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PRINCIPLES > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Name the three ways in which glucose is stored and transported. How are the latter two formed?

A

Monosaccharide, disaccharide, polysaccharide. Formed by a/B links

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2
Q

When are disaccharides particularly helpful?

A

When transporting glucose to target cells

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3
Q

In which two main structures may polysaccharides be found?

A

Cellulose and glycogen

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4
Q

What is the equation for Gibbs Free Energy?

A

dG = dH - TdS

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5
Q

Explain the concept of Gibbs Free Energy.

A

If positive (endergonic) the reaction is not favourable or spontaneous. If negative (exergonic) the reaction is favourable and spontaneous.

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6
Q

What is the difference between anabolism and catabolism?

A

Anabolism is addition, catabolism is release. Anabolism requires energy, catabolism releases it.

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7
Q

What is the name of the group of enzymes which phosphorylate ATP?

A

Kinases (ATPases too)

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8
Q

What is the name of the group of enzymes which dephosphorylate proteins?

A

Phosphatases

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9
Q

Describe the relationship between equilibrium constant and Gibbs free energy.

A

If K < 1, dG is more likely to be exergonic

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10
Q

Are hydrogen bonds straight or bent?

A

Straight

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11
Q

What is formed when oil enters water?

A

Micelles

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12
Q

Give the definition of ampipathic.

A

Has both hydrophobic and hydrophillic components

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13
Q

Describe the chemical structure of an amino acid.

A

N terminus (NH2) and C terminus (COOH)

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14
Q

What type of bond is formed when amino acids become proteins?

A

Peptide bonds.

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15
Q

What is the name of the equation which explains ion trapping?

A

Henderson-Hasselbalch

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16
Q

Give the Henderson-Hasselbalch equation.

A

pH = pKa + log ([A-]/[HA])

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17
Q

What is a zwitterion?

A

An ion which has no overall charge, but more than one charged group, so has multiple titres

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18
Q

Name the three types of secondary protein structure.

A

A-helix, B-sheet, collagen triple helix

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19
Q

Describe tertiary structure.

A

Formed by R-group interactions. Fibrous is insoluble and strong, globular is soluble

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20
Q

Describe quaternary structure.

A

Multiple sub-units. If associated with other proteins, can lead to Parkinsons etc

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21
Q

Which amino acids provide turns in B-sheets?

A

Proline, glycine

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22
Q

What is the difference between the sugars in DNA and RNA?

A

DNA - deoxyribose (H), RNA - ribose (OH)

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23
Q

What are the two classifications of bases? Which does each fall into?

A

Purines - A, G. Pyramidines - C, T, U (three pyramid)

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24
Q

In which direction are nucleotides added to a growing DNA strand?

A

5’ to 3’.

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25
Q

What is a nucleoside?

A

A sugar and a base

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26
Q

What is the name of the structure which can bind to nucleotides to prevent further DNA replication/growth?

A

An analogue

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27
Q

Describe the directions of the leading and lagging DNA strands.

A

Leading - 5’ to 3’. Lagging - 3’ to 5’. Okazaki fragments.

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28
Q

What are the three requirements to begin DNA replication?

A

Replication bubble, DNA polymerase, RNA primer.

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29
Q

What is the main difference (excluding structure) between beginning DNA and RNA synthesis?

A

RNA synthesis does not require a primer.

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30
Q

Is DNA replication conservative, semi-conservative, or dispersive?

A

Semi-conservative - One old strand and one new.

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31
Q

How do the main transcription factors begin RNA synthesis?

A

TATA binding protein (TBP) binds to TATA section. TFIID is a general factor

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32
Q

Describe the structure of the end of a new RNA chain being synthesised.

A

A hairpin with a C/G rich area, and a poly U site to terminate transcription

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33
Q

What is the main repair system for RNA synthesis?

A

3’ to 5’ exonuclease

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34
Q

Describe how stress intracellularly can cause formation of protein.

A

Stressor causes formation of stress response elements. Steroid + receptor in cytoplasm bind and cause transcription

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35
Q

Describe how transcription is degenerate.

A

Many amino acids have more than one codon.

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36
Q

Describe how transcription is unambiguous.

A

Each codon codes for only one amino acid

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37
Q

Which codon and amino acid always begin translation?

A

Methionine (Met) - AUG

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38
Q

Describe how pre-mRNA is converted into mRNA.

A

The end is cut and replaced with a poly A chain. G cap is added

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39
Q

Which chemical is responsible for directing aminoacyl-tRNA to the ribosome?

A

EF1alpha

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40
Q

Which chemical is responsible to regenerating EF1alpha?

A

EF-beta-gamma

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41
Q

Describe how tRNA collects the correct amino acid.

A

Aminoacyl-tRNA synthase directs the correct amino acid to the aminoacyl-tRNA

42
Q

Name the three ribosome sites.

A

A - minoacyl, P - olypeptide, E - xit

43
Q

Describe briefly how amino acids bind together in the ribosome, with reference to the three sites.

A

Aminoacyl binds to A site. Amino acid already bound to P site binds to amino acid on A site, releasing the tRNA from the P site. Ribosome shifts right, freeing the A space

44
Q

Name the four base mutations.

A

Missense (swap), nonsense (STOP), silent, addition/deletion (frame shift)

45
Q

Name the four chromosomal mutations.

A

Deletions, duplications, inversions, translocations

46
Q

Proteins produced by free cytoplasmic ribsomes typically end up where?

A

Cytoplasm, nucleus, mitochrondria

47
Q

Proteins produced by bound cytoplasmic ribosomes that are modified (not glycolysed) typically end up where?

A

Membrane, golgi, ER

48
Q

What does glycolysation entail and where would it occur?

A

Carbohydrates/disulfides. Golgi or ER

49
Q

Which condition may be caused by misfolding of glycolysed proteins?

A

Emphysema

50
Q

Which condition may be caused if the golgi fails to sort glycolysed proteins?

A

Mucolipidosisil

51
Q

How do enzymes affect equilibrium rate?

A

Rate at which equilibrium is reached is increased.

52
Q

Describe the pathology of glycogen storage disease.

A

An enzyme deficiency when converting glucose/glycogen to glucose-6-phosphate.

53
Q

What are cofactors and coenzymes?

A

Substances other than the substrate that must be present for enzyme function. Cofactors are metallic, coenzymes are metallic

54
Q

Name the two different types of metallic enzymes.

A

Apoenzyme (no cofactor), holoenzyme (cofactor)

55
Q

Give examples of coenzymes.

A

CoA, NAD, FAD

56
Q

Name the three main proteases.

A

Chymotrypsin, trypsin, elastase

57
Q

What is an isozyme? Give examples.

A

A different form of an enzyme. Lactic acid dehydrogenase, creatine kinase.

58
Q

Give the main form of reversible enzyme activation.

A

Phosphorylation

59
Q

Give the main form of irreversible enzyme activation.

A

Covalent modification (i.e. cutting)

60
Q

Consider the curve for enzymatic conversion [substrate] against velocity. What is [Km]?

A

The concentration of substrate at which rate is 50% of its maximum (Vmax).

61
Q

If an enzyme has a high [Km], is it efficient or not?

A

Not efficient - more is needed for higher rate

62
Q

What is [Km] otherwise known as?

A

The Michaelis constant

63
Q

What is the main formula for [Km]?

A

[Km] = (K-1 + K2)/K1

64
Q

What is the name of the equation set that allows calculation of [Km] and Vmax? What is the name of the graph when this is plotted?

A

Michaelis-Menten, and Lineweaver-Burk plot

65
Q

Why is it important the enzyme hexokinase has a low Km?

A

Must work quickly with the glucose in the blood

66
Q

Compare a normal Lineweaver-Burk plot with one with a competitive inhibitor.

A

Same Vmax (y intercept), competitive has higher gradient

67
Q

Compare a normal Lineweaver-Burk plot with one with a non-competitive inhibitor.

A

Same Km (x intercept), non-competitive has lower gradient

68
Q

Which enzyme sites do inhibitors use?

A

Competitive - orthostatic. Non-comp - allosteric

69
Q

What does a sigmoidal curve indicate?

A

Co-operativaty

70
Q

How does glucose enter the cell?

A

Na+/Glucose symporters (GLUT 1 - 5)

71
Q

Describe the substrate entry reaction in glycolysis. Describe the ATP reaction.

A

Glucose -> glucose-6-phosphate by hexokinase. ATP -> ADP + Pi

72
Q

Describe the rate limiting step of glycolysis.

A

Fructose-6-phosphate to fructose-1,6-biphosphate, by phosphofructokinase

73
Q

Which cancer drug can inhibit hexokinase?

A

2-deoxyglucose

74
Q

Which substances inhibit PFK?

A

ATP, citrate, H+

75
Q

In glycolysis, what is F-1,6-bP converted to?

A

DHAP AND G-3-P

76
Q

Describe what occurs when G3P is converted to 1,3-bPG in glycolysis.

A

2 1,3-bPG are produced. 2 NAD+ are converted to NADH

77
Q

Describe what occurs between the conversion of 1,3-bPG and phosphophenol pyruvate.

A

(2x) ATP produced, 2x H2O produced

78
Q

Which substance can inhibit the conversion of G3P to 1,3-bPG?

A

3-bromo pyruvate

79
Q

Which enzyme converts phosphenol pyruvate to pyruvate? What is the byproduct?

A

Pyruvate kinase - ATP.

80
Q

What are the end products of glycolysis?

A

2 x pyruvate, 2 x NADH, 2 x H2O, 4 x ATP

81
Q

How is pyruvate converted to lactic acid and vice versa?

A

NADH -> NAD+ (loses electron) and vice versa

82
Q

Which substance stimulates the conversion of lactic acid to pyruvate?

A

Dichloroacetate

83
Q

What substance is required to convert pyruvate to intermediates of the CAC?

A

Oxygen

84
Q

Name the intermediates of the CAC.

A

Acetyl CoA -> citrate -> 5C -> succinate -> fumerate -> malate -> oxaloacetate

85
Q

Where does the CAC occur?

A

The mitochondrial matrix

86
Q

Which enzyme converts succinate to fumerate? What is the byproduct?

A

Succinate dehydrogenase. FAD -> FADH2

87
Q

What may be the negative effect of a lack of fumerase?

A

Malignant or benign tumours

88
Q

Which two non-pyruvate substances enter the CAC, and where?

A

Lipids (acetyl CoA), amino acids (5C/fumerate)

89
Q

What are the end products of the CAC?

A

10 NADH, 2 FADH2, 6ATP

90
Q

Describe the purpose of NADH and FADH2 in the electron transport chain?

A

Provide H+ and e-. H+ is pumped into the high concentration H+ inner membrane by e-.

91
Q

What accepts the H+ and e- from the electron transport chain?

A

Oxygen (producing water).

92
Q

How is ATP produced in the electron transport chain?

A

H+ pumped through ATP synthase

93
Q

Describe the structure of ATP synthase.

A

Stator - A, B, alpha, beta

Rator - C, gamma, oopsilon

94
Q

Name the three main components of the malate-aspartate shuttle.

A

Malate -> oxaloacetate -> aspartate

95
Q

What is the main purpose of the malate-aspartate shuttle?

A

To provide NADH in the mitochondria (NADH is oxidised in glycolysis to provide an electron)

96
Q

Describe why pumping H+ through ATP synthase produces energy.

A

Creates a proto-motive force (by difference in pH and voltage)

97
Q

What are green proteins that contain a haem group called?

A

Cytochrome proteins

98
Q

Which two main factors determine ATP production?

A

P/O ratio, malate-aspartate shuttle

99
Q

How many ATP are produced from a single glucose?

A

30-32

100
Q

What is the name of the inner mitochondrial matrix?

A

Cristae

PRINCIPLES (10 decks)

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