Biochemistry Flashcards
1
Q
What charge is the N-terminus?
A
Positively charged
2
Q
What charge is the C-terminus?
A
Negatively charged
3
Q
What is defined as the start of the protein molecule?
A
The N-terminus
4
Q
What is the meaning of a zwitterion?
A
Has one of each charge but no net charge
5
Q
How much more common is trans than cis?
A
1000x
6
Q
Why is a peptide bond rigid?
A
Because it has a partial double bond character
7
Q
Which isomers are found in proteins?
A
L-isomers
8
Q
How can proteins propagate disease?
A
Two beta sheets can stick together
9
Q
Which protein is missing in cystic fibrosis?
A
Cystic fibrosis transmembrane regulator protein
10
Q
Which protein is missing in muscular dystrophy?
A
Dystrophin
11
Q
Which protein is missing in phenylketonuria?
A
Phenylalanine hydroxylase
12
Q
Which protein is missing from haemophilia?
A
Blood clotting ’factor’ proteins
13
Q
Which protein is missing in cancer?
A
Tumour suppressor genes
14
Q
Which protein is missing in type 1 diabetes?
A
Destruction of insulin producing cells needs insulin replacement therapy
15
Q
Name some structural proteins?
A
Silk-beta pleated sheet design
A-keratin
Collagen
16
Q
What is the largest protein known?
A
Titin
17
Q
What are the two structural groups of proteins?
A
Fibrous and globular
18
Q
Name 2 neuraminidase inhibitors
A
Tamiflu and relenza
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
20
Q
What is the equilibrium constant?
A
The concentration of products over reactants
21
Q
What is proximity?
A
Substrate molecules close together
22
Q
What is orientation?
A
Substrates have correct relative orientation
23
Q
What is strain/distortion?
A
Binding puts strain on bond making it easier for reaction to occur
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
25
What does Km measure and what are its units?
Measures the stability of the ES complex and is in units of concentration (M)
26
What are irreversible inhibitors?
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
27
Name some irreversible inhibitors
Aspirin, penicillin
28
What is uncompetitive inhibition?
Occurs with multisubstrate reactions
Km decreases
Vmax decreases
29
How does non competitive inhibition affect Km and Vmax?
Km is unaltered
Vmax is decreased
30
Name some examples of competitive inhibitors
Tamiflu, acarbose, statins
31
How do competitive inhibitors affect Km and Vmax?
Km increased
Vmax remains unchanged
32
Which type of interactions require ion exchange chromatography?
Charge interactions
33
What is reverse phase/hydrophobic interaction chromatography for?
Hydrophobicity
34
What is gel filtration for?
Size
35
What is affinity chromatography for?
Specific binding
36
What is eluting
When molecules leave the column
37
How to do ion exchange chromatography
Increase salt concentration of solvent or change pH
38
How to do hydrophobic chromatography
Increase hydrophobicity of solvent
39
How to do affinity chromatography
Add free ligand - change solution conditions
40
How to do size exclusion chromatography
Just time/volume dependent
41
What is an ester?
Condensation of acid and alcohol
42
What is an anhydride?
Condensation of two acid molecules
43
What is resonance?
Delocalisation of electrons
44
What is ATP synthesis coupled to?
Energy generating processes
45
What is ATP hydrolysis coupled to?
Energy requiring processes
46
When are phosphoanhydride bonds important?
In energy transfer by ATP
47
Functions of DNA
Genetic code
Storage within the cell
Accessibility for transcription
Replication
Meiosis
Genome integrity
48
What does the 5’ end carry?
Free phosphate
49
What does the 3' end carry?
Free hydroxyl
50
How much more stable is DNA than RNA?
> 100x
51
How do DNA and RNA react to hydrolysis?
-DNA resistant to hydrolysis
-RNA vulnerable to hydrolysis
52
How do DNA and RNA deal with information?
-DNA long-term storage of information
-RNA temporary transfer of information
53
How many hydrogen bonds between A and T?
2 (10kJ/mol)
54
How many hydrogen bonds between A and C?
3 (15kJ/mol)
55
What are Chargaff's rules?
1. For a particular species: [A]=[T] and [G]=[C]
2. [A]+[T]/[G]+[C] varies between organisms
56
What are the double helix dimensions?
-One turn of helix = 3.4nm
-10 base pairs per turn
-Rise per base = 0.34nm
-Helix diameter = 2nm
57
Characteristics of major groove
-22Å wide
-Information rich
58
Characteristics of minor groove
-12Å wide
-Information poor
59
Function of topoisomerase
Catalyses relaxation of supercoiled DNA
60
Function of topoisomerase 2
Catalyses untangling of DNA duplexes
61
What are Okazaki fragments?
A significant proportion of newly synthesised DNA exists as small fragments
62
Summarise pre-priming and primase
DnaA (initiator), DnaB (helicase), DnaC (control), DnaG (RNA primase)
63
Why must damage to DNA be repaired?
To ensure the integrity of the DNA molecule, large complexes of enzymes required for repair
64
Two types of termination
Factor independent and rho dependent
65
What is the primary sigma factor?
Sigma 70
66
How is transcription primarily controlled?
Regulating the initiation of transcription
67
How can transcription initiation be regulated?
Negative regulatory factor called depressors or by positive acting factors called activators
68
What is an operon?
A cluster of genes under the control of a single promoter
69
When doer high transcription of lac structural genes occur?
When lactose is present and glucose is absent
70
What are aminoacyl tRNAs?
tRNAs joined to amino acids
71
What structure does B-DNA form?
Double helix
72
What technique involves running proteins across a pH gradient?
Iso-electric focusing
73
What is the nature of the forces between stacked bases in dsDNA
Hydrophobic interaction
74
What bond links the nucleotides in the DNA chain?
Phosphodiester bond
75
Which carbon defines the D or L configuration of glucose
Carbon 5
76
At a low _________, the velocity of the reaction is directly proportional to [S]
Substrate concentration
77
What is the normal conformation of a pyranose sugar ring?
Chair
78
R-group interaction is initially involved in what level of protein structure?
Tertiary
79
What technique involves prior treatment of proteins by heating with mercaptoethanol?
SDS-PAGE
80
Which amino acid does not have D and L optical isomers?
Glycine
81
Which carbon has an axial hydroxyl in B-D-galactose?
4
82
Why is RNA less stable than DNA?
The proximity of an OH group to the phosphodiester bond
83
Why is DNA more stable than RNA?
The lack of an OH group on carbon-2 of the ribose
84
Which gel is best for separating DNA?
Agarose gel
85
Which gel is best for proteins?
Acrylamide
86
Which amino acid is used first in translation?
Methionine
87
Which amino acid is classed as aromatic and non-polar?
Phenylalanine
88
The stereochemistry at which carbon defines whether glucose is a or b?
Carbon 1
89
ATP hydrolysis is favourable due to what process?
Resonance stabilisation
90
Apart from the absolute temperature in°K, what do we need to measure in order to calculate overall change in G?
Equilibrium constant
91
Which amino acid is involved in forming disulphide bridges?
Cysteine
92
How many atoms are there in a pyranose sugar ring?
6
93
Which chemical groups are used in the formation of a peptide bond?
Amino and carboxylic
94
During which technique would you use imidazole in the purification of biomolecules?
Immobilised metal affinity chromatography
95
Define pK
The pH at which half the molecules are ionised and half are not
96
What factors are involved in elongation?
Elongation factors EF-Tu EF-Ts EF-G and GTP
97
What part of the ribosome catalyses peptide bond formation?
Peptidyl transferase which is located in the large ribosomal subunit
98
What factors are required for termination?
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
What are phototrophs?
Energy from sunlight
100
What are autotrophs?
Energy from own stores
101
What are chemotrophs?
Energy from chemical reactions
102
What are heterotrophs?
Energy from different sources
103
What are catabolic pathways?
Reactions which break down
104
What are anabolic pathways?
Reactions which build up
105
How can positive change in Gibb's free energy reactions happen?
-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
Gibb’s free energy equation
G = H - TS
107
Role of GTP
Protein metabolism
108
Role of CTP
Lipid biosynthesis
109
Role of UTP
Carbohydrate metabolism
110
What is glycolysis?
Conversion of glucose to pyruvate
111
3 stages of glycolysis
1. Investment or priming
2. Splitting
3. Energy conservation or yield
112
What is the net gain of energy in glycolysis?
2 ATP for every glucose
113
Describe step 1 of glycolysis (investment/priming)
Phosphorylation of glucose to fructose 1,6 diphosphate takes place. 2 ATPs are used
114
Describe step 2 of glycolysis (splitting)
Fructose 1-6 diphosphate split into 2 3- carbon sugar phosphates
115
Describe step 3 of glycolysis (yield)
Each 3-C sugar phosphate is oxidised by the removal of H, making NADH
116
Fates of pyruvate
-Entry into the citric acid cycle
-Converted to fatty acids
-Converted to amino acids
-Converted to lactate
-Converted to ethanol
117
What is the acronym for enzymes involved in the citric acid cycle?
Organic Acid Chemistry Is a Kangaroo Science Subject For Me
118
What does amphibole mean?
A biological pathway that involves both catabolic and anabolic reactions
119
When is ATP converted to amino acids?
During anabolic growth
120
When is pyruvate converted to fatty acids?
When ATP levels are high
121
What are oxidation and ATP synthesis coupled by?
Transmembrane proton movement
122
What does uneven distribution of protons generate?
A ph gradient and a transmembrane electrical potential that creates a proton-motive force
123
How does carbon monoxide work?
High affinity for Hb reduces amount of oxygen getting to the cells
124
How does cyanide work?
Binds to complex IV and blocks oxidative phosphorylation
125
How does salicylate work?
-Forms pores in the inner membrane
-Protons pass through without generaring ATP
126
What is complex 1?
NADH-Q oxidoreductase
127
What is coenzyme Q?
Carries the electrons from NADH and FADH2
128
What is complex III?
Q-cytochrome c oxidoreductase
129
What is Complex IV?
Cytochrome C oxidase
130
What is hypoglycaemia?
Low blood glucose concentration
131
When does blood glucose concentration decrease?
During starvation, insulin overdose, during and after exercise
132
What is hyperglycaemia?
High blood glucose concentration
133
When does hyperglycaemia occur?
Post prandial, inadequate insulin administration
134
What is gluconeogenesis?
Generation of glucose, occurs 2 hours post prandially
135
Name the sources of carbon for gluconeogenesis
-Pyruvate / lactate
-Glycerol
-Citric acid cycle intermediaries
-Amino acids
136
What are the 2 main sites of glycogen storage?
Liver and muscle
137
What is glycogenesis?
Creation of glycogen from glucose
138
4 steps of glycogenesis
Diversion, activation, polymerisation, branching
139
What does glycogen synthase require?
Glycogenin
140
What is glycogenolysis?
Breakdown of glycogen
141
What are the 2 steps of glycogenolysis?
1. Erosion of chain ends
2. Debranching
142
Symptoms of glycogen storage diseases
Muscle cramp, muscle weakness, general tiredness, hypoglycaemia
143
What is GSD type 0?
Liver glycogen synthase deficiency
144
What is GSD type 1?
Von Gurke's disease
145
What is GSD Type 3?
Cori’s disease
146
What is GSD type 4?
Andersen’s disease
147
What is GSD Type 5?
McArdle's disease
148
How are fats stored?
As triglycerides
149
Where are fats stored?
In white adipose tissue
150
What is the key enzyme controlling fatty acid synthesis?
Acetal CoA carboxylase
151
Where does catabolism of amino acids occur?
In the liver
152
What is alcohol intolerance caused by?
A mutation in aldehyde dehydrogenase
