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Biomedical Science Year 1 > Biochemistry > Flashcards

Biochemistry Flashcards

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1
Q

What charge is the N-terminus?

A

Positively charged

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2
Q

What charge is the C-terminus?

A

Negatively charged

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3
Q

What is defined as the start of the protein molecule?

A

The N-terminus

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4
Q

What is the meaning of a zwitterion?

A

Has one of each charge but no net charge

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5
Q

How much more common is trans than cis?

A

1000x

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6
Q

Why is a peptide bond rigid?

A

Because it has a partial double bond character

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7
Q

Which isomers are found in proteins?

A

L-isomers

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8
Q

How can proteins propagate disease?

A

Two beta sheets can stick together

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9
Q

Which protein is missing in cystic fibrosis?

A

Cystic fibrosis transmembrane regulator protein

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10
Q

Which protein is missing in muscular dystrophy?

A

Dystrophin

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11
Q

Which protein is missing in phenylketonuria?

A

Phenylalanine hydroxylase

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12
Q

Which protein is missing from haemophilia?

A

Blood clotting ’factor’ proteins

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13
Q

Which protein is missing in cancer?

A

Tumour suppressor genes

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14
Q

Which protein is missing in type 1 diabetes?

A

Destruction of insulin producing cells needs insulin replacement therapy

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15
Q

Name some structural proteins?

A

Silk-beta pleated sheet design
A-keratin
Collagen

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16
Q

What is the largest protein known?

A

Titin

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17
Q

What are the two structural groups of proteins?

A

Fibrous and globular

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18
Q

Name 2 neuraminidase inhibitors

A

Tamiflu and relenza

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19
Q

What does neuraminidase do?

A

Removes neuraminidase acid residues from the surface of host cells to ease the release stage of the virus life cycle

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20
Q

What is the equilibrium constant?

A

The concentration of products over reactants

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21
Q

What is proximity?

A

Substrate molecules close together

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22
Q

What is orientation?

A

Substrates have correct relative orientation

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23
Q

What is strain/distortion?

A

Binding puts strain on bond making it easier for reaction to occur

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24
Q

What is the turnover number?

A

The number of substrate molecules that can be converted to product by 1 enzyme molecule in 1 second

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25
Q

What does Km measure and what are its units?

A

Measures the stability of the ES complex and is in units of concentration (M)

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26
Q

What are irreversible inhibitors?

A

Bind irreversibly to enzyme
Usually bind via a covalent bond
Bind to an amino acid side chain at or near the active site
Commonly bind to either ser or cys side chains
Binding permanently inactivated the enzyme
Usually prevents substrate binding

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27
Q

Name some irreversible inhibitors

A

Aspirin, penicillin

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28
Q

What is uncompetitive inhibition?

A

Occurs with multisubstrate reactions
Km decreases
Vmax decreases

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29
Q

How does non competitive inhibition affect Km and Vmax?

A

Km is unaltered
Vmax is decreased

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30
Q

Name some examples of competitive inhibitors

A

Tamiflu, acarbose, statins

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31
Q

How do competitive inhibitors affect Km and Vmax?

A

Km increased
Vmax remains unchanged

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32
Q

Which type of interactions require ion exchange chromatography?

A

Charge interactions

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33
Q

What is reverse phase/hydrophobic interaction chromatography for?

A

Hydrophobicity

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34
Q

What is gel filtration for?

A

Size

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35
Q

What is affinity chromatography for?

A

Specific binding

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36
Q

What is eluting

A

When molecules leave the column

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37
Q

How to do ion exchange chromatography

A

Increase salt concentration of solvent or change pH

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38
Q

How to do hydrophobic chromatography

A

Increase hydrophobicity of solvent

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39
Q

How to do affinity chromatography

A

Add free ligand - change solution conditions

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40
Q

How to do size exclusion chromatography

A

Just time/volume dependent

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41
Q

What is an ester?

A

Condensation of acid and alcohol

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42
Q

What is an anhydride?

A

Condensation of two acid molecules

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43
Q

What is resonance?

A

Delocalisation of electrons

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44
Q

What is ATP synthesis coupled to?

A

Energy generating processes

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45
Q

What is ATP hydrolysis coupled to?

A

Energy requiring processes

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46
Q

When are phosphoanhydride bonds important?

A

In energy transfer by ATP

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47
Q

Functions of DNA

A

Genetic code
Storage within the cell
Accessibility for transcription
Replication
Meiosis
Genome integrity

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48
Q

What does the 5’ end carry?

A

Free phosphate

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49
Q

What does the 3’ end carry?

A

Free hydroxyl

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50
Q

How much more stable is DNA than RNA?

A

> 100x

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51
Q

How do DNA and RNA react to hydrolysis?

A

-DNA resistant to hydrolysis
-RNA vulnerable to hydrolysis

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52
Q

How do DNA and RNA deal with information?

A

-DNA long-term storage of information
-RNA temporary transfer of information

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53
Q

How many hydrogen bonds between A and T?

A

2 (10kJ/mol)

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54
Q

How many hydrogen bonds between A and C?

A

3 (15kJ/mol)

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55
Q

What are Chargaff’s rules?

A
  1. For a particular species: [A]=[T] and [G]=[C]
  2. [A]+[T]/[G]+[C] varies between organisms
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56
Q

What are the double helix dimensions?

A

-One turn of helix = 3.4nm
-10 base pairs per turn
-Rise per base = 0.34nm
-Helix diameter = 2nm

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57
Q

Characteristics of major groove

A

-22Å wide
-Information rich

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58
Q

Characteristics of minor groove

A

-12Å wide
-Information poor

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59
Q

Function of topoisomerase

A

Catalyses relaxation of supercoiled DNA

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60
Q

Function of topoisomerase 2

A

Catalyses untangling of DNA duplexes

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61
Q

What are Okazaki fragments?

A

A significant proportion of newly synthesised DNA exists as small fragments

62
Q

Summarise pre-priming and primase

A

DnaA (initiator), DnaB (helicase), DnaC (control), DnaG (RNA primase)

63
Q

Why must damage to DNA be repaired?

A

To ensure the integrity of the DNA molecule, large complexes of enzymes required for repair

64
Q

Two types of termination

A

Factor independent and rho dependent

65
Q

What is the primary sigma factor?

A

Sigma 70

66
Q

How is transcription primarily controlled?

A

Regulating the initiation of transcription

67
Q

How can transcription initiation be regulated?

A

Negative regulatory factor called depressors or by positive acting factors called activators

68
Q

What is an operon?

A

A cluster of genes under the control of a single promoter

69
Q

When doer high transcription of lac structural genes occur?

A

When lactose is present and glucose is absent

70
Q

What are aminoacyl tRNAs?

A

tRNAs joined to amino acids

71
Q

What structure does B-DNA form?

A

Double helix

72
Q

What technique involves running proteins across a pH gradient?

A

Iso-electric focusing

73
Q

What is the nature of the forces between stacked bases in dsDNA

A

Hydrophobic interaction

74
Q

What bond links the nucleotides in the DNA chain?

A

Phosphodiester bond

75
Q

Which carbon defines the D or L configuration of glucose

A

Carbon 5

76
Q

At a low _________, the velocity of the reaction is directly proportional to [S]

A

Substrate concentration

77
Q

What is the normal conformation of a pyranose sugar ring?

A

Chair

78
Q

R-group interaction is initially involved in what level of protein structure?

A

Tertiary

79
Q

What technique involves prior treatment of proteins by heating with mercaptoethanol?

A

SDS-PAGE

80
Q

Which amino acid does not have D and L optical isomers?

A

Glycine

81
Q

Which carbon has an axial hydroxyl in B-D-galactose?

A

4

82
Q

Why is RNA less stable than DNA?

A

The proximity of an OH group to the phosphodiester bond

83
Q

Why is DNA more stable than RNA?

A

The lack of an OH group on carbon-2 of the ribose

84
Q

Which gel is best for separating DNA?

A

Agarose gel

85
Q

Which gel is best for proteins?

A

Acrylamide

86
Q

Which amino acid is used first in translation?

A

Methionine

87
Q

Which amino acid is classed as aromatic and non-polar?

A

Phenylalanine

88
Q

The stereochemistry at which carbon defines whether glucose is a or b?

A

Carbon 1

89
Q

ATP hydrolysis is favourable due to what process?

A

Resonance stabilisation

90
Q

Apart from the absolute temperature in°K, what do we need to measure in order to calculate overall change in G?

A

Equilibrium constant

91
Q

Which amino acid is involved in forming disulphide bridges?

A

Cysteine

92
Q

How many atoms are there in a pyranose sugar ring?

A

6

93
Q

Which chemical groups are used in the formation of a peptide bond?

A

Amino and carboxylic

94
Q

During which technique would you use imidazole in the purification of biomolecules?

A

Immobilised metal affinity chromatography

95
Q

Define pK

A

The pH at which half the molecules are ionised and half are not

96
Q

What factors are involved in elongation?

A

Elongation factors EF-Tu EF-Ts EF-G and GTP

97
Q

What part of the ribosome catalyses peptide bond formation?

A

Peptidyl transferase which is located in the large ribosomal subunit

98
Q

What factors are required for termination?

A

Release factors interact with STOP codons
-RF1 recognises UAA and UAG
-RF2 recognises UAA and UGA
-RF3.GTP helps RF1 or RF2 carry out termination
-RRF and EF-G promote dissociation of the ribosome

99
Q

What are phototrophs?

A

Energy from sunlight

100
Q

What are autotrophs?

A

Energy from own stores

101
Q

What are chemotrophs?

A

Energy from chemical reactions

102
Q

What are heterotrophs?

A

Energy from different sources

103
Q

What are catabolic pathways?

A

Reactions which break down

104
Q

What are anabolic pathways?

A

Reactions which build up

105
Q

How can positive change in Gibb’s free energy reactions happen?

A

-Increase the temperature
-Increase the substrate concentrations
-Link an unfavourable positive reaction with a favourable negative reaction so that the reaction is overall negative

106
Q

Gibb’s free energy equation

A

G = H - TS

107
Q

Role of GTP

A

Protein metabolism

108
Q

Role of CTP

A

Lipid biosynthesis

109
Q

Role of UTP

A

Carbohydrate metabolism

110
Q

What is glycolysis?

A

Conversion of glucose to pyruvate

111
Q

3 stages of glycolysis

A
  1. Investment or priming
  2. Splitting
  3. Energy conservation or yield
112
Q

What is the net gain of energy in glycolysis?

A

2 ATP for every glucose

113
Q

Describe step 1 of glycolysis (investment/priming)

A

Phosphorylation of glucose to fructose 1,6 diphosphate takes place. 2 ATPs are used

114
Q

Describe step 2 of glycolysis (splitting)

A

Fructose 1-6 diphosphate split into 2 3- carbon sugar phosphates

115
Q

Describe step 3 of glycolysis (yield)

A

Each 3-C sugar phosphate is oxidised by the removal of H, making NADH

116
Q

Fates of pyruvate

A

-Entry into the citric acid cycle
-Converted to fatty acids
-Converted to amino acids
-Converted to lactate
-Converted to ethanol

117
Q

What is the acronym for enzymes involved in the citric acid cycle?

A

Organic Acid Chemistry Is a Kangaroo Science Subject For Me

118
Q

What does amphibole mean?

A

A biological pathway that involves both catabolic and anabolic reactions

119
Q

When is ATP converted to amino acids?

A

During anabolic growth

120
Q

When is pyruvate converted to fatty acids?

A

When ATP levels are high

121
Q

What are oxidation and ATP synthesis coupled by?

A

Transmembrane proton movement

122
Q

What does uneven distribution of protons generate?

A

A ph gradient and a transmembrane electrical potential that creates a proton-motive force

123
Q

How does carbon monoxide work?

A

High affinity for Hb reduces amount of oxygen getting to the cells

124
Q

How does cyanide work?

A

Binds to complex IV and blocks oxidative phosphorylation

125
Q

How does salicylate work?

A

-Forms pores in the inner membrane
-Protons pass through without generaring ATP

126
Q

What is complex 1?

A

NADH-Q oxidoreductase

127
Q

What is coenzyme Q?

A

Carries the electrons from NADH and FADH2

128
Q

What is complex III?

A

Q-cytochrome c oxidoreductase

129
Q

What is Complex IV?

A

Cytochrome C oxidase

130
Q

What is hypoglycaemia?

A

Low blood glucose concentration

131
Q

When does blood glucose concentration decrease?

A

During starvation, insulin overdose, during and after exercise

132
Q

What is hyperglycaemia?

A

High blood glucose concentration

133
Q

When does hyperglycaemia occur?

A

Post prandial, inadequate insulin administration

134
Q

What is gluconeogenesis?

A

Generation of glucose, occurs 2 hours post prandially

135
Q

Name the sources of carbon for gluconeogenesis

A

-Pyruvate / lactate
-Glycerol
-Citric acid cycle intermediaries
-Amino acids

136
Q

What are the 2 main sites of glycogen storage?

A

Liver and muscle

137
Q

What is glycogenesis?

A

Creation of glycogen from glucose

138
Q

4 steps of glycogenesis

A

Diversion, activation, polymerisation, branching

139
Q

What does glycogen synthase require?

A

Glycogenin

140
Q

What is glycogenolysis?

A

Breakdown of glycogen

141
Q

What are the 2 steps of glycogenolysis?

A
  1. Erosion of chain ends
  2. Debranching
142
Q

Symptoms of glycogen storage diseases

A

Muscle cramp, muscle weakness, general tiredness, hypoglycaemia

143
Q

What is GSD type 0?

A

Liver glycogen synthase deficiency

144
Q

What is GSD type 1?

A

Von Gurke’s disease

145
Q

What is GSD Type 3?

A

Cori’s disease

146
Q

What is GSD type 4?

A

Andersen’s disease

147
Q

What is GSD Type 5?

A

McArdle’s disease

148
Q

How are fats stored?

A

As triglycerides

149
Q

Where are fats stored?

A

In white adipose tissue

150
Q

What is the key enzyme controlling fatty acid synthesis?

A

Acetal CoA carboxylase

151
Q

Where does catabolism of amino acids occur?

A

In the liver

152
Q

What is alcohol intolerance caused by?

A

A mutation in aldehyde dehydrogenase

Biomedical Science Year 1 (8 decks)

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