Biochemistry Flashcards
(118 cards)
1
Q
Covalent bond
A
Strongest. Sharing of electron pairs
2
Q
Ionic bond
A
Attraction of opposite charges
3
Q
Hydrogen bond
A
Sharing of H atom
4
Q
Hydrophobic interaction
A
Interaction of non-polar substances in the presence of polar substances (esp. water)
5
Q
Van der Waals
A
Interaction of electrons of non-polar substances
6
Q
Bond energy
A
The amount of energy needed to separate two bonded or interacting atoms under physiological conditions
7
Q
Phosphorylation
A
addition of a phosphate group
8
Q
Dephosphorylation
A
Removal of a phosphate group
9
Q
Acylation
A
addition of C=O
10
Q
Carboxylation
A
addition of a carboxyl group COOH
11
Q
Esterification
A
Acid + Alcohol > Ester + water
12
Q
Hydrolysis
A
Splitting using water. Water added
13
Q
Oxidation states of carbon
A
alkane > alcohol > aldehyde > acid > CO2
14
Q
Standard conditions
A
T= 298K, 1 atm, 1 M conc, pH 7
15
Q
Anhydride bonds are…
A
high energy bonds
16
Q
Glycolysis
A
breakdown on glucose
17
Q
Gluconeogenesis
A
making new glucose from non-carbohydrate precursors.
e.g. pyruvate.
18
Q
Control points
A
Reactions with large -ve deltaG are used a control points
19
Q
Hydrophobic effect
A
oil and water don’t mix, as oil is non-polar so will not dissolve and results in an ‘oil slick’
20
Q
Amphipathic
A
both hydrophilic and hydrophobic
21
Q
Structure of an amino acid
A
Central carbon + COOH + NH2 + H+ + side chain
22
Q
Peptide bond formation
A
Condensation. CO-NH
23
Q
Direction of peptide
A
N terminus to C terminus
24
Q
Zwitterions
A
amino acids without charged side groups. Neutral
25
Cationic form
1+ charge
26
Anionic form
1- charge
27
Purines
A and G double ring
28
Pyrimidines
U T C single ring
29
Phosphodiester bond
Polymerisation. Formed between a free 3' OH group and 5' triphosphate. 2 Ps are released
30
Nucleic acids are only added to the free ... end
3'
31
Okazaki fragments
short segments so that the lagging strand can be replicated
32
Replication occurs in which direction?
5' to 3'
33
What is special about DNA polymerase?
It has proof-reading ability and can remove a wrong nucleotide
34
Splicing
removes introns before translation can occur
35
Free ribosomes make proteins for...
the nucleus and mitochondria
36
Bound ribosomes to rough ER make proteins for...
Golgi apparatus, secretion etc.
37
Glycosylation
addition and processing of carbohydrates in the ER and Golgi apparatus
38
RNA is made by...
RNA polymerases
39
Steps of transcription
Detection of initiation sites, DNA chain separation, transcription initiation, elongation and termination
40
Termination of transcription
an enzyme cleaves it
41
Aminoacyl-tRNA synthetases
binds amino acids to their corresponding tRNA molecule
42
Energy requirements for translation
ATP and GTP
43
Steps of translation
Initiation elongation, peptide bond formation, termination
44
most vitamins functions as...
coenzymes
45
Michaelis constant (Km)
Km= [k-1 + k2] / k1
46
Km
the substrate constant is half the maximal reaction rate
47
Vmax
intersection of line with Y axis
48
Km (graph)
intersection with X axis
49
Competitive Inhibition
Vmax does not change, Km varies
50
Non-competitive inhibition
Vmax varies, Km does not change
51
Allosteric enzymes
Sigmoid graph
52
Anabolism
synthesis of complex molecules
53
Catabolism
breakdown of complex molecules
54
NADH+ + H+ = ... and is a ... ... reaction
NAD+ and is a oxidative phosphorylation reaction
55
Fates of glucose
storage, Ribose-5-phosphate, lactate, pyruvate
56
Glucose + 2ADP + 2Pi + 2NAD+ >
2 pyruvate + 4ATP + 2H2O + 2NADH + 2H+
57
Glycolysis is the...
conversion of glucose to pyruvate
58
Control points in glycolysis
Hexokinase (controls substrate entry), Phosphofructokinase (controls rate of flow), pyruvate kinase (control product exit)
59
Hexokinase
glucose to G6P
60
Pyruvate kinase
formation of pyruvate
61
PFK activators
AMP and fructose-2,6-biphosphate. Will increase glycolysis if energy is required
62
PFK inhibitors
ATP (slow glycolysis if abundant) Citrate (slow glycolysis if abundant) H+ (slows glycolysis if too much lactic acid produced)
63
Energy charge
ATP/AMP ratio
64
Fully charged
all ATP
65
Discharged
AMP + Pi
66
Adenylate kinase
can salvage some energy from ADP forming ATP and AMP
67
Glycolysis gain of ATP, NADH and H+
net gain of 2 ATP, gain of 2 NADH and 2H+
68
NADH is used to ferment...
pyruvate to lactate
69
NADH is regenerated ...
in the TCA cycle
70
Warburg effect
up-regulation of anaerobic glycolysis in cancer cells
71
Glycolysis reduces NAD+ to
NADH + H+
72
How is NAD+ regenerated
through the oxidative metabolism of pyruvate
73
Where does the TCA cycle occur
the central matrix of the TCA cycle
74
How does pyruvate enter the mitochondria
Via the pH gradient (so H+ exchange)
75
Pyruvate to acetyl CoA
pyruvate dehydrogenase complex catalyses the oxidative carboxylation of pyruvate to acetyl CoA
76
PDC is regulated by?
phosphorylation, it is allosterically regulated
77
Overview of TCA cycle
2C + 4C= 6C which is decarboxylated twice. Then the new 4C is oxidised 4 times until the original 4C is produced.
78
Yield from TCA cycle
2CO2, 3NADH, 3H+, FADH2, GTP
79
All TCA cycle enzymes are in the matrix except...
succinate dehydrogenase which is in the inner mitochondrial membrane, which converts FAD to FADH2
80
TCA cycle control points
relate to amount of substrates present and whether there is high or low energy to the cycle will speed up or slow down
81
After glycolysis and TCA cycle net yield is
4 ATP, 10 NADH, 10H+, 2FADH2, 4CO2
82
Electrons from NADH and FADH2 are used for..
oxidising O2 to H2O
83
How does NADH get into mitochondria
using malate-aspartate shuttles, then is regenerated on the other side as part of the TCA cycle
84
Phosphoryl transfer potential
free energy change for the hydrolysis of ATP
85
Electron transfer potential
redox potential (reduction potential) of a compound
86
Negative redox potential
reduced form of X has lower affinity for electrons than H2.
87
What is the driving force of oxidative phosphorylation?
how much energy is released by the reduction of O2 by NADH
88
Two stages of oxidative phosphorylation
electron transport and ATP synthesis
89
H+ pump
the transfer of electrons along the respiratory chain is coupled to the transport of H+ across the membrane
90
ATP synthase
contains the proton channel, where protons flow back to matrix, this channel results in ATP synthesis
91
P/O ratio
a measurement of the coupling of ATP synthesis to electron transport
92
The energy for gluconeogenesis is derived from...
oxidation of fatty acids released from adipose tissue
93
What is needed for gluconeogenesis?
4 liver enzymes and oxaloacetate from TCA cycle
94
Why do we need oxaloacetate?
accepts acetyl groups (esp from fat breakdown)
95
Gluconeogenesis stoichiometry
uses 4 ATP> 4 ADP, and 2GTP>2GDP and 2 NADH> 2NAD+ etc.
96
The Cori cylce
blood delivers lactate to liver, liver converts lactate to glucose, which is released into the bloodstream
97
Fat is required for...
energy, essential fatty acids, and fat-soluble vitamins
98
Triglycerides: main energy store form in...
adipose tissue
99
Polyunsaturated fatty acids
cannot be synthesised in the body, and are essential
100
Fat digestion/absorption
Digested to glycerol, fatty acids and monoglycerides. Absorbed into mucosal cell of intestines. Converted into chylomicrons and transported away.
101
Chylomicrons transport
enter lymph then bloodstream
102
At muscle and adipose tissue, chylomicrons are attacked and cleaved by...
lipoprotein lipases
103
Fatty acid oxidation
first have to be converted into CoA derivatives, occurs in cytoplasm and requires energy. Forming- acyl CoA.
104
Carnitine shuttle
transports acyl-CoA into mitochondrial matrix by converting it to acyl-carnitine
105
B oxidation
Converts Acyl-carnitine into acetyl-CoA to enter the TCA cycle
106
Lipogenesis
fatty acid synthesis
107
Lipogenesis
Dietary starch> glucose > pyruvate > acetyl CoA > fatty acids > triglycerides
108
Lipogenesis main precursor
malonyl coA which is formed from acetyl-CoA by acetyl CoA carboxylase.
109
Fatty acid synthase
catalyses synthesis of of saturated long chain fatty acids.
110
Essential role in fatty acid synethsis and degradation
acetyl-CoA carboxylase
111
What signals the fed state?
Insulin (citrate also stimulates allosterically)
112
What signals the starved state?
Glucagon (also adrenaline)
113
Liver produces G3P from...
Adipose tissue produces G3P from...
G3P is required for...
glycerol
glucose (only occurs during fed state)
synthesis of triglycerides (involves esterification)
114
Major nitrogen containing excretory molecules
urea, uric acid, creatinine and ammonium ions
115
Synthesis of urea
transamination, deamination (involves NADH) and urea cycle
116
Amino transferases
move the amino group from one molecule to another (keto acids)
117
Major carriers of nitrogen in blood to liver
alanine, glutamine
118
Urea cycle
requires energy 2ADP and AMP
