Biochemistry: Amino Acids, Amino Acids

amino acids structure

amino acids structure

amino acids structure abbreviations

Glycine, Gly, G

Non-polar aliphatic Achiral! Doesn't rotate plane polarized light No enantiomers No absolute configuration (R,S)

Alanine, Ala, A

Non-polar aliphatic

Valine, Val, V

Non-polar aliphatic

Leucine, Leu, L

Non-polar aliphatic

Isoleucine, Ile, I

Non-polar aliphatic; * 1 of the two AA (threonine) that has a chiral carbon in its side chain

Proline, Pro, P

Non-polar aliphatic

Methionine, Met, M

Non-Polar, hydrophobic

Cysteine, Cys, C

Non-Polar Only AA with (S) absolute configuration

Phenylalanine, Phe, F

Non-polar aliphatic aromatic

Tyrosine, Tyr, Y

Polar aromatic, partial hydrophilic

Tryptophan, Trp, W

Non-Polar aromatic; Contains 2 amines but is still neutral at pH 7 (similar exception trp, gln, asn)

Serine, Ser, S

Polar neutral

Threonine, Thr, T

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

Aspartate, Asp, D

Polar acidic, negative charge

Glutamate, Glu, E

Polar acidic, negative charge

Arginine, Arg, R

Polar basic, positive charge

Lysine, Lys, K

Polar basic, positive charge

Histidine, His, H

Polar basic, positive charge

Asparagine, Asn, N

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

Glutamine, Gln, Q

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

6 types of enzyme classification

1. oxidoreductase

2. transferases

3. hydrolases

4. lyases

5. isomerases

6. ligases

Oxiodoreductases

transfer of electrons (hydride ions or H atoms)

Transferases

transfer functional groups

Hydrolases

hydrolysis reactions

isomerases

Transfer of groups within molecules to yield isomeric forms

ligases

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

non-ionic v. zwitterionic form

non-ionic= NH2 group + COOH group

zwitter = Coo- and NH3+

Pka of nh2

9

Pka of Cooh

2

peptide bond

planar with double bond chacrhter (cant rotate)

phi bond

N-Calpha

Psi bond

between the alpha carbon and carboxyl carbon

Alpha helix number of amino acid per turn

3.6

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

proline

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

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

tagging

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

what groups aborb at 280 nmn light

aromatics

gel eltrophoresis

seperate based of charge

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

sds forms what structure

miscless

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

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

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

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

K1 (NOT KEQ)

enzymes lower what G value

delta G transition state, not delta g of reacation

enzymes are complimentary to what?

transition sattes of reactions

3 catayltic streages of enzymes (can apply any combinations)

1. general acid-bas reactions

2. covalent catyalsis

3. 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

Kcat

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

whats a good indicator of catayltic effecianecy?

kcat/km

slope of line weaver burke plot:

Km/Vmax

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

1/Vmax

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

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