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Metabolism Flashcards

1
Q

Draw a basic amino acid

A

Amino group, C, R group, H, Carboxyl group

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2
Q

is there rotation around peptide bonds

A

No

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3
Q

What are the bonding types in peptides

A

hydrogen, peptide, ionic, covalent/disulphide, hydrophobic, van der waals

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4
Q

Why does ionic bonding in peptides arise

A

Electrostatic attraction between charged side chains

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5
Q

Why does hydrogen bonding arise in peptides

A

Between C=O and N-H every 4 amino acids

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6
Q

What are protein domains

A

further folding into a tertiary structure

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7
Q

give the key features of an alpha helix

A

Stabilised by H bonds
Side chains project out
RH helices due to L-AA
Proline causes kinks due to no H bonds

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8
Q

Give the key features of a beta pleated sheet

A

Stabilised by H bonds
C=O and N-H sticks out at right angles
Antiparallel strands

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9
Q

What does warfarin do

A

Causes N-linked glycosilation where a sugar us added to asparagine to make glutamate so the correct conformation is adopted

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10
Q

What are the non-polar amino acids

A

Glycine, Alanine, Proline, Valine

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11
Q

What are the polar Amino acids

A

Cysteine (CH2-SH), Aspargine, Serine, Threonine, Tyrosine, Glutamine

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12
Q

What are the hydrophilic side chain amino acids

A

Lysine (CH2)4-NH3 and Arginine (CH2)3-NH-C-(NH2)2

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13
Q

What are the hydrophobic side chain amino acids

A

Aspartate CH3-CO2 and Glutamate (CH2)2- CO2

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14
Q

Relate ATP to free energy

A

High energy anhydride bonds can be broken with energy (-31kJ/mol)

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15
Q

How do lysozyme work

A

Hydrolyse a 1-4 glycosidic bond between NAG and NAM

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16
Q

What amino acids do lysozyme require

A

Aspartic and glutamic acid

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17
Q

What is the optimum pH for lysozyme

A

5.0 as aspartic acid is deprotonated by glutamic acid is not

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18
Q

Describe/draw the process of lysozyme action

A

diagram

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19
Q

Give the three overall steps of metabolism

A

Digestion - enzymes break down larger molecule to smaller ones
Cellular metabolism I - Oxidation of molecules in the cytosol
Cellular metabolism II - oxidation of molecules generated from CM1 within the mitochondria

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20
Q

Give the process of glycolysis, including enzymes

A

10 step process

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21
Q

What are the three fates of pyruvate

A

Alcoholic fermentation
Lactate generation
Link reaction

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22
Q

Describe alcoholic fermentation

A

Pyruvate is converted to acetaldehyde using pyruvate decarboxylase (-CO2). Then conversion to ethanol using alcohol dehydrogenase

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23
Q

Describe lactate generation

A

Pyruvate is converted to lactate using lactate dehydrogenase

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24
Q

What happens to lactate produced

A

Travels to the liver where it is used to generated pyruvate

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25
Q

When will lactate dehydrogenase levels be elevated

A

Stroke, heart attack, muscle injury

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26
Q

Describe the link reaction

A

Pyruvate is converted into acetyl coA using pyruvate dehydrogenase

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27
Q

Describe the pyruvate dehydrogenase complex

A 
5 co factors and 3 enzymes. 
Pyruvate decarboxylase + TPP
Lipoamide reductase transacetylase + lipoamide
Dihydroxylipoyl dehydrogenase + FAD 
NAD + CoA
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28
Q

describe the pyruvate dehydrogenase complex mechanism

A

Decarboxylation to produce hydroxyethyl TPP
Oxidation and transfers to lipoamide (swinging arm) to produce acetyl lipoamide
Transfer of acetyl to acetyl coA
Regeneration of oxidised lipoamide and FAD, producing NADH

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29
Q

What does TPP deficiency lead to

A

Beri-Beri

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30
Q

What is Beri-Beri caused by

A

TPP deficiency

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31
Q

Compare ATP production by aerobic and anaerobic respiration

A

38 vs 4

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32
Q

How can glucose respiration be used for cancer

A

Tumour cells use a lot of glucose so using radioactively labelled glucose which emits positrons, a PET scan will detect the locations of tumours

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33
Q

Where are the TCA enzymes located

A

Mitochondrial matrix, except succinate dehydrogenase which is on the inner membrane and coupled to ubiquinone

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34
Q

What does one turn of the TCA cycle produce

A

2 CO2
3 NADH
1 FADH2
1 GTP

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35
Q

Describe the TCA cycle

A

process

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36
Q

Describe transamination

A

Transfer of the amine group from an amino acid to a keto acid. Enzyme example = alanine by alanine aminotransferase

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37
Q

What are the two ways NADH is “transported” to the mitochondrial matrix

A

Glycerol phosphate shuttle

Malate aspartate shuttle

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38
Q

Where is the glycerol phosphate shuttle used

A

Brain, skeletal muscle

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39
Q

Describe the glycerol phosphate shuttle

A

glycerol-3 phosphate dehydrogenase transfers electrons to glycerol-3-phosphate which transfers the electrons to FAD, which then passes to co-enzyme Q in the ETC

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40
Q

Where is the malate aspartate shuttle used

A

Liver, kidney, heart

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41
Q

Describe malate aspartate shuttle

A

diagram

42
Q

Compare anabolic and catabolic

A

NADPH to create molecules vs NADH used to break down molecules

43
Q

What is NADPH used in

A

Anabolic reactions
Thymidine synthesis (DNA)
Cholesterol synthesis catalysis

44
Q

How is cancer related to metabolism

A

Cancer cells rely on anaerobic respiration when there is reduced TCA activity and so even in high O2 concentration anaerobic respiration occurs (warburg)

45
Q

What is the evidence for the evolution of mitochondria

A 
can only form from existing mitochondria
circular genome
Own protein-assembly machinery
Antibiotics that affect bacterial transcription affects the mitochondria e.g. streptomycin
First amino acid of transcripts is fMet
46
Q

What is chemiosmotic theory

A

Protons are translocated to the intermembrane space where an electrical potential and pH gradient forms. protons can move back to the matrix through an ATP synthase channel

47
Q

What are the three inner membrane complexes

A

NADH dehydrogenase complex
Cytochrome B complex
Cytochrome Oxidase complex

48
Q

What are the protein transporters

A

Ubiquinone and cytochrome C

49
Q

Where do NADH and FADH2 feed their proteins into

A

NADH feeds into NADH dehydrogenase complex = 3ATP

FADH2 feeds into ubiquinone = 2ATP

50
Q

describe ATP synthase

A

ATP synthase is a multimeric enzyme that consists of F0 and F1. Protons passing through causes rotation which gives transition states with altering affinities for ATP and ADP. Generation or consuming of ATP depends on direction of proton flow

51
Q

What does the F0 unit contain

A

a,b,c units

52
Q

What does the F1 unit contain

A

alpha, beta and gamma

53
Q

Describe the process of ATP synthesis in oxidative phosphorylation

A
  1. proton flow
  2. c subunit (attached to gamma subunit) rotates
  3. alpha and beta remain stationary, being fixed by b
  4. movement causes ATP generation
54
Q

What is the effect of cyanide

A

binds to Fe3+ in cytochrome oxidase, blocking electron flow

55
Q

What is the effect of malonate

A

Competitive inhibitor of succinate dehydrogenase, slowing flow of electrons to ubiquinone

56
Q

What is the effect of oligomycin

A

Inhibits oxidative phosphorylation by binding to the ATP stalk and blocking it

57
Q

What is the effect of DNP

A

proton ionophore that can shuttle protons. DNP uncouples oxidative phosphorylation from ATP production, Increase in temp. and metabolic rate as heat is released from the ETC.

58
Q

What can acetyl coA be used for

A

TCA cycle
Sterols and fatty acid production
Ketone bodies
Protein acetylation

59
Q

Difference between saturated and unsaturated fatty acid

A

unsaturated = double bonds

60
Q

What is the structure of a triglyceride

A

1 glycerol and 3 fatty acid chains held by ester bonds

61
Q

Where are fatty acids stored

A

Stored as triglycerides in adipocytes

62
Q

How much ATP does fat produce

A

129 ATP

63
Q

What are the 4 basic steps of lipid metabolism

A

Conversion to acyl coA
Transport to the matrix
Beta oxidation
Acetyl coA production

64
Q

How is acyl coA produced

A

using Acyl coA synthesise and hydrolysing TWO anhydride bonds from ATP to produce AMP

65
Q

How is acyl coA transported to the matrix

A

Using the carnitine shuttle;e
Acyl is transferred to carnitine by carnitine acyltransferase I
Acyl carnitine is transported through translocate
Reverse occurs in the matrix

66
Q

Describe beta oxidation

A

4 steps: oxidation, hydration, oxidation, thiolysis
acyl coA dehydrogenase forms 3 hydroxyacyl and FADH2
3-hydroxyacyl hydrolase forms L-3hydroxyacyl coA
L-3hydroxyacyl coA dehydrogenase and NADH
beta ketothiolase splits into acyl coA (-2C) and acetyl coA

67
Q

How do you work out how many cycles were needed

A

/2 then -1

68
Q

How many carbons in palmitoyl coA

A

16

69
Q

What is required for acetyl coA to enter

A

balance of beta oxidation and carbohydrate metabolism to produce oxaloacetate

70
Q

What occurs if fat metabolism is greater than carb metabolism

A

Ketone body formation

71
Q

When does ketone body formation occur

A

When fat metabolism is greater than carb metabolism and during fasting

72
Q

Describe the formation of ketone bodies

A

Acetyl coA forms acetoacetyl coA
formation of 3-hydroxy-3methyl glut aryl coA (HMG coA)
formation of acetoacolate
D-3 hydroxybutyrate and acetone

73
Q

What is the basic mechanism of fatty acid synthesis

A

Decarboxylative condensation
Reduction
Dehydration
Reduction

74
Q

Describe decarboxylative condensation

A

Make a malonyl coA from acetyl coA to donate carbons using acetyl coA carboxylase and ATP
binding of malonyl coA to ACP
binding of acetyl coA to ACP
Condensation of Acetyl and malonyl coA to produce acetoacyl coA and releasing CO2

75
Q

What is ACP

A

Acyl carrier protein that acts as a swing

76
Q

After decarboxylative condensation what occurs in fatty acid synthesis

A

Reduction of acetyl coA using NADPH
Dehydration
Reduction using NADPH
After many repeats, hydrolysis of ACP

77
Q

Which enzymes catalyses fatty acid synthesis

A

acetyl coA carboxylase and fatty acid synthetase

78
Q

Compare fatty acid metabolism to synthesis

A

coA vs ACP
FAD/NADH vs NADPH
Matrix vs cytoplasm

79
Q

What is MCAD

A

Medium chain acetyl coA dehydrogenase deficiency
Autosomal recessive disease where one cannot burn fat
Cannot fast and lots of glucose must be taken
Causes SIDS
Detected via heel prick

80
Q

What is primary carnitine deficiency

A

Autosomal recessive disease
Unable to shuttle acyl coA
mutation in the gene that tajes up carnitine
Supplement given (carnitor)

81
Q

How many carbons is cholesterol

A

27C

82
Q

What is the overall mechanism for cholesterol synthesis

A

Make IPP
Condense 6 IPPs
Modification of squalene

83
Q

How is IPP made

A

Combine two acetyl coA to form acetoacetyl coA using beta ketothiolase
Add another acetyl coA to form HMG-coA using HMG-coA synthase
Reduction to form mevalonate using HMG-coA reductase
Sequential phosphorylation and decarboxylation

84
Q

What is IPP

A

Isopentyl pyrophosphate

85
Q

What does statins target

A

Formation of cholesterol by targeting the formation of mevalonate using HMG-coA reductase

86
Q

How is IPP combined

A

IPP and an isomeric form is combined to produce geranyl pyrophosphate (10C) which then forms farnesyl PP (15C).
2 of farnesyl PP are combined to form squalene (30c)

87
Q

Describe cyclization

A

Squalene is converted to lanosterol using cyclase

Lanosterol forms cholesterol (27C) in 19 steps and demethylation

88
Q

What do all 5 steroid hormones derive from

A

Pregnenolone

89
Q

What does cholesterol break down into

A

Glycocholate

Taurocholate

90
Q

What are the key features of bile salts

A

Bile salts are synthesised in the liver and stored int he gall bladder. It is needed for fat and fat soluble vitamin digestion. It is released into the small intestine to emulsify fats

91
Q

Summarise vitamin D production

A

Melanocytes in the skin

7-dehydrocholesterol conversion to pre vitamin D after exposure to UV light. Conversion to vitamin D and calcitrol.

92
Q

What does vitamin D deficiency lead to

A

Ricketts

93
Q

What is the role of lipid rafts

A

In the plasma membrane and they assist in movement of cell surface receptors

94
Q

Describe the process of lipid absorption

A

TAGs broken down into MAGs or DAGs and fatty acids by lipase
Emulsification by bile salts and cholesterol to form a mixed micelle
Mixed micelles past through the gut lining via enterocytes
MAGs and fatty acids reform TAGs
TAGs incorporated into a chylomicron with cholesterol and apoproteins
Drainage into the lymphatic system via a lacteal

95
Q

What is the structure of a chylomicron

A

TAG and cholesterol ester core

Surrounded by free cholesterol, phospholipid and apoproteins

96
Q

Where is lipoprotein lipase located and what is its function

A

Located on capillary endothelial cells in adipose and heavy skeletal muscle. in breaks down TAGs into glycerol and fatty acids

97
Q

What happens to the leftover chylomicron after breaking down by lipoprotein lipase

A

The rest travels to the liver where it forms lipoprotein: cholesterol, low density lipoproteins, high density lipoproteins

98
Q

Compare low density and high density lipoproteins

A

Low density = takes cholesterol from the liver and delivers to peripheral tissue leading to athersclerosis
High density = takes cholesterol from peripheral tissue to the liver

99
Q

What is familial hypercholesterolaemia

A

Receptor mediated endocytosis by LDL receptor in the liver usually. Mutant LDL receptor means the LDL is left in circulation.
Dominant condition
Leads to athersclerosis and heart attacks
Most cases are not from mutation, but from obesity, alcohol, diet and diabetes

100
Q

What is the treatment of hypercholesterolaemia

A

Statins which inhibit HMG-coA reductase

Resins which inhibit absorption of bile salts and cholesterol

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