TEST 1 Flashcards
carboxylic acid
ketone
amine
ester
aldehyde
peptide bond
aromatic ring
alcohol
organic phosphate
thiol
rank the following from strongest to least
hydrogen bond
covalent bond
van der waal bond
ionic bond
covalent
ionic
hydrogen
van der waal
what are the variables in this equation and what is it finding?
Energy= (Charge on particle 1*charge on particle 2) / Distance
AT H bonds
2 h bonds
GC H bonds
3 h bonds
defining chemical features of water
overall polar
high electron density at oxygen
low electron density on both hydrogens
1x10^-7 H = ?pH
7
1x10^-1 H = ?pH
1
pH equation
H x OH = what
4 classes of biomolecules
proteins
nucleic acids
carbohydrates
lipids
carbs functions
fuel
structural roles
extracellular receptors
lipid functions
hydrophobic
held together through hydrophobic interactions
fuel
intracellular signaling molecules
separates internal and external environment
eukaryotes
large
internal organelles
nucleus
usually multicellular
prokaryotes
small
no nucleus
cell wall
van der waal bond
-shortest bond length
-1
-weakest bond
-bond formed through different charges of its parent molecule
ionic bond
longest bond length
3
second strongest bond
covalent bond
medium bond length
1.5
strongest bond
hydrogen bond
1.5-2.6
second weakest bond
breaking a bond
always requires energy to break a bond
energy is always released when a bond is broken
polar
hydrophilic
ex glucose
nonpolar
hydrophobic
lipids o2 n2 co2
amphipathic
both polar and nonpolar
-second law of entropy
-for anything to be spontaneous it must increase entropy
-entropy of universe can still increase if the surroundings entropy of the surroundings increases while the systems entropy decreases
gibbs free energy
hydrophobic effect when two nonpolar molecules are suspended in water
they join by the increase of entropy of the water molecules surrounding
(creation of plasma membrane increases entropy)
autoionization of water equation
h20 == h + oh
h20+h20==h30 + oh
equilibirum constant expression
kw= [H+][OH-]=1.0x10^-14
pH equation
pH= -log[H+]
acid disassociation equation
Ka = [H+][A-]/[HA]
Ka= acid dissociation constant
H+=hydrogen concentation
A-=anion
HA=weak acid
as ka gets bigger, the acid gets stronger
COOH
carboxylic acid, H on an acid of the carboxylic acid is most likely to dissociate
pka equation
pKa= -logKa
as pka gets lower = stronger acid
as pka gets higher = weaker acid
when pka = pH
pka < pH
pka > pH
[HA] = [A-] acid and conjugate base are in equal amounts
[HA] < [A-] deprotonated conjugate base
[HA] > [A-] protonated acid
Buffering equation
amino acid constituents
carboxylic acid
amino group
variable side group
central carbon
ONLY L form of amino acids
GO OVER L/D isomer
proteins
-all made from 20 amino acids
-contain 20 different side groups
amino acid pka
Carboxylic acid group pka = ~3
protonated- COOH charge close to 0
deprotonated- COO- charge close to -1
amino group pka = ~9
protonated- NH3+
deprotonated- NH2
Glycine
non polar
Alanine
non polar
Valine
non polar
Leucine
non polar
Isoleucine
non polar
Methionine
non polar
proline
non polar
phenylalanine
non polar
Tryptophan
non polar
serine
polar
Threonine
polar
Tyrosine
polar
pka of oh hydrogen = 11
glutamine
polar
asparagine
polar
cysteine
polar
pka of sulfur hydrogen = 8
Lysine
positively charged
polar
pka of amino group = 11
Arginine
positively charged
pka of amino group = 12.5
histidine
positively charged
pka of amino group in pentyl group = 6
aspartate
negatively charged
Glutamate
negatively charged
most proteins amino acid count
50-2000
psi bond
Alpha carbon of amino acid bonded to carbon of carboxylic acid
phi bond
Alpha carbon of amino acid bonded to nitrogen of amino group
when a peptide bond forms what is lost?
H20
secondary structure of a protein
-local folded protein structure that is due to interactions between atoms in the protein backbone
-held together mostly by hydrogen bonds
-alpha helixs
-beta folded sheets
primary structure of a protein
-sequence of amino acids linked by peptide bonds
alpha helix
-3.6 amino acid residues per turn
-only right handed helixes
-hydorgen bond occurs between amino and carboxyl group 4 amino acids ahead for each amino acid
beta pleated sheets
-links strands of amino acids running parallel/antiparallel
-links dont need to be close in sequence to bond
-bonds amino and carboxyl groups
-many adopt a twisted shape
-can beta pleated sheet bond with 2 other sheets
turns/loops
-secondary structure
-hydrophilic r groups
-on surface of protein
tertiary structure of a protein
-overall three-dimensional structure resulting
from folding and covalent cross-linking of a polypeptide
-result of the interaction between R-groups
-interior usually non-polar
-exterior usually polar
-contains secondary structure inside it
-overall globular connected by short strands of peptides
Quaternary Structure of a protein
-multiple polypeptide chains (subunits) that
assemble into a functional protein
-held together by hydrogen bonds, van der Waals
interactions, electrostatic interactions
-subunits can be variable or uniform
ex. ⍺, β, ɣ
⍺2 β1 ɣ3 = 1 protein
Denaturation
loss of secondary, tertiary or quaternary
structure of a protein
active site
-site of enzyme catalysis and substate binding
-small 3D pocket
-binds via multiple weak
interactions (not usually covalent)
induced fit model
-binding of substrate and active site that creates a
conformational change in shape of protein
-makes binding site more
complementary to substrate
-correct model
transition states
-unstable molecule
-higher in free energy than substrate or product
catalysts
-lowers energy required to achieve transition state
-only affects the rate at which equilibrium is achieved
-doesnt change final equilibruim position
enzyme catalysts
-highly specific, usually only catalyzes one reaction or very closely related reactions
lock and key model
-substrate and active site fit identically into each other
-not correct
coenzymes
small organic cofactors derived from vitamins
tightly bound coenzymes
prosthetic groups
loosly bound coenzymes
cosubstrates
enzymes + cofactor
holoenzymes
enzyme without cofactor
apoenzyme
cofactors
2 main groups making up larger whole
-activation energy
-rate of reaction/how fast reaction will proceed
-lowering this value will speed up the reaction
-∆G
spontaneous reaction
keq < 1
favors products
+∆G
non spontaneous reaction
favors reactants
keq > 1
kcat
turnover number
number of substrate molecules that an enzyme can convert to a product in a given unit of time
independant of enzyme concentration
specific activity
product formed/time/mg enzyme
Vmax
highest velocity of product created
dependent on enzyme concentration
Km
independant of enzyme concentration
substrate concentration ( required for half Vmax)
low km
enzyme only requires small amount of substrate to become saturated
high km
enzyme requires large amount of substrate to become saturated
catalytic efficiency
kcat/km
used to compare enzyme preference for substrates
Covalent Catalysis
active site contains a reactive group that becomes temporarily covalently modified
General Acid-Base Catalysis
molecule other than water plays the role of proton donor or acceptor
Metal Ion Catalysis
metal ion may serve as electrophilic catalyst, may generate a nucleophile, may bind
to substrate
Approximation and Orientation
full complement of interactions only when substrate is in transition state (transition
state stabilization)
chymotrypsin
protease specific for peptide bonds on carboxyl-
terminal side of large aromatic, hydrophobic amino acids
-functions at pH 8
2 phases of chymotrypsin peptide bond formation
acylation
deacylation
acylation
-peptide bond cleavage, ester
linkage formed between peptide carbonyl
carbon and enzyme
Competitive Inhibition
-inhibitor resembles substrate and binds to the active site
results : apparent km is higher to reach vmax ; vmax unchanged ; km turns into kapp (apparent needed to then reach vmax with an increased concentration)
Noncompetitive
Inhibition
-inhibitor binds to a site other than the active site
-cannot be overcome by increasing substrate concentration
-lower v max
-km unchanged
deacylation
-ester linkage hydrolyzed and
nonacylated enzyme regenerated
hydrophobic pocket
-functions in enzyme specificity
-preference for cleaving peptide bonds just past resides with large hydrophobic side chains
oxyanion hole
-negative charge on carbonyl oxygen during formation of intermediate stabilized by hydrogen bonds
catalytic triad
serine histidine asparagine
allosteric control
-the binding of a ligand to one site affects the binding properties of another site on the same protein
bonding techniques used by the catalytic triad of chymotrypsin
general acid/base catalysis
covalent catalysis
approximation and orientation
NOT metal ion catalysis
buffer ranges
+/- 1pH around pKa value
hemoglobin
-a2B2
-more dynamic to changes in oxygen pressure in body
-when iron binds to 02 it pulls the iron into the plane of the hemoglobin, rather than hang outside of it
myoglobin
-found in muscle
-diffuses o2 to sites requiring 02, provides reserve supply of 02
-difficult to dissociate 02
T state
deoxy, low affinity for oxygen- oxygen desaturated
R state
oxy, high affinity for oxygen- oxygen saturated
intermediate states between r and t state
-out of 4 overall subunits, 1 fills with oxygen, it then influences other subunits to bind to more 02
-Hb with 1 02 bound binds 02 3x as strongly as fully deoxygenated Hb
-Hb with 3 02 bound 4 site has 20x greater affinity for 02 than fully deoxygenated Hb
other allosteric regulators for hemoglobin
2,3 biphosphoglycerate
C02- as c02 increases 02 affinity decreases
H+ - as
Bar Headed Goose
-Changes in hemoglobin amino acid sequence that stabilizes R form
-allows for survival in low 02 concentration environment
sickle cell anemia mutation
Glutamate to Valine amino acid 6
Isozymes
Different variants of the same enzyme
fetal Hb
⍺ 2 ɣ 2
gamma subunits are similar to Beta subunits however they have a lower affinity for BPG and increased affinity for 02
hexokinase and glucokinase
isozymes
hexokinase
isozyme of glucokinase
hexokinase:
located in all tissues
low km
inhibited by glucose 6 phosphate
glucokinase
isozyme of hexokinase
located in liver pancrease and brain
high km
not inhibited by glucose 6 phosphate
Reversible Covalent Modification
Addition or removal of a group to a protein via an
enzyme
phosphorylation
occurs only in groups w OH group
Tyr Ser Thr His
proteolysis
cleavage of a peptide into its
active form
ex, Proinsulin to insulin
DNA
store genetic info and pass info to next generation
deoxyribose - has H in 2’ spot
RNA
transmits and expresses info in DNA into proteins w cellular functions
ribose- has OH in 2’ spot
nucleotide composition
nitrogenous base
sugar
phosphate
can have up to 3 phosphate
purine
2 rings
GA
pyrimidine
1 ring
TCU
oligonucleotide
few nucleotides linked together
polynucleotide
many nucleotides linked together
nucleoside
base + sugar
glycosidic linkage
1’ carbon of nitrogenous base to sugar
pauling and corey model
3 strands of DNA
bases on outside
phosphates on inside
watson and crick
2 strands of dna
phosphates on outside
paired bases on inside
DNA secondary structure
-double helical structure
-anitparallel complementary backbones
-right handed helix
-minor and major grooves
chargraffs rules
ratio of purine to pyrimidine bases is equal
hydrophobic stabilizing interaction
hydrogen bonds linking complementary bases
and
van der waal interactions between bps
hydrophilic stabilizing interactions
stabilized by hydrogen bonds with the aqueous environment
A form of DNA
right handed
favored by DNA/DNA RNA/RNA complexes
most compact form of DNA
B form of DNA
right handed
standard accepted human form
found by watson and crick
Z form of DNA left handed
left handed
least compact form of DNA
stem loops
secondary structure of RNA
tertiary structure of prokaryotic DNA
circular plasmid DNA
tertiary structures of eukaryotic DNA
chromatids
quaternary structures of DNA
histones wound around DNA
what amino acids bind to DNA
positively charged ones
mostly arginine or lysine
