Biochemistry

Amino acids

a molecule with 4 groups attached to a central (a) carbon: an amino group, a carboxylic acid group, a hydrogen atom, and an R group. The R group determines the function of that amino acid

stereochemistry

The stereochemistry of the a-carbon is L for all chiral amino acids in eukaryotes. All chiral amino acids except cysteine have (S) configuration and all amino acids are chiral except for glycine

hydrophobic

hates water; alkyl chains, non-polar

hydrophillic

loves water; polar, charged

primary structure

linear sequence of amino acids in a peptide. stabilized by peptide bonds. The AA sequence is written N-terminus to C-terminus. N-terminus is positively charged due to -NH3

secondary structure

The local structure of the neighboring amino acid. Is stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups

• a-helices: a common secondary structure, clockwise coils around a central axis

• b-sheets: a common secondary structure. can be parallel or anti-parallel

• proline: can interrupt secondary structures due to its rigid cyclic structure

amphoteric

Amino acids can act as a base or an acid

tertiary structure

3D shape of a single polypeptide chain, and is stabilized by hydrophobic interactions, acid-base interactions, H-bonds, and disulfide bonds

hydrophobic interaction

push the non-polar R-groups to the interior of a protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs free energy

disulfide bonds

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

quaternary structure

The interaction between peptides in proteins that contain multiple subunits

conjugated proteins

proteins with covalently attached molecules

prosthetic group

The attached molecule is 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

aromatic

phenylalanine, tyrosine and tryptophan

nonpolar

glycine, alanine, leucine, isoleucine, methionine, proline p

polar

serine, threonine, asparagine, glutamine, and cysteine

positively charged

lysine, arginine, and histidine

negatively charged

aspartate, and glutamate

The ____ of a group is the pH at which half of the species are deprotonated; (HA) = (A-)

pKa

At low (acidic) pH, the amino acid is ___

fully protonated

At pH near the pI of the amino acid, the amino acid is a neutral ____

zwitterion

A high (alkaline) pH, amino acid is fully _____

deprotonated

isoelectric point (pI)

an amino acid without a charged side chain can be calculated by averaging the two pKa values

The titration curve is nearly ____ at the pKa values of an amino acid

flat

The titration curve is nearly _____ at the pI of the amino acid

vertical

enzymes

biological catalysts that are unchanged by the reactions they catalyze and are reusable

oxidoreductases

catalyze oxidation-reduction reactions that involve that transfer of electrons

transferases

move a functional group from one molecule to another molecule

hydrolases

catalyze cleavage with the addition of water

lyases

catalyze cleavage without the addition of water and without the transfer of electrons. The reverse reactions (synthesis) is often more important biologically

isomerases

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

ligases

responsible for joining two large biomolecules, often of the same type

exergonic rxns

release energy, G is negative

lock and key theory

the enzyme and substrate are exactly complementary

induced fit model

the enzyme and substrate undergo conformational changes to interact fully

Saturation kinetics

As substrate concentration increases, the reaction rate does as well until a maximum value is reached - Km and Vmax

• Michaelis-Menten

• Lineweaver-Burk

cooperative enzymes

sigmoidal curve bc of the change in activity with substrate binding

feedback inhibition

a regulatory mechanism whereby the catalytic activity of an enzyme is inhibited by the presence of high levels of a product 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

• noncompetitive inhibition

• mixed inhibition

• uncompetitive inhibition

competitive inhibition

The inhibitor is similar to the substrate and binds at the active site. It can be overcome by adding more substrate. Vmax is unchanged, and Km increases.

noncompetitive inhibition

Inhibitor binds with equal affinity to the enzyme and the enzyme-substrate complex. Vmax is decreased, and Km is unchanged.

mixed inhibition

Inhibitor binds with unequal affinity to the enzyme and the enzyme-substrate complex. Vmax is decreased, Km is increased or decreased depending on if the inhibitor has higher affinity for the enzyme or enzyme-substrate complex.

uncompetitive inhibition

The inhibitor binds only to the enzyme-substrate complex. Km and Vmax both decrease.

Irreversible inhibition

alters the enzyme in such a way that the active site is unavailable for a prolonged duration or permanently; a new enzyme molecules must be synthesized for the rxn to occur again

allosteric sites

can be occupied by activators, which increase either affinity or enzymatic turnover

phosphorylation

Covalent modification with phosphate or glycosylation (covalent modification with carbohydrate) can alter the activity or selectivity of enzymes

zymogens

secreted in an inactive form and are activated by cleavage

structural proteins

compose the cytoskeleton, anchoring proteins and much of the extracellular matrix

• collagen, elastin, keratin, actin, and tubulin

motor proteins

one or more heads capable of force generation through a conformational change

• have catalytic activity, acting as ATPases to power movement

• muscle contractions, vesicle movement, and cell motility

  • 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 (CAM)

allow cells to bind to other cells or surfaces

• cadherins

• intergrins

• selectins

cadherins

calcium-dependent glycoproteins that hold similar cells together

integrins

two membrane-spanning chains and permit cells to adhere to proteins in the extracellular matrix. Some also have signaling capabilities

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 a toxin

• have a constant region and variable region, variable region is responsible for antigen binding

• two identical heavy chains and two identical light chains form a single antibody

Ion channels

used for regulating ion flow into or out the cell

• ungated channels

• voltage-gated channels

• ligand-gated channels

ungated channels

always open

voltage gated channels

open within 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 second messenger cascades

G protein-coupled receptors

have a membrane-bound protein associated with a trimeric G-protein. Also, initiate second messenger systems.

native page

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

SDS-page

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

isoelectric focusing

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

chromatography

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

column chromatography

uses beads of a polar compound, with a nonpolar solvent

ion-exchange chromatography

uses a charged column and a variably saline eluent

size-exclusion chromatography

relies on porous beads. larger molecules elute first because they are not trapped in small pores

affinity chromatography

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