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Biochemistry Flashcards

1
Q

How do catalysts function?

A

They speed up reaction rate by lowering activation energy

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2
Q

What is the transition state (intermediate) in a reaction?

A

This is the unstable stage beween reactants and products

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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

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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
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5
Q

What are metal ions that contain metal cofactors called?

A

Metalloproteins

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6
Q

Like enzymes, cofactors are always ____________ at the end of a reaction

A

Regenerated

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7
Q

Tightly bound coenzymes are called what?

A

Prosthetic groups

(these confer additional function)

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8
Q

What is the term given to an enzyme without a cofactor?

A

Apoenzyme

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9
Q

An enzyme with a cofactor is called what?

A

Holoenzyme

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10
Q

Give examples of metal ions that could be used as cofactors

A
  • Zinc
  • Copper
  • Iron
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11
Q

Give examples of coenzymes

A
  • Vitamins
  • NAD
  • FAD
  • Lipoate
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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

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13
Q

Which two main factors affect enzyme fucntionality?

A
  1. Temperature
  2. pH
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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

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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

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16
Q

What are isozymes?

A

Enzymes which have almost identical function but have slightly different amino acid sequencing

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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

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18
Q

How can phosphorylation regulate enzyme activity?

A

It can convert the enzyme between inactive and active forms

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19
Q

Phosphorylation is a reversible process that involves which two enzymes?

A
  1. Kinase - adds phosphate
  2. Phosphotase - removes phosphate
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20
Q

What are zymogens?

A

Inactive precursors of an enzyme which are converted to active forms by cleavage of a covalent bond

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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+

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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

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23
Q

What is NADH required for?

A

The transfer of electrons to the respiratory electron transfer chain in stage 3 of ATP synthesis

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24
Q

What are the three diferent terms used to describe the second stage of ATP synthesis?

A
  1. Citric acid cycle
  2. Krebs cycle
  3. Tricarboxylic acid cycle (TCA)
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25
Q

Where does the TCA cycle occur?

A

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)

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26
Q

Where is pyruvate synthesised?

A

The cytosol

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27
Q

How does pyruvate enter the matrix of the mitochondria? (3)

A

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
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28
Q

Which process must pyruvate undergo to be converted to acetyl-CoA?

A

Oxidative decarboxylation

This is an irreversible reaction

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29
Q

Describe the four stages of the oxidative decarboxylation of pyruvate

A
  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
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30
Q

Describe the TCA cycle

A
  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
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31
Q

Where are all enzymes for the TCA cycle found and what is the exception?

A

Mitochondrial matrix

Succinate dehydrogenase is found in the inner mitochondral membrane - this is required to allow FADH2 to be synthesised

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32
Q

Overall, what does one molecule of glucose yield until the stage at the end of the TCA cycle?

A
  • 4 ATP
  • 10 NADH
    10 H+
  • 2FADH2
  • 6CO2
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33
Q

What is PDC deficiency?

A

A sex linked condition only survivable by carrier females.

It will largely present as a neurological diseas ein childhood.

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34
Q

What is VMAX?

A

The maximum rate at which an enzyme can function

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35
Q

What is Km?

A

The Michaelis-Menten constant

This is the concentration of substrate required to elicit a reaction rate equal to 50% of VMAX

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36
Q

How is Km calculated?

A

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.
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37
Q

What is a Lineweaver-Burk plot?

A

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
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38
Q

What are the two types of enzyme inhibition?

A
  1. Reversible
  2. Irreversible
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39
Q

What are the two types of reversible enzyme inhibition and describe them

A
  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
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40
Q

Describe irreversible enzyme inhibition

A

This is non-competitive and involves a breakage of covalent bonds and change of structure - hence it is irreversible

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41
Q

How is Vmax affected by competitive inhibition of enzyme activity?

A

Vmax does not change

With enough substrate, the inhibitor can always be outcompeted

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42
Q

How is Km affected by competitive inhibition of enzyme activity?

A

Km is increased

More substrate is now required to have the same impact as before

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43
Q

How is Vmax affected by non-competitive inhibition of enzyme activity?

A

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

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44
Q

How is Km affected by non-competitive inhibition of enzyme activity?

A

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

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45
Q

Which type of enxyme will not follow the Michaelis-Menten model of kinetics?

A

Allosteric enzymes

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46
Q

What is highlighted when Vmax is plotted against substrate concentration for allosteric enzymes?

A

The cooperation behaviour of the enzymes

A hyperbolic curve will be present on the graph

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47
Q

What is hydrolysis?

A

A reaction, when water is used to help split up a molecule

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48
Q

What is the first law of thermodynamics?

A

Energy, or matter, cannot be created or destroyed

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49
Q

What is the second law of thermodynamics?

A

When energy is converted from one form to another, energy is always lost - entropy will always increase

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50
Q

What is free energy?

A

The energy that is “free”, or available, to do work

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51
Q

How can free energy be calculated?

A

ΔG = ΔH - TΔS

or

ΔG = energy of products - energy of reactants

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52
Q

Whe calculating free energy, what is tempertaure measured in?

A

Kelvin

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53
Q

Describe exergonic reactions

A
  1. ΔG is negative
  2. The reaction is feasible
  3. The reaction can proceed spontaneously
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54
Q

Describe endergonic reactions

A
  1. ΔG is positive
  2. Energy is required in order for the reaction to proceed
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55
Q

At equilibrium, what will ΔG equal?

A

0

56
Q

What is coupling?

A

This is when an unfavourable process will combine with a favourabe process ensuring the overall reaction is feasible

57
Q

What are amphipathic molecules?

A

Molecules possessing both hydrophobic and hydrophilic properties

58
Q

What are the two types of amino acid and why do two isoforms exist?

A

L & D

They have tetrahedral molecular formations so can have stereoisomers

59
Q

What are the three types of 3D arrangement in a secondary protein structure?

A
  1. Alpha helices
  2. Beta sheets
  3. Triple helix
60
Q

What are the two directions possible in a beta sheet?

A
  1. Parallel
  2. Antiparallel
61
Q

What are the two types of tertiary structures in proteins?

A
  1. Fibrous
  2. Globular
62
Q

What are the four bases in DNA?

A
  1. Adenine
  2. Thymine
  3. Cytosine
  4. Guanine
63
Q

To which “end” of the RNA strand are more nucleotides added during transcription?

A

3’ end

64
Q

What is the catalyst for DNA replication?

A

DNA polymerase

65
Q

What is required to commence DNA synthesis and replication?

A

An RNA primer

(DNA polymerase can take over after this)

66
Q

In which two ways is DNA formed and why?

A

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
Q

The lagging stand in DNA formation must utilise which type of fragments to enable 5’ to 3’ directional growth?

A

Okazaki

68
Q

Which enzyme is reponsible for unwinding DNA?

A

DNA helicase

69
Q

Which enzyme is reponsible for synthesising an RNA primer to initiate replication on the lagging strand?

A

Primase

70
Q

Describe how Okazaki fragments aid the growth of the lagging strand

A
  • 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
Q

Which enzyme is key in proofreading?

A

DNA polymerase

72
Q

What are the three differences between DNA and RNA?

A
  1. Single vs double stranded
  2. DNA - thymine, RNA - uracil
  3. RNA - ribose sugar, DNA - deoxyribose sugar
73
Q

Which enzymes are responsible for RNA production?

A

RNA polymerases

74
Q

Which variation of RNA polymerase will synthesise mRNA?

A

Pol II

75
Q

Where will RNA polymerase bind on a section of DNA?

A

Sections of DNA called promotors

76
Q

What is characteristic about promotor regions on DNA?

A

They all have the TATA box sequence which marks the beginning of the relevant gene

77
Q

What is a transcription factor, and what is the specific one for TATA box?

A

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
Q

Once TFIID is present what does it allow for?

A

It provides a landing site for other transcription factors (RNA polymerase) and allows for the formation of the preinitiation complex

79
Q

Describe the process why which DNA strands are pulled apart

A

TFIIH - pulls a DNA strnad down into the RNA polymerase cleft

TFIID - hold the other strand in place

80
Q

What are enhancers?

A

Short regions of DNA that can be bound by protein activators to increase the liklihood of transcription

81
Q

How can enhancers have an influence if they are far from the promotor sequences?

A

Looping of the strand allows them to come into contact

82
Q

Initially exons and introns are coded together, what is the name of this strand?

A

Pre-mRNA

83
Q

How is “mature” mRNA created?

A

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
Q

Why are there many more codon oftens for relatively few amino acids?

A

The coding for amino acids is degenerate

Amino acids can be encoded by more than one codon

85
Q

What are the three tRNA binding sites in ribosomes?

A
  1. E - exit
  2. P - peptidyl
  3. A - aminoacyl
86
Q

At which point does translation begin?

A

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
Q

Where is the initiator tRNA held?

A

P site of the ribosome

88
Q

The A site of the ribosome holds what?

A

The tRNA waiting to be translated

89
Q

What does the P site in the ribosome hold?

A

The tRNA being translated

90
Q

Which enzyme catalyses the peptide bond formation between amino acids in the P and A positions

A

Peptidyl transferase

91
Q

What does the E site in the ribosome occupy?

A

The “empty” tRNA

92
Q

When does termination of translation occur?

A

When a stop codon is encountered

The is no tRNA base pairing for this, so instead release factor binds and allows for cleavage

93
Q

What is a polysome?

A

A structure formed when many ribosomes attach to an mRNA sequence

This speeds up the translation process

94
Q

What are the two forms of ribsomes?

A
  1. Free - makes proteins for cytosol, nucleus, mitochondria
  2. Bound - makes proteins for plasma membrane, ER, golgi, secretion
95
Q

What are the two main types of post-translation modification?

A
  1. Addition of chemical groups
  2. Covalent modification (proteolysis)
96
Q

Metabolism is composed of which two processes?

A
  1. Anabolism - assembly of molecule requiring energy
  2. Catabolism - breakdown of products releasing energy
97
Q

What is NAD?

A

Nicotinamide adenine dinucleotide

It is a coenzyme exising in two forms

  1. Reduced - NADH
  2. Oxidised - NAD+
98
Q

What is NAD normally involved in?

A

Catabolic pathways for ATP synthesis

99
Q

What is NADP?

A

Nicotinamide adenine dinucleotide phosphate (NADPH)

It is a cofactor that exists in two forms:

  1. Reduced - NADH
  2. Oxidised - NADP+
100
Q

What is NADP normally involved in?

A

Anabolic pathways for ATP synthesis

101
Q

What are the two equivalent forms of glucose?

A
  1. D-glucose - straight chain molecules
  2. Alpha/beta-D-glucose - cyclic molecules
102
Q

How are alpha and beta glucose differentiated?

A

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
Q

How can glucose be stored?

A
  1. Glucose molecules (monosaccharide)
  2. Disaccharide sugars (maltose, lactose etc)
  3. Long polysaccharides (cellulose or glycogen)
104
Q

How is glucose transported into cells?

A
  • Na+/glucose symporters
  • Passive diffusion glucose transporters
105
Q

What are the three pathways for glucose breakdown?

A
  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
Q

Where does glycolysis occur?

A

Cytosol

107
Q

Describe the stages of glycolysis

A
  • 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
Q

What are the products of glycolysis?

A
  • 2 ATP
  • 2NADH
  • 2H+
109
Q

What is the difference between lactate and lactic acid?

A

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
Q

What are the control points in glycolysis?

A
  • 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
Q

What are the activators of phosphofructokinase?

A
  • AMP
  • Fructose 2,6-biphosphate
112
Q

What are the inhibitors of phosphofructokinase?

A
  • 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
Q

What is energy charge?

A

The ATP/AMP ratio

It is a control mechanism for phosphofructokinase

114
Q

What is the Warburg effect?

A

The upregulation of anaerobic glycolysis in cancer cells

115
Q

Why is a high rate of ATP production achieved in cancer cells?

A

They posses low Km hexokinase allowing for more rapid substate entry

116
Q

Why do cancer patients lose weight?

A

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
Q

By the end of the TCA cycle what has been produced (including the products of glycolysis)?

A
  • 10NADH
  • 10H+
  • 2FADH2
118
Q

Where does oxidative phosphorylation occur?

A

Cristae of mitochondria

119
Q

Give a basic overview of the step of ATP synthesis

A
  • 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
Q

For the final stage of oxidative phosphorylation, how is oxygen reduced to water?

A

The hydrogen ions will bind to oxygen after it has been reduced by NADH and FADH2

121
Q

How do the 2 NADH molecules produced in the cytosol during glycolysis get into the matrix of the mitochondria?

A

Malate-aspartate shuttle

122
Q

Describe the malate aspartate shuttle

A
  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
Q

What are the two key stages in forming ATP?

A

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
Q

How many multiprotein subunits are present in the inner mitochondrial membrane that contribute to electron transport?

A

4

125
Q

At which point do electrons fron NADH enter the electron transport chain?

A

Complex I

126
Q

At which point do electrons from FADH2 enter the electron transport chain?

A

Complex II

127
Q

What is the function of co-enzyme A (Q)?

A

To transfer electrons from within the membrane that come from complex II

128
Q

Where is complex II located in relation to the mitochondria?

A

On the inner mitochondrial membrane

129
Q

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
A
  1. 4
  2. None - it is not a transmembrane protein
  3. 4
  4. 2
130
Q

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?

A

4

131
Q

How many ATP are produced from the 10NADH, 2FADH2 and two GTP?

A

30-32ATP

(per glucose)

132
Q

Name a non-competitor inhibitor of oxidative phosphorylation

A

Carbon monoxide

(binds to haem (in cytochrome C) preventing uptake and progression of electrons into the chain)

133
Q

Name a competitive inhibitor of oxidative phosphorylation

A

Cyanide

134
Q

If hydrogen ions do not enter the ATP synthase protein, where also can they enjoy and what is a side effect of this?

A

Thermogenin (uncoupling proteins)

Heat is produced instead of ATP

135
Q

Which type of fat is well adapted for thermogenesis?

A

Brown fat

136
Q

In order to activate the process of thermogenesis, what are required?

A

Fatty acids

Principles (10 decks)

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