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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
Why does glucose become trapped in the cell
Negative charge
26
What are the 3 important enzymes for glycolysis
Kinases -catalyse transfer of phosphate Isomerase - catalyses conversion to another isomer Mutase - changes position of groups
27
List the steps of glycolysis + enzymes
Check notes
28
What is produced by glycolysis
2 NADH | 2 ATP
29
What are the 3 fates of pyruvate
alcoholic fermentation Conversion to lactate Generation of Acetyl coA
30
Descrive alcoholic fermentation
Characteristic of yeast Anaerobic Pyruvate to acetaldehyde using pyruvate decarboxylase Acetaldehyde to ethanol using alcohol dehydrogenase Release of carbon dioxide then NAD+
31
Describe conversion to lactate
Anaerobic Characteristic of muscle when O2 is limiting pyruvate to lactate by lactate dehydrogenase Release of NAD+
32
Describe generation of acetyl coA
Mitochondria to enter TCA cycle Pyruvate + HS-CoA to acetyl coA and CO2 by pyruvate dehydrogenase complex Release of NADH
33
What can lactate dehydrogenase be used for clinically
Elevated levels can be used to diagnose stroke, heart attack, liver disease, muscle injury
34
What is the purpose of creatine phosphate stores
Provides phosphate for ATP regeneration
35
Describe the reaction that creatine kinase is involved in
Creatine phosphate to creatine + ATP
36
What can creatine kinase be used for clinically
Muscle damage leads to leaking of CK - elevated levels can be used to diagnose MI, muscular disease, chest pain, muscular dystrophy
37
What are the 3 overall steps of metabolism
Digestion - larger molecules break down to smaller ones Cellular metabolism I - oxidation in the cytosol Cellular metabolism II - oxidation in the mitochondria
38
Describe the pyruvate dehydrogenase complex
very large complex of 3 enzymes and 5 co-factor enzymes pyruvate decarboxylase (TPP) Lipoamide reductase transacetylase (lipoamide) dihydrolipoyl dehydrogenase (FAD) NAD + coA
39
What does a deficiency in TPP lead to
Beri Beri syndrome
40
Which factor in the pyruvate dehydrogenase complex acts as the swimming arm
lipoamide
41
Describe the process of pyruvate dehydrogenase action
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
How much ATP is produced in aerobic vs anaerobic respiration
38 ATP vs 4 ATP
43
How is metabolism involved in cancer
Tumour cells will use a lot of glucose so radioactive labelled glucose can be used, emitting positrons PET scans used for detection
44
Where are the enzymes used in the Krebs cycle found
Mitochondrial matrix except succinate dehydrogenase which is on the inner mitochondrial membrane
45
What are the products of one Krebs cycle
2 CO2 3 NADH 1 FADH2 1 GTP
46
What is oxygen required for in the Krebs cycle
Co-factor generation
47
List the steps of the Krebs cycle
Can I Keep Selling Sex For Money Officer | Refer to notes
48
Describe transanimation and give an example
amine groups are transferred from one amino acid to a keto acid e.g. alanine via alanine aminotransferase
49
Why are shuttles needed
To allow NADH to enter the mitochondria and regenerate NAD+
50
Describe the glycerol phosphate shuttle
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
Describe the malate aspartate shuttle
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
What does NADH and FADH2 yield from oxidative phosphorylation
NADH - 3 ATP | FADH2 - 2 ATP
53
Compare anabolic to catabolic reactions
anabolic - creating molecules using NADPH | catabolic - breaking down molecules using NADH
54
What can NADPH be used for
``` thymidine synthesis (DNA) Cholesterol synthesis ```
55
Describe the structure of the mitochondria
``` 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
Explain the proposed evolutionary origins of the mitochondria
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
Define the chemiosmotic theory
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
Summarise the ETC
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
Explain the role of coenzyme Q and cytochrome C
Ubiquinone (Q) transfer 2 electrons from NADH dehydrogenase to cytochrome C (hydrophobic tail confines to membrane) FADH2 passes electrons to ubiquinone
60
What feature of the ETC allows unidirectionality
Each unit has a higher affinity for electrons than the one before
61
What is the order of units in the ETC
NADH dehydrogenase complex Cytochrome b-c complex Cytochrome oxidase complex
62
Explain how ATP synthase can generate and utilise ATP
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
Explain the process of ATP synthase action in the ETC
1. proton flow 2. C and gamma rotate 3. alpha and beta remain stationary (fixed by b) 4. ATP generation/utilisation
64
How does cyanide/azides work as a poison
bind to the ferric form (Fe3+) of the hame group in cytochrome oxidase and blocking electron flow
65
How does malonate work as a poison
competitive inhibitor of succinate dehydrogenase, slowing flow to ubiquinone
66
How does oligomycin work as a poison
produced by streptomycin that binds to the ATP synthase stalk to inhibit oxidative phosphorylation
67
How does DNP work as a poison
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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