Metabolism EOT final qs

Co-enzymes of PDH

Lipoic acid

NAD+

FAD

Thiamine pyrophosphate (thiamine = B1)

Draw pyruvate to lactate

Lactate can be delivered to liver for gluconeogenesis

Draw pyruvate to ethanol

Yeast cells

Note the pyruvate decarboxylase also uses TPP

Why is too much fructose bad?

Fructose skips rate limiting step = can either go in at G6P or G3P.

Sugars like fructose and mannose skip energy investment phases and lots of ATP is produced. Thus, the glycolysis pathway is more efficient and not a heap of sugar is needed (body will store away sugar at glycogen/TGs)

Draw pathway from pyruvate to phosphoenolpyruvate

What are the precursors for gluconeogenesis?

Lactate, amino acids, glycerol

(NOT FA’s, only plants can use FAs in glyoxylate cycle)

Therefore, FA’s are not gluconeogenic

How is glycogen formed?

**Start either from glucose** __**or**__ **lactate**

Glycogen synthase - transfers glucose residue of UDP-glucose to a non-reducing end of a branch + forms alpha 1-4 linkages

Each chain is 12-14 residues

Glycogen branching enzyme - takes a terminal fragment (6-7) and adds to a chain of at least 11

Give reactants and products of TCA

2C in, 2C out, + acetyl CoA -→ 2x Co2 formed

3 NADH

1 FADH2

1 GTP

Give the anaplerotic reactions for oxaloacetate

How does oxaloacetate move from mitochondria to cytosol?

As malate via dicarboxylase carrier

gibbs free energy formula

Mitochondrial anatomy:

What processes occur in the outer membrane, inner membrane and matrix?

Outer membrane = FA elongation, phospholipid synthesis

Inner = ETC, oxidative phosphorylation

Matrix= PDH reaction, TCA, FA oxidation and amino oxidation

What type of carrier is cyt C?

Mobile carrier + peripheral protein on inner membrane sapce side of cristae membrane

What is the last step of the ETC>

Cyt a3 passing the electron to oxygen to produce water

What are oxygen reduction complications associated w mitochondria?

1e- = superoxide anion

2e-= hydrogen peroxide

3e- = hydroxyl and hydroxy radical

4e- = 2 water

What are the two major structural components of ATP synthase?

Complex V/F0F1 ATPase

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F1 = in matrix

F0 = intermembrane

What does ATPase use to make ATP?

Proton motive force

* amount of ATP is proportional to # of oxygen transferred across membrane (hence, chemiosmotic coupling)
* 3 for NADH as it gets 12 H+
* 2 for FADH2 as it gets 8 H+
* P/O (# ATP epr oxygen)

Favourable conditions for chemiosmotic couple

1. Intact membrane
2. Hydrogen ions cannot flow freely across membrane (keep gradient) and no other ions messing w the gradient
3. Key transporters are asymmetrically located and span the membrane

Absence of compounds that increase proton permeability of inner mitochondrial membrane

Two types of drugs that disrupt chemiosmotic coupling

Inhibitors: cause build up of electrons by preventing a complex’s function

Uncoupling = disrupted inner membrane (oxidative phosphorylation cannot occur)

Value for oxidation of NADH

\-220kJ/mol (need 220 kJ of free energy to get ATP created, around 31 kJ/mol for each ATP)

Why, if NADH yields 220kJ/mol and ATP needs 31kJ/mol for synthesis, does NADH not have a PO ratio of 7?

Theoretically, to get 3 ATP, only need 93 kJ. Experimentally need -220 kJ - inefficiency in coupling (leakage of protons and electrons and sometime ROS are formed instead)

NADH oxidative phosphorylation si about 42% efficienct

Energy yield for one glucose

2 ATP and 2NADH (cytosolic) for glycolysis

2 acetyl Coa and 2 NADH from PDH

2 ATP, 6 NADH and 2 FADH2 from TCA

38 ATP using malate aspartate, 36 realistically (to get NADH into matrix using glycerol phosphate shuttle, convert to FADH2 first)

What are the three inner membrane transport systems?

1. Pyruvate transport system (pyruvate in to matrix in exchange for a OH-)
2. Dicarboxylate: succ/malate/fumarate in exchange for succ/malate/fumarate/pi


1. Tricarboxylate: iso/citrate in exchange for iso/citrate (also dicarboxylic acids)

How is ATP transported?

**Adenine nucleotide translocase:** ADP goes into matrix in exchange for ATP (proton gradient helps)

**Phosphate translocase:** H2PO4- in and OH- out

Glycerol phosphate shuttle vs malate aspartate shuttle

Glycerol phosphate = faster (brain and skeletal muscle)

malate aspartate = NADH is used to transport oxaloacetate as malate into matrix from cytosol. Malate goes back to oxaloacetate to produce an NADH in the matrix.

What are the unique enzymes and their action involved in beta oxidation of unsaturated fas

Enoyl Coa Isomerase - converts C3-C4 cis double bond to trans C2-C3

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2,4-dienoyl CoA reductase = NADPH dependent (converts C2-C3 and C4-C5 cis double bonds to C3-C4 cis bond

Odd number of carbons

Last cycle has propionyl CoA -→ sub in at succinyl CoA (6 ATP in last cycle)

How is acetoacetyl CoA synthesised ?

From 2x acetyl CoA by beta-ketothiolase

Draw HMG CoA

Draw pathway of acetyl CoA being used for ketone synthesis

3x ketones are synthesised

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What are the four enzymes involved in fatty acid synthesis?

1. Condensation: beta-ketoacyl synthase
2. Ketoreduction: beta-ketoacyl reductase
3. Dehydration: 3-hydroxyacyl dehydrase
4. Saturation: Enoyl CoA reductase

How to synthesis malonyl acp?

With acetyl ACP, biocarbonic and ATP + acetyl CoA-ACP transcylase (or acetyl CoA carboxylase)

How does acetyl CoA leave the matrix?

Via citrate shuttle = combined w oxaloacetate to form citrate and then transported out

FA are elongated in ER after C16

**In ER-→ acyl CoA is now used**

What enzyme puts a double bond?

Fatty acyl CoA desaturase (up to C9)

**NEEDS OXYGEN**

How is fatty acid synthesis regulated?

Via acetyl coa carboxylase

* production of palmitoyl coa leads to inhibition
* NADPH
* Insulin (provides more acetyl CoA by activating PDH)

Nitrogen fixation process

Must be anaerobic (roots)

Oxygen deactivates

What can utilise nitrate?

Plants, bacteria and fungi (mostly)

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What are the four signals of protein destruction?

Ubiquitination (mark for destruction)

Oxidation of amino acids (esp pro, lys, arg) (mark for proteases)

PEST signals (recognition sequences for proteases)

N terminal amino acids (FLY WNK)

Type of excretion of birds, fish and humans

Birds: uric acid (very concentration)

Humans: urea

fish: ammonia

Net reaction for 1 turn of Krebs-Heinseleit

What are the essential ammino acids

Arginine

Leucine

Valine

Isoleucine

Lysine

Methionine

Phenylalanine

Tryptophan

Histidine

Threonine

Two methods of glutamate synthesis + location

Glutamate dehydrogenase (NADPH) - mitochondrial matrix

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Glutamate synthase (NADPH + glutamine )

Method of glutamine synthesis

Glutamine synthase : uses ATP + glutamine

* Two feedback mechanisms: partial inhibition by the reaction products and oxidation (adenylation) of the active site when there is high concentration of glutamine

Two types of CPS

CPSI - in matrix, uses NH4 and HCO3 + 3 ATP= carbamoyl phosphate

CPSII - in cytosol, uses transamination for NH3 source (glutamine) + HCO3- and 2ATP and 2 hydrogen

How is creatinine phosphate synthesised?

Arginine in muscle

How is proline synthesised?

Glutamic semi-aldehyde + NADPH + H+ → proline + water + water

How do plants vs animals synthesise cysteine?

Derived from serine and can directly add Sulphur

Humans require to go from methionine first

How does plants derive methionine?

Homoserine + cysteine -→ pyruvate + methionine + NH4

Function of phenylalanine hydroxylase (give chemical equation)

To make tyrosine from phenylalanine by adding an OH

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Phe + NADPH + H+ + O2 -→ tyrosine + NADP+ + water

Describe synthesis of serine

3 phosphoglycerate + NADPH + glutamate

How is glycine created (include enzyme)

Serine + THF -→ glycine

How do plants synthesis threonine?

From homoserine (which is from aspartate) -→ phosphorylation and then uses **pyroxidal phosphate**

NTs as amino acids

Glycine and glutamate are neurotransmitters

Tyrosine and tryptophan are precursors for catecholamines and serotonin

How is serotonin (the NT) synthesised?

Trp + O2 -→ serotonin + water + carbon dioxide

(peristalsis, BP, neurotransmission, light/dark)

How are the catecholamines synthesised ?

What do phosphoribosyl transferases catalyse?

Transfer of a free base to the ribose of PRPP (5-phosphribosyl pyrophosphate)

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Base + PRPP -→ NMP + pyrophosphate

Draw de novo purine synthesis

From here, go to AMP and GMP (via ASp + GTP and Gln and ATP)

What enzymes phosphorylate NMPs?

Adenylate/guanylate kinases (NMP - NDP)

Nucleoside diphosphate kinases (NDP - NTP)

3 mechanisms of regulation of de novo purine synthesis

1. AMP and GMP regulate/inhibit their own synthesis from IMP
2. ADP and GDP inhibit PRPP synthase


1. AMP, GMP and IMP inhibit PRPP aminotransferase

Draw purine degradation

Recall uric acid can break down further to allantoin and then to urea

What does HGPRT stand for and do?

hypoxanthine guanine phosphoribosyl transferase

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takes hypoxanthine and guanine back to IMP and GMP

What does uricosuric drug do?

Inhibit tubular reabsorption (more uric acid is excreted)

Why are fasting and alcohol consumption both risk factors for gout?

Fasting = ketoacidosis (inhibit secretion of urate)

Alcohol consumption = lactate formation = competes w urate for excretion

(also water/dehydration is a RF)

What do they treat ATLS with?

Recombinant uric acid oxidase = makes uric acid allantoin which is more soluble

Draw pyrimidine synthesis

Note that uTP is converted to CTP via CTP synthase w a transamination reaction (Gln) and ATP

Draw pyrimidine breakdown

Draw pyrimidine salvage

How are ribonucletides converted to deoxyribonucleotides?

Thioredoxin intermediate + ribonucleotide reductase

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NADPH → FADH2 → Thioredoxin → Ribonucleotide synthase → NDP=dNDP

How is dTMP synthesised?

How is deoxyribonucleotide synthesis controlled?

Level of ribonucleotide reductase = has two regulatory sites,

ATP binds = activated, dATP binds = inactivated

Mode of mechanism of insulin

* Increases: glucose uptake, glycogen synthase and TG synthesis (acetyl coa carboxylase), protein synthesis
* Decreases: proteolysis, lipolysis, gluconeogenesis + glycogen breakdown

Mechanism of glucagon

* Increases: TG movement, lipolysis (beta oxidation and ketogenesis), gluconeogenesis, glycogen breakdown
* Decreases: glycogen and FA synthesis

Epinephrine

Adrenal medulla: peptide hormone (still water soluble and uses second messengers)

Glycogenolysis = FAs as fuel, glycerol → gluconeogenesis

Cortisol

Adrenal cortex (long term- steroid hormone)

Increases: Proteolysis and lipolysis, gluconeogenesis, glycogen synthesis

Decrease: tissue glucose utilisation

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**Acts on muscle, liver and adipose to supply fuel to withstand stress**

Body’s response to uncontrolled diabetes mellitus

More glucose by gluconeogenesis:

* proteins broken down and amino acids used for gluconeogenesis
* TGs broken down -→ FA oxidation → acetyl coa
* not enough oxaloacetate (from condensation step)
* ketone bodies build up (acetyl coa builds up)
* acidosis

Describe hormones released by anterior and posterior pituitary

Anterior: Thyrotropin, ACTH (adrenal), somatropin, LH/FSH

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Posterior: ADH, prolactin and oxytocin

Three types of hormone

peptide (pituitary, glucagon and insulin)

amino acid (epinephrine, thyroid)

^^^^water soluble^^^^

steroid (corticosteroids) (fat soluble)

What are three ways hormones can function?

Enzyme activation/inhibition via second messengers (E and Gluc)

Stimulation of synthesis of certain proteins

Selective increases in uptake of metabolites (i.e. aldosterone binding to an ion channel)

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What form of insulin is initially synthesised in the beta cells?

Preproinsulin

4 classes of catecholamines

Function of G proteins

When a hormone binds to a receptor, G protein undergoes a conformation change. It can then go activate adenylate cyclase to make cAMP from ATP

Also activate phospholipase C (DAD and InP3)

What does cAMP do

Activated by GTP from G protein

A second messenger (as well as calcium)

Bind to PIP to increase intracellular calcium levels

 involved in the regulation of glycogen, sugar, and lipid metabolism.

How does insulin communicate?

Bind to tyrosine kinase which activate GLUT4 (receptor to uptake insulin)

How do steroid hormones work?

Directly diffuse across membrane

Go bind to hormone responsive elements (**HRE**s) in nucleus which manipulates DNA (control transcription of genes)

Is an amplification response but slower and longer lasting

Describe how alcohol affects metabolism?

1. Ethanol → Acetaldehyde (via alcohol dehydrogenase) produces NADH
* causes oxaloacetate → malate (reducing levels of oxaloacetate inhibits gluconeogenesis: **fasting state**)
2. Acetaldehyde → acetate (via acetaldehyde dehydrogenase) produces NADH
* High level of NADH inhibits Kreb’s and beta oxidation (FAs eaten cannot be metabolised so build up = steatosis)

High level of NADH causes pyruvate to be converted to lactate (via lactate dehydrogenase)

How to treat a hangover?

Hydration

Replenish vitamins loss

Increase intake of FAs + proteins to refuel

3 purposes of PPP

1. **NADPH for biosynthesis** (oxidative + non oxidative)
2. **Ribonucleotides for RNA** (just oxidative and non oxidative synthesis of R5P)
3. **Pentose dietary sugars for metabolism** (produce F6P and G3P for glycolysis to pyruvate)

describe the oxidative and non oxidative phase of the ppp

Oxidative:

G6P → 6-phosphogluconate → ribulose 5 phosphate (**2 NADPH produced total)**

Non-oxidative:

3 different pathways to get from 6 5C sugars to 5 6C sugars


1. Ru5P → Septoheludose 7P → F6P → G6P
2. Xylulose 5P → G3P → Erythrose 4P → F6P → G6P
3. Xylulose 5P → G3P (via transketolase) -→ F6P (via gluconeogenesis)

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Enzymes are transketolase and transaldolase

(Ru5P to Xylulose 5P is via epimerase)

What prevents oxidative damage in RBCs

High oxygen concentrations → prevented by glutathione peroxidase which is needed to reduce glutathione (an antioxidant which scavenges oxidative radicals)

Draw process of cholesterol synthesis

What is the rate limiting step? What controls it?

Insulin increases

Glucagon decreases

Receptor mediated endocytosis of LDL (cholesterol) decreases

What is the full name for HMG CoA?

Beta hydroxy-beta methyl- glutaryl- CoA

What is the effect of uptaking cholsterol?

1. Inhibiting HMG CoA synthesis of new cholesterol
2. Activating acyl coa acyl transferase (ACAT)
3. Decreasing expression of LDL receptor

What are derivatives of cholesterol?

Bile, steroid hormones (glucocorticoids, mineralocorticoids, androgens, oestrogens, progestins)

Describe how dTTp can be derive from uracil and thymine

1. Uracil-thymine phosphoribosyl transferase (uracil → UMP)
2. Ribonucleotide reductase (UMP → dUMP)
3. Thymidylate synthase (dUMP to dTMP using methylene THF)
4. dTMP to dTTP using nucleotide diphosphate kinase

How is dTMP synthesisised from CDP and UDP?

1. Ribonucleotide reductase (CDP → dCDP)
2. Nucleoside diphosphate kinase (dCDP → dCTP)
3. Deaminase (dCTp → dUTP)
4. dUTPase (dUTP → dUMP)
5. Thymidylate synthase (dUTP → dTMP)
6. dTMP kinase + nucleoside diphosphate kinase

Why is dUTPase important?

Excluding uracil from DNA before it acts as a substrate for DNA polymerase

What are the precursors of TG synthesis?

Fatty acyl Coa and glycer**ol** 3 phosphate

* G3P can come from DHAP from glycolysis or from phosphorylation of glycerol (by glycerol kinase using ATP)
* G3P is → phosphatidic acid (using acyl transferase)

Phosphatidic acid is used in both phospholipid and TG synthesis

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How are TG made?

Phosphatidic acid → 1,2 diacylglycerol → triacycl glycerol (using phosphatidic acid phosphatase and acyl transferase)

What is the precursor for most human phospholipids?

Phosphatidic acid + CTP → CDP diacylglycerol (precursor for PS, PE, PG, PI and CL synthesis)