Biochemistry: Amino Acids, Amino Acids

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Biology

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1

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)

<p>Non-polar aliphatic Achiral! Doesn&apos;t rotate plane polarized light No enantiomers No absolute configuration (R,S)</p>
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Alanine, Ala, A

Non-polar aliphatic

<p>Non-polar aliphatic</p>
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Valine, Val, V

Non-polar aliphatic

<p>Non-polar aliphatic</p>
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Leucine, Leu, L

Non-polar aliphatic

<p>Non-polar aliphatic</p>
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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

<p>Non-polar aliphatic; * 1 of the two AA (threonine) that has a chiral carbon in its side chain</p>
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Proline, Pro, P

Non-polar aliphatic

<p>Non-polar aliphatic</p>
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Methionine, Met, M

Non-Polar, hydrophobic

<p>Non-Polar, hydrophobic</p>
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Cysteine, Cys, C

Non-Polar Only AA with (S) absolute configuration

<p>Non-Polar Only AA with (S) absolute configuration</p>
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Phenylalanine, Phe, F

Non-polar aliphatic aromatic

<p>Non-polar aliphatic aromatic</p>
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Tyrosine, Tyr, Y

Polar aromatic, partial hydrophilic

<p>Polar aromatic, partial hydrophilic</p>
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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)

<p>Non-Polar aromatic; Contains 2 amines but is still neutral at pH 7 (similar exception trp, gln, asn)</p>
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Serine, Ser, S

Polar neutral

<p>Polar neutral</p>
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Threonine, Thr, T

Polar neutral; * 1 of the two AA (isoleucine) that has a chiral carbon in its side chain

<p>Polar neutral; * 1 of the two AA (isoleucine) that has a chiral carbon in its side chain</p>
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Aspartate, Asp, D

Polar acidic, negative charge

<p>Polar acidic, negative charge</p>
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Glutamate, Glu, E

Polar acidic, negative charge

<p>Polar acidic, negative charge</p>
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Arginine, Arg, R

Polar basic, positive charge

<p>Polar basic, positive charge</p>
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Lysine, Lys, K

Polar basic, positive charge

<p>Polar basic, positive charge</p>
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Histidine, His, H

Polar basic, positive charge

<p>Polar basic, positive charge</p>
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Asparagine, Asn, N

Polar neutral. Contains 2 NH2 but is still neutral at pH 7 (similar exception trp, gln, asn)

<p>Polar neutral. Contains 2 NH2 but is still neutral at pH 7 (similar exception trp, gln, asn)</p>
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Glutamine, Gln, Q

Polar neutral; Contains 2 NH2 but is still neutral at pH 7 (similar exception trp, gln, asn)

<p>Polar neutral; Contains 2 NH2 but is still neutral at pH 7 (similar exception trp, gln, asn)</p>
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6 types of enzyme classification

  1. oxidoreductase

  2. transferases

  3. hydrolases

  4. lyases

  5. isomerases

  6. ligases

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Oxiodoreductases

transfer of electrons (hydride ions or H atoms)

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Transferases

transfer functional groups

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Hydrolases

hydrolysis reactions

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isomerases

Transfer of groups within molecules to yield isomeric forms

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ligases

bond formation coupled with ATP hydrolysis

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What do prokaryotes lack?

nucleus and membrane bound organelles

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Gibbs free energy = -

energy released (favorable) aka exogernic

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Gibbs free energy = +

energy stored (infavorable) aka endogoremic

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Miller-Uray experiment on "chemical origins of life"

mimicked atompshere to prebiotic conditiosns to see if emergence opf biomolcues

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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

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properties of water

high melting point perfect h bonder forms 4 bonds in ice 3.4 in water good polar solvent

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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

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bicarbonate buffer

(lungs) CO2 + H2O
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non-ionic v. zwitterionic form

non-ionic= NH2 group + COOH group

zwitter = Coo- and NH3+

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Pka of nh2

9

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Pka of Cooh

2

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peptide bond

planar with double bond chacrhter (cant rotate)

<p>planar with double bond chacrhter (cant rotate)</p>
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phi bond

N-Calpha

<p>N-Calpha</p>
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Psi bond

between the alpha carbon and carboxyl carbon

<p>between the alpha carbon and carboxyl carbon</p>
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Alpha helix number of amino acid per turn

3.6

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what bonds for Alpha helix

C=O group and NH2 group 4 carbons down

side chain protudes out

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what amino acid is good for turns

proline

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Collagen

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

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Afinsen experiment

  1. Denature the protein and break disulfide bonds

  2. Remove the denaturing agents

  3. Amino acids refold into protein structure

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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

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size exchange chromatography

Separates proteins by size/shape

larger move father down (faster)

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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

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tagging

peptide binds to protein that which binds to column that can be eluted off later

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what groups aborb at 280 nmn light

aromatics

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gel eltrophoresis

seperate based of charge

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SDS-PAGE

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

<p>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</p>
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sds forms what structure

miscless

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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

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what is heme

protein bound prosthetic group that incropates into the tertiatry structure called a globin fold

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where are globin folds

hemoglobin and myoglobin

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where does oxygen bind to in blood>

hemoglobin Fe 2+

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high affinity means

a low Kd and a high (does bind super tight)

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low affinity means

a high Kd and a does not bind super tight

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r =

(L)/(kd + (L))

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when (L) = Kd

half of substrate is bound to protein

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hemoglobin v. myoglobin

Transport oxygen = hem (quartenry sturcture)

Stores oxygen = myo (monomer)

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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

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cooperativity

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

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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.

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BPG

BPG binds to T-state and stabilizes it

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what does the speed of the reaction depend on

the energy barriefr

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enzymes affect which K value

K1 (NOT KEQ)

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enzymes lower what G value

delta G transition state, not delta g of reacation

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enzymes are complimentary to what?

transition sattes of reactions

<p>transition sattes of reactions</p>
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3 catayltic streages of enzymes (can apply any combinations)

  1. general acid-bas reactions

  2. covalent catyalsis

  3. metal ion catalsis

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metal ion catalysis

metal ions function in a number of ways including serving as an electrophilic catalyst

induces negative charge to allow reactions

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why use V0?

because as the reaction goes on concenrtatin of substrate changes. you use V0 and assume concenrtation is constant

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76

what is the rate limiting steo for enzyme substate

ES = E + P

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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)

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78

What is Km equal to

1/2 Vmax (indictaion of how tightly substacte binds to enzyme)

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what does a low Km mean

you need little substrate to acheivge binding and thus have a high affinity

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Kcat

turnover number (molecules catalyzed per second in optimal conditions) Vmax / [E]

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whats a good indicator of catayltic effecianecy?

kcat/km

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slope of line weaver burke plot:

Km/Vmax

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X-intercept of Lineweaver-Burk plot

-1/Km (the closer to zero the greater the Km and the lower the affinity)

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Y intercept of a Lineweaver-Burk plot

1/Vmax

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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

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competitive inhibitor graph

all intersect in y axis

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Uncompetive inhibitor

only binds when substrate is bound

affects Km and Vmax equally by decreasing vmax and increasing Km

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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

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Mixed Inhibition Graph

same as before but all interesect left of y-axis

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transition state analogs

substrates or inhibtors compounds that mimic the form of the transition state of an enzyme reaction

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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)

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irreversible inhibtors bind by what means?

covalent or strong in the active sihgt

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what curve do allosteric enzymes follow?

non-michalesis menten (not hyperbodal). instead is sigmodal

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what does a postive modulator have

affinity high and high vmax

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Chymotrypsin structure

protease that digest proteins with aromatic

has 3 chains held together through disulfide bonds

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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

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acylation phase

the peptide bond is cleaved and an ester linkage is formed between the peptide carbonyl carbon and the enzyme

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deacylation phase

generate catlyst (starts with H20)

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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

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