BCMB 3100: EXAM 1
42 Cards in this Set
| Front | Back |
|---|---|
|
Water
|
solvent of life
polar molecule (oxygen partial negative, hydrogens partial positive)
|
|
Electrostatic interaction
|
ionic bonds or salt bridges
between distinct electrical charges on an atomNaCl in H2O
|
|
Hydrogen Bonds
|
forms between an electronegative atom (N,O,F) and a Hydrogen
occur wherever H is covalently bonded with an electroneg. atomwater disrupts hydrogen bonds (competes)
|
|
van de Waals interaction
|
between nonpolar and uncharged molecules
transient asymmetry induces complementary asymmetry
|
|
Hydrophobic effect
|
powered by the increase in the entropy of water that results when hydrophobic molecules come together
powerful organizing force (ie. membrane formation, protein folding)
|
|
pH
|
measure of H+ concentration of a solution
greater concentration of H+ lower pH
|
|
Acids
|
proton donors
form conjugate base and proton when ionized
|
|
Base
|
proton acceptor
forms hydroxide ion and conjugate acid
|
|
pKa
|
a measure of the strength of an acid
pH>pKa conj. base predominates (basic)pH<pKa acid predominates (acidic)
|
|
Buffers
|
resist changes in the pH
most effective at a pH near its pKacrucial in biological systems (ie. buffers in blood, carbonic acid and bicarbonate)
|
|
Amino Acids
|
most commonly found in the L-isomer
contain an NH3+ group, COO- group, H group, and R group side chains differ size, shape, charge, H-bonding capacity, hydrophobic character, and chemical reactivity 20 AAs
|
|
Hydrophobic Amino Acids
|
have mainly hydrocarbon side chains
Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine, TryptophanLIPPT MAG
|
|
Polar Amino Acids
|
have side chains that contain and Electronegative atoms (O,S)
Serine, Threonine, Tyrosine, Cysteine, Asparagine, GlutamineSACT GT
|
|
Positively Charged Amino Acids
|
are hydrophilic
Lysine, Arginine, HistidineHistidine can be neutral or positive HAL
|
|
Negatively Charged Amino Acids
|
have acidic side chains
Aspartate, Glutamate GA
|
|
Polypeptide bond
|
A peptide bond is a covalent chemical bond formed between two amino acid molecules.
amide bondamino terminal end is the beginning, carbonyl terminal end is the end 6 atoms in a plane, alpha carbon, NH, CO, alpha carbon of next AAin Trans configuration to reduce steric clash between R gro…
|
|
Secondary structure
|
alpha structure
beta sheet3-D structure formed by H-bonds between NH and CO groups in the main chain
|
|
Alpha Helix
|
C1 H-bonded to C5
backbone forms H-bonds to create helix shape R groups are located outside helix
|
|
Beta sheets
|
formed by adjacent beta strands
polypeptide in a beta strand is fully extended
|
|
Tertiary structure
|
protein folding
myoglobin
|
|
Quaternary structure
|
multiple peptide chains form together to create subunits that display quaternary structure
|
|
Enzymes
|
protein catalysts that accelerate the rate of a reaction
facilitate the formation of the transition state 6 major classes:oxidoreducatse catalyze oxidation-reducation rxnstransferase move functional groups between moleculeshydrolases cleave bonds w/ addn of waterlyases remove atoms to f…
|
|
Free energy (G)
|
enzymes do not alter delta G
reaction will occur if delta G is negative (exergonic)will not occur spontaneously if delta G is positive (endergonic)at equilibrium delta G=0enzymes alter the reaction rate but not the reaction equilibrium
|
|
Active Site of Enzymes
|
enzyme and substrate complex form here
this interaction promotes the formation of the transition state3-D cleft created by AAInteraction at the active site involves multiple weak interactions Enzyme specificity due to active site not lock and key fit but induced fit
|
|
Carbonic Anhydrase Case
|
H2O+CO2 --> H2CO3
In water: H2CO3 --> HCO3-+H+ HCO3- --> CO3-+H+Higher [CO2]: lower pH (due to more H+)With CA deficiency: reaction would take place slower, less acidicHistidine is neutral (can make 2 hydrogen bonds) while Tyrosine is negative (can only make one hydrogen …
|
|
Enzyme kinematics
|
reaction begins as 1st order (linear) becomes zero order
at high [S] the rate doesn't depend on [S]E+S <--> ES --> E+P k1 k2at high [S] [Etotal]=[ES]
|
|
Michaelis-Menten equation
|
Vmax = k2[Etotal] fastes that the enzyme can turnover
Km=Vmax/2 or Km=k-1+k2/k1indicates the stability of the [ES] complex / how much substrate will saturate Ekcat is the rate limiting step (turnover number) kcat=k2kcat/Km is a measure of catalytic efficiency
|
|
Lineweaver-Burk equation
|
inverse of the MM equation
1/Vo=(Km/Vmax)(1/[S])+(1/Vmax)
|
|
Km
|
Km>>[S] // Vo=(Vmax/Km)[S]
[S]>>Km // Vo=VmaxKm=[S] // Vo=Vmax/2
|
|
Kinetics Case
|
Varies: [S]
Constants: [E], temperature, pH (use buffer), timeMeasure: Vo by the product formed at certain time and [S]Wild type has larger Vmax (generates reactants to products quicker)Mutant has larger Km (less affinity to bind)Histidine substitution would result in more H-bondingMISFO…
|
|
Allosteric Enzymes
|
switch between functioning and non functioning conformations by:
1. binding of a regulator at a site distant from the active site2. cooperative binding of multiple substrate molecules (or both)Inducing quaternary structure change
|
|
Hemoglobin
|
"honorary enzyme"
4 O2 binding subunits, 2 alpha and 2 beta (pair of alpha beta dimers)Binds O2 cooperatively; as one binds, Hb conformation changes, increasing affinity for other subunitssigmodal curve (contrast with myglobin which only has one binding site -- MM curve)
|
|
Tense state (T)
|
low affinity for O2
favored until O2 has bound to one subunit of each alpha beta dimerinduces conformational change
|
|
Relaxed state (R)
|
high affinity for O2
favored until O2 is released from one complete alpha beta dimer
|
|
Molecular Basis of Hb Cooperativity
|
O2 binds to heme in Hb, Fe complexed with N of heme, Fe can form 2 add'nl bonds
Fe forms covalent bond with proximal His in HbFe2+/3+ can be oxidizedO2 pulls Fe into plane of the heme by redistributing e-*O2 binding induces conformational changes in one Hb chain, which triggers a conform…
|
|
Role of Electrostatic Interactions in Conformational Change
|
Binding of O2 induces conformational change between T and R state
T state can be stabilized by His and Asp in the beta chain Negative Asp helps stabilize positive charge on His, increasing His pKa (~7)
|
|
Bohr Effect
|
decrease in pH or increase in CO2 leads to stabilization of the T state of Hb and unloading of O2
|
|
Hemoglobin Case
|
His --> Asp disrupts salt bridge reaction, due to change in charge of the AA
R state favored due to substitution Increase in O2 affinity curve is instead sigmodal (as opposed to usual MM curve)results in O2 starvation
|
|
Competitive Inhibition
|
binds to enzyme
Vmax remains unchanged (higher [S] necessary to reach Vmax)Km increases
|
|
Uncompetitive Inhibition
|
bind to ES
Vmax changes (decreases)Km changes (decreases)
|
|
Noncompetitive Inhibition
|
binds to E and ES
Vmax changes (decreases)Km remains unchanged
|
|
Inhibitor Case
|
Acetazolamide taken to inhibit CA enzyme
Vmax changes, but Km doesn't resulting in a noncompetitive inhibitor Inhibitor works to slow down process of CA enzyme so AMS doesn't occur
|
BCMB 3100: Test 1