INTRODUCTION TO MOLECULAR BIOLOGY LS3-1 MIDTERM EXAM 1 DR. SIMONS WEDNESDAY, APRIL 28, 5:00-6:50 P.M.

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NAME: ___________________________________ SID: _________________________

DISCUSSION SECTION: ________________________ Part 1 - Ten multiple choice questions - 4 points each Part 2 - Ten fill-in-the-blank questions - 4 points each Part 3 - Four brief essay questions - 5 points each Total Points - 100

There are 12 pages in this exam booklet. Sign here ______________________ indicating you have all 12 pages. Put your name and SID on ALL pages. Write legibly - we cannot grade what we cannot read. Work steadily - you should be able to finish the exam. In some cases, you are asked to limit answers to a box. When doing so, keep the dimensions of your penmanship close to the following:

Part 1 - Ten multiple-choice questions, each worth 4 points. In each cases, circle all the correct answers OR check the box indicating there is NO correct answer. 1. According to Chargaff's Rules, in any given organism's DNA... A. B. C. ...the relative ratios of 4 bases were random. ...the molar proportion of G equaled the molar proportion of C. ...the molar proportion of purines equaled the molar proportion of pyrimidines. ...the molar proportion of C equaled the molar proportion of T.

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Name: _____________________ SID: ______________________

D.

2. Crick's "Adaptor Hypothesis"... A. B.

...just had to be correct - after all, he DID win a Nobel Prize!! ...was validated when mRNA was shown in a kinetic (time course) experiment to move from the nucleus to the cytoplasm. ...proposed that amino acids only indirectly interacted with the mRNA. ...revealed how evolution had adapted DNA to be the genetic material.

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C. D.

3. ATP... A. B. C. D. 4. DNA... A. B. C. D.

...stands for deoxyadenosine tri-phosphate. ...permanently stores energy for the cell. ...is an energy donor.

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Name: _____________________ SID: ______________________

...is a substrate for macromolecular synthesis.

...has about 10.5 amino-acid pairs per helical turn. ...is a polymer containing deoxyribose.

...has a positively charged phosphate backbone. ...has base-pairs stacked along its central axis.

5. In the DNA polymerase core... A. B.

...both of the active sites work processively in the 3'->5' direction. ...one active site works on the template strand, while the other works on the primer strand. ...the DNA helicase unwinds the dsDNA in preparation for both leading- and lagging- strand synthesis. ...ribose and deoxyribose sugars of potential substrates are distinguished.

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C.

D.

6. The replicon model... A. B. C.

...describes the origin of leprechauns.

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Name: _____________________ SID: ______________________

...defines the basic roles of the replicator and initiator. ...reveals in precise ways how different origins of replication differ at their mechanistic levels. ...envisions that mechanistically different origins of replication act largely independently of one another.

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D.

7. A transversion mutation is typified by... A. B. C. D. E.

...a deletion or insertion of no more than 1 base pair. ...a change from G:C to C:A, but not G:C to A:C. ...a change from G:C to C:G, but not A:T to G:C. ...a change from T:A to A:T, but not C:G to T:A. ...what happens to UCLA undergrads that drink too much.

8. The mismatch repair system... A.

...is able to scan in either direction from a mismatch for the nearest hemi-methylated dam site. ...is able to cleave the methylated strand on either side of a mismatch. ...recruits either 5'->3' or 3'->5' endonucleases, as needed, to excise a portion of the newly made strand across the mismatch site. ...is not able to recognize a mismatch without being part of the DNA Pol holoenzyme, but is able to carry out correction in the absence of the holoenzyme.

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Name: _____________________ SID: ______________________

B. C.

D.

9. Transcription-coupled repair differs from proofreading in that... A.

...only temporarily repairs a lesion, but will do so again and again, if the region bearing the lesion is repetitively transcribed. ...the synthetic machinery recruits a repair "machine," rather than carrying out the repair itself. ...helps to assure that lesions in highly transcribed genes are preferentially repaired. ...is error-prone.

B.

C.

D.

10. In the replication of circular chromosomes, the "end-problem"... A. B. ...is usually solved in either of two ways. ...is most often solved with an RNA-based function called the telomerase. ...will lead to a shortening of the chromosome if not solved.

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Name: _____________________ SID: ______________________

C. D.

...is faced commonly in eukaryotes, and occasionally in prokaryotes.

NB: There IS no "end problem" in a circular chromosome.

Part 2 - Ten fill-in-the-blank(s) questions, each worth 4 points. 1. For the reaction A + B -> AB, Keq is 3 x 10-7. Therefore its is __+8.89 kcal/mol____. Keq = e-)G/RT )G = -RT ln Keq

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where

Name: _____________________ SID: ______________________

)G

= (-1.987 cal/deg-mol)(298 deg)(ln 3 x 10-7) R = 1.987 cal/deg-mol T = 298K

2. H-bonds form between a covalently bound _hydrogen _ donor that has some _positive __ charge, and a covalently bound, __negatively__ charged acceptor.

3. The alpha helix is a __secondary ____ structure found in _proteins (or polypeptides) _, and has approximately 3.6 __amino acids __ per __right____handed turn.

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4. The Tm of DNA generally increases as its A:T content __decreases___, and as the salt concentration of its environment ___increases____.

5. In DNA topology, Lk = __Tw___ + ___Wr__, the writhe of a right-handed super-coil has a __negative _ sign, and the twist of Z-DNA has a _negative_ sign.

6. In the "trombone model," each iterative round of lagging-strand synthesis begins with primase associating with _helicase___, then primer synthesis, then the loading of a __clamp__ at the primer/template joint and, only then, association of this complex with __core polymerase___.

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Name: _____________________ SID: ______________________

7. In eukaryotic origins of replication, a high level of cdk activity during the _S_ phase of the cell cycle will ensure that the ___pre-RC__ will be activated to become the __RC_, and that no new ___pre-RC__ will be assembled. RC = replication complex - they need not have spelled it out. 8. With regard to the timing of the repair of DNA mismatches, proofreading is a process that occurs ___during replication ___, whereas mismatch repair occurs _after replication__, but works best if it does so before ___GATC sites are fully methylated____. 9. In SOS repair, __replication __ will be restarted, but at a cost - the process is prone to introduce ___errors_____.

10. Neutral and non-polar amino acids form primarily __hydrophobic ___ bonds, neutral and polar amino acids form primarily ___H-bonds_____ bonds, and acidic and basic amino acids form primarily __ionic__ bonds.

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Name: _____________________ SID: ______________________

Part 3 - Four brief answer or problem questions, each worth 5 points. 1. You conduct 2-factor crosses between two, true-breeding strains of the pea plant: AB and ab. For the first factor, the A allele is dominant to the a allele of the first gene, and for the second, the B allele is dominant to the b allele. The results of the F2 show a 9:3:3:1 pattern of phenotypes. In the Punnett square below, fill in the genotypes of gametes and progeny of the F2 cross.

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AB AB

Name: _____________________ SID: ______________________

Ab aB ab aABB AaBb Aabb

AABb

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AABB AABb

Ab aB ab

AaBb

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AaBb aaBB

AAbb

AaBB AaBb

Aabb

aaBb

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aabb

aaBb

NB: This is an example of how to arrange the correct data.

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2. Messelson and Stahl repeat their experiment to determine whether DNA replication is conservative or semi-conservative. This time, however, they examine the process in cells recently recovered from Mars (actually, it's not true that we found these cells in some guy's room in Hedrick Hall - this whole thing is just made up). These bacteria-like cells double every 60 minutes. After many initial generations in medium containing the light isotope of nitrogen (14N), they see the following banding patterns before (0) and after 60 and 120 min growth in medium containing the heavy nitrogen isotope (15N):

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Yes No

Name: _____________________ SID: ______________________

A. Can you conclude whether simple conservative or semi-conservative replication is occurring?

60

120

B. If you can, which type of replication is occurring? Provide a simple explanation of your reasoning, staying within the box. You needed to say that it's semi-conservative (just as in the textbook, except that the order of label transfer is the opposite), and provide a brief reasoning.

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3. Draw the structure of the typical amino acid. Define the groups. Place any charges that exist under physiological conditions.

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Name: _____________________ SID: ______________________

4. In B-form dsDNA, discuss the different informational content presented by the basepairs in the major and minor grooves, staying within the box. In the major groove, each of the 4 base-pairs arrangements displays a unique pattern of H-bond donors or acceptors, or other distinct chemical groups. In contrast, in the minor groove, there are only 2 unique patterns among the 4 base-pair displays. You need to have got this much - the basic concept, and the idea that there is half as much information (and state 2 for 4) in the minor groove as in the major (and state 4 for 4). Showing the true patterns, per se, is not needed.

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