Biochemistry Flashcards
1
Q
How do catalysts function?
A
They speed up reaction rate by lowering activation energy
2
Q
What is the transition state (intermediate) in a reaction?
A
This is the unstable stage beween reactants and products
3
Q
What is glycogen storage disease and what are its consequences?
A
It is an enzyme deficiency that results in the failure of glycogen to reach the phosphorylated transition state
This means glucose cannot be obtained from glycogen stores
Hepatomegaly (fatty liver) will result due to glycogen build up
4
Q
What are the variants of the extra molecules (as well as enzymes) that are often reqired for some enzymatic processes to proceed?
A
- Cofactors - metal ions
- Coenzymes - organic molecules
5
Q
What are metal ions that contain metal cofactors called?
A
Metalloproteins
6
Q
Like enzymes, cofactors are always ____________ at the end of a reaction
A
Regenerated
7
Q
Tightly bound coenzymes are called what?
A
Prosthetic groups
(these confer additional function)
8
Q
What is the term given to an enzyme without a cofactor?
A
Apoenzyme
9
Q
An enzyme with a cofactor is called what?
A
Holoenzyme
10
Q
Give examples of metal ions that could be used as cofactors
A
- Zinc
- Copper
- Iron
11
Q
Give examples of coenzymes
A
- Vitamins
- NAD
- FAD
- Lipoate
12
Q
Binding of a substrate to an ezyme results in what?
A
Conformational change of the enzyme around the substate
This is induced fit (due to intermolecular bonding)
The enzyme/substate complex is now formed
13
Q
Which two main factors affect enzyme fucntionality?
A
- Temperature
- pH
14
Q
Describe the how temperature can affect the rate of an enzymatic reaction
A
It will increase to a point and then sharply drop off (past the optimum temp) due to enzyme denaturing
15
Q
Describe how increasing pH affect the rate of an enzymatic reaction
A
It will increase as pH increases until the optimum rate is achieved (at optimum pH) and then will decrease again
This produces a bell curve
16
Q
What are isozymes?
A
Enzymes which have almost identical function but have slightly different amino acid sequencing
17
Q
How can the number of certain isozymes in certain tissues/blood be used to diagnose a medical condition?
A
Different isozymes are synthesised in different regions of the body or at different atges in embryonic/foetal development
Finding the “wrong” isozyme at a certain time, or location in the body may be indicative of a medical condition
18
Q
How can phosphorylation regulate enzyme activity?
A
It can convert the enzyme between inactive and active forms
19
Q
Phosphorylation is a reversible process that involves which two enzymes?
A
- Kinase - adds phosphate
- Phosphotase - removes phosphate
20
Q
What are zymogens?
A
Inactive precursors of an enzyme which are converted to active forms by cleavage of a covalent bond
21
Q
What is produced after the catabolism of glucose?
A
Two pyruvate molecules
There is also a net gain of 2ATP, 2NADH and 2H+
22
Q
What is NAD+?
A
Nicotinamide adenine dinucleotide
It is derived from niacin - a vitamin
It is used as an electron carrier by forming NADH
23
Q
What is NADH required for?
A
The transfer of electrons to the respiratory electron transfer chain in stage 3 of ATP synthesis
24
Q
What are the three diferent terms used to describe the second stage of ATP synthesis?
A
- Citric acid cycle
- Krebs cycle
- Tricarboxylic acid cycle (TCA)
25
Where does the TCA cycle occur?
Mitochondrial matrix on the inner membrane
(this is where proteins required for the electron transport chain can be found, as well as ATP synthase and transport proteins)
26
Where is pyruvate synthesised?
The cytosol
27
How does pyruvate enter the matrix of the mitochondria? (3)
It must cross two membranes
* The intermembrane space is very acidic creating a pH gradient from the cytosol to the matrix which pyruvate can follow
* There is also a electrochemical gradient and pyruvate can utilise this as it is attracted to H+
* A pyruvate symport transporter allows entry of pyruvate into the mitochondria using H+/pyruvate symport, a form of contransport, by faciliated diffusion
28
Which process must pyruvate undergo to be converted to acetyl-CoA?
Oxidative decarboxylation
This is an irreversible reaction
29
Describe the four stages of the oxidative decarboxylation of pyruvate
1. Pyruvate dehydrogenase converts pyruvate to hydroxyethyl thiamine pyrophosphate (HETPP), CO2 is given off as a by product
2. Dihydrolipoyl transacetylase transfers (and oxidises) the hydroxyethyl group to lipoic acid which forms acetyl dihydrolipoamide
3. The acetyl group is transferred to CoA forming one acetyl CoA per pyruvate
4. NAD+ reoxidises dihydrolipoamide which forms one NADH - this is mediated by dihydrolipoyl dehydrogenase
30
Describe the TCA cycle
1. Acetyl CoA forms citric acid upon binding to a four carbon subunit
2. Decarboxylation of citric acid occurs twice yielding 2CO2
3. Citric acid will also go through four oxidation reactions yielding 3NADH, 3H and FADH2
4. As a result GTP is produced, and by the end the 4-carbon subunit is reformed
31
Where are all enzymes for the TCA cycle found and what is the exception?
Mitochondrial matrix
Succinate dehydrogenase is found in the inner mitochondral membrane - this is required to allow FADH2 to be synthesised
32
Overall, what does one molecule of glucose yield until the stage at the end of the TCA cycle?
* 4 ATP
* 10 NADH
10 H+
* 2FADH2
* 6CO2
33
What is PDC deficiency?
A sex linked condition only survivable by carrier females.
It will largely present as a neurological diseas ein childhood.
34
What is VMAX?
The maximum rate at which an enzyme can function
35
What is Km?
The Michaelis-Menten constant
This is the concentration of substrate required to elicit a reaction rate equal to 50% of VMAX
36
How is Km calculated?
Km = (k2 + k-1)/k1
* k1 is the forward rate constant for enzyme association with the substrate.
* k-1 is the backwards rate constant for enzyme dissociation from the substrate.
37
What is a Lineweaver-Burk plot?
This is a method of accurately determining Vmax and Km
The Michaelis-Menten equation (V0 = (Vmax[s])/Km + [s]) can be rearranged to the form y = mx + c
Therefore it can be plotted as a straight line
* The gradient = km/Vmax
* The y intercept equals = 1/Vmax
38
What are the two types of enzyme inhibition?
1. Reversible
2. Irreversible
39
What are the two types of reversible enzyme inhibition and describe them
1. Competitive - inhibitor binds to active site used by substrate (orthosteric inhibition)
2. Non-competitive - Inhibitor binds to an allosteric site to cause inhibition by changing conformation
40
Describe irreversible enzyme inhibition
This is non-competitive and involves a breakage of covalent bonds and change of structure - hence it is irreversible
41
How is Vmax affected by competitive inhibition of enzyme activity?
Vmax does not change
With enough substrate, the inhibitor can always be outcompeted
42
How is Km affected by competitive inhibition of enzyme activity?
Km is increased
More substrate is now required to have the same impact as before
43
How is Vmax affected by non-competitive inhibition of enzyme activity?
It is reduced
Some enzymes will become inactive and no increase in substrate can cause Vmax to reach the level it once
This is because enzyme activity will become the limiting factor
44
How is Km affected by non-competitive inhibition of enzyme activity?
It does not change
This is because any increase in substrate concentration will not impact Vmax which is already at its limit under these conditions
45
Which type of enxyme will not follow the Michaelis-Menten model of kinetics?
Allosteric enzymes
46
What is highlighted when Vmax is plotted against substrate concentration for allosteric enzymes?
The cooperation behaviour of the enzymes
A hyperbolic curve will be present on the graph
47
What is hydrolysis?
A reaction, when water is used to help split up a molecule
48
What is the first law of thermodynamics?
Energy, or matter, cannot be created or destroyed
49
What is the second law of thermodynamics?
When energy is converted from one form to another, energy is always lost - entropy will always increase
50
What is free energy?
The energy that is "free", or available, to do work
51
How can free energy be calculated?
ΔG = ΔH - TΔS
or
ΔG = energy of products - energy of reactants
52
Whe calculating free energy, what is tempertaure measured in?
Kelvin
53
Describe exergonic reactions
1. ΔG is negative
2. The reaction is feasible
3. The reaction can proceed spontaneously
54
Describe endergonic reactions
1. ΔG is positive
2. Energy is required in order for the reaction to proceed
55
At equilibrium, what will ΔG equal?
0
56
What is coupling?
This is when an unfavourable process will combine with a favourabe process ensuring the overall reaction is feasible
57
What are amphipathic molecules?
Molecules possessing both hydrophobic and hydrophilic properties
58
What are the two types of amino acid and why do two isoforms exist?
L & D
They have tetrahedral molecular formations so can have stereoisomers
59
What are the three types of 3D arrangement in a secondary protein structure?
1. Alpha helices
2. Beta sheets
3. Triple helix
60
What are the two directions possible in a beta sheet?
1. Parallel
2. Antiparallel
61
What are the two types of tertiary structures in proteins?
1. Fibrous
2. Globular
62
What are the four bases in DNA?
1. Adenine
2. Thymine
3. Cytosine
4. Guanine
63
To which "end" of the RNA strand are more nucleotides added during transcription?
3' end
64
What is the catalyst for DNA replication?
DNA polymerase
65
What is required to commence DNA synthesis and replication?
An RNA primer
(DNA polymerase can take over after this)
66
In which two ways is DNA formed and why?
Continously or discontinuously
* Continuously - DNA is built up from the 5' to the 3' end easily - this is the leading strand
* Discontinuously - the other strand is built from 3' to 5' as it is orientated the other way around - this is the lagging strand
67
The lagging stand in DNA formation must utilise which type of fragments to enable 5' to 3' directional growth?
Okazaki
68
Which enzyme is reponsible for unwinding DNA?
DNA helicase
69
Which enzyme is reponsible for synthesising an RNA primer to initiate replication on the lagging strand?
Primase
70
Describe how Okazaki fragments aid the growth of the lagging strand
* Short newly synthesised DNA fragments - Okazaki fragments are added at intervals from the open DNA strands downwards
* This allows nucleotides to be sythesised in the "correct" direction by essentially filling in the gaps the Okazaki fragments created
* Each time DNA helicase opens up the strand a little more, a new Okazaki fragment can jump in and allow synthesis back down the chain
71
Which enzyme is key in proofreading?
DNA polymerase
72
What are the three differences between DNA and RNA?
1. Single vs double stranded
2. DNA - thymine, RNA - uracil
3. RNA - ribose sugar, DNA - deoxyribose sugar
73
Which enzymes are responsible for RNA production?
RNA polymerases
74
Which variation of RNA polymerase will synthesise mRNA?
Pol II
75
Where will RNA polymerase bind on a section of DNA?
Sections of DNA called promotors
76
What is characteristic about promotor regions on DNA?
They all have the TATA box sequence which marks the beginning of the relevant gene
77
What is a transcription factor, and what is the specific one for TATA box?
A protein that binds to DNA and controls the rate, or allows for transcription
TATA box binding protein will form part of the TFIID protein, the general transription factor for all pol II transcribed genes
78
Once TFIID is present what does it allow for?
It provides a landing site for other transcription factors (RNA polymerase) and allows for the formation of the preinitiation complex
79
Describe the process why which DNA strands are pulled apart
TFIIH - pulls a DNA strnad down into the RNA polymerase cleft
TFIID - hold the other strand in place
80
What are enhancers?
Short regions of DNA that can be bound by protein activators to increase the liklihood of transcription
81
How can enhancers have an influence if they are far from the promotor sequences?
Looping of the strand allows them to come into contact
82
Initially exons and introns are coded together, what is the name of this strand?
Pre-mRNA
83
How is "mature" mRNA created?
Introns are spliced out of the stand leaving only the exons
The 5' end is then capped with GTP preventing degredation
The 3' end has a poly A tail added allowing for recognition
This is **_alternative RNA splicing_**
84
Why are there many more codon oftens for relatively few amino acids?
The coding for amino acids is degenerate
Amino acids can be encoded by more than one codon
85
What are the three tRNA binding sites in ribosomes?
1. E - exit
2. P - peptidyl
3. A - aminoacyl
86
At which point does translation begin?
A ribosomal subunit binds to the 5' end of the mRNA and will move along until the AUG codon
Here, a special initiator tRNA will bind with its UAC anticodon and translation begins
87
Where is the initiator tRNA held?
P site of the ribosome
88
The A site of the ribosome holds what?
The tRNA waiting to be translated
89
What does the P site in the ribosome hold?
The tRNA being translated
90
Which enzyme catalyses the peptide bond formation between amino acids in the P and A positions
Peptidyl transferase
91
What does the E site in the ribosome occupy?
The "empty" tRNA
92
When does termination of translation occur?
When a stop codon is encountered
The is no tRNA base pairing for this, so instead release factor binds and allows for cleavage
93
What is a polysome?
A structure formed when many ribosomes attach to an mRNA sequence
This speeds up the translation process
94
What are the two forms of ribsomes?
1. Free - makes proteins for cytosol, nucleus, mitochondria
2. Bound - makes proteins for plasma membrane, ER, golgi, secretion
95
What are the two main types of post-translation modification?
1. Addition of chemical groups
2. Covalent modification (proteolysis)
96
Metabolism is composed of which two processes?
1. Anabolism - assembly of molecule requiring energy
2. Catabolism - breakdown of products releasing energy
97
What is NAD?
Nicotinamide adenine dinucleotide
It is a coenzyme exising in two forms
1. Reduced - NADH
2. Oxidised - NAD+
98
What is NAD normally involved in?
Catabolic pathways for ATP synthesis
99
What is NADP?
Nicotinamide adenine dinucleotide phosphate (NADPH)
It is a cofactor that exists in two forms:
1. Reduced - NADH
2. Oxidised - NADP+
100
What is NADP normally involved in?
Anabolic pathways for ATP synthesis
101
What are the two equivalent forms of glucose?
1. D-glucose - straight chain molecules
2. Alpha/beta-D-glucose - cyclic molecules
102
How are alpha and beta glucose differentiated?
The first carbon (counting clockwise after oxygen) is orientated up (so the hydroxyl group points up) in the beta form
The opposite is true in the beta form
103
How can glucose be stored?
1. Glucose molecules (monosaccharide)
2. Disaccharide sugars (maltose, lactose etc)
3. Long polysaccharides (cellulose or glycogen)
104
How is glucose transported into cells?
* Na+/glucose symporters
* Passive diffusion glucose transporters
105
What are the three pathways for glucose breakdown?
1. Oxidation through aerobic glycolysis - yields pyruvate
2. Fermentation anaerobic glycolysis - yields lactate
3. Oxidation through the pentose phosphate pathway - yields ribose-5-phosphate
106
Where does glycolysis occur?
Cytosol
107
Describe the stages of glycolysis
* Glucose is split using 2ATP to fructose-1,6-biphosphate
* This intermediate is broken down to 2 triose phosphates
* Each triose phosphate is oxidised by NAD to produce pyruvate
* In total 4 ATP are yielded - 2 come from each tiose phosphate oxidation
108
What are the products of glycolysis?
* 2 ATP
* 2NADH
* 2H+
109
What is the difference between lactate and lactic acid?
Latate and lactic acid are essentially the same thing
In solution (in the body) a hydrogen ion will dissociate from lactic acid (the carboxyl group) to form a conjugate base - this is lactate and is what is found in the body
110
What are the control points in glycolysis?
* Hexokinase - mediates substrate entry
* Phosphofructokinase - controls substrate movement along glycolytic pathway
* Pyruvate kinase - moderate the exit of product molecules
These are control points because they are irreversible reactions
111
What are the activators of phosphofructokinase?
* AMP
* Fructose 2,6-biphosphate
112
What are the inhibitors of phosphofructokinase?
* ATP - glycolysis slows down when energy is abundant
* Citrate - downstream pyruvate entry to the TCA cycle is slowed when energy and intermediates are already prevalent
* H+ - slows glycolysis if there is too much lactic acid being produced
113
What is energy charge?
The ATP/AMP ratio
It is a control mechanism for phosphofructokinase
114
What is the Warburg effect?
The upregulation of anaerobic glycolysis in cancer cells
115
Why is a high rate of ATP production achieved in cancer cells?
They posses low Km hexokinase allowing for more rapid substate entry
116
Why do cancer patients lose weight?
There is high glucose demand for cancer cells
The cancer cells also produce ATP very inefficiently so more glucose is used up essentially wasting body energy stores
117
By the end of the TCA cycle what has been produced (including the products of glycolysis)?
* 10NADH
* 10H+
* 2FADH2
118
Where does oxidative phosphorylation occur?
Cristae of mitochondria
119
Give a basic overview of the step of ATP synthesis
* Protons are pumped across mitochondrial matric by protein complexes into inner mitochondrial membrane space
* Protons flow back into matrix along a concentration gradient through ATP synthase generating ATP
* Water will form from the hydrogen ions and oxygen
120
For the final stage of oxidative phosphorylation, how is oxygen reduced to water?
The hydrogen ions will bind to oxygen after it has been reduced by NADH and FADH2
121
How do the 2 NADH molecules produced in the cytosol during glycolysis get into the matrix of the mitochondria?
Malate-aspartate shuttle
122
Describe the malate aspartate shuttle
1. Aspartate is converted to oxaloacetate due to α-ketoglutarate which now becomes glutamate
2. NADH is oxidised and generates malate from oxaloacetate
3. Malate transporters move malate into mitochondrial matrix
4. Malate is converted back to oxaloacetate which generates NADH from NAD+
5. Oxaloacetate is converted to aspartate by glutamate which again becomes α-ketoglutarate
6. Aspartate is pumped across the membrane through aspartate channels and the cycle can begin again
123
What are the two key stages in forming ATP?
Electron transport - electrons are transported through the respiratory chain and the enrgy produced from this causes protein complexes to pump electrons across the inner mitochondrial membrane
ATP synthesis - these elctrons re-enter and pass through ATP synthase forming ATP
124
How many multiprotein subunits are present in the inner mitochondrial membrane that contribute to electron transport?
4
125
At which point do electrons fron NADH enter the electron transport chain?
Complex I
126
At which point do electrons from FADH2 enter the electron transport chain?
Complex II
127
What is the function of co-enzyme A (Q)?
To transfer electrons from within the membrane that come from complex II
128
Where is complex II located in relation to the mitochondria?
On the inner mitochondrial membrane
129
When reduced by electrons, how many hydrogen ions do each of the following complexes pump across the inner mitochondrial membrane:
1. I
2. II
3. III
4. IV
1. 4
2. None - it is not a transmembrane protein
3. 4
4. 2
130
How many hydrogen ions will cause one ATP to be proced when they pass through the ATP synthase and back across the inner mitochondrial membrane?
4
131
How many ATP are produced from the 10NADH, 2FADH2 and two GTP?
30-32ATP
| (per glucose)
132
Name a non-competitor inhibitor of oxidative phosphorylation
Carbon monoxide
(binds to haem (in cytochrome C) preventing uptake and progression of electrons into the chain)
133
Name a competitive inhibitor of oxidative phosphorylation
Cyanide
134
If hydrogen ions do not enter the ATP synthase protein, where also can they enjoy and what is a side effect of this?
Thermogenin (uncoupling proteins)
Heat is produced instead of ATP
135
Which type of fat is well adapted for thermogenesis?
Brown fat
136
In order to activate the process of thermogenesis, what are required?
Fatty acids
