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Biochemistry > Lecture 4 - building blocks of proteins > Flashcards

Lecture 4 - building blocks of proteins Flashcards

1
Q

What makes up an amino acid? Properties of these features?

A

Amino group - basic NH2

Side chain - R group determines the characteristics (size, polarity, and pH) for each type of amino acid.

Carboxyl group - acidic COOH

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2
Q

What does it mean when you say that amino acids are chiral?

A

The chiral carbon has four different groups attached so the compound can exist as a pair of non-superimposable mirror images. There are L or D forms

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3
Q

L and D form

A

All amino acids except for glycine are stereoisomers. This means that there are mirror images of their structure. It is just like how we have left hands and right hands. These are labeled L (left-handed) and D (right-handed) to distinguish the mirror images.

L spells out CO-R-N, L form dominates nature

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4
Q

Amino acids in solution as zwitterions

A

An amino acid has this ability because at a certain pH value (different for each amino acid) nearly all the amino acid molecules exist as zwitterions. If acid is added to a solution containing the zwitterion, the carboxylate group captures a hydrogen (H+) ion, and the amino acid becomes positively charged. If base is added, ion removal of the H+ ion from the amino group of the zwitterion produces a negatively charged amino acid. In both circumstances, the amino acid acts to maintain the pH of the system—that is, to remove the added acid (H+) or base (OH−) from solution.

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5
Q

Zwitterions

A

an overall neutral species in which two or more atoms bear opposite formal charges

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6
Q

How many amino acids are there?

A

20 of them - each have a common backbone but different side chains

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7
Q

Side chains

A

Different side chains in different amino acids

In proteins these bits are arranged to carry out chemical reactions

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8
Q

4 main groups of amino acids as discussed in lectures

A 
Non polar 
Uncharged polar 
Negatively charged (acidic) polar 
Positively charged (basic) polar
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9
Q

Where in a protein would you expect to find non-polar amino acid residues?

A

On the inside of a protein structure

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10
Q

The names of the amino acids can be abbreviated in both _____ letter and _____ letter codes.

A

Three

Single

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11
Q

Non polar amino acids

A 
C - cysteine 
A - Alanine 
M - Methionine 
P - Proline 
F - Phenylalanine 
I - Isoleucine 
G - Glycine 
V - Valine 
L - Leucine 
W - Tryptophan
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12
Q

G

A 
Glycine 
Not chiral (2 same atoms) 
More flexible because it doesn’t have bulky groups hanging off of it - ends up being found in places with tight turns 
Almost in a group on its own 
R group = H
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13
Q

C

A

Cysteine
Can dorm disulphide bonds
Can she H+ and become negatively charged nucleophile and work in the active site of enzymes called cysteine proteases

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14
Q

General statement about the placement of polar and non-polar amino acids

A

Generally non-polar amino acids get put inside a protein and polar/charged amino acids decorate the surface because the cytoplasm is predominantly salt and water

Charged and polar therefore tend to be on the surface of proteins or if they are inside they will usually have their charge tied up in an ionic bond or they will be involved in the active site of an enzyme

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15
Q

F and W

A

F = Phenylalanine
W= Tryptophan
Both have aromatic rings in their side chains

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16
Q

M

A

Methionine

Quite bulky and hydrophobic

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17
Q

P

A

Proline

Quite rigid and therefore is important in structure because of this rigidity

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18
Q

Uncharged polar amino acids

A

S = Serine (alanine that has been hydroxylated)
T = Threonine, 3 carbons and internal one has been hydroxylated
Y = Tyrosine, looks like Phe only with hydroxyl attached
N = asparagine
Q= glutamine

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19
Q

negatively charged (acidic) polar amino acids

A

D = aspartic acid, involved in lots of active sites
E = Glutamic acid, extra methyl group to Asp
Donate protons

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20
Q

positively charged (basic) polar amino acids

A

K = Lysine which has 4 methyl groups and one amino group at end which makes up the R group
R= Arginine
H = Histidine
Take up protons

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21
Q

One letter abbreviations are useful for

A

Sequence alignment and mutations

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22
Q

One letter abbreviations

A

First letter - wild type or native amino acid (original amino acid)
Number - Location of amino acid
Second letter - mutated residue

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23
Q

What chemical groups would we expect to find in the R-group of an ionisable amino acid?

A

COOH, SH, OH, NH2/3+

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24
Q

Where in a protein would we often find ionisable amino acid residues?

A

Arranged on the surface in contact or near solvent

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25
Q

Which amino acids have ionisable side chains ?

A

Acidic amino acids - aspartic acid, glutamic acid (pka 4)
Basic amino acids - Histidine (pka 6), lysine (pka 10) and arginine (pka 12.5)
Non-polar - cysteine (pka 8), tyrosine (pka 10)

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26
Q

What is pka?

A

The pka value for an ionisable group on an amino acid or protein is the pH at which the group is 50% ionised

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27
Q

What is pI?

A

Isoelectric point is the pH at which the net charge on an amino acid (or protein) is zero

28
Q

Post-translational modification

A

This is defined as modifications that occurs to some amino acids after they are added to a protein

29
Q

List some common examples of post-translational modifications and their functions

A

Phosphorylation (control of enzyme activity), hydroxylation (needed to prevent connective tissue disease and scurvy),
carboxylation (needed for blood clotting)

30
Q

Cysteine and cyestine forming bonds with each other

A

If you have 2 cysteine that are close to one another in a protein and in an oxidising environment the 2 sulphide groups can form a disulphide bond - common in extracellular proteins and not so common in intracellular proteins

Example of a post-translational modification

31
Q

Amino acid modifications

A 
Phosphorylation 
Hydroxylation 
Carboxylation 
Metal binding 
Iodination 
Glycosylation 
Many others
32
Q

What can amino acid modifications do?

A

Can change solubility and activity

33
Q

Phosphorylation

A

Control of enzyme activity - often on/off

34
Q

Hydroxylation

A

Needed to prevent connective tissues diseases and scurvy

Add -OH group

35
Q

Carboxylation

A

Needed for blood clotting

Adds carboxylate group

36
Q

Peptide bond

A

Proteins are made up by joining amino acids together with a covalent bond that is called a peptide bond

37
Q

Peptide

A

A short stretch of amino acids joined together by peptide bonds is called a peptide

38
Q

Protein

A

A longer chain of amino acids joined together, usually with a defined biological function, is a protein

39
Q

Amino acid residues

A

When amino acids bond together, they are referred to as amino acid residues as they are no longer complete, individual amino acids (removed water, what remains after the reaction)

40
Q

Peptide bond defining features

A

40% double bond character leads to planarity
Planar conformation maximises pi bond overlap
Rotational barrier of 80 kj/mol
The peptide bond is predominantly trans - the alpha carbons are on opposite sides of the peptide bonds

Planar, trans, dipole

41
Q

What chemical groups would be on an R-group of an ionizable amino acid

A

OH groups and NH groups

42
Q

Alanine

A

Ala, A

43
Q

Valine

A

Val, V

44
Q

Leucine

A

Leu, L

45
Q

Isoleucine

A

Ile, I

46
Q

Glycine

A

Gly, G

47
Q

Cysteine

A

Cys, C

48
Q

Phenylalanine

A

Phe, F

49
Q

Tryptophan

A

Trp, W

50
Q

Methionine

A

Met, M

51
Q

Proline

A

Pro, P

52
Q

Serine

A

Ser, S

53
Q

Threonine

A

Thr, T

54
Q

Tyrosine

A

Tyr, Y

55
Q

Asparagine

A

Asn, N

56
Q

Glutamine

A

Gln, Q

57
Q

Aspartic acid

A

Asp, D

58
Q

Glutamic acid

A

Glu, E

59
Q

Lysine

A

Lys, K

60
Q

Arginine

A

Arg, R

61
Q

Histidine

A

His, H

62
Q

which amino acids are ionisable at physiological pH?

A

Asp, Glu, His, Lys, Arg

63
Q

which amino acids are ionisable but not at physiological pH?

A

Cys, Tyr

64
Q

rotational barrier of peptide bonds

A

80 kJ/mol

65
Q

how much of the peptide bond is double?

A

40%

66
Q

Another name for a peptide bond

A

amide bond

Biochemistry (34 decks)

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