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CHE 541 > 2 - Basic Amino Acid Structure and Chemistry > Flashcards

2 - Basic Amino Acid Structure and Chemistry Flashcards

1
Q

What are the building blocks of a cell?

A

Proteins, carbohydrates, lipids, and nucleic acids

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2
Q

What do amino acids do?

A

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

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3
Q

What do carbohydrates do?

A

Storage, generation of energy, structure, signaling

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4
Q

What do lipids do?

A

Components of cell membranes, signaling molecules

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5
Q

What do nucleic acids do?

A

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

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6
Q

What is the general structure of an amino acid?

A

H3N+ - CHR - COO-

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7
Q

What implicit conditions are present for amino acids?

A

Neutral (pH = 7.4)

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8
Q

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

A

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

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9
Q

What configuration do all natural amino acids have?

A

L configuration

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10
Q

What is the L configuration of an amino acid?

A
  1. Look down H-C bond

2. CO - R - N is clockwise

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11
Q

What stereochemistry do most amino acids have?

A

S configuration

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12
Q

Which amino acid has R configuration?

A

Cysteine

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13
Q

How come cysteine has R configuration?

A

S (side chain) has higher priority than N

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14
Q

What is S configuration?

A

Counterclockwise decrease in priority based on atomic number

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15
Q

What is R configuration?

A

Clockwise decrease in priority based on atomic number

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16
Q

True or false: all natural amino acids are L

A

True: all amino acids are L

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17
Q

True or false: all natural amino acids are S

A

False: cysteine is R, and glycine is achrial

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18
Q

True or false: all amino acids are chiral

A

False: glycine is achiral

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19
Q

How are side chains usually classified?

A

By polarity

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20
Q

What do amino acid side chains do?

A

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

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21
Q

What controls protein “collapse”?

A

Hydrophobic interactions away from water (energetics)

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22
Q

What is a big factor in ligand binding?

A

Desolvation energy

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23
Q

What roles can side chains play in enzyme catalysis?

A

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

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24
Q

What group is found on Trp?

A

Indole

25
Q

What group is found on Arg?

A

Guanidinium

26
Q

What group is found on His?

A

Imidazolium

27
Q

Which amino acid is most flexible and why?

A

Glycine, because it does not have a large R group

28
Q

Which amino acid is least flexible and why?

A

Proline, because it has a ring

29
Q

What reactions can aromatic side chains do?

A

They can accept charge well (absorbance)

30
Q

What can water do with side chains?

A

It can satisfy charges (found near the surface)

31
Q

Which amino acid(s) have two stereocenters?

A

Ile and Thr

32
Q

What is the reactivity of His?

A

Versatile - acid/base, metal coordination

33
Q

What is the reactivity of Cys?

A

Redox active, good nucleophile

34
Q

What is the reactivity of Lys?

A

Acid, base, or nucleophile

35
Q

What is the reactivity of Ser?

A

Can be a nucleophile when activated, phosphorylation

36
Q

Which N is usually more basic: sp3 or sp2?

A

sp3 (less S character, LP further away)

37
Q

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

A

The sp2

38
Q

Why is the sp2 N protonated in His?

A

It does not kill the aromaticity when protonated

39
Q

What is the reactive N used for in His?

A

Acid/base chemistry or metal coordination

40
Q

What is a tautomer?

A

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

41
Q

What is the purpose of His in carbonic anhydrase?

A

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

42
Q

What type of reaction forms disulfide bonds?

A

Oxidation

43
Q

What type of reaction breaks disulfide bonds?

A

Reduction

44
Q

What is the significance of disulfide bonds?

A

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

45
Q

Where are disulfide bonds used?

A

To facilitate folding and association

46
Q

Why is SH a good nucleophile?

A
  1. SH is less electronegative

2. SH is “softer” (more polarizable)

47
Q

How do cysteine proteases work?

A

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

48
Q

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

A

Deprotonated (active nucleophilic form)

49
Q

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

A

Protonated (positive charge)

50
Q

What is the structure of a Schiff base?

A

R1R2-C=N-R3

51
Q

How can Schiff bases be formed in biochemistry?

A

Lys can attack carbonyls (H2N)

52
Q

What does phosphonoacetaldehyde hydrolase do?

A

It cleaves C-P bonds

53
Q

How does phosphonoacetaldehyde hydrolase work?

A

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

54
Q

How is lysine used in histone methyltransferase?

A

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

55
Q

What are some examples of spontaneous reactions with amino acids?

A
  1. Oxidation of Met
  2. Beta-elimination cleavage of Asp and Pro peptide bonds
  3. Asn deamination
56
Q

What is the problem with Met oxidation?

A

It can lead to annoying heterogenicity in mass spectrometry

57
Q

What is the problem with Asn deamination?

A

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

58
Q

Where is Asn deamination a big problem?

A

In the pharmaceutical industry (low pH)

CHE 541 (20 decks)

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