Exam 3

Question 1

Which of the following is true about membrane proteins?

Answer 1

Lateral Diffusion occurs unless other cellular components restrict their movements.

Question 2

Which of the following statements describe integral membrane proteins?

Answer 2

Amino Acids that contact the membrane are usually hydrophobic.

Question 3

Which of the following is(are) not found as covalently attached anchors in lipid-linked proteins:

Answer 3

cholesterol and other sterols

Question 4

Which of the following is not a general feature of the lipid bilayer in biological membranes?

Answer 4

They are all glycoproteins.

Question 5

In humans, the fatty acid composition of membrane lipids in skin cells is different from the fatty acid composition of membrane lipids in the internal organs, because the internal organs function at a slightly higher temperature. which of the following differences in fatty acid composition is most likely to occur?

Answer 5

Skin cells show lower levels of 20:0 relative to 16:0 AND higher levels of 18:2 relative to 18:0.

Question 6

Which of the following segments of the integral membrane protein glycophorin most likely contains the membrane-spanning sequence?

Answer 6

PEITLIIFGVMAGVIGTILL

Question 7

Gap Junctions:

Answer 7

are important intercellular communication channels

Question 8

Molecular Chaperones assist proteins in the formation of

Answer 8

tertiary structure

Question 9

Oxygen triggers Hb to switch from its low affinity (T) state to its high affinity (R) state. What kind of allosteric effector is oxygen relative to Hb?

Answer 9

Homoallosteric; positive effector

Question 10

The rearrangement of T-form hemoglobin to the R-form:

Answer 10

involves the movement of the Fe(II) into the heme plane.

Question 11

Which of the following is NOT TRUE for the symmetry model of allosterism:

Answer 11

the ligand can bind to a subunit in either conformation

or

none of the above

Question 12

One of the enzymes involved in glycolysis requires Zn2+ for catalysis. Under conditions of zinc deficiency, when the enzyme may lack zinc, the enzyme would be referred to as the ________.

Answer 12

apoenzyme

Question 13

Which of the following statements is true of enzyme catalysts?

Answer 13

they bind to substrates, but are never covalently attached to substrate or product.

or

they lower activation energy for the conversion of substrate to product.

Question 14

Using this reaction, the rate of breakdown of the enzyme-substrate complex (like any reaction rate) can be described by the expression ______________.

Answer 14

k-1[ES] + k2[ES]

Question 15

To determine Km from a double reciprocal plot, you would _____.

Answer 15

multiply the reciprocal of the x-axis intercept by -1.

Question 16

A metabolic pathway proceeds according to the scheme R -> S-> T-> U-> V-> W. A regulatory enzyme, X, catalyzes the first reaction pathway. Which of the following is most likely correct for this pathway?

Answer 16

The last product, W, is likely to be a negative modulator of X, leading to feedback inhibition.

Question 17

What is the velocity of a first-order reaction when the reactant concentration is 6x10^-2 M and the rate constant is 8x10^3 sec^-1?

Answer 17

4.8 x 10^2 M*sec^-1

Question 18

Km is

Answer 18

the [S] that half-saturates the enzyme.

Question 19

Name a molecule that can be used to rearrange disulfide bonds within proteins and briefly describe how it works. (Beta-merchapthoethanol)

Answer 19

reducing agent that will cleave disulfide bonds and at low concentrations allows disulfides to reform (sometimes differently).

Question 20

Name a molecule that can be used to rearrange disulfide bonds within proteins and briefly describe how it works. PDI

Answer 20

protein disulfide isomerase - provides thiols that can replace thiols linked in another protein, which results in a shuffle or rearrangement of which thiols are covalently linked.

Question 21

What is the overall benefit of using cholesterol in membranes!

Answer 21

Cholesterol broadens the transition temperature range and at higher temps makes the membrane less fluid and at lower temps makes the membrane more fluid.

Question 22

Name two features of a membrane protein you would not see in cytoplasmic proteins.

Answer 22

transmembrane domain, signal sequence, asymmetric etc.

Question 23

Briefly describe the terminal end of a protein that has been prenylated.

Answer 23

The c-terminal end was cleaved (3 residues missing) to leave a c-terminal cys residue covalently linked to an isoprene group.

Question 24

T or F: Protein primary structures must be highly conserved to have the same active/binding site and function.

Answer 24

false

Question 25

List and briefly describe two methods that may be used to monitor protein folding events. CD

Answer 25

Circular Dichroism - spectroscopic method that monitors the optical rotation of the chiral carbons in the peptide backbone and indicates secondary structure.

Question 26

List and briefly describe two methods that may be used to monitor protein folding events. Pulsed H/D exchange

Answer 26

accessible hydrogens are exchanged for deuteriums and monitored via NMR.

Question 27

List and briefly describe two methods that may be used to monitor protein folding events. FRET

Answer 27

a fluorescence technique where energy is transferred from one fluorescent molecule (residue) to another only if they are in close proximity.

Question 28

Briefly describe how a protein can assist the folding of another protein folding.

Answer 28

proteins can provide an alternative environment (by binding or enclosing) for a portion of or a whole protein. This alternative environment typically stabilizes a portion (i.e. hydrophobic region) of the protein and allows additional folding pathways.

Question 29

Briefly describe the roles of clathrin, COPI, COPII proteins.

Answer 29

These proteins form cages around lipid vesicles to provide structural support. The various types (clathrin, COPI, COPII) are used in specific vesicle movement (i.e. clathrin from ER to plasma membrane, COPI from ER to golgi).

Question 30

Define the Levinthal Paradox.

Answer 30

Levinthal’s paradox is that finding the native folded state of a protein by a random search among all possible configurations can take an enormously long time.

Question 31

List the general steps in folding any protein.

Answer 31

1. Secondary structure forms
2. Hydrophobic collapse drives tertiary structure formation.
3. Final tertiary interactions are formed.

Question 32

Describe one important weak interaction that plays a role in stabilizing the T or R state of Hemoglobin.

Answer 32

Electrostatic interactions between BPG and his residues in the central cavity that stabilize the T-state.

or

H-bonding between the alpha and beta subunits that stabilize the R-state.

Question 33

What types of interactions play a role between 3(CO2 and Hb) and 4(BPG and Hb)?

Answer 33

3: covalent bond when CO2 forms a carbamate with Hb
4: electrostatic interactions between BPG and positive His residues

Question 34

name a detergent used in biochemistry studies

Answer 34

SDS, Triton X-100, NP-40

Question 35

What are two general ways to control the level of enzyme activity present in an organism?

Answer 35

1. Enzyme amount or level

2. Enzyme activity

Question 36

For the reaction shown above, what does the “steady state assumption” assume?

Answer 36

That the [ES] concentration is constant. The rate of ES breakdown equals the rate of formation.

Question 37

the enzyme efficiency of an enzyme, Ewild-type, was compared to a mutant version of the same enzyme Emutant… which form of the protein is most efficient for the substrate used?

Answer 37

The mutant enzyme is more efficient because the ratio of Kcat over Km is larger.

Question 38

Describe the interactions of a membrane protein with the rough ER during protein synthesis.

Answer 38

The membrane protein has a signal sequence. After this signal sequence is synthesized by the ribosome, it interacts with a protein that leads it to the ER where the signal sequence interacts with the translocon. The translocon spans the ER membrane and (1) provides a pore for the membrane to enter the ER and (2) inserts any membrane spanning regions into the ER membrane.

Question 39

Ligase

Answer 39

sticks two parts together

Question 40

Lyase

Answer 40

involves creating a double bond in carbon end product.

Question 41

Hydrolase

Answer 41

breaks apart parts and outputs water molecules