CHE 476 BIOCHEMISTRY I Hour Exam 1: Buffers, amino acids, proteins, and enzymes

06-02-16
Functional group pK
Please feel free to ask ME any questions you may have. pH = pKa + log [A-]/[HA]; V = (Vmax * [S])/(KM + [S]); -amino (lys) 10
G = -RTlnKeq; specificity constant = kcat/KM , [Etotal] = 1 for this exam; also 2.303RT = 1
o
-amino (all) 8
(40) 1. Use the table to the right for this problem. -carboxyl (all) 2
a) Draw the tetrapeptide, glutamyl-aspartyl-histidinyl-arginine as it would appear at pH 4. -carboxyl (asp) 4
-carboxyl (glu) 4
phenolic (tyr) 10
sulfhydryl (cys) 8
guanidino (arg) 12
imidazolium (his) 6

b) What would the net charge of this tetrapeptide be at:

i) pH 1? answer __________
ii) pH 13? answer __________

c) What is the pI of this tetrapeptide? answer __________

d) Draw the titration curve of this tetrapeptide.

(10) 2. Identify an amino acid which: answer __________

a) has an aromatic group. answer __________ vii) Which of these proteins would be most insoluble in water?
b) has diastereomers. answer __________ answer __________
c) has no enantiomer. answer __________ viii) Which of proteins would have the weakest quaternary attractions with other
d) has a negative charge at pH13. answer __________ same proteins at pH 3? answer
e) has a sulfur atom but no ionic capabilities. answer __________ __________
f) has the most rotational freedom around its -carbon. ix) Which of these pairs of proteins would have the strongest quaternary
answer __________ interactions at pH 7? answer __________
g) has no net charge around pH 10. answer __________ x) Which of these proteins would have the strongest quaternary repulsions at pH
h) has two negative charges at pH 9 but not pH 7. 3? answer __________
answer __________
i) has a 2o carbon in its sidechain. answer __________
j) has an amide. answer __________ (10) 4. Consider four circumstances of enzymes with the following Lineweaver-
Burk equations.
(10) 3. For the following questions, consider five proteins, each 50 amino A) y = 4 x + 4
acids long, made of just a single type of amino acid. Protein P is made of B) y = 4 x + 1
proline; K, lysine; S, serine; E, glutamic acid; F, phenylalanine. Your C) y = 1 x + 1
answers are going to be P, K, S, E, or F. D) y = 1 x + 4
E) y = 0.25 x + 1
i) Which of these proteins would have the most restricted secondary structure? i) Which of set of circumstances would have the lowest KM?
answer answer __________
__________ ii) Which of set of circumstances would have the highest Vmax?
ii) Which of these proteins would have the highest pI? answer __________
answer __________ iii) Which of set of circumstances would have the greatest specificity constant?
iii) Which of these proteins would have the highest molecular weight? answer
answer __________
__________
iv) Which of these proteins would have the strongest tertiary attractions? iv) Which of set of circumstances would most likely represent the enzymes
answer natural substrate?
__________ answer __________
v) Which of these proteins could have H-bonding in its tertiary structure at pH 2 v) Which of set of circumstances would have the smallest slope?
but not at pH 13? answer __________ answer __________
vi) Which of these proteins would have the highest A280?
(2) d. Draw RR2.
(4) e. AA1 could be one of two things from the table above. What are they?
(30) 5. You discover a new enzyme in that catalyzes the hydrolysis of a thioester Which is the better choice and why?
bond to a carboxylic acid (Product 1) and Product 2 (P2.) (2) f. RR2 is acting as a(n) __________________ when it reacts with modified
AA1.
1. This enzyme uses AA1 (amino acid 1 in the active site) to pull a (2) g. Activated R1 is acting as a(n) __________________.
proton off the smaller reactant, reactant 1 (R1), making activated (4) h. AA2 could be one thing from the table above. Which and why?
R1. (2) i. AA2 has a _______________ charge.
2. This activated R1 reacts with (attack) the least electronegative part (2) j. What is the Km for this enzyme with acetyl-CoA as a substrate?
of the the thioester (Reactant 2, R2), creating Product 1 (P1) and (2) k. Which substrate, ACOA or DACP, does this enzyme bind better?
remainder of Reactant 2 (RR2.) (2) l. Does this enzyme have a large or small active site? Does it need to have
3. During this attack, another amino acid in the active site (AA2) and the a lot tertiary interactions to stabilize the transition state? Very briefly explain your
modified AA1 stabilize RR2 ionically. answer.
4. The RR2 reacts with the modified AA1 producing P2 and
regenerating AA1.
5. This enzyme is most active at pH 9, with sharp decreases in activity
at lower and higher pHs.
6. The Lineweaver-Burk plots for this enzyme with acetyl-CoA (ACOA)
and dodecyl-ACP (DACP) are:
ACOA: 1/V = 0.1 1/[S] + 1
DACP: 1/V = 1/[S] + 1

(4) a. Draw the reactants and products of this reaction as a reaction.

Underneath each part of this reaction, indentify R1, R2, P1, and P2.

(2) b. AA1 is acting as a(n) __________________.

(2) c. What is activated R1?