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year 1 > principles biochemistry > Flashcards

principles biochemistry Flashcards

1
Q

define catabolism

A

breakdown of complex molecules into smaller ones to release energy
exergonic and oxidative
e.g. glycolysis - net gain of 2 ATP

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2
Q

define anabolism

A

synthesis of complex molecules out of smaller ones consuming energy
endergonic and reductive
e.g. gluconeogenesis - 6 ATP used for each 2 pyruvate

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3
Q

what is the formation of collagen

A 
triple helix (3 polypeptide chains- tropocollagen) - form fibrils - form fibres 
very strong structural bonds
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4
Q

what is the most abundant protein in vertebrates

A

collagen

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5
Q

what is collagen used for

A

blood clotting

connective tissue strength

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6
Q

what is the repeating sequence in collagen

A

amino acid - proline/hydroxyproline - glycine

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7
Q

what is scurvy

A

lack of vitamin C leading to a lack of hydroxyproline resulting in weakened collagen

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8
Q

what kind of interactions in protein does pH interfere with

A

electrostatic

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9
Q

what kind of interactions do detergents (urea, guanidine hydrochloride) interfere with in protein

A

hydrophobic

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10
Q

what kind of interactions do reducing agents and thiol interact with in proteins

A

disulphide bonds

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11
Q

what is the 1st law of thermodynamics

A

energy cannot be created or destroyed

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12
Q

what is the 2nd law of thermodynamics

A

when energy is converted between one form and another some of the energy becomes unavailable to do work

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13
Q

as energy is changed from one form to another, entropy increases
true/false

A

true

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14
Q

when is a reaction feasible

A

ΔG < 0

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15
Q

what is ΔG at equilibrium

A

close to 0

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16
Q

why is an exergonic reaction feasible

A

ΔG is negative
the products have less free energy than the reactants
gives out energy

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17
Q

why is an endergonic reaction not feasible

A

ΔG is positive
the products have more free energy than the reactants
requires energy

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18
Q

what is the equation for ΔG

A

ΔG = ΔH - TΔS

ΔS = entropy change
ΔH = enthalpy change
T is in kelvin

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19
Q

what is ΔG

A

change in free energy
(energy of products) - (energy of reactants)
kj/mol

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20
Q

what is the function of ribosomal RNA

A

combines with proteins to form ribosomes where protein synthesis takes place

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21
Q

what is the function of transfer RNA

A

covalently links to amino acids as a transductor molecule to bring them to the growing protein chain
anticodons - 3 nucleotides

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22
Q

what is the function of messenger RNA

A

carries genetic information for protein synthesis

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23
Q

what kind of bond is A-T

A

double hydrogen bond

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24
Q

what kind of bond is C-G

A

triple hydrogen bond

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25
Q

what 2 bases are purines and what does this mean

A

A and G

contain 2 carbon-nitrogen rings

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26
Q

what 2 bases are pyrimidines and what does this mean

A

C T and U

contain 1 carbon-nitrogen ring

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27
Q

what direction does protein synthesis run

A

5’ - 3’

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28
Q

in DNA structure where do phosphodiester bonds form

A

between 3’ OH and 5’ triphosphate

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29
Q

what makes up a nucleoside

A

base + sugar

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30
Q

what makes up a nucleotide

A

base + sugar + phosphate

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31
Q

what enzyme catalyses DNA replication

A

DNA polymerases

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32
Q

how is the leading strand replicated

A

continuously from right to left

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33
Q

how is the lagging strand replicated

A

slightly slower
in short okazaki fragments
5’ to 3’ synthesis in 3’ to 5’

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34
Q

what enzyme joins okazaki fragments

A

DNA ligase

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35
Q

what enzyme unwinds DNA

A

DNA helices
THIIH - pulls a DNA strand down to the RNA polymerase cleft
THIID - holds the other strand in place

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36
Q

what does primase do

A

makes short RNA sequences (primers) complimentary to the template strand that act as a starting point for the DNA polymerase

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37
Q

what is a coupling reaction

A

unfavourable and a favourable reaction are coupled to make the overall reaction feasible

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38
Q

what is the henderson hasselbach equation

A 
pH = pKa + log ( [A-]/[HA] )
pH = pKa - log ( [HA]/[A-] )
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39
Q

what is Ka

A

acid dissociation constant

[H+]{A-]/[HA]

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40
Q

what is the primary protein structure

A

sequence of amino acids

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41
Q

what is the secondary protein structure

A

formation of a backbone (hydrogen bonds)

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42
Q

what is the tertiary protein structure

A

3D structure

fibrous or globular

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43
Q

what is the quaternary structure

A

spatial arrangement of multiple subunits
disulphide bonds hold proteins together
association of non protein groups e.g. haem group

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44
Q

how many types of RNA polymerases do prokaryotic cells have

A

1

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45
Q

how many types of RNA polymerases do eukaryotic cells have

A

3

Pol I, II and III

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46
Q

what do each of the RNA polymerases synthesise

A

Pol II synthesises all mRNA

Pol I and III synthesise only stable RNA

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47
Q

what direction is RNA synthesised in

A

5’ - 3’

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48
Q

what is a promoter sequence that marks the start of a new gene

A

TATA

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49
Q

what is the general transcription factor for all Pol II transcribed genes

A

TFIID - provides a landing site for other transcription factors e.g. RNA polymerase and allows for formation of pre initiation complex

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50
Q

what are enhancers

A

short regions of DNA that can be bound by protein activators to increase likelihood of transcription
looping allows them to come into contact with promoter sequences

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51
Q

what kind of graph is the enzyme activity-pH graph

A

bell curve - relatively sharp decline either side of the optimum pH

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52
Q

what kind of graph is the enzyme activity-temp

A

increases until optimum temp then decreases sharply

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53
Q

how is the degradation of the mRNA prevented during splicing

A

5’ capped with GTP

3’ has a poly A tail added allowing for recognition

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54
Q

how is the degradation of the mRNA prevented during splicing

A

5’ capped with GTP

3’ has a poly A tail added allowing for recognition

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55
Q

how does translation occur

A

anticodons of tRNA form base pairs with codons of mRNA

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56
Q

what is the start codon for translation

A

AUG

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57
Q

what is in the P site

A

the tRNA being translated

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58
Q

what is in the A site

A

the tRNA waiting to be translated

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59
Q

what enzyme catalyses peptide bond formation between amino acids in P and A sites

A

peptidyl transferase

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60
Q

how does termination of translation occur

A

when A site encounters a stop codon

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61
Q

what is held in the E site

A

the empty tRNA

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62
Q

what do free ribosomes in the cytosol make proteins for

A

cytosol
nucleus
mitochondria
(post translational)

63
Q

what do ribosomes on the RER make proteins for

A 
plasma membrane
ER
Golgi
secretion
(Co-translational)
64
Q

what is a polysome

A

structure formed when multiple ribosomes attach to an mRNA sequence which speeds up translation

65
Q

what is meant by the genetic code being
unambiguous
degenerate

A

each codon codes for only one amino acid

many amino acids have more than one codon

66
Q

do catalysts effect the position of equilibrium

A

no - they speed up the rate at which equilibrium is achieved

67
Q

what are apoenzymes

A

enzymes without a cofactor

68
Q

what are zymogens

A

inactive form of enzyme

69
Q

what are metalloproteins

A

contain metal cofactors

70
Q

what is a holoenzyme

A

enzyme with a cofactor

71
Q

what are prosthetic groups

A

tightly bound coenzymes

72
Q

what enzyme synthesises ACh

A

ACh transferase

73
Q

what enzyme breaks down ACh

A

ACh etherase

74
Q

what enzymes carry out phosphorylation

A

protein kinases

75
Q

what enzymes remove a phosphate

A

phosphotase

76
Q

where is GLUT3 found

A

brain

77
Q

where is GLUT 5 found

A

gut

78
Q

what is Vmax

A

maximal rate of a reaction at unlimited substrate concentration
all enzymes are fully saturated

79
Q

what is Km

A

michaelis constant - 50% Vmax

concentration of substrate that gives a 50% maximal reaction

80
Q

what does a low Km mean in terms of affinity

A

low km
only small amount of substrate needed for 50% Vmax
enzyme has a high affinity

81
Q

what is the name of the graph km and Vmax are read off and how are they read

A

lineweaver burk plot
X axis = 1/[s]
Y axis = 1/V
gradient = km/vmax

Vmax - where line crosses Y axis = 1/vmax
Km - where line crosses X axis = -1/km

82
Q

what happens to km and vmax in competitive inhibition

A

v max is unchanged - can be outcompeted by addition of more substrate
km is increased - more substrate needed to have same impact

83
Q

what happens to km and vmax in non-competitive inhibition

A

Vmax is reduced - cannot be out competed as allosteric (bind at different site)
km is unchanged

84
Q

what kind of relationship do allosteric enzymes show

A

sigmoidal

e.g. haemoglobin

85
Q

what kind of relationship do orthosteric enzymes show

A

follow MM kinetics
hyperbolic
e.g. myoglobin

86
Q

henderson Haselbach equations are always answered with what

A

1.

87
Q

give 3 functions of cholesterol (lipid)

A

stability in cell membranes
component of myelin sheath
precursor molecule for steroid hormones, vitamin D and bile acids

88
Q

give 3 functions of triglycerides (lipid)

A

lipid bilayer membranes

highly concentrated energy stores

89
Q

how do you differentiate alpha glucose and beta glucose

A

alpha - H points up, OH points down

beta - OH points up, H points down

90
Q

where does glycolysis occur

A

cytosol

91
Q

what is the net gain of ATP in glycolysis

A

2 ATP (4 produced, 2 used)

92
Q

what is the net gain of ATP in glycolysis

A

2 ATP (4 produced, 2 used)

93
Q

what are the control points in glycolysis

A

1st 3rd and final reactions

highly exergonic so irreversible

94
Q

what enzyme phosphorylates glucose

A

hexokinase

mediates substrate entry

95
Q

what enzyme phosphorylates fructose-6-phosphate

A

phosphofructokinase

mediates substrate movement along pathway

96
Q

what enzyme converts phosphoenolpyruvate to pyruvate

A

pyruvate kinase

mediates exit of product molecules

97
Q

how many NADH + H+ are formed in glycolysis

A

2

98
Q

how is NAD+ regenerated

A

oxidative metabolism of pyruvate

99
Q

how do the 2 NADH molecules formed in glycolysis get from cytosol to matrix

A

malate-aspartate shuttle

100
Q

what happens to pyruvate in anaerobic conditions

A

alcoholic fermentation

lactic acid formation in humans (H+ dissociates to form lactate in solution)

101
Q

what happens to pyruvate in aerobic conditions

A

further oxidised in citric acid cycle

102
Q

what catalyses the formation of acetyl co A from pyruvate

A

Pyruvate Dehydrogenase Complex PDC

103
Q

where are the enzymes of the TCA cycle located

A

matrix

except succinate dehydrogenase which is integrated in the inner mitochondrial membrane (cristae)

104
Q

how do cancer cells achieve a high rate of ATP production

A

possess low Km hexokinase allowing for more rapid entry of substrate

105
Q

after glycolysis + PDC + TCA how many NADH +H+ are formed

A

10

106
Q

after glycolysis + PDC + TCA how many FADH2 are formed

A

2

107
Q

after glycolysis + PDC + TCA how many ATP are formed

A

4

108
Q

after glycolysis + PDC + TCA how many CO2 are formed

A

6

109
Q

what are the steps of glycolysis + PDC + TCA

A 
glucose
2 x pyruvate
2 x acetyl co A
joins with 4C acid to form 6C acid
in cycle reforms 4C acid
2 cycles of TCA per glucose
110
Q

what occurs in the PDC

A

2 x pyruvate to 2 x acetyl co enzyme A
NAD+ –> NADH+ +H+
coenzyme A –> CO2
per pyruvate

111
Q

in TCA cycle how many pairs of electrons are transferred in the conversion of NAD+ to NADH+ H+

A

3

112
Q

in the TCA cycle how many pairs of electrons reduce FAD to FADH2

A

1

113
Q

what is most commonly the 4C acid in the TCA cycle

A

oxaloacetate

114
Q

what is most commonly the 6C acid in the TCA cycle

A

citric

115
Q

what are the steps in glycolysis

A

glucose
fructose-1,6-bisphosphate
2 triose phosphates
2 pyruvate

116
Q

what does each TCA cycle generate

A

3 NADH+H+
1 FADH2
1 GTP
2 CO2

117
Q

where does the TCA cycle occur

A

central matrix then cristae

118
Q

what is the warburg effect

A

up regulation of anaerobic glycolysis in cancer cells - lactic acid fermentation

119
Q

where does oxidative phosphorylation occur

A

in the cristae

120
Q

what is the electron transfer potential

“standard redox potential”

A

how readily a compound donates an electron

121
Q

what is the electron transfer potential

A

measured by redox potential of a compound

122
Q

what does a negative standard redox potential mean

A

reduced form of the compound has a lower affinity for electrons than hydrogen so more likely to donate

123
Q

what does a positive standard redox potential mean

A

reduced form of the compound has a higher affinity for electrons than hydrogen so less likely to donate

124
Q

what is oxidative phosphorylation and what are the two stages

A

the coupling of respiration to ATP synthesis

electron transport and ATP synthesis

125
Q

where do electrons from NADH enter the respiratory chain

A

complex I

126
Q

where do electrons from FADH2 enter the respiratory chain

A

complex II

127
Q

what is the transfer of electrons through the respiratory chain coupled to

A

H+ transport from mitochondrial matrix to inter membrane space

128
Q

how many complexes in the ETC pump H+

A

3/4

1 2 and 4

129
Q

outline the essence of oxidative phosphorylation

A

electrons from NADH and FADH2 are used to reduce O2 to H2O
Their energy is used to pump protons (H+) form the mitochondrial membrane to the inter membrane space
the pH decreases in the inter membrane space and increases in the matrix
protons flow back across the membrane following the concentration gradient
energy of the flow is used to phosphorylate ADP to ATP (ATP synthase)

130
Q

how do CO, cyanide and azide inhibit oxidative phosphorylation

A

inhibit transfer of electrons to O2 so no proton gradient formed so no ATP formation

131
Q

Cyanide is a competitive inhibitor and CO is a non-competitive inhibitor
true/false

A

true

132
Q

how many H+ ions passing through ATP synthase forms 1 ATP

A

4

133
Q

what happens to H+ ions if they don’t enter the ATP synthase protein

A

they join thermogenin (uncoupling protein) producing heat instead of ATP

134
Q

what kind of fat is well adapted for thermogenesis

A

brown fat

135
Q

how many ATP does the TCA cycle yield

A

2 (GTP)

136
Q

how many ATP does one molecule of glucose yield

A

30-32

137
Q

cofactors are usually (metal ions/organic molecules)

A

metal ions

138
Q

coenzymes are usually (metal ions/organic molecules)

A

organic molecules

139
Q

what is the optimum pH of pepsin

A

low pH

140
Q

what is the optimum pH of salival amylase

A

neutral

141
Q

what is the optimum pH of pancreatic amylase

A

alkaline

142
Q

what enzyme is a marker of muscle damage

A

CK (M form)
(B form in brain)
(MB form in heart)

143
Q

what enzymes are markers of liver damage

A

ALT
AST (whole body)
GGT

144
Q

what enzymes are markers of pancreas damage

A

amylase

lipase

145
Q

what enzymes are markers of cardiac damage

A

CK
AST
LDH

146
Q

ATP supplies energy to run for how many seconds

A

4

147
Q

phosphocreatine supplies energy to run for how many seconds

A

15

148
Q

how long does free circulating glucose supply energy for

A

4 minutes

149
Q

how long do glycogen stores last

A

77 minutes

150
Q

how long do fat stores last

A

4+ days

151
Q

what is FiFoATPase

A

proton pore that utilises the energy yielded from the return of protons along their electrochemical gradient in a condensation reaction with ADP and Pi to yield ATP

152
Q

why do rapidly contracting human cells start producing lactic acid?

A

cells have to convert NADH to NAD+

153
Q

what is a partial agonist

A

binds to and activates receptor but only partial efficacy t receptor relative to full agonist

year 1 (45 decks)

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