Download Module 1: Review of General and Organic Chemistry

Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
Bioc 3321 Study guide
Module 1: Review of General and Organic Chemistry
1. In a hospital laboratory, a 10.0 mL sample of gastric juice, obtained several
hours after a meal, was titrated with 0.1 M NaOH to neutrality; 7.2 mL of
NaOH was required. The patient’s stomach contained no ingested food or
drink, thus assume that no buffers were present. What was the pH of the
gastric juice?
Module 2: Amino Acids, Peptides and Proteins
2. Complete the table:
Structure
Name
Three letter code
Asn
at pH=7
Leucine
at pH=12
Aliphatic / PolarUncharged / Neg.
Charged / Aromatic /
Pos. Charged
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
His
At pH=1
3. Lysine can be considered a triprotic acid with three pKas= 2.18, 8.95, 10.53.
a. Draw the structure of Lysine and identify the most acidic proton, the
second most acidic proton and the least acidic one
b. Draw the titration curve of Lysine identifying the pH zones at which
the buffer capacity is maximum
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
c. What is the Isoelectric point (pI) of Lysine?
4. State if the following peptides have a total positive, neutral or negative
charge at the given pH
a. (Gly)20 at pH 7.0
b. (Glu)20 at pH 7.0
c. (Lys–Ala)3 at pH 7.0
d. (Phe–Met)3 at pH 7.0
e. (Ala–Ser–Gly)5 at pH 6.0
f. (Asn–Ser–His)5 at pH 6.0
g. (Ala–Asp–Gly)5 at pH 3.0
h. (Asn–Ser–His)5 at pH 3.0
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
5. Below is the Ramachandran plot
a. What do the islands of color indicate in the plot above?
b. Draw the Newman projection of the Phi () angle: C-N-C-C for a
alpha-helix
c. Draw the Newman projection of the Psi (): Draw N-C-C-N for a
beta sheet
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
6. The following peptide adopts a alpha-helix secondary structure
Leu-Glu-Glu-Val-Phe-Ser-Gln-Leu-Cys-Thr-His-Val-Glu-Thr-Leu-Lys
a. By using the helical representation below. Answer why this sequence
is compatible with a alpha helix.:
b. Identify what area (circle it) of the alpha helix may be exposed to
water/hydrophilic environment and what other area is exposed to a
hydrophobic environment.
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
7. Like many things in biology, a protein’s solubility is pH dependent. Under certain
pH conditions, a protein may be quite soluble and at other pH values, the protein
may become completely insoluble. This property is sometimes used to advantage
during protein purification schemes. To understand why, answer the following
questions.
a. Suppose you have a mixture of two proteins with the following properties:
Protein A has a pI of 4.1; Protein B has a pI of 10.0. At pH 7, your
solution is clear, i.e., both proteins are soluble. You acidify your solution
with strong acid to pH 4 and observe precipitate. What has happened and
why?
b. Describe the charge states (i.e., net negative (“anionic”), or net positive
(“cationic”), or no net charge) for Proteins A & B at: pH 4, pH 7, and at
pH 10.
Module 2. Protein techniques
8. You hope to learn about an unknown protein by comparing it to known proteins
(“standards”). You mix your unknown with all the standards and apply the
mixture to a cation exchange column at low [NaCl] and buffered at pH 7.5.
Polypeptide
MW/chain
pI
standards
A
calmodulin
18,000
4.1
B
carbonic anhydrase 31,000
6.0
C
myogenin
25,000
8.7
D
serum albumin
90,000
10.6
E
trypsin inhibitor
22,000
9.6
F
transferrin
110,000
5.9
G
ubiquitin
9,000
6.6
a. Which standard proteins will NOT be retained on the column (Give the
LETTERS)? EXPLAIN why in 1 sentence.
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
b. Your unknown is retained on the column. Draw a conclusion about your
protein using the terms "acidic" or "basic" AND "pI".
9. The following diagram shows the anode, cathode, and pH gradient of an
isoelectric focusing bed:
anode+
-cathode
pH
1 2 3 4 5 6 7 8 9 10 11 12 13 14
a. Indicate if the following aminoacids and peptides will move to the
right or to the left and at what pH they may stop
Placed at pH =
Asn
Glu-Asp
Leu-His
Ser
Moving Right or
Left?
Stopping at pH=
(approx. 1 digit)
2
9
4
7
Assume that for the backbone groups, all amino groups have pKa=9.6 and
all carboxylic pKa=2.3. Amino acids with carboxlic side chains have
pKa=4.0, and amino groups pKa=10.5, imidazole groups have pKa=6.
Module 2: Protein function
10. Protein A has a binding site for ligand X with a Kd of 10−6 M. Protein B has a
binding site for ligand X with a Kd of 10−9 M.
a. Draw a plot representing binding fraction  vs ligand concentration
for the two proteins. Use a -logarithmic scale for concentration of
ligand. Indicate how Kd can be found and labels of the axis.
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
binding fraction
1
0
1 2 3 4 5 6 7 8 9 10 11 12
b. Which protein has a higher affinity for ligand X? Explain your
reasoning.
c. Convert the dissociation constant Kd to association constant Ka for
both proteins. Write the equilibrium reactions for both processes.
d. At what concentration of X will protein A have 20% of their binding
sites occupied?
-log[S]
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
Module 3: Enzymatic Catalysis
11. The reaction catalyzed by hexokinase is:
glucose + ATP  glucose-6-phosphate + ADP
A form of hexokinase called hexokinase D has a KM for glucose of 0.1 mM; the
form called glucokinase has a KM for glucose of 10 mM. Normal blood glucose
level is 4-5 mM.
e. Will either isozyme work near its maximal rate under normal blood
glucose levels? If so, which one and why?
f. Blood glucose levels increase dramatically after a meal. Which isozyme
will be more responsive to changes in blood [glucose] away from the
normal?
g. One of these isozymes is predominant in liver; the other in muscle. In
muscle, glucose is consumed for energy—a process that must occur at all
times, even in between meals. The liver isozyme’s job is to convert excess
blood glucose into glucose-6-phosphate for transport to other tissues.
Which isozyme works in which tissue? Explain your answer.
12. For an enzyme (E) catalyzed reaction that follows Michaelis-Menten kinetics,
state whether the parameters listed below will INCREASE, DECREASE, or
STAY THE SAME under the conditions listed by putting an "X" in the correct
box.
Condition #1. [E]total is increased.
Condition #2. A competitive reversible inhibitor is added.
Condition #1
Parameter Increase? Decrease? Same?
KM
Vmax
[E-S]
Condition #2
Increase? Decrease? Same?
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
V0 when
[S] = KM
kcat
Catalytic
efficiency
d[E-S]/dt
Module 4: Carbohydrates
13. In the disaccharide below
h. Identify the anomeric carbons by circling them
i.
What kind of glycosidic bond exists between the two
monosaccharides? (e.g. 14 linkage)
j.
Draw the linear form of the monosaccharide in furanose form.
14. A polysaccharide of unknown structure was isolated, subjected to exhaustive
methylation, and hydrolyzed. Analysis of the products revealed three
methylated sugars: 2,3,4-tri-O-methyl-d-glucose, 2,4-di-O-methyl-d-glucose,
and 2,3,4,6-tetra-O-methyl-d-glucose, in the ratio 20:1:1. What is the
structure of the polysaccharide?
Bioc 3321 Spring 2011
Xavier Prat-Resina Univ. Minnesota Rochester
Module 5: Lipids
1. Arachidonic acid is a fatty acid precursor of prostaglandins thromboxanes
and leukotrienes. Arachidonic acid is labeled as 20:4(5,8,11,14) .
a. Draw its structure below.
b. Is it an omega-3 or omega-6 kind of fatty acid?
c. Draw another fatty acid with the same number of carbons but with a
higher melting point.