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Biostructures, Energetics and Synthesis > Metabolism > Flashcards

Metabolism Flashcards

1
Q

Homo-oligomers vs hetero-oligomers?
What do they assemble into?

A

Homo - Many copies of the same polypeptide
Hetero - Copies of different chains

They assemble into dimers and trimers etc.

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2
Q

2 main classes of proteins?
Characteristics?

A

Globular - Surrounded by water; Hydrophobic inside and hydrophilic outside

Membrane - Hydrophobic trans membrane sequences; Hydrophilic inside

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3
Q

3 types of membrane proteins?

A

Alpha-helix
Helical bundle (several TM helices)
Beta-barrel

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4
Q

Explain each term of ∆G = ∆H – T∆S equation
Entropy equation?

A

Free energy (∆G) - Total amount of energy available to do work (conversely, the total amount of energy expended in doing work; If ∆G < 0, the reaction will go

Enthalpy (∆H) - Energy available from bonds and other bonding interactions

Entropy (∆S) - Amount of disorder in the system

∆S = klnW
k is Boltzmann’s constant
W is the number of ways of creating the system

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5
Q

What is the law of mass action?

A

If you remove products continuously, then the concentration of products is always low; This means that ∆G is kept more negative, and it pulls the reaction to the right

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6
Q

What is the equation for Coulomb’s law?

A

F ∝ k(q1xq2)/Dr^2

q1 and q2 - Represents 2 charges
r - Distance between charges
D - Dielectric constant

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7
Q

Different D values in different states? (3 states)
Meaning of higher D values?

A

Vacuum - 1
Hydrophobic interior - 2
Protein exterior - 80

Higher D means the force between charges is weaker

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8
Q

Are there many ionic bonds or charged groups inside globular proteins?
Is this the opposite for the outside?

A

Few ionic bonds and charged groups on the inside

This is the opposite for the outside as there are many interactions

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9
Q

Main type of interaction that drives secondary protein formation?
How does this affect the geometry (hint: directionality)

A

Hydrogen bonding

Highly directional so they restrict protein geometry

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10
Q

What interactions drive globular protein folding in water?

A

Hydrophobic interactions

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11
Q

Catabolism vs Anabolism?
Which produces and which uses energy?

A

Catabolism - Break down of molecules; Produces energy
Anabolism - Building of molecules; Uses energy

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12
Q

What does phosphorylation do to a molecules energy level?

A

It raises it into a higher energy form

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13
Q

Why do reactions that liberate CO2 tend to be energetically favourable? (3 reasons)

A
  • CO2 is very stable (lower free energy than the reactants)
  • CO2 easily escapes from the site of reaction; This means that the concentration of CO2 is kept low, which pulls the reaction over to the right by the law of mass action
  • Usually when a reaction generates CO2, you end up with more molecules than you started with; Favourable entropy, pushing reaction to the right
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14
Q

Why are reactions that produce CO2 wasteful?
What are the benefits of producing CO2?

A

CO2 is lost so a C atom is lost
Produces a lot of energy and helps reactions happen

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15
Q

If something is oxidised something else must _____?
What is often the subject of this?

A

Reduced
Often NAD+ to NADH, or FADH+ to FADH2

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16
Q

Anabolism is mainly reductive or oxidative?
Catabolism?

A

Anabolism is mainly a reduction
Catabolism is mainly an oxidation

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17
Q

What is a threshold enzyme?
Characteristics?

A

Enzymes which bring key elements into biosynthetic pathways

Tightly controlled
High affinity for their substrate
Non-constitutive - Regulated so that it only happens at specific times

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18
Q

What is the RNA world hypothesis?
Evidence? (4 pieces)
Problems? (2 problems)

A

RNA came before DNA, and had functions in genetic info storage and catalysis

  1. RNA is based on a standard sugar (ribose); DNA uses a very non-standard sugar, suggesting it came later in evolution
  2. RNA is capable of acting as a catalyst (ribozyme; made from entirely RNA), while DNA is not
  3. A remarkable number of important molecules are closely related to RNA
  4. Unlike DNA, RNA frequently folds up into all sorts of structures; Some of these do so to bind metals or small molecules, which is a useful behaviour for early catalysts

RNA is chemically unstable
Ribose feels too complicated to have been the first linker

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19
Q

What are many vitamins in biosynthesis?

A

Carriers

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20
Q

Name a carrier for carboxyl (C1)
What atom binds CO2 to form the carboxyl group?
What is the carrier linked to?

A

Biotin

N1 reacts well with CO2

Biotin is linked to lysine

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21
Q

Name carriers for formyl and methylene (C1)
What atoms does it bind C1 units with?

A

Tetrahydrofolate
Its 2 N atoms

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22
Q

How is tetrahydrofolate versatile?
What does the polyglutamyl chain do?

A

Can bind to many C1 units

Tail gives the molecule a high negative charge; Keeps it close to positively charged enzyme

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23
Q

What is folate used to convert?

A

Convert dUMP to dTMP

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24
Q

What is the carrier for methyl (C1) and the major donor of methyl?

A

S-Adenosylmethionine (SAM)

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25
Q

What are some important reactions that use SAM? (3 reactions)

A
  • DNA methylation is the most common mechanism for producing epigenetic changes
  • Another very important mechanism for epigenetic regulation is the methylation of lysines and arginines in histones (which wrap up DNA into nucleosomes); These form “markers” for DNA transcription; The methylation reactions use SAM
  • Ethylene is very important in plant development e.g. signal for fruit ripening; It is made using SAM
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26
Q

Name a carrier for acetyl (C2)
Structure of this carrier?

A

Coenzyme A

  • Pantothenate in the middle
  • ADP on one end
  • Thioester one other end; Involves S
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27
Q

How are thioesters better for transfer than normal esters?

A

Less stable than normal ester making it easier to transfer acetyl

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28
Q

Name the carrier for amine groups (NH2)

A

Glutamine

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29
Q

What reaction does most of the nitrogen in nucleic acid bases come from?

A

Glutamine -> Glutamate

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30
Q

What are the 2 central pathways that many feed and link into?

A

Glycolysis and Krebs cycle

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31
Q

What is the pentose phosphate pathway for?

A

Interconverting sugars; Exchanging sugars from one to another

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32
Q

What does it mean when metabolic pathways are modular?
The metabolism of amino acids, lipids and nucleotides derives from what?

A

‘Blocks’ of reactions for making certain molecules

Intermediates in carbohydrate metabolism

33
Q

What are the few reaction that link different ‘blocks’ of pathways?
Where is the control of pathways

A

Threshold reactions

Control is mainly at the beginning of pathways

34
Q

What are primary pathways?
What are primary metabolites?

A

Basic functions
Present in all cells
Largely constitutive - Happen all the time; Don’t need regulation

Primary metabolites are chemicals on main pathways e.g. sugars amino acids

35
Q

What are secondary pathways?
What are secondary metabolites?

A

Specialised functions
Present in differentiated cells
Don’t happen all the time; Inducible

Secondary metabolites are things produced in stationary phase e.g. antibiotics

36
Q

Why is glycolysis important?
Aerobic or anaerobic?
What is glucose stored as? (2 parts)

A

Glucose is the main source for energy in animals

Aerobic

Glucose is stored as glycogen when not needed; Glycogen is converted to fat when glycogen stores are full

37
Q

2 key characteristics of fat?

A

Higher energy content per gram than glycogen
Harder to mobilise

38
Q

What does glycolysis convert glucose to?
How much ATP required?
(see images on notes)

A

Converts it to 2 C3 units

Requires 2 ATP

39
Q

What are the 2 C3 units converted to in glycolysis?
Net by-products?
(see images on notes)

A

Pyruvate

Net 2 of both ATP and NADH

40
Q

What happens to pyruvate most of the time? (process name?)
How does this link back into glycolysis?

A

Pyruvate is converted to lactate, which is converted to glucose in the liver by gluconeogenesis

This can be used for further glycolysis

41
Q

What is substrate channelling?

A

When enzymes for a pathway are all in one complex
Intermediates can be directly transferred from 1 enzyme to the next without the need for long range diffusion

42
Q

What is another pathway for pyruvate (not lactate)?

A

Pyruvate is irreversibly converted to acetyl CoA + CO2

43
Q

What happens when glycogen levels and glucose levels are low?

A

Gluconeogenesis

44
Q

Why and how are glycolysis and gluconeogenesis controlled so they don’t occur at the same time?

A

Glycolysis and gluconeogenesis are essentially opposites; However they have slightly different reactions
Their reactions are control points as they produce lots of energy so they cant go backwards and happen at the same time; Futile cycling

45
Q

Why does gluconeogenesis use NADH and not NADPH?

A

NADPH generates more free energy and it would be a waste of energy here

46
Q

What is the parallel pathway to glycolysis?

A

Pentose Phosphate Pathway (PPP)

47
Q

How is PPP different to glycolysis in terms of complexity and speed?
Why?

A

PPP is more complex and not as quick

  • Produces several intermediates
  • Involves interchanging sugars
    (see image on notes)
48
Q

End goal of PPP?
Another main outcome?

A

To make a 6C and 3C sugars for glycolysis

Produces ribose for DNA and RNA; Also produces NADPH

49
Q

How does the cell decide whether to go down PPP or glycolysis?

A

Glycolysis is stimulated by low ATP
PPP is stimulated by low NADPH

50
Q

The link reaction produces CO2
What does this mean?

A

Irreversible point of regulation

51
Q

What are the main uses of acetyl CoA in the link reaction? (3 uses)

A

Feeds into the Krebs cycle
Synthesis of fatty acids
Produces energy

52
Q

What by-products of the Krebs cycle feed into the electron transport chain?

A

NADH and FADH2

53
Q

What is an anaplerotic reaction?

A

A reaction which forms an intermediate in a pathway

54
Q

What can some different reactions of the TCA cycle do at the same time?

A

Different reactions can run in 2 directions at the same time

55
Q

How is the acetyl group of acetyl CoA formed?
What does this mean in terms of pathways linking?
What happens to the fatty acid that is cleaved?

A

Beta-oxidation of fatty acids
Cleaves off 2 carbon chain with a COOH group

Fatty acid catabolism feeds directly into Krebs cycle

Fatty acid stays in the complex and continuously cleaved until it is depleted

56
Q

How does fatty acid biosynthesis occur?
What enzyme does this in mammals?

A

Fatty acid chain is continuously added onto by a carrier protein carrying 2C pieces

Fatty acid synthase

57
Q

What is the structure of fatty acid synthase? (how many functions?
How is the fatty acid moved around in the enzyme?

A

Dimeric structure
7 enzyme functions

Fatty acid is passed around different active sites in a cyclic process

58
Q

How is the amine group introduced for amino acid synthesis?
Where does the template molecule come from?

A

Ammonia is inserted into α-ketoglutarate (intermediate of Krebs cycle) to make glutamate

59
Q

What can be done with the amine group once it is in amino acids and glutamate?

A

Can be passed around between other amino acids and keto acids

60
Q

Where can carbon skeletons for amino acids come from?

A

Intermediates of Krebs cycle and glycolysis

61
Q

What are essential amino acids?

A

Amino acids taken in via the diet

62
Q

What is assembled first and then assembled after in:
- Pyrimidines?
- Purines?
What is ribose activation very intensive of in purine synthesis? (what does this mean?)

A

Pyrimidines - Base assembled first, ribose after
Purines - Ribose assembled first, Base assembled after

Ribose activation is energy intensive; ATP -> AMP; Committed step

63
Q

How are purine bases assembled?

A

Each atom added one at a time

64
Q

How are pyrimidine bases assembled? (hint: start with bicarbonate and NH3)

A

2 ATP used to make Carbamoyl phosphate which reacts with aspartate to make the pyrimidine ring
This ring then reacts with ribose pyrophosphate to give it enough energy
This results in UTP which can be converted to other pyrimidine bases

65
Q

How is it decided which pathway a molecule will go down? (give examples)

A

Bases on what the cell requires
If energy is required, glucose will go down glycolysis
If biosynthesis is required, glucose will go down PPP

66
Q

How does feedback inhibition work?
What does this avoid?

A

The last product in a pathway inhibits the initial enzyme allosterically, lowering its activity

  • Avoids doing reactions you don’t need
  • Avoids wasting energy
67
Q

Why does regulation more often involve inhibition than speeding up?

A

Enzymes tend to already be going as fast as they can; Easy to make them go slower

68
Q

How do you get better control with feedback inhibition? (hint: switch)

A

When the product of one pathway inhibits it sown pathway, but also activates an alternative

69
Q

How does the first enzyme in the pathway get regulated? (3 ways)

A

Isozymes
Single enzyme; Cumulative control
Amount of enzyme; Regulation of expression

70
Q

What is an isozyme?
Where can they be relative to another enzyme?

A

A different enzyme that does the same job as another

They can be in different tissues (mainly), or in the same tissues at different times

71
Q

Where can isozymes come from genetically? (2 options)

A

They can be in different genes to the enzyme
Can be the same gene as the enzyme but differentially spliced

72
Q

Why do different tissues use different isozymes?

A

Different tissues have different needs, so they have different isozymes to get better fine control

73
Q

What subunits are in lactate dehydrogenase?
What mix of subunits can you have?

A

Heart and Muscle (H and M); These are isozymes
Enzyme is a mixture of these and can be anywhere from H4 to M4, depending on where it is

74
Q

What metabolism occurs in heart, skeletal and liver tissue respectively?

A

Heart - Oxidative metabolism
Skeletal - Converts pyruvate to lactate anaerobically
Liver - Converts lactate to pyruvate in gluconeogenesis

75
Q

What happens in cumulative control of single enzyme?
(see notes for examples)

A

One single enzyme is inhibited independently by several different products

76
Q

How does regulation of enzyme expression occur? (2 ways)
Why is this regulation slower?
(see notes for examples)

A

End product of a pathway downregulates expression of the first enzyme in the pathway (e.g. trp)
Substrate acts to remove repression of pathway needed to handle it (e.g. lac operon)

Slower regulation as the enzyme needs to be made or broken down

77
Q

Relative speed of all 3 enzyme regulation methods?

A

Allosteric control fastest (ms)
Covalent modification middle (s)
Gene expression slowest (h)

78
Q

What does metabolic flux analysis show about altering the amount of an enzyme and its effect on rate? (hint: rate determining step)

A

Changing one enzymes amount doesn’t affect the rate too much; This is because there is no single enzyme that forms the ‘rate determining step
The control of flux is spread among many different enzymes

Biostructures, Energetics and Synthesis (2 decks)

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