Bio/Biochem Flashcards
What do the stereochemical designations of alpha and beta on a sugar mean?
They are epimers at the anomeric carbon beta: same at C5 alpha: opposite C5
What is the motor end plate?
The neuromuscular junction
What is the average molecular weight of an amino acid?
110 kDa
What is the difference between a denaturing, reducing, and native gel electrophoresis?
Denaturing: separate subunits/monomers Reducing: break disulfide bonds Native: no bonds broken, 3D shape effects migration
What is the function of SDS in SDS-PAGE?
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.
What is the equation for Vmax in enzyme kinetics?
Vmax = kcat * [E]total
What is kcat? how is it calculated?
kcat is the turnover number, how many substrate molecules an enzyme turns over per second under conditions of saturation kcat = Vmax / [E]total
What is catalytic efficiency? Equation? What does a high vs low catalytic efficiency mean?
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.
What is Kd? What does a large vs small Kd mean?
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.
When does Km = Kd ?
E + S ES E + P Kd = k-1/k1 Km = (kcat + k-1) / k1 when k-1 >>> kcat then Km = Kd
Competitive Inhibition:
Vmax, Km
Vmax constant
Km decreases
Uncompetitive inhibition: vmax, Km
Vmax decreases
Km decreases
Noncompetitive inhibition: vmax, Km
Vmas decreases
Km constant
Competitive and uncompetitive effects are equal.
Mixed inhibition: vmax, Km
Vmax decreases
Km decreases if uncompetitive effect is greater than competitive.
Km increases if competitive effect is greater than uncompetitive.
What does a hill coefficient greater/less/equal than 1 mean?
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
How is the isoelectric point of uncharged, pos, and neg charged amino acids calculated?
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
What does a low vs high pI of a peptide mean?
Low: acidic (neg charged)
High: basic (pos charged)
Define pI.
the pH at which net charge is zero
Amide vs amine
Amide: R-CO-NH2
Amine: NH3
What is Km/Vmax equivalent to on a LWB plot?
The slope
Extrinsic vs intrinsic apoptotic pathway
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
What is the function of a signal sequence?
Tags a protein to go through the secretory system of the cell (ER - golgi - membrane - etc.)
What are enhancers?
DNA sequences
What are nuclear factors?
Transcription factors
If a protein is in the cytosol what amino acids are most likely at the interface of dimerization?
hydrophobic amino acids because the polar/neg/pos will interact with water in the cytosol and prevent proper dimerization.
List the polar uncharged amino acids
asparagine, glutamine, cysteine, serine, threonine,
What are n-stacking interactions?
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.
Is glycogen phosphorylase involved in glycogen break down or synthesis?
BREAK DOWN
What enzyme catalyzes the formation of 6-phosphogluconolactone?
Glucose 6-phosphate dehydrogenase
