Name:
Chem 464
Biochemistry
Multiple choice (4 points apiece):
1.Which of the following is not correct concerning cooperative binding of a ligand to a protein?
A) It is usually a form of allosteric interaction.
B) It is usually associated with proteins with multiple subunits.
C) It rarely occurs in enzymes.
D) It results in a nonlinear Hill Plot.
E) It results in a sigmoidal binding curve.
2. The benefit of measuring the initial rate of a reaction V0 is that at the beginning of a reaction:
A) [ES] can be measured accurately.
B) changes in [S] are negligible, so [S] can be treated as a constant.
C) changes in Km are negligible, so Km can be treated as a constant.
D) V0 = Vmax.
E) varying [S] has no effect on V0.
3. How is trypsinogen converted to trypsin?
A) A protein kinase-catalyzed phosphorylation converts trypsinogen to trypsin.
B) An increase in Ca 2+ concentration promotes the conversion.
C) Proteolysis of trypsinogen forms trypsin.
D) Trypsinogen dimers bind an allosteric modulator, cAMP, causing dissociation into
active trypsin monomers.
E) Two inactive trypsinogen dimers pair to form an active trypsin tetramer.
4. From the abbreviated name of the compound Gal( â164)Glc, we know that:
A) C-4 of glucose is joined to C-1 of galactose by a glycosidic bond.
B) the compound is a D-enantiomer.
C) the galactose residue is at the reducing end.
D) the glucose is in its pyranose form.
E) the glucose residue is the â anomer.
5. Which of the following is a dominant feature of the outer membrane of the cell wall of gram
negative bacteria?
A) Amylose
B) Cellulose
C) Glycoproteins
D) Lipopolysaccharides
E) Lipoproteins
2
6. The nucleic acid bases:
A) absorb ultraviolet light maximally at 280 nm.
B) are all about the same size.
C) are relatively hydrophilic.
D) are roughly planar.
E) can all stably base-pair with one another.
7.In comparison with DNA-DNA double helices, the stability of DNA-RNA and RNA-RNA
helices is:
A) DNA-DNA > DNA-RNA > RNA-RNA.
B) DNA-DNA > RNA-RNA > DNA-RNA.
C) RNA-DNA > RNA-RNA > DNA-DNA.
D) RNA-RNA > DNA-DNA > DNA-RNA.
E) RNA-RNA > DNA-RNA > DNA-DNA.
Longer Problems 10 points each.
8. What is Bohr effect? Use a plot of è vs [O2] to explain how the binding of O2 varies with pH,
and then explain how this is accomplished in the hemoglobin structure.
The Bohr effect is the effect of pH and CO2 on oxygen binding in hemoglobin. The
binding curve should look like figure 5-16. At low pH the hemoglobin shifts to the low affinity
‘T’ form of the enzyme and releases more oxygen. At high pH hemoglobin shifts to the high
affinity ‘R’ form and binds oxygen more tightly. This effect is mediated by the binding of H+
and/or CO2 to the hemoglobin. Although H+ can be bound at several sites, the most important
site seems to be asp 94 on the beta chain and this helps to stabilize the T state. On the other hand
the CO2 binds as a carbamate on the amino terminus of both alpha and beta chains and this in
turn makes salt bridges to further stabilize the low affinity ‘T’ state
9. In class we talked about several ways an enzyme can increase the rate of a reaction by
lowering the activation energy. Give a one or two sentence explanation of these different
methods by which an enzyme can increase the rate of a reaction.
Entropy reduction - In entropy reduction two substrates are bound near each other in the
active site, greatly increasing the effective concentration of the substrates to increase the over rate
of the reaction.
Desolvation- In many reactions the sphere of hydration around ions can interfere with the
actual reaction. By binding a substrate in a way that removes the water you get rid of this
interference and increase the rate of the reaction.
General acid catalysis- In general acid catalysis an amino acid on the enzyme acts as an
electron acceptor and the placement of this electron acceptor encourages the substrate to move
into the transition state intermediate in the reaction mechanism.
covalent catalysis- In covalent catalysis a temporary covalent bond is formed between the
substrate and the enzyme. The formation of this bond provides and alternate, low energy pathway
by which the reaction can occur.
3
10.
What does V Max tell you about an enzyme and its substrate?
V max tells you the maximum rate at which an enzyme can perform a chemical reaction at
a given enzyme concentration.
What does the Specificity Constant tell you about an enzyme and its substrate?
The specificity constant, k cat /Km, is a measure of catalytic efficiency. A maximum value
of the specificity constant based on the diffusion is about 108-109 M-1 s-1. When an enzyme’s
specificity constant get near this value, the enzyme is turning all reactants that hit the active site
into product, so it is working at nearly 100% efficiency.
What is an epimer? Two sugars that differ in the configuration around only 1 carbon
atom.
What is a selectin? Selectins are a family of plasma membrane lectins that mediate cellcell recognition and adhesion.
What is a cruciform structure? It is a cross-like structure that can form in double stranded
DNA when ever the DNA sequence includes an palindrome repeat in its sequence.
11.Galactose has the same structure as glucose, except that the H and the OH are on opposite
sides at the C-4 position. Write a linear structure for galactose, and the ring structure for
â-galactose
4
12. Give me 10 points worth of information the various Glycoconjugates.
There are three types of glycoconjugates: proteoglycans, glycoproteins, and glycolipids.
Proteoglycans contain mostly carbohydrates with a small amount of protein. The carbohydrate
part consists of highly repetitive glycosaminoglycans that are attached to the protein at serine
residues. Proteoglycans are usually on the cell surface or in the extracellular matrix.
Glycoproteins consist of mostly protein, with smaller pieces of carbohydrates. The carbohydrate
portion is highly branched and structurally complex. The carbohydrate can be either linked to
serine or threonine (O-linked) or asparagine (N-linked) Most proteins secreted by mammalian
cells are glycoproteins. Glycolipds are carbohydrates covalently attached to lipids. They are
found in the cell membranes of plants, animals and bacteria
13. DNA Draw the structure of deoxy pA hydrogen bonded to the appropriate RNA complement
I did not specify the phosphates on the RNA portion, so I accepted RNA phosphates on either the
3' or the 5' end or both or neither.
14. Compare and contrast the structure of a t-RNA molecule with the structure of the double
stranded DNA molecule that coded for that sequence of RNA.
The double stranded DNA is in a B-form right-handed double helix with 10.5 base Pairs per turn
and 3.4 Å rise per turn. Kind of boring structurally. The single stranded t-RNA on the other
hand is structurally much more complex. There are four short double stranded regions that fold
together in three dimensions to make an L-shaped molecule