Amino Acids, Peptides, and Proteins

Question 1

Nonpolar, nonaromatic side chains

Answer 1

glycine, alanine, valine, leucine, and isoleucine

methionine (sulfur atom but considered relatively nonpolar)

Question 2

Chirality of amino acids in eukaryotes ?

Answer 2

L-amino acids (S) absolute configuration;

exception: cysteine –> L amino acid (has R absolute configuration)

Question 3

Only cyclic, nonpolar, nonaromatic

Answer 3

proline

Question 4

Aromatic side chains?

Answer 4

tryptophan, phenylalanine, tyrosine

Question 5

Polar side chains?

Answer 5

Serine, threonine (both have -OH groups), asparagine, glutamine (have amide side chains), cysteine (thiol, -SH)

Question 6

negatively charged (acidic) side chain

Answer 6

aspartic acid (asparatate) and glutamic acid (glutamate)

Question 7

positively charged (basic) side chains

Answer 7

lysine, arginine, histidine (has an aromatic ring with two nitrogen atoms/called a imidazole)

Question 8

hydrophobic amino acids

Answer 8

alanine, isoleucine, leucine, valine, and phenylalanine

Question 9

hydrophilic amino acids

Answer 9

charged side chains–> positively charged histidine, arginine, and lysine plus negatively charged glutamate and aspartate

Question 10

alanine

Answer 10

ala, A

Question 11

arginine

Answer 11

arg, R

Question 12

asparagine

Answer 12

Asn, N

Question 13

Aspartic acid

Answer 13

asp, D

Question 14

Cysteine

Answer 14

cys, C

Question 15

Glutamic acid

Answer 15

Glu, E

Question 16

Glutamine

Answer 16

Gln, Q

Question 17

Glycine

Answer 17

Gly, G

Question 18

Histidine

Answer 18

His, H

Question 19

Isoleucine

Answer 19

Ile, I

Question 20

Leucine

Answer 20

Leu, L

Question 21

Lysine

Answer 21

Lys, K

Question 22

Methionine

Answer 22

Met, M

Question 23

Phenylalanine

Answer 23

Phe, F

Question 24

Proline

Answer 24

Pro, P

Question 25

Serine

Answer 25

Ser, S

Question 26

Threonine

Answer 26

Thr, T

Question 27

Tryptophan

Answer 27

Trp, W

Question 28

Tyrosine

Answer 28

Tyr, Y

Question 29

Valine

Answer 29

Val, V

Question 30

amphoteric species

Answer 30

can accept a proton or donate a proton

Question 31

zwitterions

Answer 31

have a positive and negative charge

Question 32

isoelectric point

Answer 32

where the net charge is 0, pH at which the molecule is electrically neutral

Question 33

peptide bonds

Answer 33

when an amide bond is formed between the -COO- group of one amino acid and the NH3+ group of another amino acid

Question 34

What type of reaction is the formation of a peptide bond?

Answer 34

A condensation/dehydration reaction…results in the removal of a water molecule; the nucleophilic amino group of one amino acid attacks the electrophilic carbonyl group of another amino acid

Question 35

How are peptide bonds structured?

Answer 35

From N-terminus to C-terminus, free amino end on the left, carboxyl end on the right

Question 36

primary structure

Answer 36

linear arrangement of amino acids coded in an organism’s DNA, can be determined by sequencing

Question 37

secondary structure

Answer 37

local structure of neighboring amino acids, result of hydrogen bonding between nearby amino acids, most common secondary structures are alpha-helices and B-pleated sheets

Question 38

What is an important component of keratin?

Answer 38

alpha helix, keratin is a fibrous structural protein found in human skin, hair, and fingernails

Question 39

beta-pleated sheets

Answer 39

can be parallel or antiparallel, fibroin (a primary protein component of silk fibers) is composed of beta-pleated sheets, often see prolines, help turn between beta-pleated sheets

Question 40

proline’s role in secondary structure

Answer 40

helps form turns in alpha helices or beta sheets, creates a kink

Question 41

fibrous proteins

Answer 41

collagen, resembles long strands/sheets

Question 42

globular proteins

Answer 42

globin, tends to be spherical, like a globe

Question 43

tertiary structure

Answer 43

3-D shape of a protein, mostly determined by hydrophilic and hydrophobic interactions between the R groups of amino acids, have disulfide bonds

Question 44

what forms disulfide bonds?

Answer 44

two cysteine molecules become oxidized to form cystine, disulfide bonds create loops in the protein chain

Question 45

What is it called when a protein loses its tertiary structure?

Answer 45

Denaturation, it will lose its function, often irreversible

Question 46

quaternary structure

Answer 46

not all proteins have quaternary structure, need multiple subunits to have it, hemoglobin and immunoglobulins are classic examples

Question 47

prosthetic groups

Answer 47

covalently attached molecules

Question 48

What is true at the pKa

Answer 48

[HA]=[A-]

Question 49

What does the titration curve look like at the pKa values of the amino acid?

Answer 49

Nearly flat

Question 50

What does the titration curve look like at the pI of the amino acid?

Answer 50

Nearly vertical

Question 51

What type of reaction is the breaking of a peptide bond?

Answer 51

A hydrolysis reaction (water is used to break down the bonds of a particular substance)

Question 52

Hydrophobic interactions

Answer 52

push hydrophobic R groups to the interior of a protein, which increases entropy of the surrounding water molecules to create negative Gibbs free energy