MileDown MCAT Biochem

amino acids

molecules that contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur

L

stereochemistry for the alpha carbon of all amino acids in eukaryotes

cysteine

all chiral amino acids excpet ____ have (S) configuration

glycine

all amino acids are chiral except

alpha helices

clockwise coils around a central axis

beta pleated sheets

rippled strands that can be parallel or antiparallel

proline

can interrupt secondary structure because of its rigid cyclic structure

amphoteric

amino acids can act as a base or an acid

pKa

pH t which half of the species is deprotonated

low

____ pH results in amino acid that is fully protonated

pI

pH when amino acid is a neutral zwitterion

high

____ pH results in amino acid is fully deprotonated

isoelectric point

the pH at which an amino acid is in zwitterion form; the charges cancel out and make a neutra molecule

pKa

midpoint of titration is when pH = ____

pI

equivalence point of titration is when pH = ____

disulfied bonds

occur when two cysteine molecules are oxidized and create a covalent bond between their thiol groups. this forms cystine

conjugated proteins

proteins with covalently attached molecules

prosthetic group

the attached molecule in a conjugated protein. can be a metal ion, vitamin, lipid, carbohydrate, or nucleic acid.

denaturation

the loss of 3D structure, caused by heat or solute concentration

dipeptide

2 amino acids (2 residues)

tripeptide

3 residues (3 a.a.'s)

oligopeptide

less than 20 residues

polpeptides

greater than 20 residues

dehydration reaction

forming a peptide bond is a __________________. The nucleophilic amino group of one amino acid attachs the electrophilic carbonyl group of another amino acid.

amide bonds

the C-N bond of a peptide bond. rigd due to resonance

hydrolysis reaction

breaking a peptide bond is a ______ reaction

peptide bonds

primary structure of amino acids are stabilized by _______

n c

aa sequence is written ____ to ____ terminus

hydrogen bonding

secondary structure of proteins is stabilized by _____ between amino groups and nonadjacent carboxyl groups

enzymes

biological catalysts that are unchanged by the reactions they catalyze and are reusable. Enzymes do not alter the G or H, nor the final equilibrium position. They only change the rate of reaction by altering the mechanism. Catalyze both the forward and reverse reactions

exergonic reactions

release energy; delta G is negative

endergonic reactions

require energy, delta G is positive

oxidoreductases

enzymes that catalyze REDOX reactions that involve the transfer of e-'s

transferases

move a functional group from one molecule to another

hydrolases

catalyze cleavage with the addition of H2O

lyases

catalyze cleavage without the addition of H2O and without the transfer of e-'s. The reverse reaction (synthesis) is often more important biologically

isomerases

catalyze the interconversion of isomers, including both constitutional isomers and stereoisomers

ligases

join two large biomolecules, often of the same type

lipases

catalyze the hydrolysis of fats. Dietary fats are broken down into fatty acids and glycerol or other alcohols

kinases

add a phosphate group. a type of transferase

phosphatase

remove a phosphate group; a type of transferase

phosphorylases

introduces a phosphate group into an organic molecule, notably glucose

saturation kinetics

as substrate concentration increases, reaction rate increases until max value is reached

michaelis menten

hyperbolic curve describing relationship between vmax and km

lineweaver burke

line graph; Double reciprocal of Michaelis-Menten

km

the [S] at which an enzyme runs at half of its vmax. a smaller value indicates a more efficient enzyme

vmax

maximum rate at which an enzyme can catalyze a reaction. this is when all enzyme active sites are saturated with substrate

Michaelis Menten equation

v = (vmax [S])/(Km + [S])

cooperative enzymes

display a sigmoidal curve because of the change in activity with substrate binding

active site

the site of catalysis

lock and key theory

the enzyme and substrate are exactly complementary and fit together like a key into a lock

induced fit theory

the enzyme and substrate undergo conformational changes to interact fully

cofactors

metal cation that is required by some enzymes

coenzyme

organic molecule that is required by some enzymes

feedback inhibition

when an enzyme is inhibited by high levels of a product from later in the same pathway

reversible inhibition

the ability to replace the inhibitor with a compound of greater affinity or to remove it using mild laboratory treatment

competitive inhibition

when the inhibitor is similar to the substrate and binds at the active site, blocking the substrate from binding. can be overcome by adding more substrate

competitive inhibition

vmax is unchanged, km increases

uncompetitive inhibition

when the inhibitor binds only with the enzyme-substrate complex.

uncompetitive inhibition

vmax and km both decrease

noncompetitive inhibition

when the inhibitor binds with equal affinity to the enzymes and the enzyme-substrate complex.

noncompetitive inhibition

Vmax decreases, Km stays the same

mixed inhibition

when the inhibitor binds with unequal affinity to the enzyme and the enzyme-complex. vmax decreases, km is increased or decreased depending on if the inhibitor has a higher affinity for the enzyme or enzyme-substrate complex

irreversible inhibition

alters the enzyme in such a way that the active site is unavailable for a prolonged duration or permanently

suicide inhibitor

a substrate analogue that binds irreversibly to the active site via a covalent bond

allosteric effector

binds at the allosteric site and induces a change in the conformation of the enzyme so the substrate can no longer bind to the active site. Displays cooperativity, so it does not obey michaelis-mentin kinetics

positive effectors

effectors that exert a positive effect; increase activity

negative effectors

Effectors that inhibit enzyme activity

homotropic effector

an allosteric regulator that is also the substrate. ex: o2 is a _________ regulator of hemoglobin

heterotropic effector

an allosteric regulator molecule that is different from the substrate

phosphorylation

covalent modification with phosphate

catabolism

phosphorylated = active

anabolism

phosphorylated=inactive

glycosylation

covalent modification with a carbohydrate

zymogens

precursors to an enzyme. secreted in an inactive form and are activated by cleavage.

structural proteins

compose the cytoskeleton, anchoring proteins, and much of the extracellular matrix. Most common examples are collagen, elastin, keratin, actin, and tubulin. They are generally fibrous in nature

motor proteins

have one or more heads capable of force generation through a conformational change. They have catalytic activity, acting as ATPases to power movement. Common applications include muscle contraction, vesicle movement within cells, and cell motility. Examples include myosin, kinesin, and dynein

binding proteins

bind a specific substrate, either to sequester it in the body or hold its concentration at a steady state

cell adhesion molecules

allow cells to bind to other cells or surfaces

cadherins

calcium dependent glycoproteins that hold similar cells together

integrins

have 2 membrane-spanning chains and permit cells to adhere to proteins in the extracellular matrix

selectins

allow cells to adhere to carbohydrates on the surfaces of other cells and are most commonly used in the immune system

antibodies

immunoglobulins, Ig. used by the immune system to target a specific antigen, which may be a protein on the surface of a pathogen or toxin. The variable region is responsible for antigen binding

electrophoresis

uses a gel matrix to observe the migration of proteins in response to an electric field

native PAGE

maintains the proteins shape, but results are difficult to compare because the mass/charge ratio differs for each protein

SDS page

denatures the proteins and masks the native charge so the comparison of size is more accurate, but functional protein cannot be recaptured from the gel

isoelectric focusing

separates proteins by their isoelectric point (pI); the protein migrates toward an electrode until it reaches a region of the gel where pH = pI of the protein

chromatography

separates mixtures on the basis of their affinity for a stationary phase or a mobile phase.

column chromatography

uses beads of a polar compound (stationary phase) with a nonpolar solvent (mobile phase)

ion exchange chromatography

uses a charged column and a variably saline eluent

size exclusion chromatography

relies on porous beads. large molecules elute first because they are not trapped inside the small pores

affinity chromatography

uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest

ion channels

can be used for regulating ion flow into or out of a cell.

ungated ion channels

always open

voltage gated channels

open within a range of membrane potentials

ligand gated channels

open in the presence of a specific binding substance, usually a hormone or neurotransmitter

enzyme linked receptors

participate in cell signaling through extracellular ligand binding and initiation of 2nd messenger cascades

G protein coupled receptors

has a membrane-bound protein called the g-protein (alpha, beta, gamma subunits). The 1st messenger ligand initiates the 2nd messenger and the cascade response

structure

primarily determined through x-ray crystallography after the protein is isolated, although NMR can also be used

amino acid sequence

determined using the Edman Degradation