biochem module 2

what 4 groups do amino acids contain?

1. amino group

2. carboxylic acid

3. central alpha carbon (w/ a hydrogen)

4. variable side chain

are the amino acids in our body L or D?

the amino acids used to make proteins in our body are always L-amino acids

what 3 categories are amino acids sorted into?

1. nonpolar or polar

2. neutral, acidic, or basic

3. essential (not made by the body) or nonessential

amino indicates…

a protonated amine

acid indicates…

a carboxylic acid

what are the carboxylic acid and amino group in an amino acid bonded to?

the central alpha carbon

what is the alpha carbon bonded to in an amino acid?

hydrogen atom, side chain, amino group, and carboxyl group

what are the nonpolar amino acids?

glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, and tryptophan

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what are the polar amino acids?

serine, threonine, cysteine, asparagine, and glutamine

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what are the acidic amino acids?

aspartic acid and glutamic acid

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what are the basic amino acids?

arginine, lysine, histidine

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what are the 10 essential amino acids?

histidine, leucine, isoleucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and arginine

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in what amino acid is the alpha carbon not a chiral center?

glycine

what is an amphiproduct compound?

a compound that is able to act as both an acid and base

what is an equivalence point in a titration?

pH at which the moles of acid are equal to the moles of added base

what is the half equivalence point in a titration?

point along the titration at which the moles of acid = moles of base

what is the pH at half equivalence points?

the pH equals the pka

zwitterion

state of an amino acid that has no net charge

isoelectric point

pH at which the zwitterion is in the highest concentration

how do you find the isoelectric point?

by averaging the pkas or half equivalence point values surrounding the isoelectric point

compare pka and pH at mostly deprotonated form

pH>pka (deprotonated = less protons = smaller pka)

compare pka and pH at mostly protonated form

pH<pka (protonated = protons = acid = pka measure)

when are amino acids zwitterions

at physiological pH 7.4

what is the pka of the carboxyl group in amino acids

~2.0

what is the pka of the amino group in amino acids except threonine, cysteine, and lysine

~9.5

what is the pka of the amino group in threonine

10.43

what is the pka of the amino group in cysteine

10.78

what is the pka of the amino group in lysine

8.95

what is the pka of the side chain of tyrosine

10.07

what is the pka of the side chain of cysteine

8.33

what is the pka of the side chain of aspartic acid

3.86

what is the pka of the side chain glutamatic acid

4.25

what is the pka of the side chain of arginine

12.48

what is the pka of histidine’s side chain

6

what is the pka of lysine’s side chain

10.53

what group of an amino acid loses it’s proton first

the group with the lowest pka loses its proton first

what is the typical order of groups losing their protons

1. carboxylic acid

2. R-group

3. amino group

what is the isoelectric point of all neutral amino acids

5.85 (5.22 for cysteine)

isoelectric point for acidic amino acids

average the pka of the sidechain and carboxyl group

isoelectric point for basic amino acids

average the pka of the sidechain and amino group

what is the charge of a carboxyl group protonated and deprotonated?

protonated: 0

deprotonated: -1

what is the charge of an amino group protonated and deprotonated?

protonated: +1

deprotonated: 0

what is the charge of basic side chains protonated and deprotonated?

deprotonated: 0

protonated: +1

what is the charge of acidic side chains protonated and deprotonated?

deprotonated: -1

protonated: 0

what is the charge of cysteine and tyrosine’s side chain protonated and deprotonated?

protonated: 0
deprotonated: -1

alanine

glycine

isoleucine

leucine

proline

valine

phenylalanine

tryptophan

tyrosine

aspartic acid

glutamic acid

arginine

histidine

lysine

serine

threonine

cysteine

methionine

asparagine

glutamine

alanine

ala, a

glycine

gly, g

isoleucine

ile, i

leucine

leu, l

proline

pro, p

valine

val, v

phenylalanine

phe, f

tryptophan

trp, w

tyrosine

tyr, y

aspartic acid

asp, d

glutamic acid

glu, e

arginine

arg, r

histidine

his, h

lysine

lys, k

serine

ser, s

threonine

thr, t

cysteine

cys, c

methionine

met, m

asparagine

asn, n

glutamine

gln, q

what are the 4 levels of protein structure

primary, secondary, tertiary, and quaternary

primary structure

refers to the individual amino acids that make up a polypeptide chain

what are the two restrictions into the polypeptide chain

1. lack of rotation around the amide bond while free rotation around any bond connected to the alpha carbon

2. all amino acids (except proline) prefer to be in trans configuration

what is a peptide bond?

amide bond that is bonded to 2 alpha carbons, holds primary structure together

what is a condensation reaction?

carboxylate ion of one amino acid reacts with a protonated amine of a second amino acid, forms a dipeptide

N-terminal

start of an amino acid sequence, categorized by free unbonded amine group

C-terminal

end of an amino acid sequence, categorized by feee unbonded carboxylate ion

oxytocin

stimulates smooth muscle contraction in the uterus during labor and in the mammary glands during lactation

vasopressin

stimulates resorption of water by the kidneys, thus raising blood pressure

what was the first protein to have its primary structure determined?

insulin

what is the only amino acid more stable in cis confirmation

proline

secondary structure

determined by interactions in the peptide backbone largely stabilized by hydrogen bonds

what are the 2 types of secondary structures

beta pleated sheets and alpha helix

are alpha helices left or right handed?

right-handed

where are hydrogen bonds formed in alpha helices?

between the carbonyl oxygen of each residue and the backbone NH group four residues ahead