Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIOC192 > Lecture 4: BUILDING BLOCKS OF PROTEINS > Flashcards

Lecture 4: BUILDING BLOCKS OF PROTEINS Flashcards

1
Q

What do amino acids have?

A

An alpha carbon, amino group, carboxyl group and side chain (R)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What significance does amino acids having four different groups attached have?

A

It means that they are chiral

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What forms can amino acids exist in?

A

L or D but are predominantly L

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Chiral compounds can form…

A

Enantiomers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are enantiomers?

A

Non-superimposable mirror images

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the predominant form of amino acids in solution?

A

Zwitterion (COOH deprotonated and NH2 protonated)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What do the 20 amino acids have in common?

A

Backbone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is different between the amino acids?

A

Their side chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What does each amino acid have?

A

A full name, abbreviated 3 letter name and 1 letter name

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What do the amino acids have due to their different side chains?

A

Different chemical properties

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What do amino acid side chains do in proteins?

A

Carry out the biochemical reactions for which proteins are known

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How are amino acids classified?

A

Based on their chemical properties

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are most non-polar amino acids?

A

Hydrophobic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Where are hydrophobic amino acids found?

A

Typically on the inside of a protein stabilising the structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is glycine’s R group?

A

A hydrogen making it non-chiral, flexible because its R group is small meaning it is found in regions which need to get tight and close together

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is cysteine commonly found in?

A

Proteases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What do phenylalanine and tryptophan have?

A

Aromatic side chains (resonance structures)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What does the R group in proline do?

A

Bends back to the main chain N forming a 5 membered covalently closed ring. This makes it rigid and an imino acid rather than an amino acid as it contains an amine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What side chain do negatively charged polar (acidic) amino acids have?

A

One containing an acidic carboxyl group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

How are negatively charged polar (acidic) amino acids shown?

A

As the conjugate base where the protons are already donated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What side chain do positively charged polar (basic) amino acids have?

A

One containing a basic amine group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How are positively charged polar (basic) amino acids shown?

A

As conjugate acids where the protons are already accepted

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is characteristics of tyrosine?

A

Aromatic and can be phosphorylated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What amino acids contain amide groups?

A

Asparagine and glutamine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What can uncharged polar amino acids be involved in?

A

Polar, but uncharged hydrogen bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What are often learnt by biochemists and clinicians?

A

3 letter and 1 letter abbreviations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What are easy to remember?

A

3 letter abbreviations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What are one letter abbreviations useful for?

A

Sequence alignment and mutation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

One letter abbreviations are …

A

A compact way to depict sequence and great for describing mutations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What does the first letter in the 3 symbol nomenclature represent?

A

The original amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What does the second number in the 3 symbol nomenclature represent?

A

The location of the mutation in the protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What does the second letter in the 3 symbol nomenclature represent?

A

The new or mutated residue

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What do clinicians use the 3 symbol nomenclature for?

A

Noting resistance in proteins such as HIV

34
Q

What is RT?

A

Reverse Transcriptase

35
Q

What is reverse transcriptase?

A

An enzyme in the HIV virus that helps replicate the viral genome. It is essential for HIV survival

36
Q

What are the amino and carboxyl groups of amino acids usually like in solution?

A

Charged

37
Q

Some amino acid side chains are …

A

ionisable

38
Q

What do ionisable side chains contribute to?

A

The net charge of the amino acid

39
Q

How can ionisable side chains be classified?

A

By their pKa value

40
Q

What is the pKa value for an ionisable group on an amino acid?

A

The pH of which the group is 50% ionised

41
Q

What is the pI known as?

A

Isoelectric point

42
Q

What is the isoelectric point?

A

The pH at which the net charge on an amino acid or protein is zero

43
Q

What is the pKa value for alpha carboxylic acid groups?

A

About 2

44
Q

What is the pKa value for alpha amine groups?

A

About 9/10

45
Q

What os the pKa value for side chains?

A

Varies from about 4 to 12.5

46
Q

What do almost all amino acids start as?

A

One of the standard 20

47
Q

What are amino acids translated from?

A

RNA into proteins at the ribosome

48
Q

What happens to some amino acids?

A

They are modified after they are added to a protein

49
Q

What is amino acid modification called?

A

Post-translational modification

50
Q

What does cysteine sometimes do?

A

Forms a covalent bond called a disulphide bond with another nearby cysteine.

51
Q

When will disulphide bonds form?

A

In an oxidising environment

52
Q

What does disulphide bonds forming do?

A

Gives rigidity to the structure

53
Q

When will disulphide bonds break?

A

In a reducing environment

54
Q

What are types of amino acid modification?

A

Phosphorylation, hydroxylation, carboxylation, metal ending, iodination, glycosylation and many others

55
Q

What is phosphorylation?

A

Addition of a phosphate

56
Q

What is hydroxylation?

A

Addition of an OH group

57
Q

What is carboxylation?

A

Addition of a COOH group

58
Q

What is iodination?

A

Addition of iodine which isn’t very common

59
Q

What is glycosylation?

A

Addition of a carbohydrate

60
Q

What is phosphorylation often used for?

A

To control enzyme activity like a chemical ON/OFF switch

61
Q

What amino acids undergo phosphorylation?

A

Serine, threonine and tyrosine

62
Q

What is hydroxylation needed for?

A

To prevent connective tissue diseases and scurvy

63
Q

What amino acids are often involved in hydroxylation?

A

Proline and lysine

64
Q

What is required for hydroxylation?

A

Vitamin C

65
Q

What is carboxylation needed for?

A

Blood clotting

66
Q

What is often involved in carboxylation?

A

Glutamate

67
Q

What amino acids are often glycolysis?

A

Threonine and asparagine

68
Q

What is glycosylated haemoglobin, HbA1c used for?

A

To diagnose and follow patients with diabetes

69
Q

How can amino acids join together to form chains?

A

By covalent bonds called peptide bonds

70
Q

What type of reaction is the formation of a peptide bond?

A

Dehydration where water is lost

71
Q

What does the peptide bond partially have?

A

40% double bond character as there is resonance structures. This leads to planarity and planar conformation maximises pi bond overlapping

72
Q

Can peptide bonds rotate freely?

A

No, there is a rotation barrier of approximately 80kJ/mol

73
Q

What does the peptide bond have?

A

A dipole

74
Q

What is the predominant form of a peptide bond?

A

Trans

75
Q

What is a peptide?

A

A short chain of amino acids joined by peptide bonds

76
Q

What is a protein?

A

A longer chain of amino acids joined by peptide bonds which have a defined function

77
Q

What are amino acids known as in peptides or proteins?

A

Amino acid residues

78
Q

What are amino acids known as amino acid residues in peptides or proteins?

A

Because they are no longer complete

79
Q

What with regards to amino acids is often referred to?

A

Their location

80
Q

What does M184 mean?

A

There is a methionine at position 184

BIOC192 (38 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions