Bio/Biochem

Question 1

What do the stereochemical designations of alpha and beta on a sugar mean?

Answer 1

They are epimers at the anomeric carbon beta: same at C5 alpha: opposite C5

Question 2

What is the motor end plate?

Answer 2

The neuromuscular junction

Question 3

What is the average molecular weight of an amino acid?

Answer 3

110 kDa

Question 4

What is the difference between a denaturing, reducing, and native gel electrophoresis?

Answer 4

Denaturing: separate subunits/monomers Reducing: break disulfide bonds Native: no bonds broken, 3D shape effects migration

Question 5

What is the function of SDS in SDS-PAGE?

Answer 5

SDS is used to linearize proteins and to negatively charge the proteins. The binding of SDS to the polypeptide chain imparts an even distribution of charge per unit mass. As a result, negatively charged proteins will migrate towards the positive electrode and will be fractionated by approximate size only during electrophoresis.

Question 6

What is the equation for Vmax in enzyme kinetics?

Answer 6

Vmax = kcat * [E]total

Question 7

What is kcat? how is it calculated?

Answer 7

kcat is the turnover number, how many substrate molecules an enzyme turns over per second under conditions of saturation kcat = Vmax / [E]total

Question 8

What is catalytic efficiency? Equation? What does a high vs low catalytic efficiency mean?

Answer 8

kcat / Km HIGH: kcat is much larger than Km, and the enzyme complex converts a greater proportion of the substrate it binds into product LOW: kcat is much smaller than KM, and the complex converts a lesser proportion of the substrate it binds into product.

Question 9

What is Kd? What does a large vs small Kd mean?

Answer 9

Dissociation Constant, which describes the affinity of two reactants are in a reaction. Kd = k-1/k1 Large means low affinity. Small means high affinity.

Question 10

When does Km = Kd ?

Answer 10

E + S ES E + P Kd = k-1/k1 Km = (kcat + k-1) / k1 when k-1 >>> kcat then Km = Kd

Question 11

Competitive Inhibition:

Vmax, Km

Answer 11

Vmax constant

Km decreases

Question 12

Uncompetitive inhibition: vmax, Km

Answer 12

Vmax decreases

Km decreases

Question 13

Noncompetitive inhibition: vmax, Km

Answer 13

Vmas decreases

Km constant

Competitive and uncompetitive effects are equal.

Question 14

Mixed inhibition: vmax, Km

Answer 14

Vmax decreases

Km decreases if uncompetitive effect is greater than competitive.

Km increases if competitive effect is greater than uncompetitive.

Question 15

What does a hill coefficient greater/less/equal than 1 mean?

Answer 15

greater than 1 = positive cooperative binding (binding of first ligand increases affinity of binding others)

less than 1 = negative cooperative binding (binding of first ligand decreases affinity of binding others)

equal to 1 = no cooperative binding

Question 16

How is the isoelectric point of uncharged, pos, and neg charged amino acids calculated?

Answer 16

uncharged: (carboxyl + amino)/2 = (2 + 10)/2 = 6

REMEMBER TO ADD LIKE GROUPS TOGETHER.

pos: (amino + amino)/2 = (10+10)/2 = 10
neg: (carboxyl + carboxyl)/2 = (2+2)/2 = 2

Question 17

What does a low vs high pI of a peptide mean?

Answer 17

Low: acidic (neg charged)

High: basic (pos charged)

Question 18

Define pI.

Answer 18

the pH at which net charge is zero

Question 19

Amide vs amine

Answer 19

Amide: R-CO-NH2

Amine: NH3

Question 20

What is Km/Vmax equivalent to on a LWB plot?

Answer 20

The slope

Question 21

Extrinsic vs intrinsic apoptotic pathway

Answer 21

Intrinsic apoptosis is a response to ‘internal damage’ eg. damaged DNA, chromosom rearrangement, hang ups in division, hypoxia, etc. that the cell senses itself and ‘decides to commit suicide’. This is done by the mitochondrial pathway - release of cytochrome C from the mitochondria activates the caspase cascade that results in programmed cell death.

Extrinsic apoptosis: Tnfalpha, Fas ligand – both use caspases

Question 22

What is the function of a signal sequence?

Answer 22

Tags a protein to go through the secretory system of the cell (ER - golgi - membrane - etc.)

Question 23

What are enhancers?

Answer 23

DNA sequences

Question 24

What are nuclear factors?

Answer 24

Transcription factors

Question 25

If a protein is in the cytosol what amino acids are most likely at the interface of dimerization?

Answer 25

hydrophobic amino acids because the polar/neg/pos will interact with water in the cytosol and prevent proper dimerization.

Question 26

List the polar uncharged amino acids

Answer 26

asparagine, glutamine, cysteine, serine, threonine,

Question 27

What are n-stacking interactions?

Answer 27

attractive, noncovalent interactions between aromatic rings, since they contain pi bonds. These interactions are important in nucleobasestacking within DNA and RNA molecules, and protein folding.

Question 28

Is glycogen phosphorylase involved in glycogen break down or synthesis?

Answer 28

BREAK DOWN

Question 29

What enzyme catalyzes the formation of 6-phosphogluconolactone?

Answer 29

Glucose 6-phosphate dehydrogenase