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BC 351- Unit 2

protein motifs not stable on their own-> larger structures made up of secondary structures
protein motif examples beta hairpin, alpha turn alpha
protein domains stable on their own; a single polypeptide can have multiple domains
5 protein folding "rules" hydrophobic forces drive folding, alpha helices and beta sheets are separate, amino acids near each other in protein tend to be near each other in primary structure, beta sheets don't become interdigitated, beta sheets tend to twist
the structural classification of proteins is based primarily on secondary structure content and arrangement
tetramer 4 subunits, 2 sets of the same one
protomer two identical heterodimers
Leventhal's paradox protein folding would take forever to happen randomly, so it's not random
two theories of protein folding hierarchical, molten globule
hierarchical model of protein folding primary -> quaternary structures
molten globule model of protein folding hydrophobic collapse, massages into correct shape
sock model for protein folding saves time if you pair socks when you pull them out rather than just waiting for matches
experiments on denaturation and renaturation after the reduction and deoxidation of SS bonds in RNase have shown that primary sequence is sufficient to determine secondary and tertiary structure
ligands small molecules that bind reversibly through non-covalent interactions
binding sites pocket/cleft where ligand binds; should conform well with several interactions
conformation ligands can change the shape of proteins
induced fit/allostery the changes that proteins undergo when ligand binds
how does hemoglobin prevent CO from binding? distal histidine (helps somewhat but still has a high affinity)
when oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are occupied by one O2 molecule and one amino acid atom
the strength and specificity of binding between two molecules is dependent on (4) temperature, pH, binding site, number of non covalent interactions
Kd dissociation contstant; lower= higher affinity; measured in M; 1/Ka
when [L]= Kd... then 1/2 of the sites are bound
Two molecules, A and B, have a KA = 10^6 M-1 for AB complex formation. When both molecules are at 10-5 M (10 μM) the proportion of A and B in an AB complex will be >90% because 10^-5 is 10x larger than 10^-6 (which is Kd)
theta= (for oxygen binding to hemoglobin) pO2/(pO2+Kd)
T state of hemoglobin binds BPG and CO2 more tightly
R state of hemoglobin binds O2 more tightly
pH and hemoglobin tissues have a lower pH than the lungs so O2 is released here (lower pH stabilizes T state)
difference between fetal and adult hemoglobin fetal has a gamma subunit instead of beta, so gower BPG affinity
sickle cell anemia when goes to T state, it associates into large strands/fibers
four types of catalysis acid-base, covalent intermediate, reaction intermediate stabilization, orientation/proximity
ΔΔG‡cat difference between catalyzed and uncatalyzed
ΔG‡ transition state-substrate
acid and base catalysis (2) 1) involves making reactants better electrophiles and nucleophiles 2) works through transition state stabilization
transition state stabilization puts strain on S, pulling towards transition state
A mutation in an enzyme reduce the rate of the catalyzed reaction
two signals leading to apoptosis extracellular death receptor, intracellular (DNA damage and oncogene expression)
what is Km? [S] at 1/2 Vmax
Enzymes exhibit saturation behavior (become insensitive to more substrate, have a VMax) because enzymes have a fixed number of active sites where substrate binds
kcat Vmax/[Et] (reactions per second)
Lineweaver-Burk plot -1/Km (x-intercept); 1/Vmax= y intercept
two enzyme preparations have the same Km, but the bacterially expressed enzyme has a 10x lower Vmax... why? 90% of the enzyme expressed is inactive
competitive inhibition affects Km only
uncompetitive inhibition affects Km and Vmax
PGP binds hydrophobic, neutral, + charged drugs; normal functions to excrete toxins from the body
PGP inhibitors have a higher affinity for PGP binding pocket than the broad range of things that bind to it
domains stable, independently folding components of proteins
motifs not stable on their own; subset of exons that are used repeatedly
why multiple copies of a polypeptide subunit? fewer genes
two types of symmetry on oligomeric proteins helical and rotational
homoallostery change in shape leading in response to substrate binding
heteroallostery a change in shape in response to non-substrate ligand binding
four types of catalytic mechanisms acid base, covalent catalysis, transition state stabilization, proximity/orientation
covalent catalysis covalent bond is formed between a functional group on the enzyme and a substrate transition state intermediate
histidine-57 functions (2) 1) makes oxygen a better nucleophile 2) binds w/ N of peptide bond to make it a better LG
serine-195 function (1) replaces water in the hydrolysis of a peptide bond (covalent catalysis)
binding of glucose to hexokinase induces a conformational change that continues the reaction
demonstrate that at high [S], V0 approaches Vmax Km is really small, so V0= Vmax[S]/[S], so V0=Vmax
V0= Vmax [S] / Km + [S]
key conditions for M&M Km is approximately Kd
units of mcat/Km ratio s-1 M-1
proteins have regions that show specific, evolutionarily conserved patterns of folding called motifs or folds
do all protein subunits have to be identical? no
rotational symmetry (4) seen in oligomeric proteins; seen in viruses; rotation about 1 or more axis; results in closed, packed structures
will changing salt concentration result in protein denaturation? no
the average protein will not be denatured by what acid? iodoacetic acid
Leventhal's paradox is solved by proteins folding in a step-by-step, non random fashion
interactions of ligands w/ proteins are usually transient
highly specific intermolecular interactions involve as many as 15-20 hydrogen bonds
a prosthetic group is permanently associated w/ the protein
oxygen binding to myoglobin is hyperbolic
transition from T state to R state is triggered by oxygen binding
BPG is a(n) _____ allosteric modulator
BPG is found in hemoglobin where? in red blood cells
in catalyzing reactions, enzymes change what? ΔG‡ (activation energy)
transition state analogs exhibit a greater affinity for the enzyme
the serine-195 hydroxyl group does what? participates in covalent catalysis
the greater affinity of the active site for binding the substrate relative to the affinity for binding the transition state intermediate causes what? not good enzyme catalysis (hard to convert to product)
irreversible inhibition covalent linkages
Km is greater for enzymes... with lower affinities for a substrate
kcat is a function of Vmax and total E
reasons cancer patients don't respond to chemotherapy (5) increased cellular export, increased DNA repair, decreased tumor blood supply, activation of P450 detoxifying system, decreased programmed cell death signaling
ABC transporters (3) keep toxins from affecting a developing fetus, protect genomes of stem cells, keep toxins from passing blood-brain barrier
multi drug resistance proteins can interfere w/ treating brain disorders by keeping drugs from entering the brain
P-glycoprotein inhibitors also inhibit cytochrome p450 detoxification
Created by: melaniebeale
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