life science 1a practice midterm exam 1 #2 october16,...

Name: TF: Section Time

Life Science 1A Practice Midterm Exam 1 #2

October 16, 2006

Please write legibly in the space provided below each question. You may not use calculators on this exam. We prefer that you use non-erasable pen when writing your answers. A significant number of completed exams will be photocopied by the teaching staff. Please write your name on each page of the exam. There are FIVE multi-part questions in this exam. We recommend that you first read through all questions and begin with the questions that are easiest for you. Be sure to take a look at all questions before the end of the exam! All written responses should fit within the space provided. Please write your TF’s name and section time on the front page only. Question 1 /34 Question 2 /32 Question 3 /26 Question 4 /28 Question 5 /30 Total /150

Life Science 1A Spring 2006 – Midterm 1 Name_______________

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1. Amino acids and peptides can exist in different ionization states depending upon the pH of the solution and the pKa’s of the side chains.

a. (9 points) Draw the tripeptide with the one-letter amino acid abbreviation I-H-A in its most common protonation state at pH 8.0. Be sure to include formal charges if any.

A table of pKa's for the ionizable groups on the amino acids is shown below as a reference. You do not need to specify stereochemistry.

Ionizable group pKa Asp side chain 4.0 Glu side chain 4.4 His side chain 6.5 Cys side chain 9.3 Tyr side chain 10.2 Lys side chain 10.9 Arg side chain 12.0 Ser side chain 13.0 Amino terminus 9.8 Carboxy terminus 2.3

b. (4 points) Circle all of the chiral centers on the peptide drawing (1a), and indicate below the total number of possible stereoisomers that could exist.

c. (6 points) Draw this molecule in its most common protonation state at pH 5.0.


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d. (6 points) At pH 7.5, two protonation states of this molecule are present in significant concentrations. What are the net charges of these two states, and what is the ratio of their concentrations?

e. (9 points) Ubiquitin-conjugating enzymes are characterized by an active site that contains a cysteine side chain with an observed pKa of 11.3 (higher than the normal pKa of cysteine in solution; see the table above). Based on the structure of the active site of this enzyme it has been hypothesized that the proximity of side chains near this cysteine alters the pKa of the cysteine side chain. A cartoon representation of the peptide backbone (curved line) and the side chains of the cysteine and amino acids contributing to this effect are shown below.

O-

O

SH

O-

O

O-O

-OO

Explain why the pKa of this cysteine side chain is higher than the normally observed value of 9.3.


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2. The compound shown below is a toxic agent that reacts with the bases of DNA. In order to react with DNA, the compound must first undergo an intramolecular reaction to form product A as shown below. The mechanism of this reaction is depicted using arrow-pushing formalism:

NCl Cl

H

NH

Cl

product A

+ Cl-

a. (6 points) Product A can go on to react with the DNA bases. The mechanism of the reaction of product A with guanine is illustrated below using arrow-pushing formalism. Based on this mechanism, draw the product of the reaction in the box provided. Be sure to include formal charge(s).

b. (6 points) If a guanine in double-stranded DNA reacted with product A in the manner shown, would it still be able to participate in Watson-Crick base pairing with cytosine?

NH

NN

N

O

NH2

DNA

NH

Cl


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c. (6 points) Figure 1 shows a region of a protein interacting with a region of double-stranded DNA. Three amino acid side chains of the protein are depicted. On the drawing below, indicate the hydrogen bonding and ionic interactions you would expect to observe between these amino acid side chains and the DNA.

HN

N

N

NO

HN

N

N

N

OH

DNA

DNA

O

OP

O

O-O

O

O

O

P

O

O-O

O

DNA

DNA

O-

O

O

protein

H

H

HN H

HH

Figure 1: DNA-protein interaction d. (6 points) If in the absence of the protein, the guanine in Figure 1 had

reacted with product A as shown in question 2a, how would this reaction affect the protein's ability to bind this region of DNA? Describe the effects on the interactions you indicated in part c.


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e. (4 points) Many proteins that interact with DNA bind specifically to certain nucleotide sequences. Of the interactions drawn in part c, which would not be affected by changing the C-G base pair to a different Watson-Crick base pair?

f. (4 points) Which of the following changes to the side chains shown in Figure 1 would you expect to be least detrimental to the protein's ability to bind this region of DNA? Briefly explain.

(a) Ser-> Thr (b) Lys -> Phe (c) Asp -> Lys


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3. Normally, two genes in the human genome known as bcr and abl, reside on separate chromosomes. Occasionally, rearrangements of large sections of genomic DNA can occur that fuse these genes together, as shown below. This fusion causes leukemia.

a. (8 points) Beginning with one copy of the above double-stranded DNA and

an excess of primers capable of binding to region P1 of the bottom strand and region P2 of the top strand, draw the single-stranded products that would be present after two complete cycles of PCR. Please indicate on the products the positions of X1, P1, bcr, abl, P2, X2, and label the 5' and 3' ends. For example, the top strand of the DNA above would be drawn:

If there are multiple copies of a single product, you do not need to draw it multiple times; instead, you may draw the product once and indicate how many copies of that product would be produced.

5’ 3’X

1 P

1 bcr abl P

2 X

2

3’5’ 3’

5’

bcr gene abl geneX1 P1 X2P2

primer

primer


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b. (6 points) Beginning with one copy of the double-stranded DNA template, how many total single strands of DNA would theoretically be present at the end of 10 complete PCR cycles? You do not have to give a numerical value; a mathematical expression is sufficient.

c. (4 points) Which of the products drawn in question 2a will be the most abundant after 10 PCR cycles?

d. (4 points) The diagram below shows the normal arrangement of bcr and abl genes in the human genome. Regions X1, P1, P2 and X2 have the same sequences as in the leukemia-causing arrangement illustrated above.

If PCR were performed using the same primers in part (a), but using this normal human genomic DNA as a template, draw the most abundant single-stranded product(s) you would obtain after 10 cycles of PCR.

e. (4 points) Beginning with one copy of double-stranded chromosome 22 and one copy of double-stranded chromosome 9, how many total single strands of DNA would theoretically be present at the end of 10 complete PCR cycles? You do not have to give a numerical value; a mathematical expression is sufficient.

bcr geneX1 P1 abl gene X2P2

3’5’ 3’

5’3’5’

5’3’

Chromosome 22 Chromosome 9


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4. Three representations of an α-helix are illustrated below. R1-R10 represent amino acid side chains.

a. (4 points) Describe the intramolecular force(s) most important for stabilization of α-helical structure.

b. (6 points) Proline is rarely found in the middle of α-helices. Explain why.


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c. (6 points) Amino acid sequences for three different α-helices are shown below. The numbering of the amino acids corresponds to the numbering in the figure above; R1 is the side chain of amino acid 1, R2 is the side chain of amino acid 2, etc.

Amino acid: 1 2 3 4 5 6 7 8 9 10 Helix A Leu Glu Gln Ile Leu Ser Lys Leu Tyr His Helix B Gln Glu Asn Ala Lys Thr His Met Arg Ser Helix C Phe Val Gly Cys Ile Gly Trp Leu Ala Gln

Each of these three helices preferentially exists in one of three states: State 1: as a monomer in the aqueous environment inside the cell State 2: as a monomer in the interior of the cell membrane, which is composed of long hydrocarbon chains State 3: as a tetramer (structure shown below) inside the cell.

Indicate which helix you would predict to exist in each state. State 1 _____ State 2 _____ State 3 _____

d. (6 points) Explain your reasoning for assigning the specific helices (A, B, or C) to state 1 and state 2. Include intermolecular forces.

e. (6 points) Explain why helix you assigned to state 3 exists predominantly as a tetramer with this particular "vertical bundle" arrangement.

4X=

monomer tetramer


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5. Shown below is the process of DNA hybridization.

a. (6 points) Using A, B and C to represent the species shown above, write the equation for the equilibrium constant for this process.

b. (6 points) Hybridization occurs spontaneously at room temperature (25˚

C). What is the sign of ΔG˚ for DNA hybridization at room temperature? c. (6 points) When DNA is heated to 95° C, the equilibrium favors single-

stranded DNA. What is the sign of ∆G˚ for DNA hybridization at 95˚C?

d. (6 points) Which of the four cases below corresponds to the hybridization of DNA?

1. ΔH˚<0 and ΔS˚>0 2. ΔH˚>0 and ΔS˚<0 3. ΔH˚<0 and ΔS˚<0 4. ΔH˚>0 and ΔS˚>0

e. (6 points) Which of the four cases corresponds to the reverse process (DNA melting)?

1. ΔH˚<0 and ΔS˚>0 2. ΔH˚>0 and ΔS˚<0 3. ΔH˚<0 and ΔS˚<0 4. ΔH˚>0 and ΔS˚>0

life science 1a practice midterm exam 1 #2 october16,...

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