Acid/Base and Enzyme Kinetics Flashcards
Covalent bonds
equal sharing of electrons
What are the types of non-covalent bonds?
hydrogen bonds, electrostatic bonds, hydrophobic interactions and van der waals interactions
What are the characteristics of non-covalent bonds?
much weaker, require around 5 kcal/mole to break, break quite easily under physiological conditions, determine how molecules interact with each other and the shape of molecules
What are the characteristics of hydrogen bonds?
an attractive force between a H atom in a polar covalent bond and the unpaired electrons of another electronegative atom….where H is the donor and the electronegative atom is the acceptor
The strength of hydrogen bonds is dependent on?
distance and orientation
What are the characteristics of an electrostatic bond?
an attractive force between a negative and positive charged atoms where strength is dependent on distance but not orientation
What are hydrophobic interactions?
a solvent effect in water where the water molecules push non-polar molecules together
What determines strength of hydrophobic interactions?
the surrounding hydrogen bonds that push the molecules together
what is a van der waal force
the attraction between two neutral atoms
Definition of an acid
a molecule that can donate or release a H+ ion (proton)
definition of a base
a molecule that can accept or react with a hydrogen ion, H+
Conjugate base
dissociation of an acid creates a conjugate base that can accept a proton to regenerate the acid
conjugate acid
protonation of a base will produce a conjugate acid that can donate the proton to regenerate the base
what acids dissociate completely?
strong acids (HCl or H2SO4)
Weak acids and weak bases exist in_______ with their conjugate species
equilibrium
definition of pH
pH= -log[H+], higher pH means lower H+ and lower pH means higher H+
why are H+ and pH so important?
many biological molecules undergo acid-base equilibrium and the amount of acid or base is dependent on H+ concentration……the higher the H+ content the more an acid is favored (AH)
what is Ka?
the acid dissociation constant, is a measure of the position of equilibrium
ka is the H+ concentration at exactly half of A is protonated
Ka= [H+][A]/[HA]
what is pKa?
pKa=-logKa
Henderson-Hesselbalch equation
pH= pKa + log [A]/[HA]
what happens when pH=pKa?
exactly half of A is unprotonated and the other have is protonated……equilibrium
What happens when pH is one unit higher than pKa?
90% of solution is A (dissociated)
what happens when pH is two units higher than pKa?
99+% of solution is A (dissociated)
what happens when pH is one unit lower than pKa?
90% of solution will be HA (protonated)
what is buffering?
a substance that can react with either H+ or OH- to get rid of excess H+ or OH-. The buffer decreases a pH change
Buffers work well when?
pH is near their pKa
what is the most important physiological buffer?
bicarbonate
metabolism generates ______ in the body
acidity
what is the structure of amino acids?
carboxylic acid group, amino group, r group/side chain, and a H all about an alpha caarbon
the carboxyl group of an amino acid is usually _______ while the amino group is usually _______
deprotonated, protonated
What are the non-polar amino acids?
glycine, alanine, proline, valine, leucine, isoleucine, phenylalanine, methionine, tryptophan
What are the characteristics of non-polar amino acids?
have methylene side chains that cannot form hydrogen bonds, usually found in the center of protein structures, are abundant components of protein
What are the polar amino acids?
serine, threonine, tyrosine, cysteine, asparagine, glutamine
What are the characteristics of polar amino acids?
interact well with water through hydrogen bonding on their side chains, and usually found on the surface of proteins
What are the aromatic amino acids?
phenylalanine, tryptophan, tyrosine
What are the characteristics of the aromatic amino acids?
they are usually hydrophobic and buried within protein structures
tryptophan is the least abundant amino acid in proteins
what are the sulfer containing amino acids?
cysteine and methionine
what ate the characteristics of sulfer amino acids?
many extracellular proteins are held together in part by disulfide bridges
What are the negatively charged amino acids?
aspartate and glutamate
What are the positively charged amino acids?
arginine, lysine and histidine
What are the characteristics of the charged amino acids?
they mostly protrude at the surface of proteins and are often found making electrostatic interactions with other residues
what is a zwitterion?
a molecule with a positively charged amino group and negatively charged carboxyl group
What is isoelectric point?
the pH at which a molecule has no net charge pI= (pk amino group + pk carboxyl group)/2 or pI= (pk1 + pk2)/2 when there re two carboxyl groups
What is the overall protein structure?
amino acids are joined by peptide bonds/amide bonds, then many amino acids are joined end to end by peptide bonds to form polypeptides, then long polypeptides come together to form a protein
what happens in a peptide bond?
the carboxyl group of one amino acid is connected to the amino group of another amino acid and they lose their acid-base characteristics…… a water molecule is also lost
Peptide bonds have a partial ___________ that makes them planar and rigid because of ______
double bond character, electronic resonance
What level of protein structure dictates shape and function?
primary
what is the primary structure of a protein?
simple chain of amino acids
What are the two secondary protein structures?
alpha helix and beta sheets
What are the characteristics of alpha helix?
the carboxyl oxygen accepts a hydrogen from a residue 4 locations down in the sequence. this repeating interaction stabilizes the helix at which the R groups protrude at regular intervals.
What are the characteristics of beta sheets?
beta sheets form hydrogen bonds with other beta sheets, adjacent R groups interact and beta turns can be formed by the hydrogen bonding
What are triple helixes?
cable like structures of great tensile strength, only polypeptides with glycine residues every third position can be used, examples are collagen chains
*****the H on the alpha carbon sticks in the middle so no other R group can fit besides glycine
What holds primary structure together?
covalent bonds
What holds secondary structures together?
hydrogen bonds
what holds tertiary and quaternary structures together?
non-covalent bonds
What are globins?
protein structures that are primarily alphahelical, have no beta structures, but all helix connected by turns
what determines the folding structure of a protein?
amino acid sequence
what is Keq?
a way to describe equilibrium
Keq= products/reactants
when Keq>1
only a small amount of reactant is present….. it favors the products
when Keq<1
a small amount of product is present….it favors reactants
what does G0 tell us?
the same thing as keq
G0>1
the reaction is non-spontaneous, favors the reactants and absorbs energy
G0<1
the reaction is spontaneous, favors the products and produces energy
Keq and G0 tell us NOTHING about?
how fast a reaction goes
ATP is thermodynamically____but kinetically _____
unstable, stable
What is a catalyst?
lowers the energy of activation and increases the rate at which a reaction proceeds towards equilibrium
Keq and G0 depend on?
the initial and final states, which is why they are not altered by the presence of a catalyst
Enzymes do not alter the
equilibrium of a reaction
what is enzyme kinetics?
quantitative description of enzyme activity as a function of substrate concentration
what is an enzyme catalyzed reaction?
at very high substrate concentration the curve approaches a theoretical limit corresponding to the saturation of the catalyst
saturation kinetics model
E + S <—–> ES ——> E + P
the rate of product formation is proportional to the enzyme substrate complex (ES)
Additional Increase in substrate concentration will…….
not increase the reaction rate
Michaelis Menten Equation is?
reaction rate as a function of substrate concentration
What is Km?
michaelis constant, when the substrate concentration is at half of Vmax meaning half the enzyme is saturated
What is Vmax?
a measure of the maximum capacity of the enzyme. it depends on how much enzyme is present
What is enzyme inhibition?
usually refers to reversible inhibition meaning removal of inhibitor results in rapid recovery of enzyme
What is enzyme inactivation?
refers to irreversible effects
what are the two types of reversible inhibitors?
competitive and non-competitive
What are competitive inhibitors?
bind in a mutually exclusive fashion with substrate but inhibition can be overcome by high substrate concentration
what are non-competitive inhibitors?
do not compete with substrate for same binding site, can bind in the presence or absence of substrate, and inhibition cannot be overcome with high substrate concentration
Competitive inhibitors do what to km and vmax?
vmax stays the same but km increases
non-competitive inhibitors do what to km and vmax?
vmax decreases but km stays the same
lead and mercury
are heavy metals that react with -SH groups and act as irreversible inactivators of many enzymes
