Biochemistry Wk 12

Question 1

Organization of the Chemistry of Life into Metabolic Pathways

Answer 1

A metabolic pathway has many steps
That begin with a specific molecule and end with a product
That are each catalyzed by a specific enzyme

Question 2

Metabolic pathways in our bodies

Answer 2

Catabolic pathways
- breaks down complex molecules into simpler compounds

EX:
Amylase breaks complex starches into simple sugars
Cellular respiration

Question 3

Anabolic pathways

Answer 3

Consume energy to build complicated molecules

Ex:
Anabolic steroids= to build muscle
The building of a protein from a.as

Question 4

TCA Cycle

Answer 4

Also known as Krebs cycle

TCA cycle essentially involves the oxidation of acetyl CoA to CO2 and H2O.

TCA cycle –the central metabolic pathway

The TCA cycle is the final common oxidative pathway for carbohydrates, fats,
amino acids.

TCA cycle supplies energy & also provides many intermediates required for the
synthesis of amino acids, glucose, heme etc.

Question 5

Acetyl CoA Production

Answer 5

LOOK AT GOODNOTES

Question 6

Pyruvate dehydrogenase

Answer 6

⦿ Under aerobic conditions, pyruvate is converted to acetyl CoA which enters the TCA cycle to be oxidized to CO2.

⦿ ATP is generated.

⦿ Glycolysis is taking place in cytoplasm.

⦿ So pyruvate is generated in cytoplasm.

⦿ This is transported into mitochondria by a pyruvate transporter.

⦿ Inside the mitochondria, pyruvate isoxidatively decarboxylated to acetyl CoAby pyruvate dehydrogenase
(PDH).

⦿ It is a multi-enzyme complex with 5co- enzymes & 3apo-enzymes.

Question 7

Pyruvate

Answer 7

Transported into the mitochondria for:
- energy into TCA cycle
- gluconeogenesis
- outer membrane: a voltage gated porin complex
Inner: mitochondrial pyruvate carrier (MPC)

Question 8

Coenzymes

Answer 8

⦿ Thiamine pyrophosphate (TPP) ⦿ Co-enzyme A (CoA)
⦿ FAD
⦿ NAD+
⦿ Lipoamide

The lipoic acid, also called thioctic acid has two sulphur atoms & 8carbon atoms.
It can accept or donate hydrogen atoms

Question 9

Pyruvate dehydrogenase complex enzymes

Answer 9

Pyruvate decarboxylase- pyruvate-> co2

Dihydro- Lipoyl Trans acetylase- catalyzes the reaction of acetyl coenzyme A (acetyl-CoA) with dihydrolipoamide, producing coenzyme A and S-acetyldihydrolipoamide.

Dihydro lipoyl Dehydrogenase- NAD+ -> NADH

Question 10

Regulation of PDH

Answer 10

PDH is a good example for end product (acetyl CoA, NADH) inhibition.

PDH is also regulated by phosphoryIation &dephosphoryaltion.

PDH is active as a dephosphoenzyme.

PDH is inactive as a phosphoenzyme.

PDH phosphatase activity is promoted by Ca2+, Mg2+ & insulin (in adipose tissue).

Question 11

Pyruvate dehydrogenase deficiency

Answer 11

Rare inborn error of metabolism
Pyruvate shunted to alanine, lactate
Often X linked
Most common cause- mutations on PDHA1 gene
Codes for E1- alpha subunit

Key findings:
- Poor feeding
- growth failure
- developmental delays

Labs:
Elevated alanine
Lactic acidosis

Question 12

Reactions of TCA Cycle

Answer 12

Step:1 Formation of citrate
Oxaloacetate condenses with acetyl CoA to form Citrate, catalysed by the enzyme citrate synthase
Inhibited by: ATP, NADH,

Steps 2 & 3 Citrate is isomerized to isocitrate
Citrate is isomerized to isocitrate by the enzyme aconitase

This is achieved in a two stage reaction of dehydration followed by hydration through the formation of an intermediate -cis-aconiase

Question 13

Fasting stage

Answer 13

• oxaloacetate used for gluconeogenesis
• Decreased oxaloacetate for TCA cycle
• Acetyl CoA (F.A) -> Ketone bodies

Question 14

Steps 4 & 5 Formation of alpha ketoglutarate

Answer 14

Isocitrate dehydrogenase (ICDH) catalyses the conversion of (oxidative decarboxylation) of isocitrate to oxalosuccinate & then to oxalosuccinate & then to Alpha ketoglutarate

The formation of NADH & the liberation of CO2 occure at this stage.

Rate limiting step of TCA cycle Inhibited by: ATP, NADH

Activated by:ADP, Ca++

Question 15

Step: 6 Conversion of alpha ketoglutarate to succinyl CoA

Answer 15

Occurs through oxidative decarboxylation, catalysed by alpha ketoglutarate dehydrogenase complex

At this stage of TCA cycle, second NADH is produced & the second CO2 is liberated.

Similar to pyruvate dehydrogenase complex

Cofactors: Thiamine, CoA, NAD, FADH, Lipoic acid

Question 16

Succinyl Coa

Answer 16

LOOK AT GOODNOTES

Question 17

Step: 7 Formation of succinate

Answer 17

Succinyl CoA is converted to succinate by succinate thiokinase. This reaction is coupled with the phosphorylation of GDP to GTP.
This is a substrate level phosphorylation.
GTP is converted to ATP by the enzyme nucleoside diphosphate kinase.

Question 18

Step: 8,9 Conversion of succinate to fumarate to L- Malate

Answer 18

Succinate is oxidized by succinate dehydrogenase to fumarate. This reaction results in the production of FADH2.
The enzyme fumarase catalyses the conversion of fumarate to malate with the addition of H2O.

Fumarate- ALSO PRODUCED BY SEVERAL OTHER PATHWAYS
Urea cycle
Purine synthesis (formation of IMP)
Amino acid breakdown: phenylalanine, tyrosine

Question 19

Step:10 Conversion of malate to oxaloacetate

Answer 19

Malate is then oxidized to oxaloacetate by malate dehydrogenase. The third & final synthesis of NADH occurs at this stage.
The oxaloacetate is regenerated which can combine with another
molecule of acetyl CoA & continue the cycle.

Question 20

Energetics of TCA Cycle

Answer 20

Oxidation of 3 NADH by ETC coupled with oxidative phosphorylation results in the synthesis of 9 ATP.
FADH2 leads to the formation of 2ATP.

One substrate level phosphorylation.

Thus, a total of 12 ATP are produced from one
acetyl CoA.

Question 21

TCA Cycle Inhibited by:

Answer 21

-ATP
• NADH
• Acetyl CoA
• Citrate
• Succinyl CoA

Reactions; look at GOODNOTES
ATP, ACETYL COA, NADH: Pyruvate-> acetyl coA

Question 22

TCA Cycle-Activated by:

Answer 22

• ADP
• Calcium

LOOK AT GOODNOTES FOR REACTIONS