1 - Amino Acids, Peptides, Proteins

Question 1

What groups make up amino acid

Answer 1

Amine (-NH₂), carboxyl (COOH), H, R group

Question 2

Name for 20 amino acids

Answer 2

Proteinogenic amino acids

Question 3

The alpha carbon is generally ____ meaning they are optically ___

Answer 3

Chiral, active

Question 4

Which amino acid is not optically active

Answer 4

Glycine - R group is hydrogen

Question 5

Why are amino acids L-amino acids

Answer 5

NH₂ is drawn on left of Fischer projection for S configuration in eukaryotes

Question 6

Which amino acid does not have S-sterochemistry

Answer 6

Cysteine - R stereo bring L-amino acid

Question 7

Which amino acids have a chiral carbon in R group

Answer 7

Threonine (T) and isoleucine (I)

Question 8

Nonpolar, nonaromatic amino acids

Answer 8

IVGLAMP
Isoleucine, valine, glycine, leucine, alanine, methionine, proline

Question 9

Which 2 amino acids have S in it

Answer 9

Methionine (—S—), cysteine (HS—)

Question 10

Why is proline unique

Answer 10

Has cyclic R group - limits flexibility, found at start of alpha helixes or folds of ß-sheets

Question 11

Uncharged aromatic amino acids

Answer 11

FWY
Phenylalanine, tryptophan, tyrosine

Question 12

Nonpolar, aromatic amino acids

Answer 12

FW
Phenylalanine, tryptophan

Question 13

Polar, aromatic amino acids

Answer 13

Y
Tyrosine

Question 14

Why is the thiol group in cysteine important

Answer 14

Prone to oxidation (disulfide bridges)

Question 15

Polar, nonaromatic amino acids

Answer 15

STNQC
Serine, threonine, asparagine, glutamine, cysteine

Question 16

Acidic (negative) amino acids

Answer 16

DE
Aspartame (aspartic acid), glutamate (glutamic acid)

Question 17

Basic (positive) amino acids

Answer 17

KRH
Lysine, arginine, histidine

Question 18

Hydrophobic amino acids

Answer 18

ALIVF
Alanine, leucine, isoleucine, valine, phenylalanine

Question 19

Hydrophilic amino acids

Answer 19

HQDRENK
Histidine, glutamine, aspartate, arginine, glutamate, asparagine, lysine

Question 20

Why are amino acids amphoteric

Answer 20

Can become positive or negative (accept or donate proton)

Question 21

What does the first pKa refer to

Answer 21

COOH

Question 22

What does the second pKa refer to

Answer 22

NH₂

Question 23

What does zwitterion mean

Answer 23

Hybrid ion - both positive and negative charged ends

Question 24

What does the titration curve look like when pH is close to pKa

Answer 24

Slope becomes flat - implies same amount of intermediates
[NH₂—COO-] equals [NH₃+—COO-]

Question 25

What does pI mean

Answer 25

Isoelectric point - the pH where the molecule is electrically neutral

Question 26

How do you calculate pI

Answer 26

Take average of the pKa If basic, average the 2 amino pKa If acidic, average the 2 carboxyl pKa

Question 27

What are peptides made of

Answer 27

Amino acids, residues

Question 28

Oligopeptide vs polypeptide

Answer 28

Oligo: 4-20 amino acid chain Poly: 21+ amino acid chain

Question 29

How are peptide bonds formed

Answer 29

Electrophilic carbonyl is attacked by NH₃+

Question 30

What type of reaction is peptide bond formation

Answer 30

Condensation or dehydration (remove water)

Question 31

Where is there limited rotation in backbone of peptide chain

Answer 31

Between the N-C=O bond due to resonance It can become N=C-O

Question 32

What catalyzes hydrolysis

Answer 32

Hydrolytic enzymes - add H to amino side, add OH to carbonyl side

Question 33

Functions of proteins (4)

Answer 33

Enzymes, hormones, membrane pores and receptors, elements of cell structure

Question 34

What bond is involved in primary structure

Answer 34

Peptide bond (covalent)

Question 35

What bond is important in secondary structure

Answer 35

H-bonds

Question 36

Describe alpha helixes

Answer 36

Turn clockwise, stabilized by intramolecular H-bonds, R groups face out

Question 37

Describe beta sheets

Answer 37

Held together by H-bonds, R groups face up/down the plane, makes a chain

Question 38

Fibrous proteins

Answer 38

Long strands/sheets like collagen

Question 39

Globular proteins

Answer 39

Globe-like, spherical like myoglobin

Question 40

How is tertiary structure controlled

Answer 40

Hydrophobic ends go inside stabilizing protein Hydrophilic ends form electrostatic interactions outside

Question 41

What structure are disulfide bridges important in, what does it do

Answer 41

Tertiary structure, it creates loops - can determine curliness of hair

Question 42

What are intermediate steps in protein folding called

Answer 42

Molten globules

Question 43

What makes up quaternary structure

Answer 43

Aggregate of globular peptides, subunits

Question 44

4 reasons why quaternary structure is advantageous

Answer 44

Increase stability by decreasing surface area Reduce amount of DNA needed to code for that protein Bring catalytic sites closer together Cooperativity/allosteric effects - one conformational change in subunit can enhance/reduce activity of other subunits

Question 45

Conjugated vs simple proteins

Answer 45

Simple - only made of the 20 amino acids Conjugated - functions by interacting with prosthetic groups

Question 46

Examples of prosthetic groups

Answer 46

Organic molecules (vitamins) or metals (iron)

Question 47

3 different prosthetic groups attached to protein

Answer 47

Lipid - lipoprotein Carbohydrate - glycoprotein Nuclei acid - nucleoprotein

Question 48

Function of prosthetic group

Answer 48

Deliver protein to a specific location (nucleus, membrane, lysosome, ER)

Question 49

What happens during denaturation, what causes it

Answer 49

Tertiary structure is broken by heat or solutes

Question 50

How does heat denature protein

Answer 50

Overcome hydrophobic interactions and cause protein to unfold

Question 51

How do solutes denature protein

Answer 51

Urea - break disulfide bridges, overcome H-bonds in secondary structure Detergent - solubilize protein by destroying any bond (noncovalent) and promote denaturation