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Biochemistry Flashcards

1
Q

Covalent bond

A

Strongest. Sharing of electron pairs

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2
Q

Ionic bond

A

Attraction of opposite charges

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3
Q

Hydrogen bond

A

Sharing of H atom

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4
Q

Hydrophobic interaction

A

Interaction of non-polar substances in the presence of polar substances (esp. water)

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5
Q

Van der Waals

A

Interaction of electrons of non-polar substances

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6
Q

Bond energy

A

The amount of energy needed to separate two bonded or interacting atoms under physiological conditions

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7
Q

Phosphorylation

A

addition of a phosphate group

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8
Q

Dephosphorylation

A

Removal of a phosphate group

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9
Q

Acylation

A

addition of C=O

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10
Q

Carboxylation

A

addition of a carboxyl group COOH

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11
Q

Esterification

A

Acid + Alcohol > Ester + water

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12
Q

Hydrolysis

A

Splitting using water. Water added

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13
Q

Oxidation states of carbon

A

alkane > alcohol > aldehyde > acid > CO2

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14
Q

Standard conditions

A

T= 298K, 1 atm, 1 M conc, pH 7

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15
Q

Anhydride bonds are…

A

high energy bonds

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16
Q

Glycolysis

A

breakdown on glucose

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17
Q

Gluconeogenesis

A

making new glucose from non-carbohydrate precursors.

e.g. pyruvate.

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18
Q

Control points

A

Reactions with large -ve deltaG are used a control points

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19
Q

Hydrophobic effect

A

oil and water don’t mix, as oil is non-polar so will not dissolve and results in an ‘oil slick’

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20
Q

Amphipathic

A

both hydrophilic and hydrophobic

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21
Q

Structure of an amino acid

A

Central carbon + COOH + NH2 + H+ + side chain

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22
Q

Peptide bond formation

A

Condensation. CO-NH

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23
Q

Direction of peptide

A

N terminus to C terminus

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24
Q

Zwitterions

A

amino acids without charged side groups. Neutral

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25
Q

Cationic form

A

1+ charge

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26
Q

Anionic form

A

1- charge

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27
Q

Purines

A

A and G double ring

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28
Q

Pyrimidines

A

U T C single ring

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29
Q

Phosphodiester bond

A

Polymerisation. Formed between a free 3’ OH group and 5’ triphosphate. 2 Ps are released

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30
Q

Nucleic acids are only added to the free … end

A

3’

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31
Q

Okazaki fragments

A

short segments so that the lagging strand can be replicated

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32
Q

Replication occurs in which direction?

A

5’ to 3’

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33
Q

What is special about DNA polymerase?

A

It has proof-reading ability and can remove a wrong nucleotide

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34
Q

Splicing

A

removes introns before translation can occur

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35
Q

Free ribosomes make proteins for…

A

the nucleus and mitochondria

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36
Q

Bound ribosomes to rough ER make proteins for…

A

Golgi apparatus, secretion etc.

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37
Q

Glycosylation

A

addition and processing of carbohydrates in the ER and Golgi apparatus

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38
Q

RNA is made by…

A

RNA polymerases

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39
Q

Steps of transcription

A

Detection of initiation sites, DNA chain separation, transcription initiation, elongation and termination

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40
Q

Termination of transcription

A

an enzyme cleaves it

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41
Q

Aminoacyl-tRNA synthetases

A

binds amino acids to their corresponding tRNA molecule

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42
Q

Energy requirements for translation

A

ATP and GTP

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43
Q

Steps of translation

A

Initiation elongation, peptide bond formation, termination

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44
Q

most vitamins functions as…

A

coenzymes

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45
Q

Michaelis constant (Km)

A

Km= [k-1 + k2] / k1

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46
Q

Km

A

the substrate constant is half the maximal reaction rate

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47
Q

Vmax

A

intersection of line with Y axis

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48
Q

Km (graph)

A

intersection with X axis

49
Q

Competitive Inhibition

A

Vmax does not change, Km varies

50
Q

Non-competitive inhibition

A

Vmax varies, Km does not change

51
Q

Allosteric enzymes

A

Sigmoid graph

52
Q

Anabolism

A

synthesis of complex molecules

53
Q

Catabolism

A

breakdown of complex molecules

54
Q

NADH+ + H+ = … and is a … … reaction

A

NAD+ and is a oxidative phosphorylation reaction

55
Q

Fates of glucose

A

storage, Ribose-5-phosphate, lactate, pyruvate

56
Q

Glucose + 2ADP + 2Pi + 2NAD+ >

A

2 pyruvate + 4ATP + 2H2O + 2NADH + 2H+

57
Q

Glycolysis is the…

A

conversion of glucose to pyruvate

58
Q

Control points in glycolysis

A

Hexokinase (controls substrate entry), Phosphofructokinase (controls rate of flow), pyruvate kinase (control product exit)

59
Q

Hexokinase

A

glucose to G6P

60
Q

Pyruvate kinase

A

formation of pyruvate

61
Q

PFK activators

A

AMP and fructose-2,6-biphosphate. Will increase glycolysis if energy is required

62
Q

PFK inhibitors

A

ATP (slow glycolysis if abundant) Citrate (slow glycolysis if abundant) H+ (slows glycolysis if too much lactic acid produced)

63
Q

Energy charge

A

ATP/AMP ratio

64
Q

Fully charged

65
Q

Discharged

66
Q

Adenylate kinase

A

can salvage some energy from ADP forming ATP and AMP

67
Q

Glycolysis gain of ATP, NADH and H+

A

net gain of 2 ATP, gain of 2 NADH and 2H+

68
Q

NADH is used to ferment…

A

pyruvate to lactate

69
Q

NADH is regenerated …

A

in the TCA cycle

70
Q

Warburg effect

A

up-regulation of anaerobic glycolysis in cancer cells

71
Q

Glycolysis reduces NAD+ to

72
Q

How is NAD+ regenerated

A

through the oxidative metabolism of pyruvate

73
Q

Where does the TCA cycle occur

A

the central matrix of the TCA cycle

74
Q

How does pyruvate enter the mitochondria

A

Via the pH gradient (so H+ exchange)

75
Q

Pyruvate to acetyl CoA

A

pyruvate dehydrogenase complex catalyses the oxidative carboxylation of pyruvate to acetyl CoA

76
Q

PDC is regulated by?

A

phosphorylation, it is allosterically regulated

77
Q

Overview of TCA cycle

A

2C + 4C= 6C which is decarboxylated twice. Then the new 4C is oxidised 4 times until the original 4C is produced.

78
Q

Yield from TCA cycle

A

2CO2, 3NADH, 3H+, FADH2, GTP

79
Q

All TCA cycle enzymes are in the matrix except…

A

succinate dehydrogenase which is in the inner mitochondrial membrane, which converts FAD to FADH2

80
Q

TCA cycle control points

A

relate to amount of substrates present and whether there is high or low energy to the cycle will speed up or slow down

81
Q

After glycolysis and TCA cycle net yield is

A

4 ATP, 10 NADH, 10H+, 2FADH2, 4CO2

82
Q

Electrons from NADH and FADH2 are used for..

A

oxidising O2 to H2O

83
Q

How does NADH get into mitochondria

A

using malate-aspartate shuttles, then is regenerated on the other side as part of the TCA cycle

84
Q

Phosphoryl transfer potential

A

free energy change for the hydrolysis of ATP

85
Q

Electron transfer potential

A

redox potential (reduction potential) of a compound

86
Q

Negative redox potential

A

reduced form of X has lower affinity for electrons than H2.

87
Q

What is the driving force of oxidative phosphorylation?

A

how much energy is released by the reduction of O2 by NADH

88
Q

Two stages of oxidative phosphorylation

A

electron transport and ATP synthesis

89
Q

H+ pump

A

the transfer of electrons along the respiratory chain is coupled to the transport of H+ across the membrane

90
Q

ATP synthase

A

contains the proton channel, where protons flow back to matrix, this channel results in ATP synthesis

91
Q

P/O ratio

A

a measurement of the coupling of ATP synthesis to electron transport

92
Q

The energy for gluconeogenesis is derived from…

A

oxidation of fatty acids released from adipose tissue

93
Q

What is needed for gluconeogenesis?

A

4 liver enzymes and oxaloacetate from TCA cycle

94
Q

Why do we need oxaloacetate?

A

accepts acetyl groups (esp from fat breakdown)

95
Q

Gluconeogenesis stoichiometry

A

uses 4 ATP> 4 ADP, and 2GTP>2GDP and 2 NADH> 2NAD+ etc.

96
Q

The Cori cylce

A

blood delivers lactate to liver, liver converts lactate to glucose, which is released into the bloodstream

97
Q

Fat is required for…

A

energy, essential fatty acids, and fat-soluble vitamins

98
Q

Triglycerides: main energy store form in…

A

adipose tissue

99
Q

Polyunsaturated fatty acids

A

cannot be synthesised in the body, and are essential

100
Q

Fat digestion/absorption

A

Digested to glycerol, fatty acids and monoglycerides. Absorbed into mucosal cell of intestines. Converted into chylomicrons and transported away.

101
Q

Chylomicrons transport

A

enter lymph then bloodstream

102
Q

At muscle and adipose tissue, chylomicrons are attacked and cleaved by…

A

lipoprotein lipases

103
Q

Fatty acid oxidation

A

first have to be converted into CoA derivatives, occurs in cytoplasm and requires energy. Forming- acyl CoA.

104
Q

Carnitine shuttle

A

transports acyl-CoA into mitochondrial matrix by converting it to acyl-carnitine

105
Q

B oxidation

A

Converts Acyl-carnitine into acetyl-CoA to enter the TCA cycle

106
Q

Lipogenesis

A

fatty acid synthesis

107
Q

Lipogenesis

A

Dietary starch> glucose > pyruvate > acetyl CoA > fatty acids > triglycerides

108
Q

Lipogenesis main precursor

A

malonyl coA which is formed from acetyl-CoA by acetyl CoA carboxylase.

109
Q

Fatty acid synthase

A

catalyses synthesis of of saturated long chain fatty acids.

110
Q

Essential role in fatty acid synethsis and degradation

A

acetyl-CoA carboxylase

111
Q

What signals the fed state?

A

Insulin (citrate also stimulates allosterically)

112
Q

What signals the starved state?

A

Glucagon (also adrenaline)

113
Q

Liver produces G3P from…
Adipose tissue produces G3P from…
G3P is required for…

A

glycerol
glucose (only occurs during fed state)
synthesis of triglycerides (involves esterification)

114
Q

Major nitrogen containing excretory molecules

A

urea, uric acid, creatinine and ammonium ions

115
Q

Synthesis of urea

A

transamination, deamination (involves NADH) and urea cycle

116
Q

Amino transferases

A

move the amino group from one molecule to another (keto acids)

117
Q

Major carriers of nitrogen in blood to liver

A

alanine, glutamine

118
Q

Urea cycle

A

requires energy 2ADP and AMP

Principles (4 decks)

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