L18-Mitochondria and Citric Acid Cycle

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L18-Mitochondria and Citric Acid Cycle by Mind Map: L18-Mitochondria and Citric Acid Cycle

1. intro

1.1. glycolysis

1.1.1. metabolism of glucose>pyruvate

1.1.1.1. anaerobic process

1.1.1.2. only produces 2 molecules of ATP

1.1.2. takes place in the cytoplasm

1.1.2.1. pyruvate transported into the mitochondria

1.2. Citric acid cycle

1.2.1. aerobic processing of glucose

1.2.2. yields most ATP

1.2.3. process starts with complete oxidation of glucose derivatives>CO2

1.2.4. also known as

1.2.4.1. tricarboxylic acid (TCA) cycle

1.2.4.1.1. when acid not known

1.2.4.2. Kreb's cycle

1.2.4.2.1. Hans Krebs done a lot of work on stages in citric acid cycle

1.2.5. final common pathway for the oxidation of fuel molecules

1.2.5.1. carbs,proteins,fatty acids, amino acids

1.2.5.2. most enter as acetyl CoA

1.2.6. oxidizes carbon fuels in the form of acetyl CoA and serves as a source of precursors of biosynthesis

1.2.7. takes place in mitochondria

1.2.8. pyruvate is oxidatively decarboxylated to form acetyl CoA

2. Structure of mitochondria

2.1. oval shaped subcellular organelles

2.1.1. 2um length

2.1.2. 0.5um diameter

2.1.3. ~ same size as bacterium

2.2. eugene kennedy and albert lehinger

2.2.1. mitochondria contain the respiratory assembly, the enzymes of the citric acid cycle, and the enzymes of fatty acid oxidation

2.3. bounded by a double membrane

2.3.1. 2 membrane systems

2.3.1.1. outer mitochondrial membrane (OMM)

2.3.1.1.1. quite permeable to most small molecules and ions

2.3.1.1.2. mitochondrial porin

2.3.1.2. inner mitochondrial membrane (IMM)

2.3.1.2.1. extensive and highly folded

2.3.1.2.2. folds into a series of internal ridges=cristae

2.3.1.2.3. site of

2.3.1.2.4. impermeable to nearly all ions and polar molecules

2.3.1.2.5. 2 faces

2.4. 2 soluble compartments in Mt

2.4.1. inter membrane space

2.4.1.1. between the outer and inner membrane

2.4.2. matrix

2.4.2.1. bounded by the inner membrane

2.4.2.2. cristae

2.4.2.2.1. folded invaginations of the inner membrane

2.4.2.2.2. increased SA

2.4.2.3. location of

2.4.2.3.1. citric acid cycle

2.4.2.3.2. fatty acid oxidation

2.4.2.3.3. pyruvate dehydrogenase complex

2.5. has own DNA

2.5.1. can create own mitochondrial proteins

3. The endosymbiotic theory of evolution of mitochondria and chloroplasts

3.1. Mts are semiautonomous organelles that live in an endosymbiotic relation with the host cell

3.2. an endosymbiotic event is though to have occurred

3.2.1. a free living organism capable of oxidative phosphorylation was engulfed by another cell

3.3. endosymbiotic theory

3.3.1. suggests that Mt evolved from free living aerobic respiring bacteria (similar to Paracoccus denitrificans) that entered into an endosymbiotic association with the ancestors of eukaryotes

3.3.2. unable to live independently since most of their proteins are synthesised by nuclear genes

3.3.2.1. v. impt for metabolic processes

3.3.2.1.1. provide fuel in form of ATP

3.4. evidence 4 theory

3.4.1. double membrane

3.4.2. retain own circular DNA

3.4.3. mitochondrial specific transcription and translation machinery

3.4.3.1. resembles bacteria machinery

3.4.3.2. 70S rather than 80S ribosomes

3.4.3.3. synthesises few mitochondrial proteins

3.5. data suggest that mitochondria are derived from an ancestor of R. prowazekii as a result of a single endosymbiotic event

4. citric acid cycle background

4.1. citric acid cycle=central metabolic hub of the cell

4.2. function of the citric acid cycle in transforming fuel molecules into ATP

4.2.1. includes a series of oxidation-reduction rxns>oxidation of an acetyl grp to 2 molecules of CO2

4.2.2. generates high E e-s

4.2.2.1. used to power the synthesis of ATP

4.3. next steps

4.3.1. oxidative decarboxylation of pyruvate to form acetyl CoA by pyruvate dehydrogenase complex

4.3.1.1. acetyl CoA is impt 4 food hydrolysis

4.3.1.1.1. acetyl CoA (activated acetyl unit) then completely oxidized to CO2 in a series of rxns known as citric acid cycle

4.4. v. impt. deceased without this cycle

4.5. glucose is processed by glycolysis > pyruvate

4.5.1. anaerobic conditions

4.5.1.1. pyruvate is converted into lactate and ethanol depending on the organism

4.5.2. aerobic conditions

4.5.2.1. pyruvate is transported into the mitochondria by a specific carrier protein embedded in the Mt membrane

4.5.2.2. mitochondrial matrix

4.5.2.2.1. pyruvate is oxidatively decarboxylated by the pyruvate dehydrogenase complex>acetyl CoA

5. Pyruvate dehydrogenase complex

5.1. catalyses the oxidative decarboxylation of pyruvate >acetyl CoA

5.2. rxn

5.2.1. irreversible rxn=link between glycolysis and the citric acid cycle

5.3. structure

5.3.1. large

5.3.1.1. lrger than ribosomes

5.3.1.2. MR>4million-10million daltons

5.3.2. integrated complex

5.3.3. multimeric assembly

5.3.4. In E.coli

5.3.4.1. consists of 3 diff. enzymes

5.3.4.1.1. E1=a2B2 tetramer

5.3.4.1.2. transacetylase component of E2

5.3.4.1.3. E3=aB dimer

5.3.4.2. pyruvate dehydrogenase and lipoyl dehydrogenase enzymes bound to outside

5.3.4.3. 3 different active sites work in concert

5.3.4.3.1. flexible lipoamide arm of E2 subunit carries substrate from active site to active site

5.3.4.3.2. 3 diff. enzymes processes linked closely together by the flexible lipoamide arm

6. The citric acid cycle

6.1. overall stoichiometry of the cycle

6.1.1. basic rxns

6.1.1.1. citrate synthase

6.1.1.1.1. cycle starts with the condensation of acetyl CoA (C2) and oxalacetate (C4) to give citrate(C6 tricarboxylic acid)

6.1.1.2. aconitase

6.1.1.2.1. citrate isomerised to isocitrate (C6)

6.1.1.3. isocitrate dehydrogenase

6.1.1.3.1. oxidative decarboxylation produces CO2 and alpha-ketoglutarate (C5)

6.1.1.4. alpha-ketoglutarate dehydrogenase

6.1.1.4.1. oxidative decarboxylation produces CO2

6.1.1.4.2. succinyl CoA(C4)

6.1.1.5. Succinyl CoA synthetase

6.1.1.5.1. Succinyl CoA is cleaved to form succinate

6.1.1.5.2. GDP>GTP

6.1.1.6. Succinate dehydrogenase

6.1.1.6.1. succinate oxidized to fumarate (C4)

6.1.1.7. Fumarase

6.1.1.7.1. Fumarate is hydrated to form malate

6.1.1.8. Malate dehydrogenase

6.1.1.8.1. malate is oxidised to regenerate oxalacetate (C4)

6.1.1.8.2. oxalacetate (C4)

6.1.2. overview

6.1.2.1. oxidizes 2C units

6.1.2.2. produces 2 molecules of CO2

6.1.2.3. one molecule of ATP

6.1.2.4. produces high E e-s in the form of NADH and FADH2

6.2. more detail

6.2.1. coupling of favourable and unfavourable rxn

6.2.2. summarised

6.2.3. net rxn of citric acid cycle

6.2.3.1. Acetyl CoA + 3NAD+ + FAD + ADP + Pi +2H2O>2CO2+ 3NADH + FADH2+ ATP + 2H+ +CoA

6.2.3.2. generates little energy in form of ATP

6.3. Steps in the cycle

6.3.1. formation of citrate

6.3.1.1. synthase

6.3.1.1.1. an enzyme that catalyzes a synthetic rxn in which two units are joined usually without the participation of ATP

6.3.1.2. oxalacetate(C4) reacts with acetyl CoA(2C) and H2O > citrate(6C) and CoA

6.3.1.2.1. condensation rxn

6.3.1.2.2. catalyzed by citrate synthase

6.3.1.2.3. citrate=tertiary alcohol

6.3.2. formation of isocitrate

6.3.2.1. citrate is isomerized into isocitrate

6.3.2.1.1. enables the 6C unit to undergo oxidative decarboxylation

6.3.2.1.2. 2 steps of isomerization

6.3.2.2. Arginine flips citrate to form isocitrate

6.3.2.3. hydroxyl grp is not located properly for oxidative decarboxylation that follows

6.3.2.4. aconitase

6.3.2.4.1. enzyme that catalyzes the isomerization of citrate into isocitrate

6.3.2.4.2. cis-aconitate is an intermediate

6.3.2.4.3. =nonheme iron protein/iron sulfur protein

6.3.3. Formation of α-Ketoglutarate

6.3.3.1. isocitrate is oxidized and decarboxylated>α-ketoglutarate

6.3.3.2. 1st oxidative decarboxylation

6.3.3.3. isocitrate dehydrogenase catalyzes the oxidative decarboxylation of isocitrate

6.3.3.3.1. rxn

6.3.3.3.2. dehydrogenation=removal of Hydrogen

6.3.3.3.3. oxalosuccinate intermediate

6.3.3.3.4. first high transfer potential e- carrier created

6.3.4. Formation of Succinyl CoA

6.3.4.1. Succinyl CoA is formed by oxidative decarboxylation of α-ketoglutarate

6.3.4.2. rxn catalyzed by α-ketoglutarate dehydrogenase complex

6.3.4.2.1. organized assembly 3 kinds of enzymes

6.3.4.2.2. homologous to the pyruvate dehydrogenase complex

6.3.4.3. oxidative decarboxylation of α-ketoglutarate closely resembles that of pyruvate=analogous

6.3.4.3.1. formation of thioester linkage with CoA

6.3.4.3.2. decarboxylation of α-ketoacid

6.3.5. Formation of Succinate

6.3.5.1. succinyl CoA phosphorylated to form GTP/ATP

6.3.5.2. the cleavage of the thioester bond of succinyl CoA is coupled to the phosphorylation of a purine nucleoside diphosphate(ADP)

6.3.5.3. readily reversible rxn

6.3.5.4. catalyzed by succinyl CoA synthetase (succinate thiokinase)

6.3.5.4.1. mammals

6.3.5.5. yields a compound with high phosphoryl transfer potential

6.3.6. Formation of Oxaloacetate-IMM

6.3.6.1. methylene grp (CH2) is converted into a carbonyl grp (C=O)

6.3.6.1.1. 3 steps

6.3.6.2. oxalacetate is regenerated

6.3.6.3. more energy is extracted in the form of FADH2 and NADH

6.4. calculations to get stoichiometry

6.4.1. 2 carbons enter the cycle as acetyl CoA

6.4.1.1. condensation of acetyl CoA and oxaloacetate

6.4.2. 2 carbon atoms leave the cycle as CO2

6.4.2.1. successive decarboxylations catalyzed by isocitrate dehydrogenase and α-ketoglutarate dehydrogenase

6.4.3. 4 oxidation reduction reactions in the cycles

6.4.3.1. 4 NAD+ reduced

6.4.3.1.1. 2 in : oxidative decarboxylations of isocitrate and α-ketoglutarate

6.4.3.1.2. 1 in : oxidation of malate

6.4.3.1.3. 1 in : oxidative decarboxylation of pyruvate to acetyl CoA

6.4.3.2. one FAD reduced

6.4.3.2.1. oxidation of succinate

6.4.3.3. oxidation of NADH and FADH2

6.4.3.3.1. 9ATP molecules

6.4.4. one high energy phosphate bond (GTP/ATP) is formed in the cycle

6.4.4.1. usually ATP generated from cleavage of thioester linkage in succinyl CoA

6.4.5. complete oxidation of each 2C acetyl CoA>H2O and CO2

6.4.5.1. 10 high energy phosphate bonds

7. Citric acid cycle as a source of biosynthetic precursors

7.1. provides intermediates 4 biosynthesis

7.1.1. most of C atoms in porphyrins come from succinyl CoA

7.1.2. many AAs derived from α-ketoglutarate and oxaloacetate

7.1.2.1. impt. in other metabolic processes

7.2. citric acid cycle intermediates must be replenished if any are drawn off for biosynthesis

7.2.1. e.g. of anaplerotic rxns

7.2.1.1. greek for fill up

7.2.1.2. a rxn that leads to the net synthesis/replenishment of pathway components

7.2.2. replenished by formation of oxaloacetate from pyruvate

7.2.2.1. catalyzed by pyruvate carboxylase

7.2.2.2. if energy charge is high

7.2.2.2.1. oxaloacetate converted into glucose

7.2.2.3. if energy charge low

7.2.2.3.1. oxaloacetate replenishes the citric acid cycle

7.3. as citric acid cycle=cycle

7.3.1. can be replenished by generation of any intermediates

8. Control of the citric acid cycle

8.1. rate of the citric acid cycle has to meet the demand for ATP in an animal cell

8.1.1. requires careful adjustments

8.1.2. needs to be rate determined

8.2. primary control points are allosteric enzymes

8.2.1. citrate synthase

8.2.2. isocitrate dehydrogenase

8.2.3. α-ketoglutarate dehydrogenase

8.2.4. first 3 enzymes in the cycle to generate high E e-s

8.3. controlled by both

8.3.1. the energy status of the cell

8.3.1.1. 1st control point(in many bacteria)

8.3.1.1.1. funneling of 2C carbon fragments into cycle

8.3.1.1.2. synthesis of citrate from oxaloacetate and acetyl CoA is an important control point in many bacteria

8.3.1.1.3. ATP=allosteric inhibitor of citrate synthase

8.3.1.2. 2nd control site

8.3.1.2.1. isocitrate dehydrogenase

8.3.1.2.2. allosterically stimulated by ADP

8.3.1.3. 3rd control site

8.3.1.3.1. α-ketoglutarate dehydrogenase

8.3.1.3.2. inhibited by succinyl CoA and NADH

8.3.1.3.3. rate of cycle is reduced when the cell has a high level of ATP

8.3.2. rate of supply of NAD+ and FAD

8.3.2.1. downstream effect

8.3.2.2. produced by respiration when the energy status is low

8.3.2.3. cycle only operates under aerobic conditions

8.4. control of pyruvate dehydrogenase complex

8.4.1. formation of acetyl CoA from pyruvate is a irreversible step in animals

8.4.1.1. unable to convert acetyl CoA back to glucose

8.4.2. key means of regulation of complex in eukaryotes

8.4.2.1. covalent modification

8.4.2.1.1. phosphorylation of pyruvate dehydrogenase component E1 by pyruvate dehydrogenase kinase (PKD)

8.4.2.1.2. deactivation reversed by pyruvate dehydrogenase phosphatase (PDP)

8.4.2.1.3. both kinases and phosphatases are also regulated

8.4.3. regulated to respond to energy charge of the cell

8.4.3.1. complex inhibited by immediate products and ultimate product of cellular respiration

8.4.3.1.1. NADH and acetyl CoA

8.4.3.1.2. ATP

8.4.3.1.3. high energy charge

8.4.3.1.4. less acetyl CoA is formed if energy status of cell is high

8.4.3.2. complex is activated by pyruvate and ADP

8.4.3.2.1. inhibit kinase that phosphorylates PDH

8.4.3.2.2. low energy charge

8.4.4. process driven by it = key irreversible step

8.4.4.1. has to controlled and regulated the most

9. Summary

9.1. Citric acid cycle

9.1.1. in matrix

9.1.2. initiated by pyruvate dehydrogenase complex

9.1.3. 9 step cyclic process

9.1.4. generates CO2

9.1.5. yields 10 high energy phosphate bonds/acetyl CoA

9.1.6. majority of carbons for porphyrins

9.1.7. many amino acids for protein production

9.1.8. controlled by

9.1.8.1. energy status of cell

9.1.8.1.1. at 3 points

9.1.8.2. rate of supply of NAD+ and FAD

10. Beriberi

10.1. a neurologic and cardiovascular disorder

10.1.1. caused by a dietary deficiency of thiamine(vitamin B1)

10.2. characteristized by neurologic and cardiac symptoms

10.2.1. PNS

10.2.1.1. pain in limbs, weakness of musculature, distorted skin sensation

10.2.2. cardiac

10.2.2.1. enlarged heart

10.2.2.2. inadequate cardiac output

10.3. Thiamine=precursor of cofactor TPP

10.3.1. prosthetic grp of 3 impt. enzymes

10.3.1.1. pyruvate dehydrogenase

10.3.1.2. alpha-ketoglutarate dehydrogenase

10.3.1.3. transketolase

10.3.1.3.1. pentose phosphate pathway

10.4. levels of pyruvate and alpha ketoglutarate in the blood are higher than normal

10.5. leads to neurological disorders bcuz

10.5.1. NS relies on glucose for fuel

10.5.2. pyruvate=product of glycolysis

10.5.2.1. can enter only through PDH complex

10.5.2.2. PDH complex is inactivated

10.5.2.2.1. NS has no source of fuel