Biochemistry Midterm 1 Flashcards
What is the definition of a hydrogen bond?
dipole-dipole/charge-dipole interactions that arise between covalently bonded H atom and a lone pair of electrons on an electronegative atom
average number of bonds in liquid water vs ice
3.4 vs 4
why do micelles form?
by clustering non-polar tails together as a result of the hydrophobic effect, entropy is increased compared to if the hydrophobic regions were all separately interacting with water (minimized to ordered shell around micelle)
define van der waals interactions
weak interactions between atoms at the maximum between attraction (due to polarity and dipole) and repulsion (due to atom size)
van der waals qualities
between any 2 atoms, determine steric compatibility, individually easily broken, strong in numbers, stabilize macromolecules
colligative vs non colligative properties
colligative properties are only dependent on solute concentration and not on solute nature: boiling point, melting point and osmolarity
non colligative properties are dependent on solute nature: viscosity, surface tension, taste, color
adhesion vs cohesion
adhesion - binding between unlike molecules
cohesion - binding between like molecules (water surface tension)
water dissociation constant and dissociation at 25°
1.0 x 10^-14 M^2, at 25° 2 in every 10^9 molecules is dissociated
proton hopping definition
protons moving between hydrogen bonded water molecules causing net movement of a photon over long distance quickly`
ionic product of water
Kw = [H+][OH-]
A strong acid Ka and pKa
high Ka and low pKa
buffering capacity is greatest when
pH = pKa which is also when the acid is 50/50 concentration
buffer systems in vivo
phosphate, bicarbonate, histidine
peptide bonds are formed
through condensation reaction between carboxyl group and amino group of two amino acids
2 cysteine amino acids that form a disulfide bond is
cystine
histidine properties
not actively positively charged R group called imidazole but often involved in reactions as a proton donor. Imidazole is cyclic
uncommon amino acid that can be incorporated by ribosomes
selenocysteine
how do modified amino acids arise?
post-translational modifications, permanent or transient
high pH vs. low pH charged of amino acids
low pH amino acids will be positively charged (H is still attached to carboxyl group). High pH amino acids will be negatively charged (H is donated and NH2 is formed)
zwitterion
net 0 charge of amino acid, both negative and positive charges on amino acid. This occurs at pI for amino acid
how to calculate pI
without ionizable R group: average of pka1 and pka 2
with ionizable R group: average of pka closest to pkaR and pkaR
protein structures are stabilized by
non covalent forces: H bonds, ionic bonds, van der waals interactions, hydrophobic effect
why are disordered regions important
for interactions with other proteins - gives flexibility and ability for conformational change
common protein structural patterns
alpha helices, beta turns, beta sheets
why doesn’t the peptide bond rotate?
it is a resonance structure between O=C-N
phi vs. psi angle around alpha carbon
phi is amide nitrogen bond side, psi is on carbonyl carbon side
peptides are read in what direction:
amino (left) to carboxyl (right)
how are alpha helices and beta sheets stabilized?
H bonds. Alpha helices H bond between nearby residues amino acid backbones. Beta sheets stabilize parallel or antiparallel between adjacent segments (may or may not be nearby)
random coil
irregular arrangement of polypeptide (disordered)
1Å =
1x10^-10 m
residues per turn of alpha helix
3.6. Every n + 4 H bonds
alpha helix breakers and why
proline due to cyclic R ground not able to rotate and it doesn’t H bond. Glycine has a lot of flexibility because it is small, better in tight coils like collagen
5 constraints that affect helix stability
- amino acid propensity for helix (small, hydrophobic) 2. R group interactions 3-4 amino acids away. 3. bulkiness of R groups 4. Proline and glycine. 5.
proline and glycine in beta turns
proline position 2 (cis), glycine position 3
native globular form
condensed tertiary protein structure stabilized through hydrophobic effect
motifs are? Globular proteins are?
specific arrangement of many secondary structures, recur across many proteins. Globular proteins are different motifs folded together
domain is?
part of a polypeptide chain that is independently stable and functional
fibrous protein solubility
insoluble due to many hydrophobic R groups
alpha keratin description
strong double twisted left handed alpha helices. Disulfide bonds stabilize between different polypeptide twists. Found in hair, nails, and feathers.
collagen description
3 separate polypeptide alpha chains supertwisted left handed alpha chains coiled together in a right hand twist, very strong.
Cross-linking stabilizes supercoils parallel adjacent to each other. Found in connective tissue, bones and cornea
silk fibroin description
antiparallel beta sheet structures stacked with small R groups. Stabilized by weak interactions for flexibility and strength.
quaternary structure
assembly of individual polypeptides into a large functional cluster
enzymes increase specificity how?
by creating an environment in which the desire product is favored to be produced
benefits of enzymes
higher reaction rates, milder conditions, avoids side products, regulation of pathways
cofactors include:
coenzymes (organic), inorganic (minerals), prosthetic groups (tightly bound cofactor)
apoenzyme vs holoenzyme
no coenzyme, yes coenzyme
6 classes of enzymes
oxidoreductases: transfer of electrons
transferases: group transfer
hydrolases: hydrolysis (breaking of bonds using water)
lysases: cleavage of C-C, C-N, or C-O bonds
Isomerases: transfer of groups within molecule
ligases: formation of C-C, C-S, C-O or C-N bonds via condensation rxn
what is desolvation?
enzyme-substrate binding replaces H bonds water had with enzyme(which decreases entropy)
how do enzymes lower activation energy?
organizing reactive groups into proximity and proper orientation to make the reaction thermodynamically favorable
what compensates for thermodynamically unfavorable free energy change associated with induced fit?
weak interactions formed in transition state of ES complex
categories of catalysis (enzymes use one or more)
acid-base: proton transfer, often from water
covalent catalysis: transient covalent bond, requires nucleofile on enzyme
metal ion catalysis: interacts with substrate to facilitate binding
chymotrypsin function
cuts peptide bonds adjacent to aromatic amino acids
Km =
[S] when V = 1/2 Vmax
turnover number =
Kcat = K2 = Vmax/[ET]
number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at saturation
Niacin is necessary as
a precursor of NAD coenzyme required by many oxidoreductase enzymes
steady state vs equilibrium
Steady state: when rate of product creation and rate of product breakdown is is equal (amount of ES produced = amount ES broken down into product)
Equilibrium: rate of reaction is equal in both directions (forwards and backwards) and reactants and products are present
Slope at any point on a product concentration vs time graph
velocity of enzymatic reaction
Km =
[S] when V0 is 1/2 Vmax
(K2 + K-1)/K1
saturation kinetics
at high [S], velocity is not proportional to [S] (velocity flatlines due to all enzymes being occupied)
Turnover and Kcat equations
Kcat = K2
Kcat = Vmax/[ET]
turnover is equal to the slowest K
rate limit equation/enzyme efficiency
limited by specificity
kcat/Km
Lineweaver-Burk double reciprocal plot x and y intercepts
x intercept = -1/Km
y intercept = 1/Vmax
slope is Km/Vmax
reversible enzyme inhibitors
bind to and dissociate from enzymes
often structural analogs of substrates or products
competitive inhibition definition and plot
competes with substrate for enzyme, binds to active site
does not effect catalysis (Vmax)
lines intersect at y axis and apparent increase of Km
Uncompetitive inhibition definition and plot
binds to ES complex, inhibits catalysis (not substrate binding)
decrease in Vmax (and apparent decreased in Km), lines are parallel
mixed inhibition definition/noncompetitive inhibition and plot
binds enzyme (with or without S)
inhibits both substrate binding and catalysis
lines intersect left of the y axis
allosteric inhibitor
noncompetitive inhibitor or uncompetitive inhibitor which binds to a part of the enzyme outside the active site
myosin structure
2 heavy chains of supercoiled alpha helices with amino terminal globular heads
enzymes differ from other catalysts in that only enzymes…
display specificity towards a single reactant
what does Keq equilibrium constant say about free energy?
Keq = [P]/[S] reflects the lower energy state of the product compared to the substrate
a catalyzed reaction where at equilibrium there is more product than substrate is thermodynamically favorable
Transition state definition
momentary perfect bind match with enzyme and substrate after it has changed conformation
