Biochemistry: Amino Acids, Amino Acids

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amino acids structure
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amino acids structure abbreviations
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Glycine, Gly, G
Non-polar aliphatic Achiral! Doesn't rotate plane polarized light No enantiomers No absolute configuration (R,S)
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Alanine, Ala, A
Non-polar aliphatic
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Valine, Val, V
Non-polar aliphatic
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Leucine, Leu, L
Non-polar aliphatic
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Isoleucine, Ile, I
Non-polar aliphatic; * 1 of the two AA (threonine) that has a chiral carbon in its side chain
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Proline, Pro, P
Non-polar aliphatic
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Methionine, Met, M
Non-Polar, hydrophobic
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Cysteine, Cys, C
Non-Polar Only AA with (S) absolute configuration
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Phenylalanine, Phe, F
Non-polar aliphatic aromatic
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Tyrosine, Tyr, Y
Polar aromatic, partial hydrophilic
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Tryptophan, Trp, W
Non-Polar aromatic; Contains 2 amines but is still neutral at pH 7 (similar exception trp, gln, asn)
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Serine, Ser, S
Polar neutral
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Threonine, Thr, T
Polar neutral; * 1 of the two AA (isoleucine) that has a chiral carbon in its side chain
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Aspartate, Asp, D
Polar acidic, negative charge
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Glutamate, Glu, E
Polar acidic, negative charge
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Arginine, Arg, R
Polar basic, positive charge
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Lysine, Lys, K
Polar basic, positive charge
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Histidine, His, H
Polar basic, positive charge
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Asparagine, Asn, N
Polar neutral. Contains 2 NH2 but is still neutral at pH 7 (similar exception trp, gln, asn)
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Glutamine, Gln, Q
Polar neutral; Contains 2 NH2 but is still neutral at pH 7 (similar exception trp, gln, asn)
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6 types of enzyme classification
1. oxidoreductase 2. transferases 3. hydrolases 4. lyases 5. isomerases 6. ligases
transfer of electrons (hydride ions or H atoms)
transfer functional groups
hydrolysis reactions
Transfer of groups within molecules to yield isomeric forms
bond formation coupled with ATP hydrolysis
What do prokaryotes lack?
nucleus and membrane bound organelles
Gibbs free energy = -
energy released (favorable) aka exogernic
Gibbs free energy = +
energy stored (infavorable) aka endogoremic
Miller-Uray experiment on "chemical origins of life"
mimicked atompshere to prebiotic conditiosns to see if emergence opf biomolcues
RNA world hypothesis
hypothesis that RNA served as the genetic information of early life. why? - single stranded can form shapes DNA cant -can act like enzyeme -can reverse transcript (RNA->DNA) -carry geentic info
properties of water
high melting point perfect h bonder forms 4 bonds in ice 3.4 in water good polar solvent
hydrophobic effect
The exclusion of nonpolar molecules by polar molecules, which drives biological processes such as the formation of cell membranes and the folding of proteins. helps stabilze enzyme substrate complex
bicarbonate buffer
(lungs) CO2 + H2O <--> H2CO3 <--> HCO3- + H+ (blood)
non-ionic v. zwitterionic form
non-ionic= NH2 group + COOH group zwitter = Coo- and NH3+
Pka of nh2
Pka of Cooh
peptide bond
planar with double bond chacrhter (cant rotate)
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phi bond
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Psi bond
between the alpha carbon and carboxyl carbon
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Alpha helix number of amino acid per turn
what bonds for Alpha helix
C=O group and NH2 group 4 carbons down side chain protudes out
what amino acid is good for turns
A glycoprotein in the extracellular matrix of animal cells that forms strong fibers, found extensively in connective tissue and bone; the most abundant protein in the animal kingdom. triple helix of Gly, Pro, Hyp
Afinsen experiment
1. Denature the protein and break disulfide bonds 2. Remove the denaturing agents 3. Amino acids refold into protein structure
ion exchange chromatography
Protein Purfication -stationary phase is made of negatively (attract & bind compounds that have opposite charge) **more negative flow faster -salt is added to elute proteins stuck to column
size exchange chromatography
Separates proteins by size/shape larger move father down (faster)
affinity chromatography
uses a bound receptor or ligand and an eluent with free ligand or a receptor for the protein of interest eluted by excess ligand
peptide binds to protein that which binds to column that can be eluted off later
what groups aborb at 280 nmn light
gel eltrophoresis
seperate based of charge
denatures the proteins and masks the native charge so that comparison of size is more accurate, but the functional protein cannot be recaptured from the gel
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sds forms what structure
mass spectrometry
a technique that separates particles according to their mass need small strands however (can use proteases to cut up) lighter things go farther
what is heme
protein bound prosthetic group that incropates into the tertiatry structure called a globin fold
where are globin folds
hemoglobin and myoglobin
where does oxygen bind to in blood>
hemoglobin Fe 2+
high affinity means
a low Kd and a high (does bind super tight)
low affinity means
a high Kd and a does not bind super tight
r =
(L)/(kd + (L))
when (L) = Kd
half of substrate is bound to protein
hemoglobin v. myoglobin
Transport oxygen = hem (quartenry sturcture) Stores oxygen = myo (monomer)
T State and R State of Hemoglobin
T-state: high affinity state, holds does not bind tightly to Oxygen (low affinity) R-State: has oxygen binding ability (relaxid state) high affinity
A kind of allosteric regulation whereby a shape change in one subunit of a protein caused by substrate binding is transmitted to all the other subunits, facilitating binding of additional substrate molecules to those subunits. creates sigmodial curve in hemoglbin
Bohr effect
Binding affinity decreases as a result of the lower Ph of tissue and relases oxygen . the low Ph stabilize the T-state and this favors the uptake of protons.
BPG binds to T-state and stabilizes it
what does the speed of the reaction depend on
the energy barriefr
enzymes affect which K value
enzymes lower what G value
delta G transition state, not delta g of reacation
enzymes are complimentary to what?
transition sattes of reactions
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3 catayltic streages of enzymes (can apply any combinations)
1. general acid-bas reactions 2. covalent catyalsis 2. metal ion catalsis
metal ion catalysis
metal ions function in a number of ways including serving as an electrophilic catalyst induces negative charge to allow reactions
why use V0?
because as the reaction goes on concenrtatin of substrate changes. you use V0 and assume concenrtation is constant
what is the rate limiting steo for enzyme substate
ES = E + P
michael menton equation assumptions
1. k-2 is ignored (the reverse of ES = E +pp) 2. v0 is determined by rate of breadown of ES 3. ES concenrtation is constant. this os steady state (formation = breakdown)
What is Km equal to
1/2 Vmax (indictaion of how tightly substacte binds to enzyme)
what does a low Km mean
you need little substrate to acheivge binding and thus have a high affinity
turnover number (molecules catalyzed per second in optimal conditions) Vmax / [E]
whats a good indicator of catayltic effecianecy?
slope of line weaver burke plot:
X-intercept of Lineweaver-Burk plot
-1/Km (the closer to zero the greater the Km and the lower the affinity)
Y intercept of a Lineweaver-Burk plot
Competitive inhibition of enzymes
occurs when a substance other than the substrate binds to the active site of an enzyme (does affect Km but does not affect Vmax) Need more substate to reach K
competitive inhibitor graph
all intersect in y axis
Uncompetive inhibitor
only binds when substrate is bound affects Km and Vmax equally by decreasing vmax and increasing Km
Uncompetive inhibitor graph
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mixed inhibition
can bind to enzyme alone or when subrtate is bound affect both Km and Vmax unequally
Mixed Inhibition Graph
same as before but all interesect left of y-axis
transition state analogs
substrates or inhibtors compounds that mimic the form of the transition state of an enzyme reaction
3 kinds of regulatory enzymes
Allosteric Enzymes (undergo confromation change) Covalently Modified Enzymes (regulatory compoiyd that are attached that can be taken off) Zymogens (need to be cleaved to become actvive)
irreversible inhibtors bind by what means?
covalent or strong in the active sihgt
what curve do allosteric enzymes follow?
non-michalesis menten (not hyperbodal). instead is sigmodal
what does a postive modulator have
affinity high and high vmax
Chymotrypsin structure
protease that digest proteins with aromatic has 3 chains held together through disulfide bonds
7 steps of chymotrypsin
1. substate binding in hydrophobic pocket (h-bond of serine to to enzyme) 2. general base and covalent chemistry: transition state stabilized by oxyanion hole. forms carbon terthdyal with slight negative charge on oxygen with 3 bonds 3. breakage of peptide bond via acid chemistry. forms C=O double bond. forms product 1 4. water deportation by general base form OH- which attacks forming another carbon terthdryal 5. formation of secound transition state stabilized by oxyanion hole 6. collaspe of TS 2 forms product 2 7. relases of product 2
acylation phase
the peptide bond is cleaved and an ester linkage is formed between the peptide carbonyl carbon and the enzyme
deacylation phase
generate catlyst (starts with H20)
important features of Chymotrypsin active site
1. Ser: covalent catalyst (aclyation) 2. His: general acid base 3. Oxyion anion hole: lower activation energu by stabilzing oxyanion in transition state 4. hydropbic pocket: substarte binding 5. Asp: h-bonds to his to stabilie + charge on his
what does penicillin do?
inhibits cell wall synthesis by inhibting by irreverible binding to ser group. via carbonyl on b-lam ring bacteria explodes. bacteria evolved to have water take place and make caboybl into carbylxtate humans respond by using structure that mimics b-lactmase and binds ireevibly to ser
triaclyglycerol structure
lipids from fatty acids for LONG TERM storage (NEUTRAL) good because better reduction (c-h hold good energu) dehydartedt and are less space metablize more slowly
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3 types of lipids in membranes
phospholipids, cholesterol, glycolipids
phospholipids that contain a glycerol backbone glyercol + phosphate with OH polar
long fatty acid chain polar head group backbone=amino alcohol (not glycerol) PO4 + Cl + sprling head
lipid that acts as secoundary mesenger across membrane
sphinglopids sturcture
backbone different + middle FA + amide linkage to fatty acid