Biochem review

What are amino acids

What are amino acids

they have an amino (NH4) and a carboxyl acid (COOH)

what is a a-amino acid

amino and carboxyl group are on the same carbon

most amino acids are optically active true or false

true

define optically active

capable of rotating the plane of vibration of polarized light to the right or left

all amino acids but cysteine are R or S

S

all amino acids but glycine are chiral or achiral

chiral

amino acids whit long alkyl side chains are all hydrophobic or hydrophilic

hydrophobic

amino acids whith charged side chains are all hydrophobic or hydrophilic

hydrophilic

abbreviations of alanine

Ala, A

abbreviations of Arginine

Arg, R

abbreviations of Asparagine

Asn, N

abbreviations of Cystesine

Cys, C

abbreviations of glutamic acid

Glu, E

abbreviations of glutamine

Gln. Q

abbreviations of glycine

Gly, G

abbreviations of histidine

His, H

abbreviations of isoleucine

Ile, I

abbreviations of leucine

Leu, L

abbreviations of lysine

Lys, K

abbreviations of methionine

Met. M

abbreviations of phenylalanine

Phe, F

abbreviations of proline

Pro, P

abbreviations of serine

Ser, S

abbreviations of theronine

Thr, T

abbreviations of tryptophan

Trp, W

abbreviations of tyrosine

Tyr, Y

abbreviations of valine

Val, V

What are the 4 groups attached to the central a carbon of a proteinogenic amino acid?

amino, carboxylic, hydrogen, and R group

Where do hydrophobic amino acids tend to reside within a protein?

inside proteins

Where do hydrophilic amino acids tend to reside within a protein?

on the outside of proteins

define amphoteric species

as they can either accept a proton or donate a proton;

ionizable groups tend to gain protons under acidic or basic conditions and lose them under acidic or basic conditions

acid, basic

define zwitterions/dipolar ions

a molecule that has both positive charge and a negative charge

When the pH of a solution is approximately equal to the pka of the solute, the solution acts as a

buffer

what does pI stand for

isoelectric point

pI neutral amino acid =

(pkaNH4 + pkaCOOH)/2

pI acidic amino acid =

(pkaR group + pkaCOOH)/2

pI basic amino acid =

(pkaNH4 + pkaR group)/2

What amino acid

glycine

What amino acid

alanine

what amino acid

valine

what amino acid

leucine

what amino acid

isoleucine

what amino acid

methionine

what amino acid

proline

what amino acid

tryptophan

what amino acid

phenylalanine

what amino acid

tyrosine

what amino acid

serine

what amino acid

theronine

what amino acid

asparagine

what amino acid

glutamine

what amino acid

cysteine

what amino acid

aspartate

what amino acid

glutamate

what amino acid

arginine

what amino acid

lysine

what amino acid

histidine

For a generic amino, NH2CRHCOOH, with an uncharged side chain, what would be the predominant form at a pH=1

+NH3CRHCOOH

For a generic amino, NH2CRHCOOH, with an uncharged side chain, what would be the predominant form at a pH=7

+NH3CRHCOO-

For a generic amino, NH2CRHCOOH, with an uncharged side chain, what would be the predominant form at a pH=11

NH2CRHCOO-

What is the value of the pI for aspartic acid (pka1=1.88, pka2=3.65, pka3=9.60)

(1.88+3.65)/2=2.77

What is the value of the pI for arginine (pka1=2.17, pka2=9.04, pka3=12.48)

(9.04+12.48)/2=10.76

What is the value of the pI for valine (pka1=2.32, pka2=9.62)

(2.32+9.62)/2=5.97

peptides are composed of

residues

what is a residue

an amino acid subunit

what is a dipeptide

has 2 residues

what is a tripeptides

have 3 residues

what is a oligopeptide

have less than 20 residues

what is a polypeptide

have more than 20 residues

how are residues in peptides joined together

peptide bonds

why is a peptide bond formation an example of a condensation/dehydration/acyl substitution

because it results in the removal of a water molecule

how does a peptide bond form

the electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic amino group of the carboxylic acid is kicked off

what is amino terminus or N-terminus

free amino end

what is carboxy terminus or C-terminus

free carboxyl end

by convention how are peptides drawn

with the N-terminus on the left and the C-terminus on the right

in living organisms how is hydrolysis done

by enzymes such as trypsin and chymotrypsin by breaking apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon

what molecule is released during formation of a peptide bond

water

If chymotrypsin cleaves at the carboxyl end of phenylalanine, tryptophan, and tyrosine, how many oligopeptides would be formed in enzymatic cleavage of the following molecule with chymotrypsin? Val − Phe − Glu − Lys − Tyr − Phe − Trp − Ile − Met − Tyr − Gly − Ala

4: Val − Phe; Glu − Lys − Tyr; Ile − Met − Tyr; Gly−Ala.

what are proteins classified as

polypeptide

what is the primary structure of a protein

linear arrangement of amino acids coded in an organisms DNA

the primary structure of a protein encodes what?

all the information needed for folding at all the higher structural levels

what is the secondary structure of a protein

the local structure of neighboring amino acids

what are the 2 most common secondary structures

a-helices and b-pleated sheets

What role does proline serve in secondary structures

prolines rigid structure causes it to introduce kinks in a-helices and create turns in B-pleated sheets

Describe the key structural features of a-helix

α-helix is a rod-like structure in which the peptide chain coils clockwise around a central axis

Describe the key structural features of B-pleated sheets

In β-pleated sheets the peptide chains lie alongside one another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain.

what are the stabilizing bonds in primary proteins

peptide (amide) bond

what are the stabilizing bonds in secondary proteins

hydrogen bonds

proteins can be broadly divided between what 2 groups

fibrous proteins and globular proteins

what is the tertiary structure of a protein

3d shape

what is denaturation

the loss of the tertiary structure and loss of function along with it

what is the tertiary structure a result of

moving hydrophobic amino acid side chains into the interior of the protein

what does the disulfide bond do in tertiary structure

create loops in the protein chains

what is a disulfide bond

the bonds that form when 2 cysteine molecules become oxidized to form cysteine

what does disulfide bonds require to form

oxidization

describe the basic idea of folding

the basic idea of folding is that the secondary structures probably form first and then hydrophobic interactions and hydrogen bonds cause the protein to collapse into its proper 3d structure. Along the way it adopts intermediate states known as molten globules

what kind of proteins have quaternary structure

proteins that contain more than one polypeptide chain

what is the quaternary structure in proteins

is an aggregate of smaller globular peptides or subunits and represents the functional form of protein

what does the quaternary structure in proteins do (4)

1. they can be more stable, by further reducing the surface area of the protein complex

2. they can reduce the amount of DNA needed to encode the protein complex

3. they can bring catalytic sites closer together, allowing intermediates from one reaction to be directly shuttled to a second reaction

4. they can induce cooperativity or allosteric effects