Amino Acids & Intro to Peptides

Question 1

What 4 components make up amino acids?

What is at the center of an amino acid?

Answer 1

NH3+ (Amino Group)
COO- (Carboxylic Acid)
R Group
H (Hydrogen)

A central tetrahedral carbon is the ⍺-carbon (C⍺), and is at the center of all amino acids.

Question 2

What atoms/molecules are present in the Non-variable region of amino acids?

What do amino acids differ by?

Answer 2

They only differ by the variable region (R)

Question 3

How many amino acids are found in proteins?

Answer 3

20 different amino acids are found in proteins

Question 4

What are the 2 conformations that Amino Acids can assume?

Answer 4

L & D

Question 5

What confirmation are all Amino Acids found in proteins in?

Describe the conformation and its counterpart

Answer 5

L conformation

In the L conformation the Amine is on the left

In the D conformation the Amine is on the right

Question 6

Glycine
Gly G

R?

Answer 6

Question 7

Alanine
Ala A

R?

Answer 7

Question 8

Proline
Pro P

R?

Answer 8

Question 9

Valine
Val V

R?

Answer 9

Question 10

Leucine
Leu L

R?

Answer 10

Question 11

Isoleucine
Ile I

R?

Answer 11

Question 12

Methionine
Met M

R?

Answer 12

Question 13

Name the 7 Amino Acids with Nonpolar, aliphatic R Groups

Answer 13

1) Glycine - Gly G
2) Alanine - Ala A
3) Proline - Pro P
4) Valine - Val V
5) Leucine - Leu L
6) Isoleucine - Ile I
7) Methionine - Met M

Question 14

Aspartate
Asp D

R?

Answer 14

Question 15

Glutamate
Glu E

R?

Answer 15

Question 16

Name the 2 Amino Acids with Negatively charged R groups

Answer 16

1) Asparate - Asp D
2) Glutamate - Glu E

Question 17

Lysine
Lys K

R?

Answer 17

Question 18

Arginine
Arg R

R?

Answer 18

Question 19

Histidine
His H

Answer 19

Question 20

What is unique about His?

Answer 20

His gets conditionallly charged at physiological pH

Physiological pH – The pH that normally prevails in the human body. ~7.4

Question 21

Name the 3 Amino Acids with Positivley charged R Groups?

Answer 21

1) Lysine - Lys K
2) Arginine - Arg R
3) Histidine - His H

Question 22

Serine
Ser S

R?

Answer 22

Question 23

Theonine
Thr T

R?

Answer 23

Question 24

Cysteine
Cys C

Answer 24

Question 25

What is unique about Cysteine side chains?

Answer 25

They can be oxidized to form Disulfide Bonds

Question 26

Asparagine Asn N | R?

Answer 26

Question 27

Glutamine Gln Q

Answer 27

Question 28

Name the 5 Amino Acids with Polar, uncharged R Groups

Answer 28

1) Serine - Ser S 2) Threonine - Thr T 3) Cysteine - Cys C 4) Asparagine - Asn N 5) Glutamine - Gln Q

Question 29

Phenylalanine Phe F | R?

Answer 29

Question 30

Tyrosine Tyr Y

Answer 30

Question 31

Tryptophan Trp W | R?

Answer 31

Question 32

Name the 3 Amino Acids with Aromatic R Groups?

Answer 32

1) Phenylalanine - Phe F 2) Tyrosine - Tyr Y 3) Tryptophan - Trp W

Question 33

What form do Amino Acids take in acidic conditions?

Answer 33

Cationic form

Question 34

What form do Amino Acids take in nuetral conditions?

Answer 34

Zwitterion form (neutral)

Question 35

What form do Amino Acids take in basic conditions?

Answer 35

Anionic form

Question 36

Describe the functional groups of an Amino Acid in relation to pH conditions of the solution that surround them

Answer 36

Functional groups are ionizable – Their structure will change based on the pH of the solution around it

Question 37

Define Isoelectric Point/pI

Answer 37

The pH ar which the net electric charge of a molecule is zero

Question 38

What is the formula to find the pI of a molecule?

Answer 38

Question 39

What does the pI of a molecule depend on?

Answer 39

1) The number of ionizable functional groups it has 2) pH of the solution

Question 40

Define Peptide Bonds

Answer 40

Bonds formed between 2 amino acids by a condensation reaction

Question 41

What is the chemical structure of a peptide bond?

Answer 41

Question 42

Define the N-terminus

Answer 42

the start of a protein or a polypetide, refffering to the free amine group on the end of a polypeptide

Question 43

Define the C-terminus

Answer 43

the end of the amnio acid chain, terminated by a free carboxyl group

Question 44

What is unique about the length of a peptide bond? Explain what makes it unique

Answer 44

Peptide bonds have partial double bond characteristics, there for their length is inbetween that of a C-N and C=N bond This is due to the fact that electron density os shared between the C, N and O

Question 45

What is the length of a C-N bond?

Answer 45

.145nm

Question 46

What is the length of a C=N bond?

Answer 46

.123nm

Question 47

What is the length of a Peptide bond?

Answer 47

.133nm

Question 48

What plane do the 6 atoms surrounding a peptide bond lie in?

Answer 48

They lie in the same flat amide plane

Question 49

What is parts of a polypeptide are able to rotate?

Answer 49

The bonds before and after the C⍺ can rotate forming phi (ɸ) and psi (Ψ) angles

Question 50

Define the phi (ɸ) angle

Answer 50

The phi angle is formed between the N-C⍺ bond in a polypeptide phi (ɸ) = N-C

Question 51

Define the psi(Ψ) angle

Answer 51

The psi(Ψ) angle is formed between the C⍺–C bond in a polypeptide psi(Ψ) = C⍺-C