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IMS topic 1 > Proteins > Flashcards

Proteins Flashcards

1
Q

Define acid

A

A molecule that can donate protons (H+)

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2
Q

Define base

A

A molecule that produces OH- ions in water

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3
Q

What is the structure of an amino acid at normal body pH?

A

A zwitterion; ionised to from NH3+ and COO-

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4
Q

Define enantiomers

A

Two stereoisomers that have the same molecular formula but their mirror images cannot be superimposed on each other, due to the presence of a central chiral carbon

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5
Q

What is the basic amino acid structure?

A

Nh2, R group, H, COOH, central chiral carbon

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6
Q

How many of the 20 amino acids are ESSENTIAL? (because they cannot be manufactured from metabolic intermediates)

A

8

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7
Q

What is the difference between proline and other amino acids?

A

Proline is an IMINO acid; it has -NH- not -NH2-

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8
Q

Give the 6 different amino acid groups

A 
Non-polar aliphatic
Non-polar aromatic 
Polar uncharged
Polar -ve charge
Polar +ve charge
Sulphur containing (can form a disulphide bond)
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9
Q

Why is rotation of amino acids limited?

A

There is limited rotation around he single covalent peptide bond, as it has some of the rigidity of a delve bond because electrons are unevenly shared between COHN atoms. Rotation still occurs around the a-carbon.

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10
Q

Define denaturation

A

The tertiary structure of proteins can be disrupted by heating, chemicals or reducing agents, which abolishes biological activity. This can recover when the denaturing agent is removed (shows that tertiary structure is entirely dependent on primary structure)

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11
Q

What is the role of a molecular chaperone?

A

Aids the folding of a protein chain, and increases the rate of folding (efficiency)

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12
Q

Define acetylation. Why is this done?

A

Addition of an acetyl (CH3CO) group to the N-terminal.

This reduce the rate of degradation

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13
Q

Define glycosylation. Why is this done?

A

Addition of carbohydrate molecules to form glycoproteins

Used in recognition, signal sequences, cell components

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14
Q

Define phosphorylation. Why is this done?

A

Adding a phosphate group (POOO) to a hydroxyl group

To increase or decrease a protein’s activity

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15
Q

Define genome

A

The complete set of genes in an organism

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16
Q

Define proteome?

A

The full set of proteins encoded by the human genome

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17
Q

Why are the genome and proteome not an equal number?

A

One gene does not equal just one protein because;
alternative splicing
changes in a base in DNA
addition of sugars/phosphates after translation

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18
Q

What is phenylketonuria?

A

The enzyme phenylalanine hydroxylase is not present, so phenylalanine (AA) cannot be broke down. Food can’t be broken down = can lead to brain damage in children as it builds up in the brain .

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19
Q

Give an example of a disease caused by a mutation in transport/storage proteins

A

Sickle cell anaemia

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20
Q

Give an example of a disease caused by a mutation in motion/muscle proteins

A

Duchenne muscular dystrophy; changes in muscle fibres mean muscles can’t function

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21
Q

Give an example of a disease caused by a mutation in communication proteins

A

Type 2 diabetes (non-insulin dependent); insulin receptor is unavailable

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22
Q

Give an example of a disease caused by a mutation in structural proteins

A 
Osteogenesis imperfecta (collagen)
Scurvy (collagen); lack of Vit C (aspartic acid) which is needed to make collagen
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23
Q

Give an example of a disease caused by a mutation in channel/transporter proteins

A

cystic fibrosis; the CFTR channel is affected so salts can’t be transported across the membrane

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24
Q

Give an example of a disease caused by a mutation in regulation proteins

A

Insulin dependent diabetes (type 1); no insulin is produced in the pancreas = kidney failure

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25
Q

Give an example of a disease caused by a mutation in immune proteins

A

Myasthenia Gravis; muscle weakness because of damage to the communication between nerves and muscles (immune system response)

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26
Q

How are amino acids named?

A

According to the R group

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27
Q

What is pKa?

A

The pH at which a group is 50% ionised (acid dissociation constant)

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28
Q

What does a lower pKa mean?

A

A stronger acid (more H+)

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29
Q

What does a higher pKa mean?

A

A weaker acid (less H+)

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30
Q

Is the pKa for carboxylic acid groups high or low?

A

Low

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31
Q

Is the pKa for amino groups (NH3+) high or low?

A

High

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32
Q

What is special about the pKa for the amino acid histine?

A

It is 6.0, so histone can be found either positively charged or neutral depending on the medium’s pH

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33
Q

What is indicated if the pH is BELOW the pKa?

A

The group will have a H attached

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34
Q

What is indicated if the pH is above the pKa?

A

Group will lose H+

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35
Q

What is the N-terminal of a polypeptide chain?

A

The free amino group at one end

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36
Q

What is the C-terminal of a polypeptide chain?

A

The free carboxylic acid group at one end of the chain

37
Q

What reaction forms peptide bonds?

A

Condensation

38
Q

Why is there limited rotation around the peptide bond

A

It has double bond characteristics so it more rigid

39
Q

In a peptide bond exhibiting double bond characteristics, are the hydrogen and oxygen atoms in the cis or trans position?

A

trans

40
Q

Explain the structure of an alpha helix

A

The backbone forms the main helix and the side chains extend outside of it. A right hand helix. INTRACHAIN hydrogen bonds at REGULAR INTERVALS between N-H and C=O stabilise the helix. Each oxygen binds to a hydrogen on the NH FOUR RESIDUES ALONG. e.g. 1 bonds with 5, 3 bonds with 7.

41
Q

Does an alpha helix have elasticity? why/why not?

A

Yes, because the hydrogen bonds lay parallel to the helix

42
Q

What types of bonding are present in the secondary structure of a protein?

A

Alpha helixes and beta pleated sheets

43
Q

Explain the structure of a beta pleated sheet

A

Strands of the polypeptide chain run along side each other (parallel or anti-parallel), with intrachain (in the same chain) and interchain (between different chains) hydrogen bonds. The side chains lie ABOVE and BELOW the plane of the sheet, and the backbone is fully extended. Loops and turns between strands allow for a change in direction. Tetrahedral angles around the carbon make it look pleated.

44
Q

Does a beta pleated sheet have any elasticity? why/ why not?

A

No, backbone is fully extended

45
Q

Which amino acids will be incorporated into the middle of the tertiary structure, and which will be on the outside?

A

Hydrophobic in the middle, hydrophilic (polar) on the outside.

46
Q

What is the quaternary structure of a protein? What types of proteins are these normally?

A

Multiple polypeptide chains (subunits) arranged together. Each subunit has a different function.
Structural, transport

47
Q

What is a dilsuphide bond? Which amino acids does it form between?

A

Between two cystine residues, oxidation occurs. A covalent bond between two sulphur atoms, eliminated 2H+

48
Q

What are electrostatic interactions? Give an example of this.

A

Interactions between oppositely charged side chains, e.g. salt bridges between ion pairs. Or, side chains with the same charge can repel each other and destabilise the molecule

49
Q

Explain Van Der Waals forces

A

Weak interactions between molecules with electrically different polarities in ELECTRICALLY NEUTRAL molecules. Relies on the formation of dipoles, when a molecule contains two elements of different electronegativity (the ability to attract the bonding electrons in a covalent bond). An instantaneous dipole induces a dipole in another molecule forming a polar bond.

50
Q

Explain hydrophobic effect

A

Non-polar residues try to minimise contact with water, so are buried in the core of the protein = lots of folding. Polar residues are found on the surface of the molecule.

51
Q

Define molecular chaperones

A

proteins that bind to short segments of a protein to help it fold correctly and efficiently

52
Q

What is the role of chaperonins?

A

Barrel shaped chambers; the protein enters the chamber to become correctly folded

53
Q

Give an example of an disease caused by a misfolded amyloid protein

A

Alzheimer’s

54
Q

Give an example of a disease caused by a misfolded prion protein

A

Creutzfelt-Jacbo disease
Scope
BSE
(an infectious protein agent causes a change in a normal protein)

55
Q

Give 3 symptoms of alzheimer’s

A 
memory loss
loss of language
poor judgement
increased aggression
confusion
restlessness
mood swings
56
Q

What causes Alzheimer’s? Which protein is affected?

A

A loss of neurones from the cerebral cortex. A normal membrane protein, amyloid precursor protein (APP), is cleaved by protease enzymes to form Amyloid Beta, which forms insole fibrils outside of the cell. These aggregate to form plaques which damage and destroy neurones.

57
Q

Why does amyloid beta form insoluble fibrils outside of the cell in Alzheimer’s disease? Why are these fibrils are problem?

A

APP (amyloid precursor protein) from normal membranes is cleaved by proteases to form Amyloid Beta which has a high concentration of beta pleated sheets
The fibrils aggregate to form plaques which damage and destroy neurones.

58
Q

What is Creutzfeldt-Jacob disease? What causes it?

A

Loss of neurological function, memory loss and coordinaton loss
Caused by the ingestion of an infectious agent, the Prion Protein (not a virus), likely from animals. It is similar to Scrapie in sheep and BSE in cows.
Prion protein PrP^sc has an identical primary sequence to a normal membrane protein but with more beta pleated sheets, making it insoluble and resistant to proteases. This also changes the form of the normal prion protein, forming clumps f insoluble aggregate proteins.

59
Q

Why do amino acids have optical activity?

A

The right amino acid in the enantiomer is the D isomer (dextrorotatory) and the left is the L isomer (Levorotatory). They reflect light in different ways.

60
Q

Which form of amino acid enantiomers is found in proteins?

A

L isomer (levorotatory)

61
Q

Where can D isomers of amino acids be found?

A

The cell walls of bacteria (can be targets for antibiotics)

62
Q

What are the features of a globular protein? Give two examples of these

A

Compact, soluble, hydrophobic residues inside

enzymes, haemoglobin

63
Q

What are the features of fibrous proteins? give two examples

A

Elongated, insoluble due to high hydrophobic residue content, large, often have repeated amino acid sequences
keratin, collagen

64
Q

What are the features of membrane proteins? give one example

A

Embedded fully or partially in the membrane, have to be both hydrophilic and hydrophobic
ion channels

65
Q

Define haemoglobinpathies

A

A genetic defect that results in abnormal structure of one of the globin chains of the hemoglobin molecule

66
Q

Why does oxygen need a transport protein and storage?

A

It is too large to be soluble in the blood

67
Q

What is the role of myoglobin

A

Oxygen store

68
Q

Where is the highest concentration of myoglobin?

A

Skeletal and cardiac muscle

69
Q

What type of protein is myoglobin?

A

Globular (mostly a-helix)

70
Q

What does the haem group consist of? What is the bonding in this?

A

Fe2+ in a protoporphyrin ring. Fe2+ acts as the central metal ion and forms dative bonds with 6 different ligands; 4 with the nitrogen atoms in the polyporphyrin ring, one with a histidine residue and one with the oxygen that binds.

71
Q

How does the binding of oxygen to the haem group change the structure?

A

Fe2+ is normally below the centre of the ring; when it bonds datively with O2 it moves up to become parallel to the plane of the ring. === relaxed state

72
Q

Why must a haem be associated to a protein?

A

This keeps Fe2+ in this form and not Fe3+ (which can’t bind O2).
This also inhibits the binding of other small molecules

73
Q

What is the danger of carbon dioxide?

A

It has a higher affinity to haem then O2 does so will bind over it, and cells become started of oxygen. (nausea, dizziness, confusion)

74
Q

What is the structure of haemoglobin? How many O2 can each haemoglobin bind?

A

Four polypeptide chains held together by non-covalent chains. 2 alpha and 2 beta chains. Each chain has a haem group, so haemoglobin can bind four O2. This gives a spherical shape.

Similar structure to myoglobin but 83% of residues are different

75
Q

Why is haemoglobin an allosteric protein?

A

The binding of O2 to one subunit affects interactions to the other subunit, making it easier for more O2 to bind (cooperative binding)

76
Q

Define cooperative binding

A

When a ligand binding to one site affects the binding of a ligand to another site

77
Q

Which has a greater affinity for oxygen, myoglobin or haemoglobin?

A

Myoglobin

78
Q

How does the binding of O2 affect the quaternary structure of haemoglobin?

A

Fe2+ moves down into the plane of the ring, dragging the helix into a different position, which causes some interchain salt bridges to rupture, putting the molecule into the relaxed state (easier for more O2 to bind)

79
Q

Which state of haemoglobin, tense or relaxed, has more salt bridges?

A

Tense

80
Q

Describe the Bohr effect. How is this effected by exercise?

A

A change in pH affects the affinity of haemoglobin for oxygen. At a lower pH (more H+), the affinity for O2 decreases, so more O2 is released.
During anaerobic exercise, lactic acid is produced and pH is lowered, so more O2 is released from haemoglobin to the muscles.

81
Q

How does pH affect haemoglobin?

A

pH affects the protonation state of amino acids in haemoglobin (particularly histidine). At pH 6.0 histidine is positively charged, at a higher pH (lower pKa) it is less positively charged.
As pH drops, more positively charged residues are present so MORE salt bridges are formed, putting haemoglobin back into the tense state = less affinity for oxygen.

82
Q

How does BPG regulate haemoglobin?

A

It is found in high concentrations in RBCs, when O2 levels are low, BPG levels increase (e.g. in hypoxia or at altitude). BPG interacts with hB to decrease the affinity for O2, so more is released.
BPG binds into the centre space of Hb between beta subunits in the T-state only. Negative charges on BPG interact with positive charges on residues lining the space.

83
Q

What compound is formed when CO2 binds to Hb?

A

carbaminohaemoglobin

This means O2 can’t bind

84
Q

Which 3 factors regulate the uptake of O2 by haemoglobin? Why is it important that these act at different sites?

A

pH (H+); BPG, CO2

They act at different sites so the effects can be additive

85
Q

What is the difference between normal and foetal haemoglobin?

A

Foetal haemoglobin does not have b-subunits, they are replaced with gamma subunits which have a higher affinity for oxygen because it does not bind to BPG as efficiently.

86
Q

Who will win between foetus and mother in a competition for oxygen? Why?

A

Foetus, it has a higher affinity for oxygen because BPG cannot bind as readily to the gamma subunits

87
Q

Give two examples of heamogolbinopathies

A

sickle cell anaemia (alters the outside of haemoglobin so molecules become ‘sticky’)
Beta thalassaemia; not enough beta haemoglobin causes anaemia

88
Q

Why don’t mutations always cause disease?

A

It depends on position of the mutation (are the residues critical?) and type of mutation (conservative or non-conservative)

89
Q

What are conservative and non-conservative substitution mutations?

A

Conservative substitutions maintain the hydrophobic interior of the molecule; the residue is switched for one with similar properties.
Non-conservative substitutions have a major effect on structure and function

IMS topic 1 (7 decks)

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