Biochem Flashcards
Where do D amino acids exist
prokaryotes
Nonpolar, nonaromatic amino acids
glycine, alanine, valine, leucine, isoleucine, methionine, proline
Aromatic amino acids
tryptophan, phenylalanine, tyrosine
Polar Amino acids
Serine, threonine, asparagine, glutamine, cysteine
Negatively charged amino acids
aspartate, glutamate
Positively charged amino acids
lysine, arginine, histidine
Nature of amino acid at low PH
fully protonated
Nature of Amino acid at high PH
fully deprotonated
Nature of Amino Acid at isoelectric point
zwitterion
PI of amino acids without charged side chains
6
peptide formation is what type of reaction
dehydration
conjugated proteins
have attached molecules called prosthetic groups which can be metal ions, vitamins, lipids, carbs, or nucleic acids
Oxidoreductase
catalyzes REDOX reactions
transferase
move a functional group from one molecule to another
hydrolase
cleaves with water
lysase
cleaves without water
isomerase
interconversion of isomers including constitutional isomers and stereoisomers
how do enzymes work
by stabilizing the transition state
Michaelis Mentin Plot info
plots substrate concentration (x) and reaction velocity (y)
Km value occurs at 1/2 vmax
v = (vmax[s])/(Km+[S])
vmax = [E]kcat
v=(Kcat/Km +[S])[E][S] but at low substrate concentration S can be negated and the equation is v=(Kcat/Km)[E][S]
Lineweaver-Burn Plot info
plots 1/v (y) against 1/[S] (x)
x intercept is (-1/Km) Y intercept is (1/vmax)
Catalytic Intensity
Kcat/Km
Hills coefficient
describes cooperative binding. Above one indicates cooperative binding, below one indicates negative cooperative binding, a value of 1 indicates no cooperative binding
Competitive inhibition
when inhibitor is similar to subtrate and binds to active site. Can be overcome by adding more substrate. Has no effect on vmax, but Km increases
Noncompetitive inhibition
inhibitor binds with equal affinity to enzyme and enzyme-substrate complex. Vmax is decreased Km stays the same
Mixed inhibition
inhibitor with unequal affinity for enzyme and enzyme substrate complex. Vmax is decreased and Km increases or decreases depending on the inhibitors affinity
uncompetitive inhibition
inhibitor only binds with enzyme-substrate complex so both Km and vmax decrease
zymogens
inactive forms of an enzyme that are activated by cleavage
Migration velocity
v=Ez/f
Cadherins
calcium dependent glycoproteins hat hold similar cells together
integrins
have two membrane spanning chains to permit cells to adhere to extracellular proteins
selectins
allow cells to adhere to carbohydrates on surfaces of other cells. found in the immune system
antibody makeup
two heavy chains and two light chains held together by disulfide linkages and noncovalent interactions
G protein receptor cascade
Ligand engages G protein. GDP becomes GTP and the alpha subunit dissociates from beta and lambda subunits. Alpha subunit activates adenyl cyclase or phospholipase C and GTP becomes GDP and alpha subunit reassociates.
Equation for number of stereoisomers with common backbone
=2^n where n is the number of chiral carbons
Benedicts reagent
oxidizes glucose to gluconic acid and creates red precipitate to test for the presence of aldehyde
Tollens reagent
makes a silvery substance when reacted with an aldehyde
Esterification of glucose reagents
acetic anhydride, 273K, pyridine
Phosphorylation of glucose
ATP usually occurs with an enzyme
maltose
(glucose-alpha-1,4-glucose)
cellobiose
beta 1,4 linkage of two glucose molecule
Sucrose
(glucose-alpha-1,2-fructose)
Lactose
(galactose-beta-1,4-glucose)
cellulose
string of cellubiose (beta 1,4 linkage of two glucose molecule)
Amylopectin
amylose but also has alpha1,6 bonds
amylose is glucose-alpha-1,4-glucose
amylose
glucose-alpha-1,4-glucose
glycogen
highly branched glucose polymer with alpha1,6 bonds more than amylopectin. Highly branched
saturated fatty acid
has only single bonds (thus saturated with hydrogen)
unsaturated fatty acid
has some double bonds
glycerophosphate
As a head group (x) linked to a glycerol backbone via a phosphodiester linkage. Called phosphatidyl-x. examples include phosphatidylcholine and phosphatidylethanolamine
sphingolipids
have a sphingosine backbone with long chain nonpolar fatty acid tails and polar head groups. Can be phospholipids or glycolipids.
Classes of sphingolipids
ceramides, sphingomyelin, glycosphingolipids, gangliosides
ceramides
sphingolipid with Hydrogen as a head group
sphingomyelin
sphingolipids that are also phospholipids. Usually have phosphatidylcholine or phosphatidylethanolamine as the head group
