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Biological Chemistry- Samiyah > Amino Acids And Peptide Bonds > Flashcards

Amino Acids And Peptide Bonds Flashcards

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1
Q

At pH 7 what do amino acids exist as

A

Exist as zwitterions

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2
Q

What are the different parts of an amino acid and draw the general structure of amino acids

A

Amino acids can form enantiomers since they have a chiral centre

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3
Q

How are amino acid enantiomers named

A

Left and right handedness defined using L and D
L= Levo
D= dextro
Amino acids are named relative to glyceraldehyde= relative stereochemistry

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4
Q

What is racimisation

A

The enantiomers of amino acids can interconvert between them (but this would take 10 years to happen)
So L enantiomers can convert to D enantiomers and vice versa

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5
Q

What is absolute stereochemistry *

A

Based on opposite orientation

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6
Q

what form of enantiomer are amino acids always found in proteins

A

All amino acids in proteins are L enantiomers
They’ll have the same stereochemistry

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7
Q

How is a peptide formed from amino acids

A

Dehydration/condensation reaction to form an amide bond between the carbonyl group of one amino acid and amine group of another (and water)
(OH group comes off carboxylic acid)

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8
Q

What is the ‘backbone’ of a peptide

A
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9
Q

What is the definition of a peptide

A

2 or more amino acids linked by peptide bonds

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10
Q

What is the definition of a polypeptide

A

Lots of amino acids joined together by peptide bonds

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11
Q

What is the C-terminus and N-terminus

A
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12
Q

What is an amino acid residue

A
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13
Q

What is the primary structure of a protein and how is it represented

A
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14
Q

What kind of hybridisation does the carbon, oxygen and nitrogen atom undergo and what shape is the c=o bond

A

Sp2 hybridisation
Trigonal planar

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15
Q

How do amino acids behave 60% of the time.

A

There is a c=o bond the p orbital of oxygen and carbon overlap so they share a pair of electrons (which is how the double bond forms)
(Ignore red)

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16
Q

How do amino acids behave 40% of the time

A

Nitrogen donates one of its electrons from its p orbital to oxygen so that oxygen has a negative charge and nitrogen has a positive charge
This allows for the p orbitals of carbon and nitrogen to overlap forming a double bond between them (instead of between the carbon and oxygen
Because of this, a peptide bond has partial double bond character

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17
Q

How are the electrons arranged in each of the orbitals of the atoms in an amino acid in a peptide bond

A
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18
Q

Why is a peptide bond polar

A

After nitrogen donates its electrons to oxygen it pulls the electrons in the N-H bond towards itself due to its higher electronegativity, inducing a sight positive charge on the hydrogen
Meanwhile oxygen has a slight negative charge as it accepts an electron from nitrogen

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19
Q

What is meant by the peptide bond having partial double bond character

A

Double bond can form between C and N or between C and O
So if there’s a double bond between N and C there wont be one between C and O

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20
Q

What is meant by a peptide bond being planar

A

All of the atoms attached to the bond are in the same plane

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21
Q

Illustrate the plane of the peptide

A
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22
Q

What would the trans configuration of a peptide be

A

Alpha carbons are opposite eachother

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23
Q

What would the cis configuration of a peptide be

A

2 alpha carbons are on the same side

24
Q

Is the cis or trans isomer of peptides more energetically favourable and why

A

The trans configuration is more energetically favourable
Less repulsion between atoms as they’re less crowded

25
Q

What is the energy difference between the cis/trans orientations of peptides

A

10 kj mol-1

26
Q

What is the structure, 3 letter code and one letter code for alanine

A
27
Q

What is the structure, 3 letter code and one letter code for valine

A
28
Q

What is the structure, 3 letter code and one letter code for leucine

A
29
Q

What is the structure, 3 letter code and one letter code for isoleucine

A
30
Q

What is the structure, 3 letter code and one letter code for glycine

A
31
Q

What is the structure, 3 letter code and one letter code for proline

A
32
Q

What is the structure, 3 letter code and one letter code for cysteine

A
33
Q

What is the structure, 3 letter code and one letter code for methionine

A
34
Q

What is the structure, 3 letter code and one letter code for histidine

A
35
Q

What is the structure, 3 letter code and one letter code for phenylalanine

A
36
Q

What is the structure, 3 letter code and one letter code for tyrosine

A
37
Q

What is the structure, 3 letter code and one letter code for tryptophan

A
38
Q

What is the structure, 3 letter code and one letter code for asparagine

A
39
Q

What is the structure, 3 letter code and one letter code for serine

A
40
Q

What is the structure, 3 letter code and one letter code for glutamine

A
41
Q

What is the structure, 3 letter code and one letter code for threonine

A
42
Q

What is the structure, 3 letter code and one letter code for lysine

A
43
Q

What is the structure, 3 letter code and one letter code for arginine

A
44
Q

What is the structure, 3 letter code and one letter code for aspartic acid

A
45
Q

What is the structure, 3 letter code and one letter code for glutamic acid

A
46
Q

What are the diastereomers of isoleucine and the mirror images

A
47
Q

What are the three classifications of amino acids

A

Standard amino acids
Protein amino acids
Essential amino acid

48
Q

What are standard amino acids

A

The 20 amino acids encoded in the genetic code

49
Q

What are the protein amino acids

A

The different forms of the amino acids that you could have
There are more than 100 of them

50
Q

What are essential amino acids

A

Required in the diet as they can’t be made in the body

51
Q

List the essential amino acids

A

HIS
ILE
LEU
MET
THR
LYS
TRP
PHE
VAL

52
Q

List the aliphatic amino acids

A

Alanine
Valine
Leucine
Isoleucine

53
Q

List the non polar amino acids

A

Glycine
Proline
Cysteine
Methionine

54
Q

Name the aromatic amino acids

A

Histidine
Phenylalanine
Tyrosine
Tryptophan

55
Q

Name the polar amino acids

A

Asparagine
Glutamine
SER in
Threonine

56
Q

Name the charged amino acids

A

Lysine
Arginine
Aspartic acid
Glutamic acid

57
Q

What is the structure of glutamate

A

Biological Chemistry- Samiyah (24 decks)

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