2 - Basic Amino Acid Structure and Chemistry

Question 1

What are the building blocks of a cell?

Answer 1

Proteins, carbohydrates, lipids, and nucleic acids

Question 2

What do amino acids do?

Answer 2

Determine shape/function of proteins, specific chemical reactions (catalysis)

Question 3

What do carbohydrates do?

Answer 3

Storage, generation of energy, structure, signaling

Question 4

What do lipids do?

Answer 4

Components of cell membranes, signaling molecules

Question 5

What do nucleic acids do?

Answer 5

Building blocks of DNA/RNA, source of energy in coupled reactions (ATP), signaling, activation of substrates

Question 6

What is the general structure of an amino acid?

Answer 6

H3N+ - CHR - COO-

Question 7

What implicit conditions are present for amino acids?

Answer 7

Neutral (pH = 7.4)

Question 8

What is the charge on a general amino acid at pH = 7.4?

Answer 8

Positive amine (protonated), negative carboxylic acid (deprotonated)

Question 9

What configuration do all natural amino acids have?

Answer 9

L configuration

Question 10

What is the L configuration of an amino acid?

Answer 10

1. Look down H-C bond

2. CO - R - N is clockwise

Question 11

What stereochemistry do most amino acids have?

Answer 11

S configuration

Question 12

Which amino acid has R configuration?

Answer 12

Cysteine

Question 13

How come cysteine has R configuration?

Answer 13

S (side chain) has higher priority than N

Question 14

What is S configuration?

Answer 14

Counterclockwise decrease in priority based on atomic number

Question 15

What is R configuration?

Answer 15

Clockwise decrease in priority based on atomic number

Question 16

True or false: all natural amino acids are L

Answer 16

True: all amino acids are L

Question 17

True or false: all natural amino acids are S

Answer 17

False: cysteine is R, and glycine is achrial

Question 18

True or false: all amino acids are chiral

Answer 18

False: glycine is achiral

Question 19

How are side chains usually classified?

Answer 19

By polarity

Question 20

What do amino acid side chains do?

Answer 20

Control structure and properties of proteins, involved in nonpolar and electrostatic interactions, involved in enzyme catalysis

Question 21

What controls protein “collapse”?

Answer 21

Hydrophobic interactions away from water (energetics)

Question 22

What is a big factor in ligand binding?

Answer 22

Desolvation energy

Question 23

What roles can side chains play in enzyme catalysis?

Answer 23

Nucleophilic catalysis, acid/base catalysis, transition state stabilization (electrostatics)

Question 24

What group is found on Trp?

Answer 24

Indole

Question 25

What group is found on Arg?

Answer 25

Guanidinium

Question 26

What group is found on His?

Answer 26

Imidazolium

Question 27

Which amino acid is most flexible and why?

Answer 27

Glycine, because it does not have a large R group

Question 28

Which amino acid is least flexible and why?

Answer 28

Proline, because it has a ring

Question 29

What reactions can aromatic side chains do?

Answer 29

They can accept charge well (absorbance)

Question 30

What can water do with side chains?

Answer 30

It can satisfy charges (found near the surface)

Question 31

Which amino acid(s) have two stereocenters?

Answer 31

Ile and Thr

Question 32

What is the reactivity of His?

Answer 32

Versatile - acid/base, metal coordination

Question 33

What is the reactivity of Cys?

Answer 33

Redox active, good nucleophile

Question 34

What is the reactivity of Lys?

Answer 34

Acid, base, or nucleophile

Question 35

What is the reactivity of Ser?

Answer 35

Can be a nucleophile when activated, phosphorylation

Question 36

Which N is usually more basic: sp3 or sp2?

Answer 36

sp3 (less S character, LP further away)

Question 37

Which N is protonated in His (sp2 or sp3)?

Answer 37

The sp2

Question 38

Why is the sp2 N protonated in His?

Answer 38

It does not kill the aromaticity when protonated

Question 39

What is the reactive N used for in His?

Answer 39

Acid/base chemistry or metal coordination

Question 40

What is a tautomer?

Answer 40

An isomer where atoms switch places (not a resonance structure)

Question 41

What is the purpose of His in carbonic anhydrase?

Answer 41

It forms a coordination complex around zinc, which is used to make water more electropositive to attack CO2

Question 42

What type of reaction forms disulfide bonds?

Answer 42

Oxidation

Question 43

What type of reaction breaks disulfide bonds?

Answer 43

Reduction

Question 44

What is the significance of disulfide bonds?

Answer 44

They are covalent bonds, so they are less dynamic than electrostatics and H-bonds

Question 45

Where are disulfide bonds used?

Answer 45

To facilitate folding and association

Question 46

Why is SH a good nucleophile?

Answer 46

1. SH is less electronegative | 2. SH is "softer" (more polarizable)

Question 47

How do cysteine proteases work?

Answer 47

S- acts as a nucleophile to attack and break amide bonds

Question 48

If Lys is to be used as a nucleophile, what state is it in?

Answer 48

Deprotonated (active nucleophilic form)

Question 49

If Lys is to be used for electrostatic interactions, what state is it in?

Answer 49

Protonated (positive charge)

Question 50

What is the structure of a Schiff base?

Answer 50

R1R2-C=N-R3

Question 51

How can Schiff bases be formed in biochemistry?

Answer 51

Lys can attack carbonyls (H2N)

Question 52

What does phosphonoacetaldehyde hydrolase do?

Answer 52

It cleaves C-P bonds

Question 53

How does phosphonoacetaldehyde hydrolase work?

Answer 53

Lys forms the Schiff base, which activates the phosphate bond, allowing water to attack and break the bond

Question 54

How is lysine used in histone methyltransferase?

Answer 54

It can help form a good leaving group to break methyl-sulfur bond

Question 55

What are some examples of spontaneous reactions with amino acids?

Answer 55

1. Oxidation of Met 2. Beta-elimination cleavage of Asp and Pro peptide bonds 3. Asn deamination

Question 56

What is the problem with Met oxidation?

Answer 56

It can lead to annoying heterogenicity in mass spectrometry

Question 57

What is the problem with Asn deamination?

Answer 57

It can break down into Asp (change amide into hydroxyl), change the backbone (alpha to beta), and can add a double bond in the system

Question 58

Where is Asn deamination a big problem?

Answer 58

In the pharmaceutical industry (low pH)