Kaplan Biochemistry: Chapter 3 Protein Functions Flashcards
What is Kd
Kd is the dissociation constant. It tells you how well a specific substrate will bind to the enzyme.
E + S ES -> E + P
Kd= [E][S]/[ES]
The smaller the Kd, the stronger the Substrate is bound to the Enzyme.
What is Kcat
Kcat is the rate of reaction of the enzyme; turnover of substrate to product / unit time.
Vmax = Kcat [Enzyme]
what is a hydrolase
an enzyme that catalyzes the hydrolysis of a particular substrate.
a hydroxylase is a type of enzyme within a broader category of enzymes called:
oxidoreductases.
The protein channel Na+/K+ ATPase exchanges ___ Na+ for ___ K+
3 Na+ out; 2 K+ in
- maintains an overall negative charge inside the cell.
what is the primary structure of a protein
peptide bonds. the amino acid sequence
what forces stabilize the secondary structure of a protein
stabilized by H bonding between backbone molecules in the alpha helix of beta pleated sheet conformation
what forces stabilize the tertiary and quarternary structure of a protein
stabilized by the side chain interactions: H bonding, disulfide bonds, dipole dipole bonds.
a competitive inhibitor graph looks like:
What state does the comp inhibitor bind to?
what kinetic parameters are constant? Which varies?
-looks like a cross over at the y axis
binds to ENZYME ONLY
Km increases, Vmax is constant
an UNcompetitive inhibitor graph looks like:
What state does the UNcomp inhibitor bind to?
what kinetic parameters are constant? Which varies?
-looks like two parallel lines
binds to E-S
Km decreases, Vmax decreases
a NONcompetitive inhibitor graph looks like:
What state does the NONcomp inhibitor bind to?
what kinetic parameters are constant? Which varies?
a non comp inhibitor crosses over at the x axis.
binds to ES or E
Km stays the same, Vmax decreases.
What is suicide inhibition
irreversible enzyme inhibition. Usually inhibits via covalent bond-hard to break.
kinesin brings vesicles towards the ___ end of the microtubule
POSITIVE end. Ex/ to the synaptic terminal— positive end is the end where the microtubules DIDN’T originate from.
Dyneins bring vesicles towards the ___ end
NEGATIVE ends. Ex/ towards the SOMA.
homotropic regulation
when a molecule serves as a substrate for its target enzyme, as well as a regulatory molecule of the enzyme’s activity.
3 possible outcomes when an antibody binds to its antigen
1) neutralizing the antigen: making the pathogen unable to exerts its effects
2) opsonization: marking the pathogen for immediate destruction by WBCs
3) agglutinating: clumping together the antigen and antibody into large INSOLUBLE protein complexes that can be phagocytized by macrophages.
____ are Ca2+ mediated glycoproteins that hold similar types of cells together.
Cadherin
in G proteins, when____ is replaced with ___-, the alpha subunit is able to dissociate from the beta and gamma subunits.
when GDP is replaced with GTP.
in Native PAGE, the negative charge proteins will migrate:
towars the positive charge electode. therefore, native page varies with mass-to-charge ratio and mass-to-size ratio.
SDS PAGE separates proteins on the basis of ___
mass. SDS page coats the entire protein so it is all negative. charge doesn’t matter, they will all migrate to the same pole. but the larger proteins will not migrate as fast on the gel.
what is isoelectric focusing
protein separation based on isoelectric point. when the protein is neutral.
in isoelectric focusing, what acts as the anode? as the cathode?
acidic gel is at the POSITIvE anode (its electrochemical cell), and basic gel is at the NEGATIVE cathode. it is neutral in the middle of the gel.
proteins that are + charged will begin to migrate to the cathode where the basic gel is. the proteins that are negatively charged will begin migrating toward the anode, where the acidic gel is.
in anion exhange chromatography, the column is ____ charged. What charge elutes faster?
column is POSITIVELY charged. attracts the negative proteins. POSTIVE charged particles will elute faster.
therefore, in anion exchange chromatography, you exchange anions for positive ions.
in size exclusion chromatography, which sized proteins elut faster?
larger proteins elute faster.
what type of protein would be best seen under UV spec?
aromatic proteins. UV light excites the conjugated systems of double bonds.
