Midterm I terms - biochem

metabolic pathway

one set molecule is converted step-by-step to other molecules

metabolite

any one of a single molecule involved in metabolism

metabolome

the total number of metabolites in a given cell, tissue, or organism

metabolomics

the study of all the metabolites as they interact in a given tissue, cell, or sample

functional groups

a group of atoms responsible for characteristic reactions of a particular compound

catabolism

exergonic breakdown of complex molecules in living organisms to form simpler ones together with the release of energy

anabolism

build up endergonic, the synthesis of complex molecules in living organisms from simpler molecules together with the storage of energy

L-amino acid

every single biological amino acid is this, it is one of two possible mirror images of the molecule with the amino group always being on the left side in a fischer projection

peptide bond

amide linkage between a carboxyl group and an amino group

C-terminus

carboxyl-terminal end of a polypeptide chain

N-terminus

amino-terminal end of a polypeptide chain

residue

a single unit that makes up a polymer such as an amino acid, polypeptide or protein

alpha helix

a common, tightly coiled, right-handed secondary structure in proteins, stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the amide hydrogen of an amino acid four residues away

beta sheet

consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet

1,2,3,4 degree structures

1 is amino acid residues, 2 is alpha helix, 3 is polypeptide chain, 4 is assembled subunits

cofactor

a molecule other than an amino acid whose presence is essential for the activity of an enzyme

enzyme

a protein that acts as a biological catalyst, accelerating the rate of specific chemical reactions in living organisms

steady state

condition where concentrations of molecules or ions within a cell or organ remain relatively constant over time despite a continuous flow of materials and energy through biochemical pathways

substrate

a molecule or substance that an enzyme acts upon to catalzye a chemical reaction

product

molecules formed as a result of a chemical reaction

reaction

reaction coordinate diagram

activation energy (delta G+)

entropy reduction

ensures two molecules are sufficiently restricted so that they have a higher chance of finding each other

acid-base catalysis

acid or base accelerates a chemical reaction without being consumed in the process.

metal ion catalysis

act as catalysts by binding to reactants, orienting them, and/or stabilizing transition states

covalent intermediate

a transition state formed during an enzyme-catalyzed reaction where a covalent bond forms between the enzyme and the substrate

non-covalent bonds

interaction between atoms dues to electrostatic forces

ionic

complete transfer of electrons between atoms, typically a metal and non-metal

van der waals

weak electrostatic forces that attract neutral molecules to each other

hydrogen bond

electrostatic attraction between a proton in one atom and an electronegative atom in the other

hydrophobic

relation between water and nonpolar molecules that have a long chain of carbons that do not interact with water molecules typically

ligand

small molecule that binds to large molecule binding site (like a protein)

Kd

the dissociation constant for concentration of ligand bound to binding site

saturation

occurs when all available enzyme active sites are occupied by substrate molecules, preventing any further increase in reaction rate

fraction saturation (L/(L+Kd))

the concentration of ligand that is bound to the binding site

active site

the region of eznyme that binds to a protein or other substance during a reaction

competitive inhibitor

competes with the substrate for binding to an active site

chymotrypsin

a selective protease (this enzyme only cleaves proteins that have correctly oriented aromatic R groups)

catalytic triad

3 different amino acids/R groups that are at the right place at the right time, an example of the three members of a catalytic triad is serine, proton acceptor, and a third member of the triad that helps the acceptor be a little more charged (ser, his, asp are the three this is talking about)

hydrophobic pocket

helps selectively bind and cleave peptide bonds with aromatic amino acids

oxyanion hole

stabilizes the transition site (tetrahedral intermediate) giving lower activation energy

Michaelis-menton equation

this equation tells us how the rate of an enzyme-catalyzed reaction changes as the substrate concentration changes

Vmax

the maximum rate of an enzymatic reaction when the enzyme is fully saturated with substrate

Kcat

the turnover number, the maximum number of substrate molecules an enzyme can convert to product per active site per unit of time when the enzyme is saturated with substrate

Km

the substrate concentration at which the reaction rate is half of the maximum reaction rate (Vmax)

myoglobin

constant K, one subunit/monomeric, hyperbola, found in skeletal and cardiac muscles, oxygen storage

hemoglobin

sigmoidal curve, K is not constant/cooperative binding, tetrameric subunit, binds and releases oxygen

sigmoidal/cooperative binding

the binding of one substrate/subunit has an impact on the binding affinity for other subunits of the same ligand

allosteric enzyme

proteins that regulate their activity by binding effector molecules at sites separate from the active site, causing conformational changes that alter enzyme function

sigmoidal isotherm

a type of isotherm that exhibits an S-shaped curve

hill coefficient

describes the degree of sigmoidal behavior, never observed something of over 4

allosteric inhibitor

a molecule that binds to an enzyme at a site other than the active site, altering the enzymes shape and preventing it from binding to its substrate effectively

allosteric activator

binds to the enzyme at a site other than the active site, increasing the enzymes activity

chorismate mutase

substrate of chorismate and product of prehenate. Chorismate mutase is an example of a simple allosteric enzyme

Lineweaver-Burke plot

a graphical representation of enzyme kinetics derived from the michaelis-menten equation that helps analyze the constant Km and maximum reaction velocity Vmax

Gibbs free energy

the energy available to do work at a constant temperature and pressure

enthalpy (deltaH)

heat

entropy (deltaS)

order, number of states something can occupy

deltaG knot

deltaG

the change in free energy

Keq

spontaneous

phosphoanhydride bond

ATP, ADP, AMP, P-P

Pi

hydrolysis

dehydration condensation