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Biochemistry Flashcards

1
Q

What is covalent bonding?

A

Sharing of electron pairs

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2
Q

What is ionic bonding

A

Attraction of opposite charges

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3
Q

What is hydrogen bonding?

A

Sharing of a hydrogen atom

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4
Q

What is hydrophobic attraction?

A

Interaction of non polar substances in the presence of polar substances

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5
Q

What are Van de Waals interactions?

A

Interactions of electrons of non polar substances

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6
Q

What is electron negativity

A

The attractive force that an atomic nucleus exerts on electrons

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7
Q

What is the final product of catabolism?

A

Carbon dioxide

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8
Q

Give some examples of mono, di and poly saccharides?

A 
Mono = Glucose, Ribose
Di = Lactose, Sucrose, Fructose and Maltose 
Poly = Glycogen and cellulose
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9
Q

2 laws of thermodynamics?

A

1) Energy is neither created or destryed. When energy is converted the total energy before and after is the same
2) When energy is converted, some of that energy becomes unavailable to do work. No energy transfer is 100% efficient

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10
Q

What is enthalpy?

A

Heat content (H)

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11
Q

What is entropy?

A

Level of disorder (S)

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12
Q

What is the equation for the change in free energy?

A

Delta G = deltaH - TxdeltaS

OR free energy change = (enery of products) - (energy if reactants)

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13
Q

What is an exogonic reaction?

A

Total free energy of the products is less than the total free energy of reactants. Free energy change is negative.
Reactions are fesable and spontaneous.
Drive disease pathways

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14
Q

What is an endogonic reaction?

A

Total free energy of the products is greater than the total free energy of reactants. Free energy change is positive.
Reactions are unfesable and not spontaneous.
Require an energy input

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15
Q

What are the standard conditions for biochemists?

A

T = 298K
1 atmosphere of pressure
1mol/litre concentration of reactnts (except H+)
pH = 7
Standard conditions in the body, the temperature is higher

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16
Q

How can you tell if a reaction is reversible or close to equilibrium?

A

The free energy change should be close to 0

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17
Q

Many cellular processes are unfavourable so how do they happen?

A

Coupling to to a highly favorable process such as ATP hydrolysis (Free energy change = -30kJ/mol)

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18
Q

Why is ATP less stable than ADP?

A

The negative phosphate group charges close together create electrostatic repulsion within the molocule

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19
Q

Where is the utilisation energy stored in ATP?

A

Anhydride bonds between the phosphate groups are high energy bonds

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20
Q

How is ATP regenerated?

A

Creatinine phosphate or 2ADP ATP + AMP

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21
Q

What is metabolism?

A

All the reactions taking place in the body

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22
Q

What is anabolism?

A

Synthesising complex molecules from smaller molecules. Energy consuming

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23
Q

WHat is catabolism?

A

Breakdown of complex molecules into smaller ones. Releases energy
NB: There are some energy consuming steps within catabolic pathways

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24
Q

What type of reactions are used as control points in metabolic reactions?

A

Reactions with large negative free energy changes. Not readily reversible reactions. Controlled by enzymes

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25
Q

Where can hydrogen bonding take place?

A

Covenlent bond between a hydrogen and a more elecronegative atom creates a polarised bond. Bonds tend to be linnear bonds, weaker than covelent bonds individually but strong collectively

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26
Q

What is the hydrophobic effect?

A

When non polar substances are placed in water they are insoluble. There is a strong attraction between water molecules and water excludes the non polar substance

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27
Q

What is a amphipathic molocule and what do they form in water?

A

A molocule with a hydrophobic and a hydrophillic part.

they form Micelles in water keeping the hydrophobic parts hidden inside

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28
Q

With a membrane, proteins that span the bilayer are hydrophobic/ampipathic and proteins on the surface are ampipathic/hydrophillic?

A

Span the bilayer = ampipathic

On the surface = hydrophillic

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29
Q

Proteins are made from L or D amino acids?

A

20 L amino acids (rotate light anticlockwise)

Some D amino acids are found in bacterial cell walls

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30
Q

In an amino acid what is the alpha carbon bound to and what shape is formed?

A

Tetrahedral

NH2, H, COOH, R

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31
Q

What are the 8 non polar/hydrophobic amino acids?

A 
Leucine 
Proline
Alenine
Valine
Methionine
Tryptophan
Phenylalanine
Isoleucine
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32
Q

What are the 7 polar/hydrophilic amino acids?

A 
Glycine
Serine
Asparagine
Glutamine
Cysteine 
Threonine 
Tyrosine
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33
Q

What are the 2 acidic amino acids?

A

Aspartic acid and glutamic acid

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34
Q

What are the 3 basic amino acids?

A

Lysine
Argenine
Histidine

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35
Q

Peptides have a direction- which direction are they read?

A

N terminus to C terminus

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36
Q

Why do peptides have a partial double bond character?

A

Pair of unpaired electrons oscillate across the peptide bond => rotation of the peptde bond is restricted. Peptide bonds are strong, planar and ridgid

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37
Q

What is a zwitterion?

A

An amino acid without a charged side group in a neutral solution with no net charge
Distribution of charge will change as a result of the pH of the surrounding fluid.

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38
Q

How many titratable groups and pKa values do amino acids have?

A

2 of each

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39
Q

What is the term for the pH at which the amino acid has no net charge?

A

The isoelectric pH

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40
Q

Why can proteins act as buffers?

A

Ends and side groups of proteins can be ionised.

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41
Q

How do you measure the strength of an acid?

A

Acid dissociation constant

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42
Q

What is pH?

A

A measure of the amount of protons in solutions

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43
Q

What is a buffer?

A

A soltion to control the pH of a reaction mixture

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44
Q

When does pH=pKa?

A

When the concentration of acid is equal to the concentration of conjugate base

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45
Q

When will buffers resist a change in pH?

A

When the pH is close to their pKa value

46
Q

What is the primary structure of a protein?

A

A sequence of amino acid residues where polypeptides can rotate around bonds to the alpha cardon but not the peptide bond

47
Q

What is the secondary structure of a protein?

A

A hydrogen bonded 3D arrangement of a polypeptide chain which considers the backbone of the polypeptide

48
Q

What are the 3 types of decondary structure of a protein?

A

Alpha helix- right handed hydrogen bond between amino acids 4 residues away
Beta sheets- parallel or antiparralel sheets
Colagen triple helix- 3 left handed helix chains twisted to forma a right handed super helix

49
Q

Which amino acid will cause a right angled bend?

A

Proline

50
Q

What is the most common protein found in humans and where is it found?

A

Collagen- bones and connective tissue. Insoluble in water but soluble in strong alkili

51
Q

WHat is tropocollagen?

A

Repeating X-Y-Gly

where X is any amino acid, Y is proline or hydroxyproline

52
Q

How can a vitamin C defficieny weaken collagen?

A

The enzyme required to hydroxylate proline requires vitamin C (Ascorbic acid). To maintain health you need hydroxyproline so a vitamin C defficieny will weaken collagen

53
Q

What is the tertiary structure of a protein?

A

Arrangement of all amino acids of a polypeptide in space.Fibrous or globular proteins

54
Q

What is a fibrous protein?

A

polypeptide chains organised roughly parallel along a single axis. Long fibres, mechanically strong and insoluble in water and salt solution
Eg. Keratin, collagen, cartilage in bone an dteeth

55
Q

What is a globular protein?

A

proteins folded into a spherical shape.
Soluble in water and salt solutions, form micelles and have lots of alpha helix and beta sheet.
Eg myoglobin, haemoglobin

56
Q

What are the bonds found in tertiary protein structures?

A

Disulphide bonds (redox susceptible)
Electrostatic and hydrophobic attractions
Hydrogen bonds
Complex formation with metal ions

57
Q

When and where is a disulphide bond usually found?

A

Between cyctine aminoacids and its formed in reducing conditions

58
Q

Folding of a protein can occur spontaneously but this is erroneous. What molecules are used to help fold proteins?

A

Chaperones

59
Q

What will denatre a protein structure?

A

Heat: increases vibrations in a protein
pH: electrostatic attraction interrupted
Detergents/urea: disrpt hydrophobic interaction
Thiol agents/reducing agents: Disrupt the disulphide bonds

60
Q

What is myoglobin?

A

A globular protein which stores oxygen in muscles

61
Q

What subunits does haemoglobin contain?

A

2 alpha and 2 beta subunits

62
Q

What happens in stage one of glycolysis?

A

Glucose is trapped and stabalised

63
Q

What are the control points in stage 1 of glycolysis?

A

Only the irreversible reactioncatalysed by hexokinase (controls substrate entry) and phosphofructokinase (controls rate of flow)

64
Q

What happens in stage 2 of glycolysis?

A

2 interconvertable 3 carbon molecules are formed

65
Q

What happens in stage 3 of glycolysis?

A

Generation of ATP

66
Q

What is the contraol point in satge 3 of glycolysis?

A

Pyruvate kinase which controls the product exit

67
Q

What are the products of glycolysis?

A

2 pyruvate, 2NADH + 2H+ and 2ATP

68
Q

What happens if there is no oxygen for respiration?

A

No terminal electron acceptor therefore the electron transport chain and TCA cycle stop. But electrons are dangerous and you must continure to generate ATP
Pyruvate –> lactate catalysed by lactate dehydrogenase and NAD+ is produced to be used in glycolysis for ATP production

69
Q

What ion can be used to neutralise the charge on lactate?

A

Ca++

70
Q

Which enzyme catalyses the pyruvate –> lactate reaction?

A

Lactate dehydrogenase

71
Q

What are the activators and inhibators of phosphofructokinase?

A

Activators: AMP, Fructose 2-6 bisphosphate
Inhibators: ATP, Citrate, H+ (too much lactic acid produced)

72
Q

When is the cell charges and discharged?

A

Charged when adenylate nucleotides are in ATP

Discharged when adenylate nucleotides are in AMP + Pi

73
Q

Which enzyme catalyses the reaction of 2ADP -> AMP + ATP

A

Adenylate kinase

74
Q

Which cell types require glucose as an energy source?

A

Erythrocytes, renal medulla, retina, brain, all cancer cells

75
Q

WHat can happen to glucose in the cell?

A

Storage
Oxidation through aerobic glycolysis
Fermentation by anaerobic gylcolysis
Oxidation through the pentose phosphate pathway

76
Q

What is involved in the pentose phosphate pathway?

A

Ribose 5 phosphate
pre-cursor for nucleotide synthesis and DNA repair
Essential for growth

77
Q

How is glucose transported into cells

A

Na+/glucose symporters

Passive facilitated diffusion glucose transporters (GLUT 1-5)

78
Q 
Where are the fallowing found?
GLUT1 =
GLUT2 =
GLUT3 =
GLUT4 =
GLUT5 =
A 
GLUT1 = Brain (low Km)
GLUT2 = Liver and beta cells of the pancreas (high Km)
GLUT3 = Brain (low Km)
GLUT4 = Muscle and adipose tissue
GLUT5 = Small and large intestine (fructose transport)
79
Q

What is the Warburg effect?

A

Upregulation of anaerobic gylcolysis
Cancer cells produce energy by a high rate of glucose metabolism to lactate as cancer cells have a hexokinase with a low Km

80
Q

What are the advantages and disadvantages of the Warburg effect for cancer cells?

A

+ Rapid energy production
+ Supports other pathways needed for nucleotide synthesis
+ Supports rapid proliferation
+ tumour core is very hypoxic or anoxic so anaerobic is important
- Produces H+ and lactate
- very inefficient ATP synthesis
- High glucose consumption demand- cancer patients loose weight

81
Q

How can 2 deoxyglucose be used to treat cancer patients?

A

Initially phosphorylated to 2 deoxyglucose-6-phosphate which competitively inhibits phophoglucose isomerase and non competitively inhibits hexokinase.
Blocks further metabolism of glucose-6-phosphate

82
Q

How can 3 bromopyruvate be used to treat cancer patients?

A

Competitive inhibator or glyceraldehyde-3-phosphate dehydrogenase. Prevents production of 1,3-bisphosphate

83
Q

How can Dichloroacetate be used to treat cancer patients?

A

Promotes conversion of lactic acid to pyruvate by re-engaging mitochondrial metabolism and then slows the glycolytic rate.
Cells can no longer sustain nucleotide synthesis.
The ribose-5-phosphate production through pentose phosphate pathway is inhibited

84
Q

What is PDC?

A

Pyruvate dehydrogenase complex

85
Q

What happens during the PDC reactions?

A

1) Pyruvate is decarboxylated and CO2 is formed with hydroxyethyl TTP
2) Hydroxyethyl group is transferred to lipoic acid and oxidises to form acetyl dihydrolipoamide
3) Acetyl group is transferred to CoA
4) Dihydrolipoamide is reoxidised to form lipoic acid

86
Q

What can inhibit the PDC reactions?

A

ATP, Acetyl CoA and NADH

87
Q

What are the intermediates in the TCA cycle?

A 
A Clown In Kilimanjaro Sings Songs For Money Only
Acetyl CoA
Cirtate
Isocitrate
Ketoglutarate (alpha)
Succinyl-CoA
Succinate
Fumerate
Malate
Oxaloaccetate
88
Q

Where are the 3 control points of the TCA cycle?

A

1) Oxaloaccetate –> Citrate (citrate synthase)
Inhibited by ATP, NADH, succinyl CoA and citrate
2) Isocitrate –> alpha ketoglutarate (Isocitrate dehydrogenase)
Inhibited by ATP and NADH and stimulated by ADP and NAD+
3) Alpha ketoglutarate –> Succinyl CoA (alpha ketoglutarate dehydrogenase)
Inhibited by ATP and NADH and Succinyl CoA

89
Q

Where does the TCA cycle occur and why?

A

Mitochondrial matrix as it contains all the enzymes for the TCA cycle except succinate dehydrogenase which is integrated into the inner mitochondrial membrane

90
Q

How does pyruvate enter the mitochondrial matrix?

A

H+ gradient from cyctol to matrix and there is a H+/pyruvate symport protein which uses facilitated diffusion. NB: Pi also enters coupled with H+.

91
Q

Can pyruvate be converted back to accetyl CoA?

A

No the reaction is irreversible

92
Q

What are the products of the TCA cycle?

A

2CO2
3NADH + 3H+
1FADH2
1GTP (substrate level phosphorylation)

93
Q

What is the yield from one glucose at the end of the TCA cycle?

A

6ATP, 10H+, 10NADH, 2FADH2 and 6CO2

94
Q

What is PDC deficiency?

A

X linked neurological disease in children. Gene for pyruvate dehydrogenase is on the X chromosome. Female carriers get adolescent onset and males result in a still birth

95
Q

What are the symptoms of PDC deficiency?

A

Poor muscle tone and lack of coordination, retardation and seizures, persistent lactic acidosis and respiratory problems

96
Q

What is fumerase deficiency and Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC)

A

Defect in fumerase => multiple system benign and malignant tumours particularity in the kindey

97
Q

In the respiratory chain their are 4 multisubunit complexes. Where do electrons form NADH and FADH2 enter?

A

NADH enter at complex 1 and FADH2 enter at complex 2

98
Q

In the respiratory chain, do electrons move from higher to lower or lower to higher redox potentials?

A

Higher to lower and the energy released is used to actively transport H+ across the membrane

99
Q

What is the terminal electron acceptor?

A

Oxygen and it is reduced to water

100
Q

What is UQ in oxidative phosphorylation?

A

Ubiquinone co-enzyme Q which is hydrophobic and shuttles rapidly in the membrane

101
Q

What is CytC in oxidative phosphorylation?

A

Soluble protein which contains a haem group as a functional cofactor which contains a FE++ group which can take up ad release electrons

102
Q

In oxidative phosphorylation Transport of electrons through the respiratory chain is coupled to what?

A

Transport of H+ from the matrix to the intermembrane space. Requires energy released form electrons moving from a higher to lower redox potential

103
Q

Which 3 multi subunit complexes pump H+ in oxidative phosphorylation?

A

1, 3 and 4

104
Q

What happens when there are more protons in the intermembrane space than the matrix?

A

Protons diffuse back into the matrix and this is coupled to ATP synthesis.

105
Q

NADH is produced in glycolysis but cannot cross the mitochondial membrane for oxidative phosphorylation. How is this overcome?

A

Malate- Aspartate shuttle

1) NADH is used to generate malate from oxaloacetate in cystol
2) Malate transporters transfer malate into the mitochondrial matrix
3) Malate conversion to oxaloacetate in the TCA cycle generates NADH in addition to the malate that arises from fumerate.

106
Q

What does a negative and positive edution potential imply?

A

Negative implies a lower affinity for electrons than hydrogen (reducing agent)
Positive implies a higher affinity for electrons than hydrogen (oxidising agent)

107
Q

What makes up ATP synthase?

A

F1 subunit- round and protrudes into the mitochondrial matrix
F0 subunit is a hydrophobic complex in the inner membrane
a, b, alpha, beta and delta form the stator
c, gamma and epsilon form the rotor (mostly F0)
Flow of protons turns the rotor and a conformational change leads to ATP synthesis

108
Q

What substances can inhibit oxidative phosphorylation?

A

Cyanide, azide and CO inhibit the transfer of electrons to oxygen meaning no proton gradient is formed and no ATP synthesised

109
Q

What happens with uncoupling of electron transport and phosphorylation?

A

Protons return to the matrix via UCP uncoupling protein rather than ATP synthase
=> non shivering thermogenesis and maintains body temperature in hibernating mammals and newborns.
Brown adipose tissue contains UCP. This proton leas consumes oxygen and generates heat and requires fatty acids. ?Obesity therapy

110
Q

What is the P/O ratio?

A

Number of molecules of Pi incorporated into ADP per atom of oxygen used

111
Q

What is the P/O for NADH and FADH2?

A

NADH is 2.5 and FADH2 is 1.5

112
Q

How many ATP are generated through 1 glucose in aerobic respiration?

A

30-32

Principles (12 decks)

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