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Y2 Biostructures > Metabolism > Flashcards

Metabolism Flashcards

1
Q

How are globular proteins arranged?

A

Spherical, hydrophobic on the inside, hydrophilic outside

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2
Q

What are the main ways energy can be lost from polypeptides?

A

Not having peptide bonds
Hydrogen bonding

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3
Q

What is enthalpy?

A

Energy available from bonding interactions

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4
Q

Which sorts of reactions usually produce energy?

A

Catabolic reactions

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5
Q

Why is CO2 an important by-product of reactions?

A

By-product of energetically favourable reactions. Increases entropy
CO2 has very stable bonds (enthalpic)
Easily escapes site of reaction
Difficult to reincorporate, so it is a committed step

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6
Q

What is an anaplerotic reaction?

A

Reaction which forms intermediates in a metabolic pathway
Usually replenishes carbon

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7
Q

How is the micheales menton constant calculated?

A

(Vmax[S])/(Km + [S])

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8
Q

What is vitamin B a carrier for?

A

NAD
FAD
Acyls
CO2
Aldehydes

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9
Q

What are vitamins

A

Nutrients humans cannot synthesise themselves. Presumably from pathways lost

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10
Q

What does biotin act as a carrier for?

A

Bicarbonate group
Pyruvate carboxylase catalyses the formation of oxaloacetate from pyruvate and COO

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11
Q

How does folic acid (vitamin B9) act as a carrier?

A

The polyglutamyl chain has a high negative charge which attracts to the enzyme surface.
Used to convert dUMP to dTMP (nucleotide precursor)

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12
Q

Outline folate catalysing dTMP production

A

Folate is converted to DH4-Folate. This is activated to TH4-Folate by dihydrofolate reductase and NADPH.
This is converted to 5, 10-Methylene-folate which catalyses dUMP to dTMP.

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13
Q

Where does folic acid take its methyl group from?

A

Serine -> glycine conversion

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14
Q

What can dihydrofolate reductase inhibitors be used as?

A

Anticancer drugs as they prevent dTMP synthesis

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15
Q

What does folic acid carry?

A

Methyl groups

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16
Q

What carries C2 units?

A

Panthotheic acid
Coenzyme A

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17
Q

Why are thioester bonds more favourable than esters for carriers?

A

Thioester bonds are less stable, making it easier to transfer the acetyl group

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18
Q

What are 5 carbon molecules usually used for?

A

Steroids
Terpenes
Vitamin A

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19
Q

What are N2 groups usually donated from?

A

Glutamine

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20
Q

What are primary metabolic pathways?

A

Basic housekeeping pathways. Mainly happen constitutively

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21
Q

What are secondary metabolic pathways?

A

Pathways for specialised functions. Inducible, e.g antibiotics and plant oils

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22
Q

What are terpenes?

A

Unsaturated hydrocarbons produced by plants. (C5H8)n for n>1
Lipid derived
Terpenoids are modified terpenes containing additional functional groups

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23
Q

What are terpenes used to synthesis?

A

Natural rubber, rosin.
Rosin can be used for inks, varnishes and adhesives

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24
Q

How are isoprene units made in plants?

A

Dimethylallyl pyrophosphate (DMAPP) and isopentenyl pyrophosphate (IPP) are produced in the melvonate pathway
This creates C5 units from acetyl-CoA and non-sterols such as heme-A and ubiquinone

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25
Outline glycolysis
Glucose is phosphorylated to fructose 1,6 bisphosphate with 2 ATP. This splits into 2 glyceraldehyde 3-phosphate molecules and for each, NAD is used to form pyruvate, producing 2 ATP and 1 NADH
26
What is the net gain of glycolysis of one glucose molecule?
2 ATP, 2NADH
27
What is substrate channelling?
Process where substrates are passed from one enzyme to the next
28
What pathways can pyruvate move into?
Fermentation Lactate formation Link reaction
29
What is gluconeogenesis used for?
Maintaining blood glucose levels when they run down Reverse glycolysis
30
How is α-ketoglutarate produced?
Glutamate + Pyruvate -> Alanine + α-ketoglutarate. Catalysed by alanine transaminase
31
Where does gluconeogenesis mainly take place?
Liver
32
What are the end products of the pentose phosphate pathway?
Pyruvate and intermediates
33
In gluconeogenesis, what does pyruvate initially react with?
Oxaloacetate
34
Outline the steps of gluconeogenesis
1. Pyruvate reacts with oxaloacetate and CO2 is lost to form a 6 carbon intermediate 2. A series of reactions is undergone, using 2ATP until fructose 1,6-bisphosphate is reached. 3. This is dephosphorylated to glucose-6-phosphate 4. Glucose-6-phosphatase convers this to glucose
35
What stimulates the need for the pentose phosphate pathway?
Need for ribulose
36
What is acetyl CoA used for?
Krebs cycle, terpene production and fatty acid synthesis
37
What is the link reaction?
Pyruvate + NAD+ -> Acetyl CoA + CO2 + NADH
38
What are some of the products of the krebs cycle used for?
Oxaloacetate and α-ketoglutarate are used for amino acid biosynthesis Succinyl CoA is used in haem, chrorophyll and vitamin b12 Citric acid is a fatty acid precursor
39
When fatty acids are degraded, where do the products go?
They are oxidised into acetyl groups which move to the link reaction NADH and FADH2 move to the krebs cycle
40
Describe fatty acid synthase
7 different functions in 1 polypeptide chain Dimeric Fatty acids join at one point and pass around the different active sites. The fatty acids extends in a cyclic process until it is long enough
41
Outline fatty acid biosynthesis
Acetyl groups join together. Each addition of a monomer creates a ketone group which is subsequently reduced
42
How is glutamate synthesised?
α-ketoglutarate is taken from the krebs cycle and ammonia is added. Adding the amine group os the most difficult part
43
What is the cofactor in dUMT production?
Folic acid
44
How are pyrimadines synthesised?
Bases ae assembled from the pentose phosphate pathway and amino acids. Ribose is then attached
45
How are purines synthesised?
Rings are assembled onto ribose, then groups are added bit by bit. Ribose activation is very energy intensive: the first committed step requires a hydrolysis of ATP to AMP Ribose pyrophosphate is used 2 ATP are required to activate the bicarbonate and add it on
46
How is metabolism generally controlled?
Feedback inhibition. This is to avoid unnecessary energy wasting
47
Describe how aspartate transcarbamoylase is inhibited
Carbamoyl +aspartate <-> N-carbamoyaspartate <-> cyditine triphosphate (CTP) CTP is an allosteric inhibitor of N-carbamoylaspartate formation
48
How is isoleucine production regulated?
When pyruvate is converted to valine, isoleucine synthesis is promoted. Isoleucine blocks its own production from pyruvate and threonine
49
What are isozymes?
Enzymes which are the same but encoded by different genes to work in certain tissues. These arise from alternatively spliced genes
50
Describe the different isozymes of lactate dehydrogenase
Pyruvate <-> lactate 4 subunits which can be H (heart) or M (muscle) depending on the isozyme. The H form is allosterically activated by pyruvate. The H form is promoted by endurance training
51
What is glutamine synthetase inhibited by?
Glutamine α-ketoglutarate
52
What is the most common type of regulating enzymes by covalent modification?
Reversible phosphorylation
53
Outline the mechanism of glycogen phosphorylase
When active, it removes glucose from glycogen. Glycogen kinase phosphorylates glycogen, making it inactive. Glycogen phosphorylase removes the phosphate groups and the inactive shape reverts to the active shape.
54
How is the lac operon regulated?
Presence of lactose and absence of glucose removes the repressor, switching on gene expression
55
How is tryptophan regulated?
If there is enough tryptophan, it binds to the Trp repressor and shuts it down. The trp operon is activated, leading to a 23-fold increase of expression Positive feedback
56
What are the 4 ways metabolism can be controlled?
Enzyme multiplicity (isozymes) Cumulative control of a single enzyme Enzyme expression regulation Change in substrate concentration
57
What is the flux coefficient?
An enzyme's importance in the overall rate through the whole pathway. Changing substrate concentration has little effect on overall flux
58
What is an example of enzyme concentration having little effect on reaction rate
Overexpressing phosphofructokinase in glycolysis results in almost no change
59
How is urea produced?
Breakdown of amino acids in the urea cycle
60
How is carbamoyl phosphate synthase regulated in the urea cycle?
Regulated allosterically by NAG (N-acetylglutamate) Covalent modification
61
What reaction does carbamoyl phosphate synthase catalyse?
Conversion of ammonia and CO2 to carbamoyl phosphate
62
Outline the urea cycle
1. Ammonia and CO2 react in a reaction catalysed by carbamoyl phosphate synthase to form carbamoyl phosphate 2. This reacts with ornithine in the mitochondrial matrix, forming citrulline 3. Citrulline reacts with aspartate to form arginino-succinate 4. This splits into arginine and fumarate 5. Arginine reacts with water, forming urea and ornithine
63
Where does glycolysis take place?
Respiring cells

Y2 Biostructures (5 decks)

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