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NA > Amino Acids & Intro to Peptides > Flashcards

Amino Acids & Intro to Peptides Flashcards

Lecture 1

1
Q

What 4 components make up amino acids?

What is at the center of an amino acid?

A

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.

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2
Q

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

What do amino acids differ by?

A

They only differ by the variable region (R)

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3
Q

How many amino acids are found in proteins?

A

20 different amino acids are found in proteins

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4
Q

What are the 2 conformations that Amino Acids can assume?

A

L & D

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5
Q

What confirmation are all Amino Acids found in proteins in?

Describe the conformation and its counterpart

A

L conformation

In the L conformation the Amine is on the left

In the D conformation the Amine is on the right

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6
Q

Glycine
Gly G

R?

A
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7
Q

Alanine
Ala A

R?

A
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8
Q

Proline
Pro P

R?

A
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9
Q

Valine
Val V

R?

A
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10
Q

Leucine
Leu L

R?

A
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11
Q

Isoleucine
Ile I

R?

A
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12
Q

Methionine
Met M

R?

A
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13
Q

Name the 7 Amino Acids with Nonpolar, aliphatic R Groups

A

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

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14
Q

Aspartate
Asp D

R?

A
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15
Q

Glutamate
Glu E

R?

A
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16
Q

Name the 2 Amino Acids with Negatively charged R groups

A

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

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17
Q

Lysine
Lys K

R?

A
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18
Q

Arginine
Arg R

R?

A
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19
Q

Histidine
His H

A
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20
Q

What is unique about His?

A

His gets conditionallly charged at physiological pH

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

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21
Q

Name the 3 Amino Acids with Positivley charged R Groups?

A

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

22
Q

Serine
Ser S

R?

A
23
Q

Theonine
Thr T

R?

A
24
Q

Cysteine
Cys C

A
25
Q

What is unique about Cysteine side chains?

A

They can be oxidized to form Disulfide Bonds

26
Q

Asparagine
Asn N

R?

A
27
Q

Glutamine
Gln Q

A
28
Q

Name the 5 Amino Acids with Polar, uncharged R Groups

A

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

29
Q

Phenylalanine
Phe F

R?

A
30
Q

Tyrosine
Tyr Y

A
31
Q

Tryptophan
Trp W

R?

A
32
Q

Name the 3 Amino Acids with Aromatic R Groups?

A

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

33
Q

What form do Amino Acids take in acidic conditions?

A

Cationic form

34
Q

What form do Amino Acids take in nuetral conditions?

A

Zwitterion form
(neutral)

35
Q

What form do Amino Acids take in basic conditions?

A

Anionic form

36
Q

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

A

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

37
Q

Define Isoelectric Point/pI

A

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

38
Q

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

A
39
Q

What does the pI of a molecule depend on?

A

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

40
Q

Define Peptide Bonds

A

Bonds formed between 2 amino acids by a condensation reaction

41
Q

What is the chemical structure of a peptide bond?

A
42
Q

Define the N-terminus

A

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

43
Q

Define the C-terminus

A

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

44
Q

What is unique about the length of a peptide bond?

Explain what makes it unique

A

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

45
Q

What is the length of a C-N bond?

A

.145nm

46
Q

What is the length of a C=N bond?

A

.123nm

47
Q

What is the length of a Peptide bond?

A

.133nm

48
Q

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

A

They lie in the same flat amide plane

49
Q

What is parts of a polypeptide are able to rotate?

A

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

50
Q

Define the phi (ɸ) angle

A

The phi angle is formed between the N-C⍺ bond in a polypeptide

phi (ɸ) = N-C

51
Q

Define the psi(Ψ) angle

A

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

psi(Ψ) = C⍺-C

NA (6 decks)

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