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BoC > Michaelmas > Flashcards

Michaelmas Flashcards

1
Q

Hormone involved in parturition and its receptor

A

Oxytocin
Oxytocin receptor (GPCR)

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2
Q

What are muscarinic receptors?

A

GPCRs
Activated by ACh
Mainly in parasympathetic pathway
Found in hear, brain, intestine

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3
Q

What are NAChR?

A

Nicotinic acetylcholine receptors, ligand gated ion channels
Allow movement of K+ and Na+
Found on post synaptic vesicle

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4
Q

Which route does the efferent fibre take?

A

Efferent- action (leave)
Ventral route

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5
Q

Which route does the afferent fibre take?

A

Afferent- sensory
Dorsal route

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6
Q

Which neurotransmitter is released by Parasympathetic NS?

A

Acetylcholine

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7
Q

Which neurotransmitter is released by the sympathetic NS?

A

Adrenaline or noradrenaline

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8
Q

What type of receptors do adrenaline and noradrenaline work on?

A

Adrenoreceptors- (GPCRs)
Alpha- inhibitory
Beta- Excitatory

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9
Q

Secondary messenger involved in control of the heart

A

cAMP
Broken down by phosphodiesterase

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10
Q

What is Ficks first law for small uncharged particles

A

Rate of diffusion= permeability x conc gradient

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11
Q

What did Watson and Crick discover?

A

DNA, double helix structure, And base pairing, A-T, C-G
- found out structure by using X-ray crystallography

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12
Q

What is the Edman Degradation method?

A

Purification of protein by sequentially removing a residue at a time from a polypeptide. Can help determine amino acid sequence. Use hydrolyzing agent and chromatography to analyse residue removed

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13
Q

What are the two ways to determine amino acid sequence?

A

Mass spectrometry and Edman degradation

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14
Q

Disulphide bridges are commonly found between which residues?

A

Cysteine

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15
Q

What is a Rossman fold?

A

Type of tertiary fold that allows proteins to bind to nucleotides, for example in adenine in NAD, NADP, FAD

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16
Q

What is an amyloid?

A

When a protein folds incorrectly

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17
Q

Methods for determining protein structure

A

1) X-ray diffraction
2) Cryo EM
3) Circular dichroism
4) NMR spectroscopy
5) Atomic force spectroscopy

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18
Q

Differences between alpha and beta hairpin

A

Beta contains H bonds, Alpha doesn’t. Alpha has van der Waals forces. Beta is anti-parallel strands

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19
Q

What is the standard free energy change of hydrolysis of ATP?

A

-31kJmol-1

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20
Q

What equation uses the charges of solutes to calculate membrane potential/ concentration of solutes?

A

Nernst equation

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21
Q

How does endocytosis occur?

A

Vesicle binds to protein adapter-> Activates Clathrin-> Activates triskelion-> forms coated pits-> then uncoated by chaperone proteins

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22
Q

What is substrate level phosphorylation?

A

Direct transfer of Pi from substrate to make ATP to GTP

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23
Q

What is the phosphoryl-transfer potential?

A

Potential for a molecule to phosphorylate something. ATP has an intermediate phosphoryl-transfer potential

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24
Q

What is feed forward stimulation? Give an example

A

When products of an earlier reaction stimulate enzymes involved at the end of a pathway. For example fructose 1,6- bisphosphate stimulating pyruvate kinase

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25
Q

Where are hexokinase and glucokinase located?

A

Hexokinase- muscles
Glucokinase- liver

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26
Q

What inhibits hexokinase?

A

Glucose 6- phosphate

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27
Q

Name the type of glucose transporters and their locations

A

GluT 1-3 = insulin independent- on liver, brain, erythrocytes
GluT4= insulin dependent- on fat and muscle

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28
Q

What is the significance of creating 1,3 - bisphosphoglycerate?

A

It has a high phosphoryl-transfer potential so able to phosphorylate ADP to make ATP

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29
Q

What regulates production of ATP/ NADH in bacteria?

A

Rusticyanin

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30
Q

How can bacteria produce ATP and NADH?

A

By reversing F-type ATPase, changing the use of the pmf created by cytochrome c oxidase

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31
Q

How can bacteria produce ATP and NADH?

A

By reversing F-type ATPase, changing the use of the pmf created by cytochrome c oxidase

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32
Q

Describe the structure of a photosystem

A

Contains Light Harvesting Complex and Reaction Centre

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33
Q

What ion is contained in chlorophyll?

A

Mg2+

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34
Q

How is light energy transferred to the reaction centre?

A

Resonance energy transfer

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35
Q

What are the 2 mobile electron carriers in the light dependent part of photosynthesis?

A

Plastoquinone
Plastocyanin

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36
Q

How is the H+ gradient established in photosynthesis?

A

1) NADH made in the stroma removes H+
2) formation of PQH2 takes up H+
3) photolysis of water

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37
Q

What are the 3 key steps of CBB cycle?

A

1) CO2 fixation by RuBisCO (RuBP-> 2x 3-PGA)
2) Reduction using ATP, NADH (3PGA- > GAP)
3)Regeneration of RuBP using ATP

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38
Q

What side reaction does RuBisCO carry out?

A

Oxygenation, forming 3PGA and phosphoglycolate which is toxic and requires ATP to be removed

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39
Q

How are damaged metabolites dealt with?

A

1) Repair pathway- return the molecule back into its original state (e.g NAD(P)HX back to NAD(P)H)
2) Pre- emption- Convert metabolite into a normal product (e.g XuBP to to Xu5P)

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40
Q

Why is regulation of metabolic reactions needed?

A

Avoid futile cycles
Respond to changes

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41
Q

Why is glucose important, and what’s special about muscle glucose?

A

1) Brain uses glucose
2) Muscle serves muscle only

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42
Q

How are enzymes controlled?

A

1) Change in enzyme concentration
2) Metabolic control (feedback inhibition ATP inhibits pyruvate kinase an PFK)
3) Allosteric inhibition- inhibition where molecule binds to another site (e.g. citrate synthase by ATP)

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43
Q

How is metabolism controlled intracellularly and extraccellularly?

A

Intra- allosteric inhibition
Extra- by hormones leading to phosphorylation

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44
Q

What occurs in the gluconeogenesis reaction step 1?

A

Pyruvate unable to go directly back to PEP, so intermediate of oxaloacetate is made. Requiring 2xCO2, ATP and GTP
Enzymes- pyruvate carboxylase and PEP- CK

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45
Q

What are the 2 allosteric inhibitors of PFK-1?

A

ATP and citrate

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46
Q

Why is glycolysis different from glycogenolysis?

A

2ATP from glycolysis however 3 ATP from glycogenolysis because only Pi required to make G -1-P instead of an ATP

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47
Q

What does each turn of the TCA cycle make?

A

3x NADH
1x FADH2
1x GTP

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48
Q

How is pyruvate turned into Acetyl CoA

A

Enzyme pyruvate dehydrogenase
Making a molecule of NADH

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49
Q

What is an anaplerotic reaction? And an example.

A

A reaction that produces an intermediate of the TCA cycle that can be used to replenish the cycle. Pyruvate to oxaloacetate catalysed by pyruvate decarboxylase

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50
Q

How can you measure the rate of the citric acid cycle?

A

coupling the cycle with oxygen consumption
1) Oxygen electrode
2) fMRI
3) Carbon labelling

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51
Q

How can pyruvate to Acetyl CoA be regulated?

A

Catalysed by PDH, when phosphorylated its inactive and vice versa
Lots of pyruvate and Ca2+ will activate PDH

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52
Q

How can the formation of citrate be controlled?

A

citrate synthase is allosterically inhibited by ATP
so allows reactants to be used in other reactions
oxaloacetate- gluconeogenesis
Acetyl CoA- ketone bodies

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53
Q

How is the formation of oxaloacetate controlled?

A

1) Substrate availability- pyruvate or aspartate, from pyruvate requires pyruvate carboxylase which requires biotin
2) Regulation of enzymes- e.g. pyruvate carboxylase, allosterically activated by acetyl CoA, inhibited by ADP
3) Hormones- glucagon, stimulate formation of oxaloacetate by promoting gluconeogenesis (requiring oxaloacetate to make glucose)

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54
Q

What is beta oxidation?

A

Production of Acetyl CoA from fatty acids, occurs in mitochondria and peroxisomes

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55
Q

What are the steps in beta oxidation?

A

1) Fatty acid binds to carnitine shuttle ( by carnitine actyltransferase I)
2) Moved through the membrane
3) fatty acid released and reacts with CoA-SH (by carnitine acyltransferase II)
4) Carnitine moves back out into cytosol

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56
Q

What are the steps of energy production in high energy sport?

A

1) Phosphocreatine is used
2) ATP broken down to release Pi
3) Pi phosphorylates glycogen to make glucose 1-P
4) Further stimulated by Ca2+ and adrenaline

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57
Q

What are the steps of energy production in long term exercise?

A

Glycogen oxidised, then fatty acids

58
Q

What is the effect of increase of AMP in exercise?

A

AMP is deaminated to IMP
IMP stimulates gluconeogenesis
IMP further degraded to adenosine
adenosine causes vasodilation

59
Q

What are the types of bacteria that can fix N2?

A

1) cyanobacteria
2) Soil bacteria (Rhizobium)

60
Q

How does direct N2 fixation occur?

A

Nitrogenase enzyme

61
Q

Describe the structure of the nitrogenase enzyme

A

Fe- reduced by ferredoxin, gives e- and reducing power
MoFe- 2 alpha and 2 beta subunits

62
Q

What occurs when ATP is hydrolysed in nitrogenase?

A

Conformational change bringing Fe closer to MoFe, ATP hydrolysis also coupled to electron transfer

63
Q

What is a negative of nitrogenase and what are the solutions around it?

A

Sensitive to inactivation by oxygen
1) remove PSII so no water hydrolysis
2) Symbitoic relationship O2 transfer by haemoglobin

64
Q

What are steps to get from nitrate to ammonia?

A

Nitrate -> Nitrite
Nitrite -> Ammonia

65
Q

How do you get from nitrate to nitrite?

A

Nitrate reductase- containing Mo cofactor
Requires e- donor (NAD(P)H)
Requires FAD, heme and Mo

66
Q

How do you get from nitrite to ammonia?

A

Nitrite reductase
Contains sirohaem and Fe4S4
Reducing power Ferredoxin

67
Q

How is ammonia incorporated into amino acids?

A

Via production of glutamate
via reductive amination of 2-oxoglutarate or
formation by initially incorporation of glutamate

68
Q

What is reductive amination of 2-oxoglutarate?

A

Occurs in animals and fungi
catalysed by glutamate dehydrogenase
1) forms Schiff base
2) Schiff base reduced by NAD(P)H

69
Q

Describe how glutamate is used to make more glutamate

A

1) form glutamine
catalysed by glutamine synthetase
2) glutamine + 2-oxoglutarate + NADH
catalysed by glutamate synthase
produces 2 glutamate

70
Q

How are amino groups transferred from glutamate?

A

1) Transamination
2) Carbon skeleton alteration

71
Q

Describe how transamination occurs

A

Catalysed by aminotransferases
Glutamate +pyruvate makes Alanine + oxoglutarate

72
Q

Describe the structure and function of aminotransferases/ transminases

A

Contain Vit B6 (pyridoxal phosphate (PLP) cofactor)
Transfer amine groups, e.g. from amino acids in amino acid catabolism
Also production of amino acids

73
Q

Describe how carbon skeleton alteration produces amino acids

A

Rearrangement of the glutamate
Requires - 2x NADPH and ATP
produces Proline

74
Q

Where does the C skeleton for amino acid synthesis come from?

A

Oxoglutarate in citric acid cycle
also known as alpha-ketoglutarate

75
Q

How is oxaloacetate replenished?

A

Carboxylation of C3 intermediate compounds
1) CO2 converted into HCO3-
by carbonic anhydrase
2) HCO3- incorporated
pyruvate carboxylase (animals)
PEP (plants and bacteria)

76
Q

Who proposed the chemiosmotic theory and when?

A

Peter Mitchell in 1961

77
Q

What is the chemiosmotic theory?

A

Based on the ETC and ATP synthesis coupled to a proton gradient (pmf)

78
Q

What are the 2 components of the pmf?

A

chemical and charge gradients

79
Q

What is the main component of the pmf in chloroplasts and mitochondria?

A

Mitochondria= charge
Chloroplast= pH/ chemical

80
Q

What are the 4 pieces of evidence for the pmf?

A

1) detergent stopping gradient
2) hydrophobic anions and bases (create H+ channel) dissipating gradient
3) Inhibitors of ATP synthesis
4) Artificial membrane, showing only H+ gradient and ATP synthase needed, ETC not actually needed

81
Q

What is the structure of F-type ATP synthase like?

A

F0 in the membrane which causes rotation
F1 catalytic area creating ATP

82
Q

What does the proton gradient actually do in the ATP synthase?

A

Allow the release of ATP, by moving through F0 which causes conformational change in beta subunit. DOES NOT CAUSE ATP SYNTHESIS.

83
Q

Which subunit rotates the alpha and beta ring?

A

Gamma subunit

84
Q

Which way and by how many degrees does the F1 rotate?

A

120 degrees counter clockwise

85
Q

Why is ATP synthase regulated?

A

Working backwards would cause ATP to be used up and wasteful processes to occur

86
Q

Examples of ATP synthase regulation

A

Chloroplast- high inhibition overnight
Anaerobic bacteria- weak inhibition, use backwards reaction to allow ion movement and flagella motility

87
Q

Features of ion channels

A

Conformational change
Aqueous pore
Size of chanel
Charge channel

88
Q

Describe an experiment that tests for rotational movement of F-ATPase sub-units.

A

Single Molecule Fluorescent Microscopy
1) Fluorescent dye added
2) F-ATPase immobilized onto surface
3) Proton gradient added, for the function
4) F1 subunit rotates, and is detected

89
Q

Outline the likely journey of a nitrogen atom from the atmosphere to a beef sandwich

A

N2 turned into ammonia
via bacteria (nitrogenase), lightning or Harber Process
Then ammonia absorbed by roots of plants, converted to amino acids & nucleic acids
Cows eat the plants, taking up the nitrogen
Amino acids reworked into proteins in cows which can be present in the muscle of the cow that is eaten as beef

90
Q

In metabolism what are activated carriers and why are they so common in metabolic pathways?

A

Activated carriers- carry electrons or chemicals between reactions
e.g. ATP, NAD+ and NADH+, FAD and CoA
Common- link different metabolic reactions, act as reducing agents etc, for reactions

91
Q

Describe the role of sigma factors in promoter recognition in prokaryotes

A

Present in RNA polymerase
Function is to allow binding to specific promoters, to initiate transcription
Examples include sigma-70 recognises genes for growth and sigma-32 is for transcribing heat shock proteins
Also helps stabilizes the interaction between RNA polymerase and DNA

92
Q

How does p53 function as a tumour suppressor?

A

p53 controls aspects of the cell cycle
Is activated when there is damage and stops the cell cycle
If damage severe will cause apoptosis
It inhibits the activity of CDK

93
Q

In protein structure, why are β -sheets made of antiparallel β -strands more stable than those of parallel strands? Why therefore is a βαβ super-secondary structure common?

A

Antiparallel= H bonds are more linear so stronger
Greater van der Waals interactions
βαβ incorporates flexiblity of alpha helix, with stability/rigidity of β

94
Q

How can “flip-flop” of a phospholipid in a bilayer be demonstrated?

A

1) FRAP -flip flop increases rate of recovery, because flip of other phospholipids can help recover fluorescence quicker
2) Spin labelling- molecule with stable radical added, if flip flop occurs changes in electron spin resonance detected
3) Modify membrane so that only one side can react with chemical, put the chemical on the opposite side and if reaction occurs, means that flipping has occured

95
Q

Excluding DNA replication, summarise two ways in which the information encoded in DNA sequence can be “read” by cellular processes

A

Transcription (describe)
DNA binding proteins- in major and minor groove e.g. Sigma factor, binding to promoter region

96
Q

Briefly outline the different mechanisms used by organisms to synthesize glutamate.

A

Animals/Fungi- form schiff base
2- oxoglutarate + NH4+ -> glutamate (glutamate dehydrogenase)
Plant/Fungi- use glutamate
glutamate + NH4+ -> glutamine (glutamine synthetase)
glutamine+ 2-oxoglutarate -> 2x glutamate (glutamate synthase)

97
Q

Name, and briefly describe, the characteristics and functions of three types of RNA involved in the process of protein translation

A

mRNA- messenger, provides the code for translation, produced in nucleus
tRNA- transfer RNA, anticodon, brings amino acid to ribosome
rRNA- forms part of the ribosome, which is the organelle that carries out translation

98
Q

Name and briefly contrast two alternative cycles of viral replication.

A

Lytic- fast replication cycle, causes build up of virus, and lysis of cells
Lysogenic- slower cycle, may integrate virus DNA into host DNA, then enters lytic cycle

99
Q

How does the presence of sterols influence animal plasma membranes as the temperature changes

A

e.g. Chlosterol
At low temp- maintain fluidity, stop membrane too rigid
At high temp- stops leakage, restrict movement, present for stability

100
Q

What are the three main redox carriers used in metabolism? Provide an example of a pathway in which each operates and the role of the carrier in that pathway

A

NAD/NADH- in respiration becomes reduced to NADH, releases H in oxidative phosphorylation, for ATP synthesis
NADPH- present in plants for photosynthesis, required to fix carbon in Calvin cycle
FADH- present in respiration, reducing agent, providing H+ for proton gradient

101
Q

Briefly compare and contrast enzyme regulation by phosphorylation and allostery

A

Phosphorylation- extracellular signals, rapid, reversible control
Allosteric- intracellular signals, sustained regulation and feedback control, ATP + Citrate inhibitors of PFK1

102
Q

What reaction does nitrogenase catalyse and what is the role of Fe (iron) in this process?

A

Nitrogenase reacts N2 to form ammonia
Important for nitrogen fixation in bacteria
Fe is oxidised and reduce
Provides e- for MoFe subunit to allow reaction to occur

103
Q

Briefly describe the differences between embryonic and somatic cell cycles in animals.

A

Embryonic- little growth between divisions
Somatic- growth, distinct phases G1, S, G2, M

104
Q

Discuss the contribution of studies in model organisms for understanding fundamental controls of the human cell cycle

A

CDKs- discovered using yeast and frogs eggs
p53- discovery through mice
More ethical

105
Q

Describe 3 ways in which enzymes can be controlled in the eukaryotic cell

A

Competitive inhibition: Blocks active site - succinate dehydrogenase inhibition by malonate (since malonate has similar structure to succinate) preventing fumarate formation
Allosteric inhibition: conformation change to active site shape, reducing affinity - hexokinase inhibition in muscles by glucose 6-phosphate (less immediate and weaker)
Compartmentalisation - lysozymes in lysosomes - isolated to prevent unwanted protein degradation within cell (no substrate available so inhibited)
Covalent modification (e.g. phosphorylation, methylation): similar to allostery but temporary addition of covalently bonded molecule - rapid and reversible - phosphorylation of transcription factors by protein kinase enzyme to stop gene expression

106
Q

Describe 3 similarities between the cytochrome b6f complex in chloroplasts and complex III of mitochondria

A

Multi-subunit transmembrane complexes
Are electron acceptors- b6f from plastoquinol, complex III from ubiquinol
Translocate H+ across membranes
Both contain embedded e- carriers (b6f= haem, complex III= FeS clusters)

107
Q

Explain why uracil is one of the four bases in RNA, but DNA contains thymine instead.

A

Difference- Thymine has extra methyl on C5
-Uracil resistant to oxidation
Important because RNA has to leave the nucleus and still be stable
-Thymine more resistant to damage by UV
Uracil not stable in DNA and can be formed by deamination of cytosine, so mechanism developed to turn Uracil into thymine
-Evolutionary- Uracil and RNA came first

108
Q

Explain the structural basis of phospholipid diversity using a labelled diagram

A

Phosphate head- hydrophillic, exposed to inside and outside of cell
Fatty acid tail- hydrophobic

109
Q

How have scanning and transmission electron microscopy aided the study of cell biology?

A

Broken the diffraction limit
Higher resolution
No antibodies needed, no fluorescent tagging required but can still be used together
Scanning EM allows 3D image

110
Q

How is fluorescence microscopy used to show protein mobility in membranes?

A

Stain with Green Fluorescent protein (GFP)
FRAP- F recovery after P
- bleached, and intensity measured overtime
FLIP- F loss in P
- Measure change in intensity of neighboring protein

111
Q

Why are membranes so important for life?

A
  • Compartmentalisation, of enzymes, toxic compounds, allow gradient build up (pmf)
  • Storage, lipid droplets, BAT
  • Insulation, Schwann cells, saltatory conduction
  • Chemiosmosis
112
Q

What is the 5’/3’ structure of nucleotides and why is it significant?

A

Number is for specific C
Important for formation of phosphodiester bond
Polymerases and ribosomes synthesis 5’ to 3’
All nucleotides in same orientation and 2 complementary strand forms

113
Q

Explain why NADH and NADPH are used in metabolism

A

Small easy to synthesise
Good reduction and oxidation molecules, carry e- and H+
Important for metabolism e.g. oxidative phosphorylation, glycolysis and Calvin Cycle
Present in anabolic and catabolic reactions

114
Q

How do protein pigment complexes allow efficient harvesting of light energy?

A

Contain Mg2+ held between 4N, e- can be excited
Large surface area
Resonance E transfer allows transfer to special pair in reaction site
Can be densely packed together, make harvesting more efficient

115
Q

Importance of the hydrolysis aceytl-coA have ΔG = -31.4KJmol-1

A

-ve so reactions occurs spontaneously
Releases energy, to sustain TCA cycle
Close to hydrolysis value of ATP
Allows continuous addition of C into cycle

116
Q

How does GLUT4 regulate glycolysis in skeletal muscle and adipose tissue?

A

GLUT 4 not always present on the membrane, usually stored in vesicles
When activated increases the amount of glucose coming in for glycolysis
Activated by insulin

117
Q

In metabolism outline how the role of NADPH differs from that of NAD+

A

NADPH reducing agent whereas NAD+ is an oxidising agent
NADPH involved in reductive biosynthesis (anabolism)
NAD+ involved in oxidative phosphorylation
NAD+ used in nitrate reductase (anabolism)
NADPH not used in catabolism

118
Q

What is the oxidative pentose phosphate pathway and what are its roles?

A

Oxidation of Glucose-6-phophate to produce NADPH and pentose
NADPH and pentose sugars important for other biosynthesis, e.g. fatty acids and DNA/RNA respectively
Some energy production when G-6-P turned to ribulose-5- phosphate

119
Q

How does DNA exemplify the properties required of any molecule used to store genetic information in a biological system?

A

Stable- can withstand processes without losing integrity
Extracted/ accessed- via transcription and DNA binding proteins
Variability- can undergo mutations and changes
Replication- can be replicated very accurately, during DNA replication

120
Q

What is the anomeric carbon atom in polymers of D-glucose? Why is it important?

A

Anomeric carbon- new chiral carbon that forms
-Can be in 2 configurations alpha or beta, which then effects the shape of D-glucose
-Leading to different stereoisomers
-Alpha being more flat and beta being more vertical
-Beta for cellulose and plants
-Alpha for animals, and energy storage

121
Q

Describe three pieces of evidence for chemiosmosis

A

Artificial membrane- of just light activated H+ pump and ATPsynthase
Detergents- diffuse the H+ gradient
Uncoupler- diffuse the H+ gradient, e.g. DNP
pH of membrane- more acidic in the intermembrane space
Overall shows that the two processes are separate, but linked via the proton gradient

122
Q

Most unsaturated carbon bonds of membrane phospholipids are in the cis formation. Why is this important?

A

Doesn’t allow tight packing, cis forms kinks
- Fluidity
Maintain liquid crystal state
- Permeability
- Unsaturated helps deal with changes in temp

123
Q

What is the Cori Cycle and why is it important during exercise?

A

Cori cycle is means of regenerating NAD+ for glycolysis and the production of ATP, by forming lactate
Lactate is then transported to the liver, where it is turned into pyruvate, and then glucose by gluconeogenesis
This stops the build up of lactate, and reforms NAD+ for glycolysis to make 2ATP in anaerobic conditions

124
Q

What is the function of the ribosome? How could the ability of a single RNA to bind to multiple ribosomes be demonstrated?

A

Ribosomes carry out protein synthesis through translation
Polysome profiling to see multiple ribosomes attached to RNA
1) Cross linker preserve RNA-ribosome interactions
2) Cell lysed, lysate centrifuged and separated by size and density on a sucrose density gradient
3) Fractions from the gradient show polysomes

125
Q

Briefly, describe an experiment that tests for rotational movement of F-ATPase sub-units

A

Beta subunit anchored by nickel covered beads
Attached to fluorescent actin
Rotor driven artificially by add ATP
Fluorescent microscope used to detect rotation of actin filament

126
Q

Explain why uracil is one of the four bases in RNA, but DNA contains thymine instead

A

Uracil is less stable
Thymine more stable, important for long term info storage
Thymine more easily oxidised, in nucleus it’s OK, however cytosol is a more oxidative environment
C can be deaminated into U, which would lead to many mutations

127
Q

Describe the structural differences between a beta strand and alpha helix including the forces involved to stabilise these protein secondary structures

A

alpha
- low phi and psi angles
- compact helical shape
- stabilised by H bonds between CO and NH (every 5th residue)
Beta
- High phi and psi angles
- Antiparallel gives strongest alignment
- best alignment of CO/NH bonds

128
Q

How do protein-pigment complexes in photosynthetic membranes allow efficient harvesting of light?

A
  • Multiple pigments present to absorb light e.g. chlorophyll
  • Closely located to allow for efficient energy transfer by resonance
  • reaction centre is where an electron is excited
  • ‘funneling’ of energy allows excitation even in dim light
129
Q

Discuss the importance of the fact that the hydrolysis of Acetyl CoA has a standard Gibbs free energy of -31.4kJ/mol

A

-ve which means it releases energy
Occurs spontaneously
Likely to be more negative due to high conc of water in the cell
Activated form of acetate, making some reactions more favourable

130
Q

Briefly discuss why the conversion of glucose to glucose-6-phosphate is an important regulatory step in glycolysis

A

Muscles- hexokinase, liver- glucokinase
Prevents leaving of glucose by glucose transporters (e.g. SGLT1)
Primes glucose for degradation to make energy
G-6-P an allosteric inhibitor of hexokinase

131
Q

How have scanning and transmission EM aided the study of cell biology?

A

Higher resolving power
Resolution (few nms from light (100s nm))
SEM- can create 3D images
EM- allows visualization of organelles
No requirement for antibodies or staining

132
Q

Outline 3 techniques you might use to determine PROTEIN structure. What are the advantages and disadvantages?

A

X-ray crystallography
- require crystals
+ atomic level structure
NMR
- may require labelling
+ can identify flexible regions
Cryo-EM
- artefacts may form when freezing, low Res
+ cheap
Atom force microscopy
- poor width measurment
+ cheap, good for general shape

133
Q

In metabolism what are activated carriers and why are they so common in metabolic pathways?

A
  • high energy intermediates
  • used in energy storage and redox reactions
  • versatile and can be used in many reactions
  • ATP- stores energy in form of phosphate bonds
  • NADH- electron carrier, involved in glycolysis, TCA cycle, oxidative phosphorylation
134
Q

Briefly explain how non-photosynthetic cells make NADPH. Why do they need to?

A

NADH important as an electron transfer molecule. It accepts an electron, is reduced, in glycolysis. This is important in creating ATP
Important molecule for the synthesis of molecules, such as fatty acids

135
Q

What is the role of Coenzyme A in metabolism?

A
  • Carrier molecule for acyl groups
  • Functions as a coenzyme so helps other enzymes carry out their role
  • important in fatty acid metabolism, as well as amino acid metabolism
136
Q

What is the role of Coenzyme A in metabolism?

A
  • Carrier molecule for acyl groups
  • Functions as a coenzyme so helps other enzymes carry out their role
  • important in fatty acid metabolism, as well as amino acid metabolism
  • Present in the TCA cycle and produces ATP, NADH and FADH2
137
Q

Describe the differences between the flagella of prokaryotes and eukaryotes

A

Eukaryotes more complex
Prokaryote made of flagellin, Eukaryote made of tubulin
Prokaryote move via rotation, using ion gradient, Eukaryote move by bending/ whipping, using motor proteins (dyneins)

138
Q

Describe electron flow in the light dependent reaction

A

Occurs in photosynthesis
i) electron lost at PSII due to absorption of light 680nm
ii) electron passed down ETC, cause movement og H+
iii) electron passed on to PSI
iv) from PSI passed down ETC
v) goes on to reduce NADP+ to NADPH
vi) photolysis of water replenishes e- lost at PSI

139
Q

The primary sequence of a protein is always the same, but this is not true for polysaccharides. Explain why this is the case

A

Protein amino acid sequence is dependent on the mRNA which it is translated from. The sequence needs to be the same because the folding needs to be the same.
Polysaccharides can form glycosidic bonds at C4 or C6 with C1 to form different branched structures
They aren’t coded for so their sequence can vary
Different monomers such as fructose or galactose can be used instead of glucose
They can also exist as isomers alpha and beta forms

140
Q

Why does ATP have such a high free energy of hydrolysis?

A

High energy phosphate bonds are present
Negatively charge so repel each other
Balanced by resonance stabilization, which contributes to the high energy content
Around -31kJ/mol

BoC (4 decks)

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