) They are ribozymes.
                      (D) They are translated.
B) They initially contain introns.
          (E) They are synthesized in the cytosol.
C) They are single-stranded.

24. DNA ligase is to DNA fragments during  _____, as _____ is to exons during RNA processing.
A) DNA replication, snRNA
                (D) proofreading, RNA pol II
B) DNA replication, telomerase
          (E) telomere extension, ribosomes
C) proofreading, snRNA
                                                         [submitted by NN, modified]

25. If a eukaryotic ribosome encounters non-sense where non-sense should not be, the result will
A) depend on whether the non-sense is in an intron, or in an exon.
B) probably be a shortened polypeptide.
C) probably be a polypeptide of normal length, but with a different amino acid sequence.
D) be frameshift.
E) definitely be deleterious.
                                                                [inspired by JJ]

26. Polyribosome activity ultimately has the same overall affect on the amount of a single protein as
           
1. alternative RNA splicing.
           
2. circularization of mRNA.
           
3. removal of cap and tail from mRNA.
           
4. multiple RNA pols reading the same transcription unit simultaneously.
           
5. telomerase activity.
A) 1 & 2
           (B) 2 & 4          (C) 2 & 5         (D) 3 & 4         (E) 4 & 5

27. What types of monomers comprise a charged tRNA molecule?
A) deoxyribonucleotides
                     (D) both (A) & (C)
B) ribonucleotides
                               (E) both (B) & (C)
C) amino acids
                                                                        [submitted by KM, modified]

28. If cap and/or tail are not added to the primary transcript, then what will be the result, and where will this result occur?
A) increase in free deoxyribonucleotides, cytosol
B) increase in free ribonucleotides, cytosol
C) increase in free deoxyribonucleotides, nucleus
D) increase in free ribonucleotides, nucleus

29. At the A site of a ribosome, complementary base pairing is supposed to occur between
A) tRNA and mRNA.
              (D) DNA and mRNA.
B) tRNA and rRNA.
                (E) rRNA and mRNA.
C) amino acids and tRNA.

30. Which of the following play a role (direct or indirect) in increasing genetic variation?
                       
I. introns                                              III. independent assortment
                       
II. crossing-over                                  IV. mutations
A) I & IV
          (B) II & III         (C) I, II, & III         (D) I, III, & IV              (E) all four                                   [submitted by NN, modified]

Proceed to Part 2 and read the directions carefully.

 Part 2 directions: (40 points) Use indelible ink and write in paragraphs to answer the 2 essay questions on these 2 pages. You may continue an answer on the reverse side, but NOT on another sheet. Do NOT add your name or any identifying marks to these pages. Enter your essay numeral in the blank on the front page of your test booklet. Besides being correct, answers must be legible, complete, concise, and well organized to receive full credit (20 points each).

1a (9 pts). Given the exonic, non-template DNA sequence below, and a copy of the dictionary of the genetic code, show the two intermediate sequences necessary to determine the corresponding amino acid sequence, as well as the amino acid sequence itself. Label each sequence, always work from left to right, and assume that the leftmost nucleotide in the sequence below corresponds to the 1st nucleotide of a codon.

Non-template DNA:
-- A A G C A G T G C A G T G A G –

1b (5 pts). Using the attached chart of amino acid structures, describe the level(s) of protein structure – beyond the primary level – that this amino acid sequence (determined in 1a above) should NOT be able to participate in, and explain why not. (NOTE: If you don’t get 1a correct, it is unlikely that you will get credit for 1b.)

1c (6 pts). If the 7th nucleotide from the right (9th nucleotide from the left) in the original, non-template DNA sequence above changes from C to A, then without having to make any assumptions, what are the three specific types of mutation that this change can be described as? Why is each term appropriate?

2. Below is a drawing of transcription occurring in a eukaryotic cell. Depicted are two molecules of RNA pol I and associated transcription factors (circles), at work on the same transcription unit: a rRNA gene, where P is the location of this gene’s promoter. There are five major errors in this drawing. Identify only four of them, briefly describing why each is an error in the context of the description given above.

Drawing unavailable

ANSWER KEY?

BIOL 1403                                          Test #2                                   _____________

Fall 2011                                             100 points                              Essay Numeral

Dr. Dini                                               Form 1

 

Part 1 Directions (60 points).  Be sure your R# grid and form bubble are correctly bubbled in on the scantron.  Enter essay numeral in the space above.  For each test item, choose the letter that represents the BEST response (2 points each, except where indicated).  Dominate!

 

1. What is true of a 1-polypeptide, allosteric enzyme that, by itself, is in its active conformation?

A) It is probably located at the final step of the metabolic pathway that it regulates.

B) The bonding of an allosteric inhibitor changes its 3° structure.

C) A competitive inhibitor bonds to its allosteric site.

D) Its activity requires an allosteric activator.

E) It is inactivated by receiving positive feedback.

 

2. A protein’s function is directly dependent on _____, which is/are maintained by _____, which are determined by _____, which is ultimately determined by _____.

A) its shape, its bonds, its amino acid sequence, a nucleotide sequence

B) its bonds, its shape, its amino acid sequence, a nucleotide sequence

C) its amino acid sequence, its bonds, its shape, a nucleotide sequence

D) its shape, its bonds, its nucleotide sequence, an amino acid sequence

E) its amino acid sequence, its shape, its bonds, a nucleotide sequence

 

3. Which does NOT belong with the others?
A) Okazaki fragments                                    (D) looping of the template strand

B) multiple primers present                 (E) discontinuous DNA replication

C) leading strand

 

Match the prokaryotic replisome components on the right with the functions on the left. Responses may be used once, more than once, or not at all (1 point each).

 

4. Proofreading                                                                       (A) DNA pol III

                                                                                                (B) DNA pol I

5. Removal of primers                                                                        (C) DNA ligase

                                                                                                (D) all three of these

6. Can catalyze formation of phosphodiester bonds              (E) two of these

 

7. Chief DNA-building enzyme

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

8. The action of helicase produces conditions that make necessary the action of _____, and of _____ before any new nucleic acids can be synthesized.

A) primase, SSBs                   (C) primase, topoisomerase      (E) DNA ligase, telomerase

B) SSBs, topoisomerase        (D) primase, DNA ligase

 

 

 

 

9. Which does NOT belong with the others?

A) transcription factors           (C) mRNA circularization                   (E) GTP cap

B) spliceosomes                     (D) operons                             [submitted by BK, modified]

 

10. The “trombone model” pertains to current thinking about the way

A) introns are removed from primary transcripts.

B) prokaryotes can perform transcription and translation of the same mRNA molecule at the same time.

C) mature mRNA is transported by NPCs to the cytoplasm following cap and tail addition.

D) DNA replication occurs on the lagging strand.

E) both (A) & (C)

 

11. Lipids carry out many more types of functions in organisms than do carbohydrates.  The chief explanation for this is the

A) structural diversity of lipids compared to carbs.

B) hydrophobic nature of lipids in general.

C) high caloric content of lipids compared to carbs.

D) extraordinary strength of the covalent bonds that hold lipids together.

E) monomers and polymers that comprise lipids.

 

12. Polymers of alpha-glucose primarily function in/as _____, whereas polymers of beta-glucose primarily function in/as _____.

A) fuel, energy storage                       (D) fuel, cell-cell recognition              

B) structures, cell-cell recognition      (E) energy storage, cell-cell recognition

C) energy storage, structures

 

13. Hydrolysis of all of the ester bonds of a triglyceride should produce

A) one H2O, one glycerol, and 3 fatty acids.

B) one glycerol and 3 fatty acids.

C) a phosphate group, 3 fatty acids, and glycerol.    

D) a phosphate group, 2 fatty acids, and a glycerol.

E) one H2O, one phosphate group, one glycerol, and 2 fatty acids.

 

14. Those hormones that are modifications of a cholesterol precursor

A) are mostly hydrophilic.

B) are usually transported in the bloodstream by being attached to proteins.

C) are called “peptide hormones,” and more specifically, “biogenic amines.”

D) have roughly half as many calories per unit mass as the oligosaccharides that are attached to the outsides of animal plasma membranes.

E) are amphipathic, except where there is an –OH group attached, in which case the hormone is completely hydrophobic.

 

 

 

 

 

 

 

15. In enzyme-catalyzed hydrolysis reactions, one could properly expect that the enzyme

            1. might provide the necessary microenvironment for the reaction to occur.

            2. should eliminate the energy of activation.

            3. might bring together reactive side groups of multiple substrates in the correct     arrangement for the reaction to proceed.

            4. might cause a covalent bond of the substrate to break.

A) 1 & 3           (B) 1 & 4          (C) 2 & 4         (D) 1, 2, & 3         (E) 1, 2, & 4

 

16. Which of these partial concept maps most accurately depicts the relationship between these 11 concepts?

 

Figure could not be duplicated in this format.  Sorry.

17. Which of these can change the 1° structure of an enzyme that consists of a single polypeptide?

A) adding just enough heat to bring the enzyme to its optimal temperature

B) breaking all of its disulfide bonds

C) breaking all of its hydrogen bonds

D) mutating the gene that codes for the enzyme

E) exposing the enzyme to a nuclease

 

18. If a transport protein allows a specific material to flow through a membrane, down its concentration gradient, without itself (the protein) undergoing any conformational change, then

A) mostly charged or polar amino acids of the transport protein should be in closest proximity to the material as it moves through the protein.

B) mostly charged or polar amino acids of the transport protein should be in closest proximity to the fatty acids of the neighboring phospholipids.

C) mostly neutral or non-polar amino acids of the transport protein should be in closest proximity to the material as it moves through the protein.

D) mostly neutral or non-polar amino acids of the transport protein should be in closest proximity to the phosphate groups of the neighboring phospholipids.

 

19. Reversible denaturation may disrupt all but

            1. 1° structure.                        2. 2° structure.                        3. 3° structure.

A) #1 only        (B) #2 only      (C) #3 only      (D) 1 & 3         (E) 2 & 3

                                                                                                [submitted by BK, modified]

 

The next two questions are based on the information below:

A hypothetical, mature eukaryotic mRNA molecule is 1,000 ribonucleotides long, not including the cap and tail.

 

20. About how many amino acids should the corresponding polypeptide consist of, assuming no post-translational processing?

A) 300             (B) 333            (C) 1,000         (D) 3,000           (E) 3,300

 

21. If the gene that codes for this mRNA is 10% exonic, then how many base pairs should comprise the intronic portions of this gene?

A) 1,000          (B) 2,000         (C) 9,000         (D) 10,000       (E) 18,000

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

 

22. Which of the following are true of both dsDNA molecules and tRNA molecules?

                                    1. both have hydrogen bonds

                                    2. both contain anticodons

                                    3. both have sugar-phosphate backbone(s)

                                    4. both contain the nitrogenous base, uracil

                                    5. both contain phosphodiester bonds

A) 1 & 3           (B) 2 & 5          (C) 3 & 5         (D) 1, 3, & 5          (E) 2, 3, & 4

                                                                                                [submitted by EL, modified]

 

 

23. If eukaryotic DNA lacked introns, then it is likely that

A) introns would, instead, be more common in bacterial genomes.

B) DNA replication would no longer be limited to S phase.

C) there would be no need for differences in replication of the leading and lagging strands.

D) introns would continue to be parts of eukaryotic primary transcripts.

E) there would be fewer instances of crossing-over during Prophase I.

 

24. Which exonic mutation(s) cannot result in frameshift?

            1. substitution mutation           4. inversion

            2. 1-base insertion                   5. 3-base insertion

            3. 2-base deletion

A) 1 & 2           (B) 1 & 4          (C) 3 & 5         (D) 1, 4, & 5        (E) 3, 4, & 5

 

25. Which does NOT belong with the others?

A) insertion mutation               (C) substitution mutation              (E) deleterious mutation

B) deletion mutation                (D) inversion mutation                    [submitted by JTBS, modified]

 

26. If a species’ DNA pols lacked proofreading capability, and if the species also lacked DNA-repair enzymes, then one should expect

A) relatively more individuals within this species to have genetic defects than in other species.

B) the gene pool of this species to have relatively more genetic variability than species with proofreading capability and DNA-repair enzymes.

C) the species to be able to adapt rapidly in a changing environment.

D) absolutely faithful DNA replication during S phase.

E) more than one of these.

 

27. How many of the following statements concerning telomerase are true?

            1. It is an enzyme used by both prokaryotic and eukaryotic species.

            2. It catalyzes the lengthening of telomeres.

            3. It contains an RNA molecule that acts as a template.

            4. It can catalyze RNA-directed DNA synthesis.

            5. Its activity is limited to healthy somatic cells.

A) only one statement is true              (C) three statements               (E) all five are true

B) two statements                               (D) four statements

 

28. Restriction enzymes are to molecular _____, as DNA ligase is to molecular ____.

A) scalpels, probes                 (C) forceps, scalpels               (E) sponges, forceps

B) scalpels, sutures                 (D) forceps, sutures

 

29. What is/are reason(s) that eukaryotic chromosomes cannot be used to produce eukaryotic proteins if placed into prokaryotic cells aboard cloning vectors?

A) Eukaryotic chromosomes are linear.         (D) both (A) & (B)

B) Eukaryotic chromosomes have histones.   (E) both (B) & (C)

C) Eukaryotic chromosomes have introns.

 

 

 

30. What is the correct sequence in which the following steps are performed to introduce eukaryotic DNA into prokaryotic cloning vectors?

            1. Use DNA ligase.

            2. Use restriction enzyme.

            3. Use reverse transcriptase.

            4. Harvest and purify the mature eukaryotic mRNA of interest.

            5. Harvest and purify the cDNA.

            6. Mix opened plasmids and cDNA together.

A) 3,2,6,1,5,4              (C) 3,6,2,1,5,4             (E) 4,5,2,6,1,3

B) 4,1,3,5,2,6              (D) 4,3,5,2,6,1

 

The next two questions are based on the following paragraph:

On October 9, 2011, the scientific journal, Nature, published an article about a group of researchers from the University of Cambridge who, for the first time, corrected a human gene mutation in a patient's stem cells. The study focused on the gene, alpha1-antitrypsin, a gene active in the liver and responsible for producing a protein that is released from the liver and helps fight inflammation. When people inherit a mutated version of this gene, the proteins that are created are incapable of leaving the liver, thus causing cirrhosis and lung emphysema.

 

31. Which of the following can be properly inferred about this mutation from the paragraph above?

            1. It is an induced mutation.

            2. It can be found in somatic cells.

            3. It has a deleterious affect on protein function.

            4. It can be found in germ line cells.

            5. It results from third-base wobble.

A) 1 and 3       (B) 1 and 5      (C) 2 and 3           (D) 2, 3 and 4         (E) 3, 4 and 5

                                                                                                [submitted by KS, modified]

 

32. Given that the mutated protein is synthesized by, but cannot be secreted from, liver cells, which of these parts of the alpha1 antitrypsin gene is the most likely location of the mutation?  The part of the gene that corresponds to

A) the protein’s signal peptide.

B) the mRNA’s ribosome binding sequence.

C) the interior of an intron that is always treated as an intron.

D) the interior of an exon that is treated as an intron in the case of alpha1 antitrypsin.

E) either (C) or (D) are equally likely.

 

Proceed to Part 2 and read the directions carefully.

 

Part 2 directions: (40 points) Use indelible ink and write in paragraphs to answer the 2 essay questions on these 2 pages.  You may continue an answer on the reverse side, but NOT on another sheet.  Do NOT add your name or any identifying marks to these pages.  Enter your essay numeral in the blank on the front page of your test booklet.  Besides being correct, answers must be legible, complete, concise, and well organized to receive full credit (20 points each).

 

1.  Given the sequence of deoxyribonucleotides from the exonic non-transcribed strand below, a copy of the dictionary of the genetic code, and always working from left to right, determine the corresponding sequence of (a) the transcribed strand, (b) the mRNA codons, (c) the tRNA anti-codons, and (d) amino acids, entering them in the spaces provided for each.  Then, using Table 2, name the type of secondary structure in which the amino acids from part (d) above are most likely to be involved.

 

non-transcribed DNA strand:         T  G  G  G  T  C  T  T  C  T  G  G  A  G  G

 

A) transcribed DNA strand:

 

B) mRNA codons:

 

C) tRNA anti-codons:

 

D) amino acids:

 

Table 2: Statistical preferences of various amino acids for participation in 2° structures

2° structures

Amino Acids

Beta Pleated Sheets

Val, Ile, Phe, Thr, Trp

Reverse Turns

Ser, Asp, Asn, Gly, Pro

No Preference

Arg

Alpha Helices

all others

 

E) 2° structure:

 

 

Part 2 directions: (40 points) Use indelible ink and write in paragraphs to answer the 2 essay questions on these 2 pages.  You may continue an answer on the reverse side, but NOT on another sheet.  Do NOT add your name or any identifying marks to these pages.  Enter your essay numeral in the blank on the front page of your test booklet.  Besides being correct, answers must be legible, complete, concise, and well organized to receive full credit (20 points each).

 

1.  Given the sequence of deoxyribonucleotides from the exonic non-transcribed strand below, a copy of the dictionary of the genetic code, and always working from left to right, determine the corresponding sequence of (a) the transcribed strand, (b) the mRNA codons, (c) the tRNA anti-codons, and (d) amino acids, entering them in the spaces provided for each.  Then, using Table 2, name the type of secondary structure in which the amino acids from part (d) above are most likely to be involved.

 

non-transcribed DNA strand:         G  G  A  C  G  C  G  G  C  G  G  T  G  G  G

 

A) transcribed DNA strand:

 

B) mRNA codons:

 

C) tRNA anti-codons:

 

D) amino acids:

 

Table 2: Statistical preferences of various amino acids for participation in 2° structures

2° structures

Amino Acids

Beta Pleated Sheets

Val, Ile, Phe, Thr, Trp

Reverse Turns

Ser, Asp, Asn, Gly, Pro

No Preference

Arg

Alpha Helices

all others

 

E) 2° structure:

 

 

2. Which major ribozyme do prokaryotic cells have in common with eukaryotic cells?  What is the functional significance of this ribozyme?  Which major ribozyme do prokaryotic cells lack that eukaryotic cells have?  How does this lack affect the rDNA lab procedure for inserting eukaryotic DNA into prokaryotic plasmids?

 

ANSWER KEY?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

BIOL 1403                                          Test #2                                   _____________

Fall 2012                                             100 points                              Essay Numeral

Dr. Dini                                               Form 1

 

Part 1 Directions (60 points).  Be sure your R# grid and form bubble are correctly bubbled in on the scantron.  Enter essay numeral in the space above.  For each test item, choose the letter that represents the BEST response (2 points each, except where indicated).  Dominate!

 

1. If two different polypeptides share the same primary structures, but have quite different tertiary structures, then this might be because

A) the sequence of their amino acids is different.

B) the environment in which each works may have different pH, temperature, etc.

C) one, but not the other, may have been assisted by a chaperonin.

D) all three of these    (E) only two of these

 

2. If a 50-base-pair stretch of DNA is 10% adenine (A), then what should be the proportion of guanine (G)?        

A) 10%      (B) 20%              (C) 30%       (D) 40%        (E) 50%

 

3. If a 50-base-pair stretch of DNA is 10% adenine (A), then how many hydrogen bonds should hold the two strands together in this stretch of DNA?

A) 135             (B) 145            (C) 150            (D) 155            (E) 160

 

4. How is telomerase like a ribosome?

A) It catalyzes translation.    (C) It is a ribozyme.  (E) It consists of both RNA and protein.

B) It synthesizes protein.      (D) it synthesizes DNA.

 

5. Which of these require(s) the process of transcription (either forward or reverse)?

A) making primers                  (D) making primary mRNA transcripts

B) making telomeres              (E) all of these

C) making rRNA

 

6. The direct action of telomerase is to add

A) DNA to the 3’ overhang.                (C) RNA to the 3’ overhang.

B) DNA to the 5’ underhang.              (D) RNA to the 5’ underhang.

 

7. What do spliceosomes and ribosomes have in common?

A) They contain ribozymes.                                                                (D) all three of these

B) They are made of protein and RNA.                                             (E) two of these

C) They contain RNA that serves as a template for DNA synthesis.

 

8. The significance of introns in eukaryotic genomes is that they are thought to allow

A) for an increased frequency of crossing-over.

B) for the storage of extra ribonucleotides in the cell cytoplasm.

C) for a single gene to code for multiple polypeptides.

D) both (A) & (B)

E) both (A) & (C)

 

9. Which enzyme synthesizes a different product than the others?

A) telomerase             (C) RNA pol                (E) reverse transcriptase

B) DNA pol I                (D) DNA pol III

 

10. How is prokaryotic transcription different from that occurring in eukaryotes?

A) Eukaryotic genes cannot handle multiple RNA pols simultaneously transcribing them.

B) Eukaryotic transcription can only occur during S phase.

C) Eukaryotic transcription does not require RNA polymerase.

D) Eukaryotic transcription requires lots of transcription factors.

E) Eukaryotic transcription does not transcribe the entire transcription unit.

 

11. If a 100,000-base-pair gene is 90% intronic, then

of about how many bases should the primary transcript consist,

of about how many bases should the mature mRNA (excluding cap and tail) consist, and of about how many amino acids should the corresponding polypeptide consist?

A) 100,000;  10,000;  3,333                (D) 50,000;  90,000;  30,000

B) 50,000;  10,000;  3,333                  (E) none; 10,000;  3,333

C) 100,000;  90,000;  30,000

 

12. Circularization of eukaryotic mRNA has the same overall effect on protein synthesis as which of these other features?

A) polyribosomes.

B) highly effective promoters.

C) multiple RNA pols transcribing the same transcription unit simultaneously.

D) an abundant supply of ribonucleases.

E) all except (D).

 

13. Which of these is a correct sequence in which the following events occur during translation?             

                                    1. charged initiator tRNA bonds to small ribosomal subunit

                                    2. large ribosomal subunit attaches

                                    3. small ribosomal subunit/initiator tRNA attaches to mRNA

                                    4. initiator tRNA departs from E site

                                    5. next charged tRNA enters A site

A) 4,1,2,3,5         (B) 1,4,5,2,3            (C) 4,1,3,2,5        (D) 1,3,2,4,5            (E) 4,1,3,5,2

 

14. Which is NOT an example of post-translational protein processing?

A) removal of the signal peptide                     (D) splicing exons together

B) removal of C peptide from pro-insulin       (E) adding sugars to polypeptides

C) chaperonin activity

 

15. The ribosomal component that directly hydrogen-bonds with mRNA is _____, whereas the ribosomal component that directly catalyzes peptide bond formation is _____.

A) rRNA of the large subunit, rRNA of the small subunit

B) rRNA of the small subunit, rRNA of the large subunit

C) rRNA of the small subunit, protein of the large subunit

D) rRNA of the large subunit, protein of the large subunit

E) protein of the small subunit, rRNA of the small subunit

 

16. Spontaneous mutations are those caused by

A) UV.             (C) DNA pols/repair enzymes.           (E) all of these.

B) mutagens.  (D) external factors.   

 

17. Theoretically, which parts of plants should be most likely to store excess calories as oil, rather than as carbohydrate, and what accounts for this?

A) leaves, they make oils                   (D) seeds, they disperse in the environment

B) roots, they store oils                       (E) stems, they transport oils

C) flowers, are colored by oils

 

18. All of these statements are true of triglycerides (TGIs), except

A) polyunsaturated ones are typically solid.

B) they consist of three fatty acids and a glycerol.

C) they are similar to phospholipids, but in TGIs a fatty acid replaces the phosphate group.

D) the lengths of their fatty acids can vary.

E) they can store energy, serve as insulation, or as padding.

 

The next three questions refer to the drawing and description below:

Erythritol, one of the sweeteners in TruviaÔ, is a 4-carbon

sugar alcohol with the formula C4H10O4.  It is not found in

stevia plants, but is produced commercially by enzymatically

converting wheat starch or corn starch to glucose, which is

then fermented to erythritol by food-grade yeasts, the erythritol     Drawing could not be duplicated in this format.

then being separated from the fermentation broth.  In humans,

90% of erythritol is absorbed by the small intestine, and

remains unchanged in the bloodstream for less than 24 h,

before being excreted, unchanged, by the kidneys.

 

19. How are sugar alcohols different from true sugars, such as glucose?  Sugar alcohols

A) have a higher proportion of carbon.           (D) have proportionately fewer hydroxides.

B) have a higher proportion of hydrogen.       (E) lack double bonds.

C) have a higher proportion of oxygen.

 

20. Erythritol is a byproduct of the metabolism of

A) fructose.     (B) galactose.    (C) alpha-glucose.    (D) beta-glucose.      (E) two of these

 

21. Given the way that erythritol is treated within the human body, what should be true?

A) Erythritol is a negligible nutritional source for bacteria in the large intestine.

B) Erythritol makes a negligible contribution to human metabolism.

C) Erythritol makes a negligible contribution to human growth.

D) all three of these are true.

E) two of these are true.

 

22. If a gram of lipid contains X calories, then how many calories should be present in a gram of carbohydrates?           

A) 0.25X          (B) 0.5X           (C) X        (D) 2X        (E) 4X

 

Match the level of protein structure on the right with the correct bonds that maintain it on the left.  Answers may be used once, more than once, or not at all. 1 point each

23. Hydrogen bonds between R groups                                 (A) primary

24. Hydrogen bonds between backbone elements                (B) secondary

25. Peptide bonds                                                                   (C) tertiary

26. Electrical interactions                                                        (D) quaternary

                                                                                                (E) two of these

 

27. Consider an enzyme in an aqueous environment.  Which statements should be true?

            1. Alpha-helices are more likely to be found in the interiors of such enzymes.

            2. Their active sites should predominately feature hydrophilic R groups.

            3. Their allosteric sites should predominantly feature hydrophobic R groups.

            4. b pleated sheets are likely to be found on the exteriors of such enzymes.

A) 1 & 2           (B) 1 & 4          (C) 2 & 3         (D) 2 & 4         (E) 3 & 4

 

28. Consider a transmembrane protein that has a receptor site for a ligand.  The ligand is sometimes present on the exterior of the cell.  How many of these statements should be true?            1. Alpha-helices are more likely to be found on the exteriors of such proteins, next to the fatty acid tails of neighboring phospholipids.

            2. Their receptor sites should feature hydrophilic R groups.

            3. Such proteins are susceptible to the phenomenon known as “saturation.”

            4. Charged or polar R groups of this protein are likely to predominate on the transmembrane ends of this protein, or deep within its interior.

A) none           (B) only one           (C) two                 (D) three          (E) all four

 

29. The enzyme, sucrase, catalyzes the hydrolysis of sucrose.  What prevents sucrase from also catalyzing the hydrolysis of maltose?

A) Maltose is heavier than sucrose.

B) Maltose has a different form of glucose than has sucrose.

C) Maltose has a different shape and chemistry than has sucrose.

D) Maltose is not as sweet as sucrose.

E) Maltose has a higher free energy than has sucrose.

 

30. What is the correct chronological sequence in which the following act to determine the 3-D conformation of an enzyme?

            1. Substrate            2. DNA                 3. Chaperonins              4. Ribosomes

A) 1,2,3,4        (B) 2,4,3,1       (C) 1,2,4,3       (D) 2,3,4,1       (E) 3,4,2,1

 

31. Which does NOT belong with the others?
A) the trombone model           (D) continuous DNA replication

B) Okazaki fragments             (E) more catalytic activity by primase, ligase, & DNA pol I

C) lagging strand

 

32. Watson-Crick base pairing helped to explain

A) how phosphodiester bonds are catalyzed.

B) the existence of “the 5’ to 3’ rule.”

C) Chargaff’s rules.

D) why DNA polymerases can only extend previously existing nucleotides.

E) why primers consist of RNA, rather than DNA.

Part 2 directions: (40 points) Use indelible ink and write in paragraphs to answer the 2nd essay question.  You may continue an answer on the reverse side, but NOT on another sheet.  Do NOT add your name or any identifying marks to these pages.  Enter your essay numeral in the blank on the front page of your test booklet.  Besides being correct, answers must be legible, complete, concise, and well organized to receive full credit (20 points each).

 

1.  Given the sequence of deoxyribonucleotides from the exonic non-transcribed strand below, a copy of the dictionary of the genetic code, and always working from left to right, determine the corresponding sequence of (A) the transcribed strand, (B) the mRNA codons, (C) the tRNA anti-codons, and (D) amino acids, entering them in the spaces provided for each.  Then, if nucleotide T1 is mutated to A, what are all of the terms that could be appropriately used to describe this mutation, including its impact on 1° protein structure and protein function?  If nucleotide G2 is mutated to C, what are all of the terms that could be appropriately used to describe this mutation, including its impact on 1° protein structure and protein function?

 

non-transcribed DNA strand:         G  T  C  A  T  T  T  T  T1  G  G  A  T  T  C  T  G  G2

 

A) transcribed DNA strand:

 

B) mRNA codons:

 

C) tRNA anti-codons:

 

D) amino acid sequence:

 

E) T1 mutation types:

 

F) G2 mutation types:

 

 

2. Complete the drawing below to include the rest of this chromosome as it would exist during G2, assuming perfectly faithful replication and providing the same level of detail.  Then, if replication had not been perfectly faithful, explain what can occur in cells to make it more nearly so.  Finally, discuss a possible advantage of imperfectly faithful replication to a species over time.

 

Answer Key?