Jack Westin Amino Acids (not finished)

Question 1

Which two amino acids act as weak acids?

Answer 1

Cysteine and tyrosine

Question 2

What is a weak acid?

Answer 2

A molecule that can donate a proton

Question 3

What does pKa measure?

Answer 3

How easily molecules lose protons (aka acidity)

Question 4

What does pKa represent?

Answer 4

The pH at which half of the molecules are protonated

Question 5

What part of cysteine’s side chain is acidic?

Answer 5

The thiol group

Question 6

What is the pKa of cysteine’s side chain?

Answer 6

8.3

Question 7

What part of tyrosine’s side chain is acidic?

Answer 7

The alcohol group

Question 8

What is the pKa of tyrosine’s side chain?

Answer 8

10.1

Question 9

What environment does tyrosine need for deprotonation?

Answer 9

A basic environment

Question 10

How are non-polar amino acids typically oriented in the protein?

Answer 10

Towards the inside of the protein (avoiding the aqueous environment)

Question 11

Which protein structures are influenced by the hydrogen bonds from the hydroxyl group in serine and threonine?

Answer 11

Secondary and tertiary

Question 12

What are a few of the interactions that can occur with the hydroxyl group of serine and threonine?

Answer 12

Hydrogen bonds, phosphorylation

Question 13

What can phosphorylation of tyrosine, threonine, or serine regulate?

Answer 13

To regulate protein activity, signaling pathways, and cellular processes

Question 14

What can phosphorylation alter in a protein?

Answer 14

The function, localization, and/or interactions

Question 15

The amide groups in glutamine and asparagine can be involved in what type of bonding?

Answer 15

Hydrogen bonding

Question 16

What are the three components of an amino acid?

Answer 16

An amino group, a carboxyl group, a distinct side chain (R)

Question 17

What is an amino group?

Answer 17

NH₂

Question 18

What is a protonated amino group?

Answer 18

NH₃⁺

Question 19

What is a carboxyl group?

Answer 19

COOH

Question 20

What is physiological pH?

Answer 20

7.4

Question 21

What are the charges on an amino acid at physiological pH?

Answer 21

Amino group → (+) NH₃, Carboxyl group → (-) COO

Question 22

What is a zwitterion?

Answer 22

A molecule with a positive and negative charge

Question 23

What does isoelectric mean?

Answer 23

The net charge is zero

Question 24

Where is the chiral center in most amino acids?

Answer 24

The alpha carbon

Question 25

Which amino acid is achiral?

Answer 25

Glycine

Question 26

In a Fischer projection, where is the amino group for an L configuration?

Answer 26

On the left

Question 27

What is the configuration for chiral amino acids (L or D)?

Answer 27

L

Question 28

What is the chirality of most chiral amino acids (R or S)?

Answer 28

S

Question 29

What does L and D describe about a chiral molecule?

Answer 29

The configuration

Question 30

In the L configuration, which amino acid has R chirality?

Answer 30

Cysteine

Question 31

Which amino acids are exceptions to the configurations/steriochemistry that our body prefers?

Answer 31

Glycine → achiral (≠ L or D), Cysteine → is R not S

Question 32

What's the equation for the number of stereoisomers each molecule has?

Answer 32

2ⁿ, where n = number of chiral centers

Question 33

What's a special characteristic of proline?

Answer 33

Its side chain is bonded to the amino group

Question 34

What is a significant application of proline?

Answer 34

It can initiate kinks/turns in a protein's structure

Question 35

What's a special characteristic of glycine?

Answer 35

It's the only achiral amino acid

Question 36

What's a special characteristic of serine?

Answer 36

It has a hydroxyl group

Question 37

What are 3 significant applications of serine?

Answer 37

It can be involved in phosphorylation, form hydrogen bonds, participate in catalytic mechanisms

Question 38

What's a special characteristic of threonine?

Answer 38

It has a hydroxyl group

Question 39

What are 3 significant applications of threonine?

Answer 39

It can be involved in phosphorylation, form hydrogen bonds, participate in catalytic mechanisms

Question 40

What's a special characteristic of tyrosine?

Answer 40

It has an aromatic ring and a hydroxyl group that is weakly acidic

Question 41

What are significant applications of tyrosine?

Answer 41

Phosphorylation, forming hydrogen bonds, acting as a weak acid/base in enzymatic reactions (contributing to catalytic mechanisms)

Question 42

What's a special characteristic of cysteine?

Answer 42

It has a terminal thiol group

Question 43

What is a significant application of cysteine?

Answer 43

It can create disulfide bonds and be involved in redox reactions

Question 44

What's a special characteristic of histidine?

Answer 44

Its side chain has a pKa of 6

Question 45

What does aliphatic mean?

Answer 45

Non-aromatic

Question 46

List all of the non-polar aliphatic amino acids (7).

Answer 46

Glycine, alanine, valine, leucine, isoleucine, proline, methionine

Question 47

List all of the polar uncharged amino acids (6).

Answer 47

Serine, threonine, cysteine, asparagine, glutamine, tyrosine

Question 48

List all of the positively charged amino acids (3).

Answer 48

Lysine, arginine, histidine

Question 49

List all of the negatively charged amino acids (2).

Answer 49

Aspartic acid, glutamic acid

Question 50

List all of the aromatic amino acids (3).

Answer 50

Phenylalanine, tryptophan, tyrosine

Question 51

What is the abbreviation (3 letter and 1 letter) for serine?

Answer 51

Ser, S

Question 52

What is the abbreviation (3 letter and 1 letter) for threonine?

Answer 52

Thr, T

Question 53

What is the abbreviation (3 letter and 1 letter) for tyrosine?

Answer 53

Tyr, Y

Question 54

What is the abbreviation (3 letter and 1 letter) for cysteine?

Answer 54

Cys, C

Question 55

What is the abbreviation (3 letter and 1 letter) for asparagine?

Answer 55

Asn, N

Question 56

What is the abbreviation (3 letter and 1 letter) for glutamine?

Answer 56

Gln, Q

Question 57

Where are serine and threonine often found?

Answer 57

On the surface of proteins where they can interact with an aqueous environment

Question 58

Why are serine and threonine often found on the surface of proteins?

Answer 58

Because it allows their hydroxyl group to interact with an aqueous environment

Question 59

What is the pKa on tyrosine's hydroxyl group?

Answer 59

10

Question 60

What R group is formed when tyrosine is deprotonated?

Answer 60

A nucleophilic phenoxide ion

Question 61

What are 3 significant applications of a deprotonated tyrosine (phenoxide ion R group)?

Answer 61

It's behavior in enzyme active sites, covalent bond formation, help stabilize transition states

Question 62

Describe tyrosine's involvement in enzymatic reactions when it's deprotonated.

Answer 62

1.) The nucleophilic R group (phenoxide ion) is electrophilic allowing it to be involved in catalysis with electrophilic substrates. 2.) Its oxygen ion can stabilize charges in proton transfer steps.

Question 63

What is a thiol?

Answer 63

SH

Question 64

Which two amino acids have thiols?

Answer 64

Cysteine and methionine

Question 65

What is the abbreviation (3 letter and 1 letter) for methionine?

Answer 65

Met, M

Question 66

What is a disulfide bond?

Answer 66

A covalent bond between two cysteine molecules through their thiol groups

Question 67

What level of protein structures are influenced by disulfide bonds?

Answer 67

Tertiary and quaternary

Question 68

How are disulfide bonds formed?

Answer 68

Through oxidation reactions

Question 69

How are disulfide bonds broken?

Answer 69

Through reduction reactions