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
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
3
Q
what is the formation of collagen
A
triple helix (3 polypeptide chains- tropocollagen) - form fibrils - form fibres very strong structural bonds
4
Q
what is the most abundant protein in vertebrates
A
collagen
5
Q
what is collagen used for
A
blood clotting
connective tissue strength
6
Q
what is the repeating sequence in collagen
A
amino acid - proline/hydroxyproline - glycine
7
Q
what is scurvy
A
lack of vitamin C leading to a lack of hydroxyproline resulting in weakened collagen
8
Q
what kind of interactions in protein does pH interfere with
A
electrostatic
9
Q
what kind of interactions do detergents (urea, guanidine hydrochloride) interfere with in protein
A
hydrophobic
10
Q
what kind of interactions do reducing agents and thiol interact with in proteins
A
disulphide bonds
11
Q
what is the 1st law of thermodynamics
A
energy cannot be created or destroyed
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
13
Q
as energy is changed from one form to another, entropy increases
true/false
A
true
14
Q
when is a reaction feasible
A
ΔG < 0
15
Q
what is ΔG at equilibrium
A
close to 0
16
Q
why is an exergonic reaction feasible
A
ΔG is negative
the products have less free energy than the reactants
gives out energy
17
Q
why is an endergonic reaction not feasible
A
ΔG is positive
the products have more free energy than the reactants
requires energy
18
Q
what is the equation for ΔG
A
ΔG = ΔH - TΔS
ΔS = entropy change
ΔH = enthalpy change
T is in kelvin
19
Q
what is ΔG
A
change in free energy
(energy of products) - (energy of reactants)
kj/mol
20
Q
what is the function of ribosomal RNA
A
combines with proteins to form ribosomes where protein synthesis takes place
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
22
Q
what is the function of messenger RNA
A
carries genetic information for protein synthesis
23
Q
what kind of bond is A-T
A
double hydrogen bond
24
Q
what kind of bond is C-G
A
triple hydrogen bond
25
what 2 bases are purines and what does this mean
A and G
| contain 2 carbon-nitrogen rings
26
what 2 bases are pyrimidines and what does this mean
C T and U
| contain 1 carbon-nitrogen ring
27
what direction does protein synthesis run
5' - 3'
28
in DNA structure where do phosphodiester bonds form
between 3' OH and 5' triphosphate
29
what makes up a nucleoside
base + sugar
30
what makes up a nucleotide
base + sugar + phosphate
31
what enzyme catalyses DNA replication
DNA polymerases
32
how is the leading strand replicated
continuously from right to left
33
how is the lagging strand replicated
slightly slower
in short okazaki fragments
5' to 3' synthesis in 3' to 5'
34
what enzyme joins okazaki fragments
DNA ligase
35
what enzyme unwinds DNA
DNA helices
THIIH - pulls a DNA strand down to the RNA polymerase cleft
THIID - holds the other strand in place
36
what does primase do
makes short RNA sequences (primers) complimentary to the template strand that act as a starting point for the DNA polymerase
37
what is a coupling reaction
unfavourable and a favourable reaction are coupled to make the overall reaction feasible
38
what is the henderson hasselbach equation
```
pH = pKa + log ( [A-]/[HA] )
pH = pKa - log ( [HA]/[A-] )
```
39
what is Ka
acid dissociation constant
| [H+]{A-]/[HA]
40
what is the primary protein structure
sequence of amino acids
41
what is the secondary protein structure
formation of a backbone (hydrogen bonds)
42
what is the tertiary protein structure
3D structure
| fibrous or globular
43
what is the quaternary structure
spatial arrangement of multiple subunits
disulphide bonds hold proteins together
association of non protein groups e.g. haem group
44
how many types of RNA polymerases do prokaryotic cells have
1
45
how many types of RNA polymerases do eukaryotic cells have
3
| Pol I, II and III
46
what do each of the RNA polymerases synthesise
Pol II synthesises all mRNA
| Pol I and III synthesise only stable RNA
47
what direction is RNA synthesised in
5' - 3'
48
what is a promoter sequence that marks the start of a new gene
TATA
49
what is the general transcription factor for all Pol II transcribed genes
TFIID - provides a landing site for other transcription factors e.g. RNA polymerase and allows for formation of pre initiation complex
50
what are enhancers
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
51
what kind of graph is the enzyme activity-pH graph
bell curve - relatively sharp decline either side of the optimum pH
52
what kind of graph is the enzyme activity-temp
increases until optimum temp then decreases sharply
53
how is the degradation of the mRNA prevented during splicing
5' capped with GTP
| 3' has a poly A tail added allowing for recognition
54
how is the degradation of the mRNA prevented during splicing
5' capped with GTP
| 3' has a poly A tail added allowing for recognition
55
how does translation occur
anticodons of tRNA form base pairs with codons of mRNA
56
what is the start codon for translation
AUG
57
what is in the P site
the tRNA being translated
58
what is in the A site
the tRNA waiting to be translated
59
what enzyme catalyses peptide bond formation between amino acids in P and A sites
peptidyl transferase
60
how does termination of translation occur
when A site encounters a stop codon
61
what is held in the E site
the empty tRNA
62
what do free ribosomes in the cytosol make proteins for
cytosol
nucleus
mitochondria
(post translational)
63
what do ribosomes on the RER make proteins for
```
plasma membrane
ER
Golgi
secretion
(Co-translational)
```
64
what is a polysome
structure formed when multiple ribosomes attach to an mRNA sequence which speeds up translation
65
what is meant by the genetic code being
unambiguous
degenerate
each codon codes for only one amino acid
| many amino acids have more than one codon
66
do catalysts effect the position of equilibrium
no - they speed up the rate at which equilibrium is achieved
67
what are apoenzymes
enzymes without a cofactor
68
what are zymogens
inactive form of enzyme
69
what are metalloproteins
contain metal cofactors
70
what is a holoenzyme
enzyme with a cofactor
71
what are prosthetic groups
tightly bound coenzymes
72
what enzyme synthesises ACh
ACh transferase
73
what enzyme breaks down ACh
ACh etherase
74
what enzymes carry out phosphorylation
protein kinases
75
what enzymes remove a phosphate
phosphotase
76
where is GLUT3 found
brain
77
where is GLUT 5 found
gut
78
what is Vmax
maximal rate of a reaction at unlimited substrate concentration
all enzymes are fully saturated
79
what is Km
michaelis constant - 50% Vmax
| concentration of substrate that gives a 50% maximal reaction
80
what does a low Km mean in terms of affinity
low km
only small amount of substrate needed for 50% Vmax
enzyme has a high affinity
81
what is the name of the graph km and Vmax are read off and how are they read
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
what happens to km and vmax in competitive inhibition
v max is unchanged - can be outcompeted by addition of more substrate
km is increased - more substrate needed to have same impact
83
what happens to km and vmax in non-competitive inhibition
Vmax is reduced - cannot be out competed as allosteric (bind at different site)
km is unchanged
84
what kind of relationship do allosteric enzymes show
sigmoidal
| e.g. haemoglobin
85
what kind of relationship do orthosteric enzymes show
follow MM kinetics
hyperbolic
e.g. myoglobin
86
henderson Haselbach equations are always answered with what
1.
87
give 3 functions of cholesterol (lipid)
stability in cell membranes
component of myelin sheath
precursor molecule for steroid hormones, vitamin D and bile acids
88
give 3 functions of triglycerides (lipid)
lipid bilayer membranes
| highly concentrated energy stores
89
how do you differentiate alpha glucose and beta glucose
alpha - H points up, OH points down
| beta - OH points up, H points down
90
where does glycolysis occur
cytosol
91
what is the net gain of ATP in glycolysis
2 ATP (4 produced, 2 used)
92
what is the net gain of ATP in glycolysis
2 ATP (4 produced, 2 used)
93
what are the control points in glycolysis
1st 3rd and final reactions
| highly exergonic so irreversible
94
what enzyme phosphorylates glucose
hexokinase
| mediates substrate entry
95
what enzyme phosphorylates fructose-6-phosphate
phosphofructokinase
| mediates substrate movement along pathway
96
what enzyme converts phosphoenolpyruvate to pyruvate
pyruvate kinase
| mediates exit of product molecules
97
how many NADH + H+ are formed in glycolysis
2
98
how is NAD+ regenerated
oxidative metabolism of pyruvate
99
how do the 2 NADH molecules formed in glycolysis get from cytosol to matrix
malate-aspartate shuttle
100
what happens to pyruvate in anaerobic conditions
alcoholic fermentation
| lactic acid formation in humans (H+ dissociates to form lactate in solution)
101
what happens to pyruvate in aerobic conditions
further oxidised in citric acid cycle
102
what catalyses the formation of acetyl co A from pyruvate
Pyruvate Dehydrogenase Complex PDC
103
where are the enzymes of the TCA cycle located
matrix
| except succinate dehydrogenase which is integrated in the inner mitochondrial membrane (cristae)
104
how do cancer cells achieve a high rate of ATP production
possess low Km hexokinase allowing for more rapid entry of substrate
105
after glycolysis + PDC + TCA how many NADH +H+ are formed
10
106
after glycolysis + PDC + TCA how many FADH2 are formed
2
107
after glycolysis + PDC + TCA how many ATP are formed
4
108
after glycolysis + PDC + TCA how many CO2 are formed
6
109
what are the steps of glycolysis + PDC + TCA
```
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
what occurs in the PDC
2 x pyruvate to 2 x acetyl co enzyme A
NAD+ --> NADH+ +H+
coenzyme A --> CO2
per pyruvate
111
in TCA cycle how many pairs of electrons are transferred in the conversion of NAD+ to NADH+ H+
3
112
in the TCA cycle how many pairs of electrons reduce FAD to FADH2
1
113
what is most commonly the 4C acid in the TCA cycle
oxaloacetate
114
what is most commonly the 6C acid in the TCA cycle
citric
115
what are the steps in glycolysis
glucose
fructose-1,6-bisphosphate
2 triose phosphates
2 pyruvate
116
what does each TCA cycle generate
3 NADH+H+
1 FADH2
1 GTP
2 CO2
117
where does the TCA cycle occur
central matrix then cristae
118
what is the warburg effect
up regulation of anaerobic glycolysis in cancer cells - lactic acid fermentation
119
where does oxidative phosphorylation occur
in the cristae
120
what is the electron transfer potential
| "standard redox potential"
how readily a compound donates an electron
121
what is the electron transfer potential
measured by redox potential of a compound
122
what does a negative standard redox potential mean
reduced form of the compound has a lower affinity for electrons than hydrogen so more likely to donate
123
what does a positive standard redox potential mean
reduced form of the compound has a higher affinity for electrons than hydrogen so less likely to donate
124
what is oxidative phosphorylation and what are the two stages
the coupling of respiration to ATP synthesis
| electron transport and ATP synthesis
125
where do electrons from NADH enter the respiratory chain
complex I
126
where do electrons from FADH2 enter the respiratory chain
complex II
127
what is the transfer of electrons through the respiratory chain coupled to
H+ transport from mitochondrial matrix to inter membrane space
128
how many complexes in the ETC pump H+
3/4
| 1 2 and 4
129
outline the essence of oxidative phosphorylation
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
how do CO, cyanide and azide inhibit oxidative phosphorylation
inhibit transfer of electrons to O2 so no proton gradient formed so no ATP formation
131
Cyanide is a competitive inhibitor and CO is a non-competitive inhibitor
true/false
true
132
how many H+ ions passing through ATP synthase forms 1 ATP
4
133
what happens to H+ ions if they don't enter the ATP synthase protein
they join thermogenin (uncoupling protein) producing heat instead of ATP
134
what kind of fat is well adapted for thermogenesis
brown fat
135
how many ATP does the TCA cycle yield
2 (GTP)
136
how many ATP does one molecule of glucose yield
30-32
137
cofactors are usually (metal ions/organic molecules)
metal ions
138
coenzymes are usually (metal ions/organic molecules)
organic molecules
139
what is the optimum pH of pepsin
low pH
140
what is the optimum pH of salival amylase
neutral
141
what is the optimum pH of pancreatic amylase
alkaline
142
what enzyme is a marker of muscle damage
CK (M form)
(B form in brain)
(MB form in heart)
143
what enzymes are markers of liver damage
ALT
AST (whole body)
GGT
144
what enzymes are markers of pancreas damage
amylase
| lipase
145
what enzymes are markers of cardiac damage
CK
AST
LDH
146
ATP supplies energy to run for how many seconds
4
147
phosphocreatine supplies energy to run for how many seconds
15
148
how long does free circulating glucose supply energy for
4 minutes
149
how long do glycogen stores last
77 minutes
150
how long do fat stores last
4+ days
151
what is FiFoATPase
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
why do rapidly contracting human cells start producing lactic acid?
cells have to convert NADH to NAD+
153
what is a partial agonist
binds to and activates receptor but only partial efficacy t receptor relative to full agonist
