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Semester 1 > MGD > Flashcards

MGD Flashcards

0
Q

When pH>pK which form of an acid forms the dominant?

A

De protonated

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1
Q

Define pK

A

The stronger the tendency of an acid to dissociate, the lower the pK value

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2
Q

When pH<pK which for of an acid takes the dominant?

A

Protonated

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3
Q

What are the 3 classes of amino acids based upon charge?

A

Nonpolar hydrophobic
Polar, uncharged, hydrophilic,
Polar, charged, hydrophilic,

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4
Q

What are the 2 classes of amino acids based upon structure? Give an example of each

A

Ring = Aromatic eg tyrosine

Without a ring = aliphatic eg lysine

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5
Q

Give 2 examples of positively charged amino acids.

A

Lysine, Arginine, Histadine.

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6
Q

Give 2 examples of negatively charged amino acids.

A

Aspartate, glutamate.

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7
Q

Give an example of a non polar amino acid.

A

Valine

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8
Q

Give an example of a polar, uncharged amino acid.

A

Serine

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9
Q

Define pI

A

The isoelectric point

pH at which the protein has no overall charge.

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10
Q

Which type of charge is dominant in amino acids making up an acidic protein?

A

Negative. Low pI

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11
Q

Which type of charge is dominant in amino acids that form a basic protein?

A

Positive. High pI

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12
Q

What type of bond forms between two amino acids?

A

Peptide bond

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13
Q

When drawing a polypeptide, what orientation is it drawn?

A

Trans, hence Carbonyl O and amine H are on opposite sides.

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14
Q

What is an amyloidose?

A

Improper folding of tertiary structure of proteins.

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15
Q

What is the name when the polypeptides are the same in quarternary strucure?

A

Homomeric

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16
Q

What is the name when the polypeptides are different in quarternary strucure?

A

Heterogenous

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17
Q

What type of structure is found in fibrous proteins?

A

Repeating primary structure.

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18
Q

What types of proteins have several secondary folding structures?

A

Globular

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19
Q

What is the pitch and number of amino acids per turn of an alpha helix of a polypeptide. Which direction does it turn?

A

0.54nm
3.6 amino acids per turn
Right hand

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20
Q

What type of amino acid acts as a helix fixer? Eg?

A

Small hydrophobic amino acids, eg Ala + Leu

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21
Q

Which two amino acids act as helix breakers and why?

A

Pro - no rotation around N-C

Gly - small R group supports other conformations

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22
Q

What are the two states of deoxyhaemoglobin? Which has the higher affinity for oxygen?

A

The tense and relaxed state.

R state has a higher affinity for oxygen

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23
Q

What is the full name for BPG?

A

2,3 bisphosphoglycerate.

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24
Q

What does BPG do to haemoglobin. Curve effect?

A

Decreases its affinity for oxygen, curve shifts to the right.

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25
Q

Describe the Bohr effect.

A

CO2 and H+ causes the affinity of haemoglobin to decrease, hence curve shifts to the right.
More offload of oxygen at actively restoring tissues.

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26
Q

What inheritance pattern is displayed by sickle cell anaemia?

A

Autosomal recessive

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27
Q

What substitution of amino acids is made in sickle cell anaemia?

A

Glutamate to Valine

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28
Q

Why does the substitution of glutamate to valine cause sickle cell anaemia?

A

Valine is hydrophobic and sits on the outcode of the cell. Hence Hb polymerises and forms a sickle shape.

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29
Q

What problems are caused by sickle cell anaemia?

A

Blockage of micro vascular

Premature lysis of RBC leading to anaemia and jaundice.

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30
Q

Describe alpha thalassaemias

A

A decrease or absence of alpha polypeptide chans in Hb
Beta chains form stable terameters with increased affinity for oxygen
Onset before birth

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31
Q

Describe beta thalassaemias.

A

A decrease or absence of beta polypeptide chains in Hb.
Alpha chains cannot form stable tetramers
Symptoms appear after birth.

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32
Q

How do enzymes catalyse reactions?

A

Provide a lower activation energy by:
Increasing local concentration of reactants.
Stabilise the formation of the high energy transition state.

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33
Q

What is the Michaelis-Menton equation?

A

Vmax x [S] / Km + [S]

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34
Q

What does Vmax stand for?

A

The maximum rate of reaction when the enzymes are saturated with a substrate.

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35
Q

What does Km stand for?

A

The concentration of a substrate that gives 1/2 Vmax

The Michaelis constant.

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36
Q

What effect does non-competitive inhibiton have on Km and Vmax?

A

Reaction will not reach Vmax

No change to Km

37
Q

What effect does competitive inhibition have on Vmax and Km?

How is this overcome?

A

Km increases
No effect on Vmax
Can be over come by adding more substrate

38
Q

Describe allosteric modification.

A

Enzymes with more then 1 subunit, when substrate is bound to one active site, then this will enhance/disrupt substrate binding at another active site.

39
Q

Give an example of allosteric inhibition and activation in glycolysis.

A

Phosphofructo kinase is:
Activated by AMP
Inhibited by ATP, citrate and H+

40
Q

Describe the main method of covalent modification of enzymes.

A

A large, charged phosphate group is added to an amino acid in the protein, hence disrupting its structure.
Added by kinase enzymes
Removed by phosphotase enzymes.

41
Q

Describe proteolytic activation of enzymes.

A

Enzymes are secreted as inactive precursors (zymogens).

These enzymes are cleaved by protease enzymes to activate them.

42
Q

Define a zymogen.

A

An inactive precursor enzyme.

43
Q

Describe an enzyme cascade.

A

When enzymes activate other enzymes, ie activation of zymogens.

44
Q

What is the precursor of pepsin?

A

Pepsinogen

45
Q

What is the enzyme formed from trypsinogen?

A

Trypsin

46
Q

What is the precursor enzyme of elastase?

A

Proelastase

47
Q

What factor is activated by the intrinsic pathway of the clotting cascade?

A

Factor XII

48
Q

What factor is activated by the external pathway of the clotting cascade?

A

Factor III

49
Q

What is the first factor that the intrinsic and extrinsic pathways of the clotting cascade have in common?

A

Factor X

50
Q

What zymogen is activated by factor X in the clotting cascade and hence what enzyme is formed?

A

Prothrombin to Thrombin

51
Q

What zymogen is activated by Thrombin in the clotting cascade and hence what enzyme is formed?

A

Fibrinogen to fibrin

52
Q

What enzyme provides positive feedback in the clotting cascade?

A

Thrombin

53
Q

How does fibrin produce a clot?

A

It forms a fibrin mesh, as father cleavage globular domains are exposed and so bind together. Cross linking then occurs between the polymers between lysine and glutamine

54
Q

Which factor has a defect in haemophilia a?

A

Factor VIII

55
Q

What are the methods of regulation in the clotting cascade?

A

Inactive zymogens at low concentration.
Enzyme cascade.
Localisation of clotting.
Feedback by thrombin

56
Q

What is the relevance of Gla and Ca2+ in the clotting cascade?

A

Some glutamate in factors have a carboxyl group added to them. This will bind to Ca2+. Ca2+ binds to platelets, ie the area of damage. Hence localisation of the factors.

57
Q

How is the clotting cascade stopped, and the clot removed?

A

Dilution of clotting factors by blood flow and the liver.
Anti thrombin III is activated by heparin.
Protein C is activated by thrombin binding to endothelial receptors. This protein degrades factors by stimulating proteases hence fibrinolytic.

58
Q

How many rings do purines have?

A

2

59
Q

How many rings does pyrimadines have?

A

1

60
Q

What are the purine bases?

A

Adenine and guanine.

61
Q

What are the pyrimadines?

A

Cytosine, Thymine and Uracil.

62
Q

What nucleotide base binds to Adenine? How many hydrogen bonds are formed?

A

Thymine, 2

63
Q

What nucleotide base binds to Guanine? How many hydrogen bonds are formed?

A

Cytosine, 3

64
Q

How many hydrogen bonds between Cytosine and Guanine?

A

3

65
Q

How many hydrogen binds between adenine and thymine?

A

2

66
Q

What group is free at the 5’ end of a DNA helix?

A

Phosphate

67
Q

What group is free at the 3’ end of a DNA helix?

A

Hydroxyl

68
Q

What type of bond is formed between nucleotides?

A

Phosphodiester bonds

69
Q

What is an RNA stem loop?

A

When RNA loops back on itself and hydrogen bonds form between complimentary bases, hence 1 strand is anti parallel to the other eg tRNA

70
Q

What is the pitch of DNA double helix?

A

0.34nm

71
Q

How many base pairs make up a full revolution of a DNA helix?

A

10

72
Q

What is the significance if purines and pyrimadines being planar and unsaturated?

A

They can lie ontop of each other well ie less space required in the DNA helix

73
Q

What are the two grooves in a DNA helix?

A

Major and minor

74
Q

Describe a nucleosome.

A

DNA wound around a charged his tone core.

75
Q

Describe a solenoid.

A

Nucleosome a coiled to form solenoid structures.

76
Q

Which form of chromosome is condensed and the genome is not expressed, hence it can’t be replicated?

A

Mitotic chromosome.

77
Q

Which form of the chromosome is decondensed, the genome is expressed and so can be replicated?

A

Interphase chromosome (chromatin)

78
Q

Describe the three main processes of initiation of DNA replication.

A

Recognition of an origin of replication.
DNA is unravelled by helicase.
Primase forms a primer of dNTPs.

79
Q

What is the full name of dNTPs?

A

Deoxyribonucleic triphosphate.

80
Q

What occurs in the elongation stage of DNA replication?

A

DNA polymerase adds dNTPs to an already existing chain.

81
Q

In which direction does DNA polymerase form new Polynucleotides? What is the name of the segments that are formed due to this?

A

5’ to 3’

Okazaki fragments.

82
Q

What enzyme binds Okazaki fragments together?

A

DNA ligase.

83
Q

What is the name of the polynucleotide strand comprised of Okazaki fragments?

A

The lagging strand.

84
Q

What is required for DNA polymerase, DNA primate, DNA ligase and DNA helicase all to work?

A

ATP

85
Q

What enzyme recoils the polynucleotide chains after DNA replication has occurred?

A

Helicase

86
Q

What occurs the the phase G1

A

Cell growth

87
Q

What occurs in the S phase of a cell?

A

Replication of DNA

88
Q

What occurs in the G2 phase of a cell?

A

Checking of polynucleotide sequences, preparation to divide.

89
Q

What occurs in the M stage of a cell?

A

Cell division.

Semester 1 (2 decks)

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