109c quiz 3 + amino acids

Alanine Ala or A

Arginine Arg or R

Asparagine Asn or N

Aspartate Asp or D

Cysteine Cys or C

Glutamate Glu or E

Glutamine Gln or Q

Glycine Gly or G

Histidine His or H

Isoleucine Ile or I

Leucine Leu or L

Lysine Lys or K

Methionine Met or M

Phenylalanine Phe or F

Proline Pro or P

Serine Ser or S

Threonine Thr or T

Tryptophan Trp or W

Tyrosine Tyr or Y

Valine Val or V

catalysis

substance that increases the rate of a chemical rxn w/o being consumed

decreases activation energy

catalysis speed up a rxn by

1. increase the reactivity of the electrophile

2. increase the reactivity of the nucleophile

3. increase the l.g. propensity

4. increase the stability of the TS

acid catalysts

will increase the rate of rxn by donating a proton to the reactant

acid-catalyzed ester hydrolysis

two types of acid catalysts

1. specific-acid catalysts

2. general-acid catalysis

specific-acid catalysis

proton is fully transferred to the reactant before the slow step. seen w/ strong acids

general-acid catalysts

proton is transferred to the reactant during the slow step. seen w/ weak acids

specific-acid

is this the first slow step of specific or general acid?

general-acid

is this the first slow step of specific or general acid?

specific-acid

is this the second slow step of specific or general acid?

general acid

is this the second slow step of specific or general acid?

base catalysis

will increase the rate of rxn by removing a proton from the reactant

specific base catalysis

proton is completely removed before the slow step. seen w/ strong bases

general-base catalysis

proton is removed during the slow step. seen w/ weak bases

specific-base catalysis

general-base catalysis

enzymes use ___ catalysts, acid + base

general

nucleophilic catalysis

will increase the rate of rxn by reacting as a nuc to form a covalent bond w/ the reactant

examples of nucleophile catalysis

SN₂ rxn, ester hydrolysis

catalyzed SN₂ rxn (nucleophile catalysis)

catalyzed ester hydrolysis (nucleophile catalysis)

metal ion catalysis

use lewis acids to speed up a rxn

how do lewis acids work to speed up rxns (metal ion catalysis)

1. Make the electrophile more electrophilic

2. make a leaving group into a better leaving group (weaker base)

3. increase the rate of hydrolysis by increasing H₂O nucleophilicity

metal ion catalysis

decarboxylation

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are biological catalysts

enzymes

substrate —^?—> product

enzyme

active site

region of an enzyme that binds the substrate to carry out a chemical reaction

lock-and-key model

enzyme (lock) and substrate (key) that have specific features that fit exactly into one another (outdated)

induced-fit model

enzyme and substrate bonding model that says the active site doesn’t become completely complimentary to the shape of the substrate until the enzyme has bound the substrate (enter into active site and gets encapsulated once enzyme binds)

how enzymes catalyze reactions

1. Hold reacting groups in proper orientation for a rxn to occur.

2. aa side-chains act as acid, base, or nucleophilic catalysts (many 1/3 also have metal ions)

3. aa side-chains can stabilize the t.s. through H-bonding, electrostatic interactions, or LDF’s

*can use many at the same time

endopeptidase

all known as serine proteasees because they use serine to catalyze peptide bond cleavage

endopeptidase catalyte triad

acid: Asp

base: His

nucleophilic: Ser

endopeptidases

trypsin, chymotrypsin, elastase

trypsin

cleaves peptide bond on C-terminal side of Arg + Lys

chymotrypsin

cleaves peptide bond on C-terminal side of Phe, Tyr, and Trp

Elastase

cleaves peptide bond on C-terminal side of Gly, Ala, Ser, and Val

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is what gives specificity

binding pockets

site specific mutagenesis

a technique that replaces a single aa in the primary sequence with another

metal ion cofactor

• helps to bind and hold a substrate in a particular orientation in the active site

• helps to catalyze the rxn

• coordinate with groups on the enzyme to stabalize

how does the metal ion cofactor help catalyze the rxn

by increasing substrate electrophilicity or H₂O nucleophilicity

organic molecular cofactors “coenzymes”

used to help carry out reactions that amino acid side chains cannot on their own

what are organic molecular cofactors “coenzymes” derived from

vitamins

examples of organic molecular cofactors “coenzymes”

NAD⁺, NADPH, FAD, Biotin, TPP

What reactions do organic molecular cofactors “coenzymes” help carry out that aa side chains cannot on their own?

redox rxns, act as electron sinks, activating groups, provide stronger base/nucleophile

electron sink

groups that electrons can be delocalized into

Niacin is needed for ____ reaction

redox

what role does Niacin play in redox rxns

oxidizes or reduces the substrate

Oxidizes:

• NAD⁺ is reduced to NADH (NAD⁺ acts as electron sink)e

Reduces:

• NADPH is oxidized to NADD⁺

FAD is reduced to

FADH₂

FAD enzymes are also often dependent on ______ to reoxidize

FADH₂ —> FAD

NAD⁺

TPP is used to

catalyze the transfer of acyl groups to electrophiles

Hell-Volhard-Zelinkski rxn description

adds bromo to alpha carbon of carboxylic acid

Hell-Volhard-Zelinkski Reagents

1. Br₂, PBr₃

2. H₂O

1° structure

sequence of aa and location of disulfide bridges

2° structure

description of the backbone of a protein

3° structure

3-D structure of a protein

4° structure

(if more than one polypeptide) the way dif chains are arranged with respect to each other

1st step in determining sequence of amino acids?

reducing disulfide bride to obtain an external chain

polypeptide —^?—-> aa

6 M HCl

100°c for 24 hours

how to determine the N terminal amino acid?

(left end) use edman’s reagent

how to determine the C terminal amino acid?

(right end) use a carboxypeptidase

endopeptidases

enzymes that catalyze the hydrolysis of a peptide bond that is not at the end of the peptide chain

trypsin, chymotrypsin, elastase

Where does trypsin cleave?

the c-side of Arg and Lys

where does chymotrypsin cleave?

c-side of aromatic 6-membered rings (Phe, tyr, trp)

where does elastase cleave?

c-side of small aa’s Gly, ala, ser, val

cyanogen bromide purpose

hydrolyzes the peptide bond on the c-side of methionine (cleaves)

factors that determine backbone folding

1. regional planarity of each peptide bond (limits conformation)

2. H-bonding between carbonyl O of one aa and amide H of another

3. the need for seperation between neighboring R groups to avoid steric strain and repulsion of like charges

description of alpha helix

side chains of the aa’s protrude outward (less steric strain), stabalized by H-bonds, clockwise direction

description of beta pleated sheet

H-bonding occurs BETWEEN neighboring peptide chains

for 3° structure, each stabalizing interaction releases what?

free energy (-delta G°)

stabilizing interactions for tertiary structure

disulfide bonds, H-bonds, electrostatic attractions (between opp. charges), hydrophobic interactions

• can be between peptide groups, side chains, or both

electrostatic attractions definition

between opposite charges

hydrophobic interactions

between nonpolar groups in the protein, increased stability by increased entrophy of water molecules

what are quarternary structure subunits held together by

hydrophobic interactions, H-bonding, and electrostatic attraction

for quarternary structure, greates S.A.: volume ratio = ?

highest % of polar aa’s

what can degrade proteins?

1. changing pH (disrupt electrostatic attraction)

2. urea + guanidine (form stronger H-bonds)

3. organic solvents (associate w/ nonpolar groups. and disrupt hydrophobic interactions)

4. heat/agitation (disrupt attractive force)

what aa’s will have lower pka values?

electron withdrawing, more electroneg=more electron withdrawing

trypsin will not cleave if lys or arg is followed by ___?

Pro

which aa will be eluded first?

the most positive, the most neg will be eluded last

free energy diagram for specific or general acid catalysts?

specific-acid catalyst