BIOL 231 Summer

26 Jun BIOL 231 Summer

Question
BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

BIOLOGY 231 Summer 2015 Exam 1

KEY

June 5, 2015

GENERAL INSTRUCTIONS:

1. Answer all questions IN INK without white-out (especially if you might want regrades).

2. NO CALCULATORS.

3. Confine each answer to the BOX provided. You are free to use any space outside the boxes for scratch work, but ONLY what is written in the box will be graded!

4. SHOW YOUR WORK in all calculations. Be careful to use the right UNITS.

5. Make sure that your name and PU ID is PRINTED LEGIBLY on the FRONT OF EACH PAGE. The pages may be separated for grading.

6. This exam consists of 9 questions on 12 pages and it is worth a total of 100 points, plus 5 bonus points.

Information that may be useful:

For the reaction A + B <==> C + D

DG =DGo + RTln([C][D]/[A][B]) and RTln(X) = 5.7 kJ/mol*log(X)

At equilibrium,DG = 0 and ([C][D]/[A][B]) = Keq thereforeDGo =- 5.7 kJ/mol*log(Keq) log (10X) = X; 10log(X) = X

For an enzyme that obeys Michaelis-Menten kinetics, the relationship between v and [S] is:

v =Vmax [S] Km+[S]

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Or

1

K

m

æ

1

ö

1

=

ç

÷

+

v

ç

÷

Vmax

Vmax è

[S ]ø

An amino acid has the following structure (amino and carboxy groups shown in their charged form):

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

R groups of some amino acids, shown in their charged form, if relevant:

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

1. Size and scale of chemical and biological objects.

(a) 5 pts.In the table below, indicate the approximate sizeof each object.Note that the approximations described in lecture are good enough (in fact,

they’re preferred). Be sure to indicate the size as a fraction of a meter (e.g. something “1 nm” large should be entered as “10-9 meter”).

Object

Size as a fraction of a meter

A bacterial cell

A eucaryotic cell (a typical small one, not

a dinosaur egg)

A covalent bond between two carbon

atoms

A nitrogen atom

The optimal van der Waals distance

between two atoms

2. Cellular organelles and compartments

(a) 7 pts.Please indicate which organelle/compartment has the followingfunctions. There may be one, more than one, or zero organelles for each function. The same organelle may be used once, more than once, or not at all.

Function

Organelle(s)

Synthesizes cell-membrane components

and proteins to be secreted from the cell

Contains three kinds of protein filaments

(Hint, not the cytoplasm/cytosol)

Modifies proteins destined for secretion

Digests food particles brought into the cell

The sites of protein synthesis by ribosomes

The location of reactions involving

hydrogen peroxide

Consumes carbon dioxide and releases

oxygen

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

3. A “sizes” question.

9 pts. Numbereach of the following structures so that 1 is the largest and 9 isthe smallest by mass.

_____ a fatty acid molecule

_____ human chromosome #1 (about 100 million nucleotides)

____ an oxygen gas molecule (O2)

______ a water molecule

______ the enzyme hexokinase (about 600 amino acids)

______ a triglyceride molecule

____ a proton

_____ a human cell nucleus

_____ a glycerol molecule

4. Protein structure.

Consider the dipeptide with a sequence: N term-Ser-Glu-C term

(a) 5 pts. Draw the structureof this dipeptide in the box below. For eachfunctional group that can be charged (ionizable group), show it in the charged form as it would be at pH = 2.5in your drawing (Hints, you can ignore fractionalcharges from the Henderson-Hasselbach equation. Be sure you’ve indicated all

bond acceptors (either because they are positively charged or because their electrons are involved in resonance). However, nothing in the course has taught this, and so these are OK answers.

(b) 2 pts.Draw an arrow pointing to eachpeptide bond in your drawing.

(c) 4 pts.In your drawing, mark a Dnext to all possible hydrogen bond donors,and mark an A next to all possible hydrogen bond acceptors. You can use arrows along with the D’s and A’s, if there is any possible confusion. (Hint, not all hydrogen atoms are possible hydrogen bond donors. Recall, what else is needed to make a hydrogen a possible hydrogen bond donor.)

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

(d) 8 pts. Determine the total chargeon the dipeptide at each of the followingpH values. Be sure to include the correct sign (positive or negative). You can ignore fractional charges for pH 1, 7, 13. However, you must include fractional chargesfrom Henderson-Hasselbach for pH 7.8.

What is the total charge at pH = 1?

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What is the total charge at pH = 5?

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What is the total charge at pH = 10?

0

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What is the total charge at pH = 7.8? (Hints, remember to include Henderson-

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Hasselbach and it’s simple math.)

–

5. Reaction energies.

You have isolated an enzyme, creatine kinase, which catalyzes the reaction:

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creatine + ATP <=> phosphocreatine + ADP

In a test tube, you combine a tiny amount of pure creatine kinase and a mixture of creatine and ATP and find that the equilibrium constant, Keq = 100.

(a) 5 pts. Using the Keq, calculate DGo for this reaction. Show your work.

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

(b) 5 pts. You want to see whether this reaction is spontaneous under theconditions in a cell. You develop the appropriate assays and find that a cell has:

[creatine] = 0.1 mM [phosphocreatine] = 5 mM

[ATP] = 10 mM [ADP] = 2 mM

What will be theDG (not DGo) of the reaction starting from these conditions?

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D

(c) 2 pts. Will this reaction proceed spontaneously from left to right (aswritten above) or right to left (as written above) starting from the conditions found inside the cell? Please answer L->R or R->L.

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(d) 3 pts. Please explain part (c).There are at least 2 ways to explain part (c),but the preferred way (for full credit) will be based on an understanding of the Gfrom part (b). Other ways receive partial credit. (3 sentences or fewer)

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(e) 5 Bonus pts. Even under conditions where the reaction proceedsspontaneously, it is very slow. Please explain (in 3 sentences or fewer) how a reaction can be spontaneous and slow? If theDG is calculated above, what other energydo we need to know to explain the slow reaction. (Hint, a suitablediagram is an excellent way to answer this question.)

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

6. Enzyme kinetics.

You are studying the hexokinase enzyme of glycolysis from two different species, the short-lived rodent, the pocket gopher of North America (below left) and the related long-lived rodent, the naked mole rat of East Africa (below right). Interestingly, the naked mole rat is one of the few mammals that is eusocial, having a social organization like that found in ants. It is also the only mammal that does not maintain a constant body temperature.

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You measure the velocity of the two enzymes (in mmoles of product produced per minute per nmole of enzyme) at several different substrate concentrations. Then you plot your data using the Lineweaver-Burk equation. The best lines through your data points are shown below.

A = naked mole rat; B = pocket gopher.

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BIOL 231 Summer 2015 Exam 1 Name:____ KEY _____________________

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PU ID: _____________________________

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(a) 8 pts.In the box below, calculatethe KM (left) and vMAX (right) of the twoenzymes. Be careful to include the correct units. Show your work.

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-> enzyme.

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

(b) 4 pts. Will one of these enzymes have a smaller velocityat every substrateconcentration? If so, which one? Please explain you answers. (3 sentences or fewer)

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7. Molecular structure and inhibitor types.

Examine the two molecules shown below. The top molecule is the important vitamin and metabolite folate. Consumption of adequate folate is important for both male and female fertility and an important nutrient for pregnant women in preventing birth defects. The bottom molecule is an anticancer drug called methotrexate.

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Folate

Methotrexate

Inside cells folate is first reduced to dihydrofolate. Dihydrofolate is then a substrate in the following reaction catalyzed by the enzyme dihydrofolate reductase (DHFR)

Dihydrofolate + NADPH ß à Tetrahydrofolate + NADP+

Tetrahydrofolate is then used in the synthesis of purines, the pyrimdine nucleotide TMP and several of the amino acids. All of these syntheses can be stopped by inhibiting DHFR, so there’s been an intense search for inhibitors of

DHFR as anticancer, antiparasite and antibiotic drugs. One of the best reversible inhibitors of DHFR is methotrexate.

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

(a) 3 pts.Based on the structure of methotrexate, what kind of reversible inhibitoris it? Please explain(in three sentences or fewer).

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(b) 3 pts. Whereon DHFR would you expect methotrexate to bind? Please explain(in three sentences or fewer).

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(c) 3 pts. Please explainwhy irreversible inhibitors of DHFR are unlikely to beuseful as drugs (in 3 sentences or fewer).

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8. Hierarchy of protein structure.

As discussed in lecture protein structure is organized into a hierarchy of primary, secondary, tertiary and quaternary.

(a) 5 pts.Please explain how the regular secondary structures are compatible with a large number of amino acid sequences?Hints: Whichatoms are involved in the hydrogen bonding that promotes regular secondary structure? Where are the amino acid side chains located in the regular secondary structures?

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

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(b) 5 pts. What elements make up tertiary structure?Hint, there are thesecondary structure elements (name them in your answer) and something(s) else.

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9. Protein folding.

Many kinds of interactions (bonding) play a role in protein folding.

(a) 5 pts. List the various kinds of interactions (bonding)that play some rolein protein folding.

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.

(b) 3 pts. Which one(s) of these interactions is responsible for providing the free energyto make protein folding spontaneous? Please explain(3sentences or fewer).

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BIOL 231 Summer 2015 Exam 1

Name:____ KEY _____________________

PU ID: _____________________________

(c) 3 pts. Which one(s) of these interactionsplays a large role in the formationof protein secondary structure? Please explain in 3 sentences or fewer.

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(d) 3 pts. Which one(s) of these interactionshelps shape the final structure ofthe protein making sure the protein atoms are well-packed (without much empty space), but not too close to each other? Please explain (3 sentences or fewer).