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Introduction to Medical Sciences > Proteins and Enzymes > Flashcards

Proteins and Enzymes Flashcards

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USMLE® Step 1 flashcards
1
Q

How many coding genes are there in the genome? How many proteins are in the proteome?

A

20,000 genes but around 200,000 proteins.

This is possible due to alternative splicing and modification of translated polypeptides

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2
Q

What are the common ways of classing amino acids?

A

Size, aliphatic vs. aromatic, polarity, charge

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3
Q

All amino acids are chiral, apart from which?

A

Glycine

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4
Q

How do amino acids exist at physiological conditions?

A

Zwitterions

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5
Q

What is the ‘backbone’ of a protein?

A

The amino acid chain

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6
Q

What are the ‘side chains’ in a protein?

A

The R groups of the amino acids

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7
Q

What is a ‘residue’ in terms of proteins?

A

One amino acid in the protein

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8
Q

Which terminuses are used to display a polypeptide chain. Which side is which?

A

N terminus: on the left
C terminus: on the right
(this is the order of translation)

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9
Q

True or False?

Peptide bonds are only single covalent bonds

A

False
The peptide can exist as a single bond (and allow free rotation) or a double bond caused by the donation of an electron by a carbonyl (hence not allowing free rotation). This has a large influence on protein shape.

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10
Q

At what interval do hydrogen bonds occur between residues to make the secondary structure?

A

Every 4 residues

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11
Q

Describe the structure and properties of alpha helices

A

Right-handed helix, H bonds parallel to axis of helix, side chains extend away from helix, allows some elasticity

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12
Q

Describe the structure and properties of beta pleats

A

May form along the same polypeptide (intrachain) or different polypeptides (interchain), side chains extend above and below, pleats may run parallel or antiparallel to each other, allow no elasticity

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13
Q

What property do amino acids in the centre of soluble proteins have?

A

Hydrophobic (whilst outside has hydrophilic residues)

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14
Q

Name the interactions between residues that form the tertiary structure

A

Disulphide bridges (formed between two thiol groups), electrostatic interactions (form salt bridges), hydrogen bonds, Van der Waals interactions, hydrophobic interactions (repulsion of hydrophobic residues forces them into the centre)

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15
Q

What do molecular chaperones do?

A

Bind to sections of protein to facilitate correct folding

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16
Q

What are chaperonins and what do they do?

A

Large protein chambers that provide the correct environment for folding of the protein

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17
Q

What structures are abundant in insoluble proteins?

A

Beta pleats

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18
Q

What are amyloid diseases? Give an example

A

Diseases caused by abnormal amyloid proteins, such as Alzheimer’s disease. Here, cleavage of amyloid precursor proteins create a toxic fragment (amyloid beta) which accumulates to form plaques that cause cell death

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19
Q

What are prion diseases?

Give an example

A

Diseases caused by abnormal prion protein. The protein becomes infectious. E.g. Creutzfeldt-Jakob disease. Here prion protein mutates, becomes infectious and insoluble aggregates form creating vacuoles in the brain (spongiform encephalopathy)

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20
Q

Does adipose (fat) tissue contain protein?

A

Yes. These tissues contain cells!

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21
Q

What is the role of myoglobin?

A

Stores oxygen

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22
Q

What is the structure of myoglobin?

A

One polypeptide with one haem group. Mostly alpha helical

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23
Q

What is the role and structure of haemoglobin?

A

Oxygen transport. 4 polypeptides; 2 alpha and 2 beta chains each containing one haem group.

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24
Q

What is meant by ‘allosteric’ in terms of Hb?

A

the binding of one oxygen molecule affects the interactions with other subunits

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25
Q

What is the structure of the haem prosthetic group?

A

Iron (II) bonded with 4 coordinate bonds to protoporphyrin IX ring. The Iron (II) has one coordinate bond with the polypeptide chain at the F8 histidine position and another with a potential oxygen molecule

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26
Q

When an oxygen molecule associates to a haem group, there is a change in structure of the Hb molecule. How does this come about?

A

When the oxygen binds, position of the Fe (II) changes and the proximal F8 histidine is pulled in, allowing a distal histidine at position E7 to bond to the oxygen. This causes alpha helices to shift, causing some interchain salt bridges to rupture

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27
Q

Name the two states of a Hb molecule and the affinity for oxygen at each one.

A

T state: No oxygen associated so more salt bridges between subunits. Low affinity.
R state: Fewer salt bridges caused by oxygen association, so haem groups more accessible. High affinity

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28
Q

How does the Bohr effect change the affinity for oxygen of Hb molecule?

A

Lowers the affinity. This occurs at low pH. Here, there are more H+ ions, so more residues act as bases by gaining a H+. This allows more salt bridges to form, stabilising the T state and lowering the affinity for oxygen

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29
Q

What is BPG?

A

Biphosphogylcerate: binds to Hb in the T state. It encourages the Hb to release any remaining associated oxygen, further lowering the affinity of the Hb

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30
Q

True or False?

Carbon dioxide is transported by haem groups on Hb molecules

A

False

Carbon dioxide bonds to residues on the Hb polypeptides, forming carbaminoheamoglobin

31
Q

Does foetal Hb have a higher or lower affinity than adult Hb? Why is this and what causes this difference?

A

HbF has a higher affinity than HbA. This is so that the foetus can upload oxygen across the placenta from the mother’s haemoglobin - so it must have a higher affinity than the mother’s Hb. HbF does not bind BPG as effectively as HbA, so has a higher affinity

32
Q

What is the structural difference between HbF and HbA?

A

HbF: 2 alpha subunits and 2 gamma subunits
HbA: 2 alpha subunits and 2 beta subunits

33
Q

What are the differences between the properties of Hb and Mb?

A

Mb has greater affinity than Hb.
Hb is cooperative (change in structure in response to oxygen association), Mb is non-cooperative
Oxygen affinity for Hb is affected by pH and carbon dioxide, Mb affinity is not

34
Q

What causes sickle cell anaemia?

A

Point mutation in which val replaces glu, forming HbS.. Hb becomes less soluble and polymerises into crystals. This distorts the red blood cells into a sickle shape. Sickle cells have a shorter half life than healthy erythrocytes, causing anaemia

35
Q

What is a sickle cell crisis?

A

When sickle cells cause blockage in capillaries, blocking off blood flow and hence oxygen supply to tissue. This causes pain in the affected area and can last around 7 days (until the cells degrade)

36
Q

What is beta-thalassaemia?

A

A mutation in the gene for the beta subunit of haemoglobin, causing it to be silenced. Less Hb can be syntheses leading to anaemia

37
Q

Why don’t all mutations that cause a change in amino acid sequence of a protein cause disease?

A

1) Position of mutated residue may not have a substantial impact on protein function.
2) The mutation may be conservative (the mutated residue has a similar property to the original one, so won’t cause an issue)

38
Q

Name and describe the role of the 3 types of collagen

A

Fibril-forming: form long fibrils (most common)
Fibril-associated: crosslinks the major fibril-forming collagen
Network-forming: forms a 2D matrix, important in the basal lamina (the foundation for which tissues sit on)

39
Q

In what cell is collagen made? Up to which structure level does this cell process the collagen?

A 
Fibroblasts
Processes procollagen (up to the tertiary structure). The quaternary structure is processed extracellularly
40
Q

What are the 3 residues in collagen? Note: two are modified

What is the repeating unit for the sequence of these residues?

A

Gylcine, Hydroxyproline, Hydroxylysine

(Gly - X - Y)n

41
Q

Describe the structure of procollagen

A

Left-handed helix

Glycine is located in the centre (to allow a tight coil) whilst the hydroxylated residues are on the outside.

42
Q

Describe the structure of tropocollagen (the quaternary structure)

A

Right-handed helix

43
Q

What is the name of the protein that holds procollagen in place whilst the quaternary structure is being processed?

A

Extension peptides

44
Q

What is allysine? How is it formed and what is its role in collagen?

A

A deaminated hydroxylysine residue found in tropocollagen. This forms covalent bonds between tropocollagen molecules to make strong collagen

45
Q

What is Dupuytren’s contracture? How is this treated?

A

A disease caused by excess collagen production, affecting the connective tissue of the hand. Collagenases are used to breakdown the excess collagen.

46
Q

What is osteogenesis imperfecta? What causes it?

A

“brittle bone disease” - where bones easily fracture. Many types caused by different mutations, e.g. one where glycine is substituted for a larger residue so the tropocollagen can’t wind as tightly. This occurs in every tropocollagen molecule, resulting in brittle bone.

47
Q

What is Ehlers-Danlos syndrome? What causes it?

A

A disease of abnormal collagen resulting in fragile, stretchy skin and hyperextendable joints. Caused by mutation in the procollagen genes

48
Q

What is scurvy? What causes it?

A

Vitamin C deficiency. Vitamin C acts as a cofactor of hydroxylases so accelerates the hydroxylation of procollagen residues and hence production of collagen. A deficiency in vitamin C impairs collagen production, causing problems in wound healing, bone formation and capillary structure - resulting in abnormal bleeding

49
Q

State the equilibrium constant (where reactants are A and products are B)
What effect do catalysts/enzymes have on the constant?

A

K = [B]/[A]
No effect. Catalysts speed up the forward and backward reactions, so there is no proportional change and hence no change to K

50
Q

What is an enzyme assay?

A

A procedure for measuring enzyme activity

51
Q

What is the Michaelis constant, Km?

A

The concentration of substrate needed to reach half the reaction velocity (rate). This indicates the affinity an enzyme has for its substrate

52
Q

What is Vmax?

A

The maximum reaction velocity (rate) of a given reaction.

53
Q

True or False?

Half Vmax = Km

A

True

54
Q

What features of the substrate/rate graphs are affected by competitive inhibitors?

A 
Km increased (is extrinsic)
Higher [S] needed to reach the same Km
No change to Vmax (is intrinsic)
55
Q

What features of the substrate/rate graphs are affected by non-competitive inhibitors?

A 
Vmax decreased (is extrinsic)
No change to Km (is intrinsic)
Increasing [S] has no effect
56
Q

What does IC50 measure? What do the values indicate in terms of drugs?

A

Inhibitor concentration needed to knock out half the enzyme activity. This tells us the strength of the inhibitor. Smaller concentration/IC50 means stronger and more effective inhibitor

57
Q

What is blood serum?

A

Blood plasma without platelets

58
Q

What is the isoform of an enzyme?

A

A specific form of an enzyme; specific to one tissue

59
Q

Presence of glutamate-pyruvate transaminase (GPT/ALT), glutamate-oxaloacetate transaminase (GOT/AST) and bilirubin in the blood indicates what condition?

A

Liver failure

60
Q

Bilirubin builds up in the blood due to liver failure. What is this condition called? What molecule is it the by-product of the breakdown of?

A

When it enters the blood, it causes yellowing of the skin. This is jaundice.
It is formed from the breakdown of haemoglobin by the liver

61
Q

Presence of creatine kinase (CK) and lactate dehydrogenase (LDH) in the blood indicates what condition?

A

Acute myocardial infarction (AMI)

62
Q

What is the role of creatine kinase?

A

Phosphorylates creatine. This can convert ADP to ATP, hence creating a storage of ATP for the cell

63
Q

What is the isoform of creatine kinase used by the heart that indicates AMI if present in the blood?

A

CK-MB (1x M and 1x B subunits)

64
Q

What two protein ratios in the blood are used in the diagnosis of AMI?

A

CK-MB:tCK (total CK)

LDH1:LDH2 (should usually be less than 1 but in AMI flips to more than 1)

65
Q

What is the role of lactate dehydrogenase (LDH)?

A

Catalyses both the forward and backward reaction of lactate to pyruvate

66
Q

How many isoforms of LDH are there?

A

5

67
Q

What isoform of LDH is present in the heart? What is significant about this isoform that makes it suitable for use by the heart?

A

LDH-H4 (4x H subunits) or LDH1
Not inhibited by pyruvate so can continuosly facilitate the anaerobic reaction (lactate to pyruvate) even in aerobic conditions

68
Q

What toxic group of compounds are produced when the liver breaks down excess paracetamol?

A

quinone

69
Q

What is the treatment for paracetamol poisoning? How does it work?

A

N-acetly methionine
Encourages the primary mechanism of paracetamol breakdown (excretion by the kidneys) instead of the back up mechanism (formation of quinone by the liver)

70
Q

What is the problem with using N-acetyl methionine to treat paracetamol poisoning? What precautions are taken to limit this?

A

N-acetyl methionine is toxic. The correct dosage is given by measuring the levels of excess paracetamol in the blood. This is done using a bacterial enzyme that converts the paracetamol into p-aminophenol. This reacts with ortho-cresol in the presence of copper ions to form a coloured dye. A spectrophotometer is used to quantify the colour produced which is representative of the excess paracetamol present

71
Q

Glucose levels in the blood can be measured using a biochemical assay. Here, glucose is oxidised, producing hydrogen peroxide. This reacts with chromagen to make a coloured dye. A spectrophotometer is used to quantify the colour which is linear to the glucose level. What colour is the dye?

A

Blue

72
Q

What enzyme is used to convert chromagen to the coloured dye used in assays to measure metabolite concentrations?

A

Compound specific oxidases

73
Q

What enzyme are tumour cells deficient in, meaning that when the substrate is broken down by therapeutic enzymes, the tumour cells cannot synthesise the substrate and hence die?

A

Asparagine synthetase (synthesises asparagine used in DNA synthesis/cell replication)

Introduction to Medical Sciences (2 decks)

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