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MCD > Metabolism 1 > Flashcards

Metabolism 1 Flashcards

1
Q

Summarise the reaction by which amino acids are joined together

A

Condensation reaction using the energy from hydrolysis of ATP, releasing water and join gin by peptide bonds

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2
Q

Distinguish between the different types of bond that stabilises protein conformation (peptide, ionic, covalent, van der Waals)

A

Peptide - no free rotation, only conformations where side chains do not clash allowed
Ionic - salt bridge, electrostatic attraction between charged side chains
Covalent/ disulphide - cysteine side chains oxidised
Van der Waals - weak but large no

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3
Q

Where are hydrogen bonds in a protein

A

between C=O and N-H every 4 amino acids, found between side chains and the backbone/water

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4
Q

What is the significance of hydrophobic bonds

A

Creates a hydrophobic core and hydrophilic core as hydrophobic side chains are in the interior

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5
Q

What is the structure of the following: glycine, alanine, valine

A

H

CH3

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6
Q

What is the structure of the following: Serine, threonine, cysteine

A

CH2-OH
CH-CH3-OH
CH2-SH

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7
Q

What is the structure of the following: Lysine, Arginine, Aspartate, Glutamate

A

(CH2)4-NH3+
(CH2)3-NH-C-(NH2)2
CH2-COO-
(CH2)2-COO-

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8
Q

Which are positively charged and negatively charged: Aspartate, arginine, glutamate, lysine

A

Arginine and lysine +ve

Aspartate and glutamate -ve

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9
Q

Describe the structure of a beta pleated sheet

A

NH and C=O groups point out at right angles

Alternate strands run in different directions, parallel or anti parallel

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10
Q

Describe the structure of a alpha helix

A

side chains project out of the helix

Right handed helices favoured due to L-AAs

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11
Q

What happens to the structure of a protein when proline is present

A

NH group is lost so the side chain cannot H-bond, distorting the helix and putting in a “kink”

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12
Q

Summarise the different levels of conformation of a protein

A

Primary: Single polypeptide chain
Secondary: Polypeptide chain folded into an alpha helix or beta pleated sheet
Tertiary: Further folding with hydrogen and disulphide bonding to keep shape into domains
Quaternary: two or more polypeptide chains

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13
Q

Summarise N-linked glycosylation

A

addition of sugar groups to asparagine to ensure it adopts the correct conformation in the cell membrane

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14
Q

How can free energy be used to produce outcome of a reaction

A

if the free energy (kJ/mol) is -ve then the reaction is spontaneous
Reactions proceed in the direction of more disorder

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15
Q

Why may a reaction not occur even if free energy is -ve and how can it be overcome

A

There may be a high activation energy that must be overcome. Energetically unfavourable reactions can occur by coupling them with favourable ones

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16
Q

How does ATP act as a carrier of free energy

A

3 phosphate groups bonded by high energy anhydride bonds that release a lot of energy (largely -ve free) when broken
This release can overcome activation energies for other reactions

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17
Q

Explain how enzymes act as catalysts of reactions

A

Enzymes are biological catalysts that act without being used up, lowering the activation energy through a different reaction pathway

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18
Q

How does lysozyme work

A

Hydrolysis of the 1-4 glycosidic bond between NAG and NAM in the cell wall of bacteria

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19
Q

Describe the process of lysozyme action

A
  1. Glu-35 protonates the O in the bond to split the sugars
  2. Asp-52 neutralises the positive charge on the NAM
  3. A water molecule is deprotonated by the Glu-35 with a negative O
  4. The remaining OH attacks the NAM
  5. Asp-52 and Glu-35 return to the original state
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20
Q

What pH does lysozyme work at and why

A

5.0 as aspartic acid is ionised while Glucose-35 is not

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21
Q

What is the difference between lock and ket and induced fit

A

Lock and key - substrate perfectly fits the active site

Induced - active site changes as the substrate binds

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22
Q

Draw graphs to show the effect of pH, substrate concentration and temp. on enzyme reactions

A

pH - almost symmetrical curve
temp - curve that peaks at greater temps
SC - increase then plateau

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23
Q

What is the role of NAD in the reaction catalysed by lactate dehydrogenase

A

Accepts H atom, 2 electrons

Usually catalyses “oxidation” from -OH to =O

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24
Q

What type of reaction is involved in formation of covalent bonds

A

Ligation requiring ATP cleavage

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25
Q

Why does glucose become trapped in the cell

A

Negative charge

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26
Q

What are the 3 important enzymes for glycolysis

A

Kinases -catalyse transfer of phosphate
Isomerase - catalyses conversion to another isomer
Mutase - changes position of groups

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27
Q

List the steps of glycolysis + enzymes

A

Check notes

28
Q

What is produced by glycolysis

A

2 NADH

2 ATP

29
Q

What are the 3 fates of pyruvate

A

alcoholic fermentation
Conversion to lactate
Generation of Acetyl coA

30
Q

Descrive alcoholic fermentation

A

Characteristic of yeast
Anaerobic
Pyruvate to acetaldehyde using pyruvate decarboxylase
Acetaldehyde to ethanol using alcohol dehydrogenase
Release of carbon dioxide then NAD+

31
Q

Describe conversion to lactate

A

Anaerobic
Characteristic of muscle when O2 is limiting
pyruvate to lactate by lactate dehydrogenase
Release of NAD+

32
Q

Describe generation of acetyl coA

A

Mitochondria to enter TCA cycle
Pyruvate + HS-CoA to acetyl coA and CO2 by pyruvate dehydrogenase complex
Release of NADH

33
Q

What can lactate dehydrogenase be used for clinically

A

Elevated levels can be used to diagnose stroke, heart attack, liver disease, muscle injury

34
Q

What is the purpose of creatine phosphate stores

A

Provides phosphate for ATP regeneration

35
Q

Describe the reaction that creatine kinase is involved in

A

Creatine phosphate to creatine + ATP

36
Q

What can creatine kinase be used for clinically

A

Muscle damage leads to leaking of CK - elevated levels can be used to diagnose MI, muscular disease, chest pain, muscular dystrophy

37
Q

What are the 3 overall steps of metabolism

A

Digestion - larger molecules break down to smaller ones
Cellular metabolism I - oxidation in the cytosol
Cellular metabolism II - oxidation in the mitochondria

38
Q

Describe the pyruvate dehydrogenase complex

A

very large complex of 3 enzymes and 5 co-factor enzymes
pyruvate decarboxylase (TPP)
Lipoamide reductase transacetylase (lipoamide)
dihydrolipoyl dehydrogenase (FAD)
NAD + coA

39
Q

What does a deficiency in TPP lead to

A

Beri Beri syndrome

40
Q

Which factor in the pyruvate dehydrogenase complex acts as the swimming arm

A

lipoamide

41
Q

Describe the process of pyruvate dehydrogenase action

A
  1. decarboxylation -> hydroxyethyl TPP
  2. oxidation and transfer to lipoamide -> acetyl lipoamide
  3. transfer of acetyl -> acetyl coA
  4. regeneration of oxidase lipoamide + FAD -> NADH
42
Q

How much ATP is produced in aerobic vs anaerobic respiration

A

38 ATP vs 4 ATP

43
Q

How is metabolism involved in cancer

A

Tumour cells will use a lot of glucose so radioactive labelled glucose can be used, emitting positrons
PET scans used for detection

44
Q

Where are the enzymes used in the Krebs cycle found

A

Mitochondrial matrix except succinate dehydrogenase which is on the inner mitochondrial membrane

45
Q

What are the products of one Krebs cycle

A

2 CO2
3 NADH
1 FADH2
1 GTP

46
Q

What is oxygen required for in the Krebs cycle

A

Co-factor generation

47
Q

List the steps of the Krebs cycle

A

Can I Keep Selling Sex For Money Officer

Refer to notes

48
Q

Describe transanimation and give an example

A

amine groups are transferred from one amino acid to a keto acid e.g. alanine via alanine aminotransferase

49
Q

Why are shuttles needed

A

To allow NADH to enter the mitochondria and regenerate NAD+

50
Q

Describe the glycerol phosphate shuttle

A

Skeletal muscle, brain
glycerol-3-phosphate dehydrogenase transfers electrons to DHAP to generate G-3-P
The same enzyme in the membrane transfers electrons to FAD, then passed to co-enzyme Q in the ETC

51
Q

Describe the malate aspartate shuttle

A

Liver, kidney, heart
2 membranes, 4 enzymes
H- transferred from NADH to oxaloacetate to give malate (malate dehydrogenase)
Malate transported into the mitochondria, re-oxidation by NAD+
Refer to notes

52
Q

What does NADH and FADH2 yield from oxidative phosphorylation

A

NADH - 3 ATP

FADH2 - 2 ATP

53
Q

Compare anabolic to catabolic reactions

A

anabolic - creating molecules using NADPH

catabolic - breaking down molecules using NADH

54
Q

What can NADPH be used for

A 
thymidine synthesis (DNA)
Cholesterol synthesis
55
Q

Describe the structure of the mitochondria

A 
Infoldings - cristae to increase SA
oxidative phosphorylation in the inner membrane 
Krebs cycle in the matrix
Several copies of the genome 
mtDNA is through the ovum so from mother
56
Q

Explain the proposed evolutionary origins of the mitochondria

A

Evolutionary descendants of a prokaryote that established an endosymbiotic relationship
Only arises from pre-existing mitochondria
Own circular genome
Own protein-synthesising machinery
First amino acid of transcripts is a fMet (bacteria) and not Met (eukaryotes)
Antibiotics that affect bacterial protein synthesis can also affect mitochondria (but not eukaryotes)

57
Q

Define the chemiosmotic theory

A

Translocation of protons from within the matrix is controlled by the electron transport or respiratory chain
Pumping of a proton through ATP synthase creates a gradient. The proton motive force that drives h+ consists of both a pH and a transmembrane electrical potential

58
Q

Summarise the ETC

A

Proteins accept electrons and a proton
Electrons pass through complexes so that protons are pumped into the inter membrane space
Cytochrome oxidase receives 4 electrons before the cycle repeats
Electrons passed to oxygen to generate water

59
Q

Explain the role of coenzyme Q and cytochrome C

A

Ubiquinone (Q) transfer 2 electrons from NADH dehydrogenase to cytochrome C (hydrophobic tail confines to membrane)
FADH2 passes electrons to ubiquinone

60
Q

What feature of the ETC allows unidirectionality

A

Each unit has a higher affinity for electrons than the one before

61
Q

What is the order of units in the ETC

A

NADH dehydrogenase complex
Cytochrome b-c complex
Cytochrome oxidase complex

62
Q

Explain how ATP synthase can generate and utilise ATP

A

Contains F0 and F1
F0 - a,b,c
F1 - 𝛼,β,𝛾
Protons passing through causes rotation with transition states with altering affinities for ATP and ADP
Generation or utilisation depends on direction of flow

63
Q

Explain the process of ATP synthase action in the ETC

A
  1. proton flow
  2. C and gamma rotate
  3. alpha and beta remain stationary (fixed by b)
  4. ATP generation/utilisation
64
Q

How does cyanide/azides work as a poison

A

bind to the ferric form (Fe3+) of the hame group in cytochrome oxidase and blocking electron flow

65
Q

How does malonate work as a poison

A

competitive inhibitor of succinate dehydrogenase, slowing flow to ubiquinone

66
Q

How does oligomycin work as a poison

A

produced by streptomycin that binds to the ATP synthase stalk to inhibit oxidative phosphorylation

67
Q

How does DNP work as a poison

A

proton ionophore that can shuttle protons
Uncouples oxidative phosphorylation from ATP production
Heat is released from the ETC
Leads to weight loss, increase in temp. and metabolic rate

MCD (13 decks)

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