Respirasi

Heterotrof
Heterotrof membutuhkan molekul organik sebagai makanan.
Energinya diperoleh dari ikatan kimia di dalam molekul makanan seperti karbohidrat, lemak dan protein.

Autotrof
Autotrof merupakan organisme yang dapat menggunakan sumber energi dasar (sinar matahari) untuk membuat energi. Mis: tumbuhan dan beberapa mikroorganisme 2 Types
Photosynthetic autotrophs Chemosynthetic autotrophs

Chemosynthesis
Chemosynthesis is a process used by prokaryotic organisms to use inorganic chemical reactions as a source of energy to make larger organic molecules. Chemosynthesis adalah proses yang digunakan oleh organisme prokariotik menggunakan reaksi kimia anorganik sebagai sumber energi untuk membuat molekul organik yang lebih besar.

Aerobic Vs. Anaerobic

Aerobic respiration requires oxygen. Anaerobic respiration does not require oxygen.

Aerobic Respiration
Aerobic cellular respiration is a specific series of enzyme controlled chemical reactions in which oxygen is involved in the breakdown of glucose into carbondioxide and water. The chemical-bond energy is released in the form of ATP. Sugar + Oxygen carbon dioxide + water + energy (ATP)

Summary: 3 steps: 1st glycolysis 2nd Krebs cycle 3rd Electron Transport Chain (ETC)

A Road Map for Cellular Respiration

Cytosol Mitochondrion High-energy electrons carried by NADH Glycolysis Glucose 2 Pyruvic acid Krebs Cycle Electron Transport High-energy electrons carried mainly by NADH

Figure 6.7

Glycolysis
Stage 1: splitting glucose molecule (C6) into two PGALD (C3). 2 ATPs are used per glucose metabolism.

Stage 2: catalyzes the oxidation of PGALD to pyrvate. Generate s 4 ATPs per glucose metabolism.

glucose ATP ADP glucose-6-phosphate Hexokinase

Glycolysis

Phosphoglucose Isomerase fructose-6-phosphate ATP Phosphofructokinase ADP fructose-1,6-bisphosphate Aldolase glyceraldehyde-3-phosphate + dihydroxyacetone-phosphate Triosephosphate Isomerase Glycolysis continued

glyceraldehyde-3-phosphate NAD+ + Pi Glyceraldehyde-3-phosphate Dehydrogenase NADH + H+

Glycolysis continued. Recall that there are 2 GAP per glucose.

1,3-bisphosphoglycerate ADP Phosphoglycerate Kinase ATP 3-phosphoglycerate Phosphoglycerate Mutase 2-phosphoglycerate Enolase H2O phosphoenolpyruvate ADP Pyruvate Kinase ATP pyruvate

6 CH 2OH

H
4

O H
2

ATP ADP H H
1 4

6 CH OPO 2 2 3 5

O H
2

H
1

H OH
3

OH

OH

Mg2+ OH

H OH
3

OH

OH

Hexokinase

OH

glucose

glucose-6-phosphate

1. Hexokinase catalyzes: Glucose + ATP glucose-6-P + ADP

The reaction involves nucleophilic attack of the C6 hydroxyl O of glucose on P of the terminal phosphate of ATP. ATP binds to the enzyme as a complex with Mg++.

6 CH OPO 2 2 3

H
4

O H
2

H
1

6 CH OPO 2 2 3

H OH
3

1 CH 2OH

H
4

HO H

OH

OH

3 OH

OH

OH

Phosphoglucose Isomerase glucose-6-phosphate fructose-6-phosphate

2. Phosphoglucose Isomerase catalyzes: glucose-6-P (aldose) fructose-6-P (ketose)

The isomerization is an electron shift where 2 electron from C2 carbon reduce the C1 aldehyde of the glucose6-phosphte molecule to an alcohol.

Phosphofructokinase
6 CH OPO 2 2 3

1CH2OH

6 CH OPO 2 2 3

ATP ADP HO H
2 5

1CH2OPO32

H
4

H
4

HO H

3 OH

Mg2+

3 OH

OH

OH

fructose-6-phosphate

fructose-1,6-bisphosphate

3. Phosphofructokinase catalyzes: fructose-6-P + ATP fructose-1,6-bisP + ADP

This highly spontaneous reaction has a mechanism similar to that of Hexokinase.

The Phosphofructokinase reaction is the ratelimiting step of Glycolysis. .

1CH 2OPO3 2C

O H OH OH

HO 3C H 4C H
5

Aldolase

2 CH OPO 2 3 3

H
1C

2C

1CH 2OH

H 2C OH 2 3 CH 2OPO3

2 CH OPO 2 3 6

fructose-1,6bisphosphate

dihydroxyacetone phosphate

glyceraldehyde-3phosphate

Triosephosphate Isomerase

4.Aldolase catalyzes: fructose-1,6-bisphosphate dihydroxyacetone-P + glyceraldehyde-3-P The reaction is an aldol cleavage, the reverse of an aldol condensation.
Note that C atoms are renumbered in products of Aldolase.

1CH 2OPO3 2C

O H OH OH

HO 3C H 4C H
5

Aldolase

2 CH OPO 2 3 3

H
1C

2C

1CH 2OH

H 2C OH 2 3 CH 2OPO3

2 CH OPO 2 3 6

fructose-1,6bisphosphate

dihydroxyacetone phosphate

glyceraldehyde-3phosphate

Triosephosphate Isomerase

5. Triose Phosphate Isomerase (TIM) catalyzes: dihydroxyacetone-P glyceraldehyde-3-P The dihidroxyacetone-P is isomerized to PGALD, thus this stage produce 2 molecules PGAL pe 1 glucose

Triosephosphate Isomerase
H H C C OH O H H
+ +

H C C

OH OH

H H

H C H C

O OH

CH 2OPO32

CH 2OPO32

CH 2OPO32

dihydroxyacetone phosphate

enediol intermediate

glyceraldehyde3-phosphate

The ketose/aldose conversion involves acid/base catalysis, and is thought to proceed via an enediol intermediate, as with Phosphoglucose Isomerase. Active site Glu and His residues are thought to extract and donate protons during catalysis.

Glyceraldehyde-3-phosphate Dehydrogenase
H
1C

O C OH

NAD+ + Pi

OPO32 + H+ O NADH 1C H
2 CH OPO 2 3 3

2 CH OPO 2 3 3

OH

glyceraldehyde3-phosphate

1,3-bisphosphoglycerate

6. Glyceraldehyde-3-phosphate Dehydrogenase catalyzes: glyceraldehyde-3-P + NAD+ + Pi 1,3-bisphosphoglycerate + NADH + H+

Glyceraldehyde-3-phosphate Dehydrogenase
H
1C

O C OH

NAD+ + Pi

OPO32 + H+ O NADH 1C H
2 CH OPO 2 3 3

2 CH OPO 2 3 3

OH

glyceraldehyde3-phosphate

1,3-bisphosphoglycerate

Exergonic oxidation of the aldehyde in glyceraldehyde- 3phosphate, to a carboxylic acid, drives formation of an acyl phosphate, a "high energy" bond (~P). This is the only step in Glycolysis in which NAD+ is reduced to NADH.

Phosphoglycerate Kinase
O
1C

OPO32 ADP ATP O

1

O C

H 2C OH 2 CH OPO 2 3 3

Mg2+

H 2C OH 2 CH OPO 2 3 3

1,3-bisphosphoglycerate

3-phosphoglycerate

7. Phosphoglycerate Kinase catalyzes: 1,3-bisphosphoglycerate + ADP 3-phosphoglycerate + ATP This phosphate transfer is reversible (low DG), since one ~P bond is cleaved & another synthesized.
The enzyme undergoes substrate-induced conformational change similar to that of Hexokinase.

Phosphoglycerate Mutase
O
1

O C

O
1

O C

H 2C OH 2 CH OPO 2 3 3

H 2C OPO32 3 CH 2OH

3-phosphoglycerate

2-phosphoglycerate

8. Phosphoglycerate Mutase catalyzes: 3-phosphoglycerate 2-phosphoglycerate Phosphate is shifted from the OH on C3 to the OH on C2.

Enolase
O
1

O C

O C C

OH

O
1

O C OPO32

H 2 C OPO32 3 CH2OH

OPO32

2C

CH2OH

3 CH2

2-phosphoglycerate enolate intermediate phosphoenolpyruvate

9. Enolase catalyzes: 2-phosphoglycerate phosphoenolpyruvate + H2O

Pyruvate Kinase
O C 1 C 2 O OPO32 ADP ATP O
1 2

O C C O

3 CH 2

3 CH 3

phosphoenolpyruvate

pyruvate

10. Pyruvate Kinase catalyzes: phosphoenolpyruvate + ADP pyruvate + ATP

Krebs Cycle
Makes ATP Makes NADH Makes FADH2

Conversion of pyruvate to Acetyl CoA

O H3C O pyruvate O
pyruvate dehydrogenase complex

NAD+

NADH

HSCoA

CO2 H3C

O SCoA

acetyl CoA

2 per glucose (all of Krebs) Oxidative decarboxylation Makes NADH

Net From Krebs

Oxidative process
3 NADH FADH2 GTP

X 2 per glucose
6 NADH 2 FADH2 2 GTP

All ultimately turned into ATP (oxidative phosphorylationlater)

Citrate Synthase Reaction (First)

Aconitase Reaction
O O
O HO

HO

C CH2 O C C O CH2 C
O

O O O

aconitase

C CH HC C CH2 C
O O

citrate

isocitrate

Forms isocitrate Goes through alkene intermediate (cis-aconitate)

Hydroxyl moved and changed from tertiary to secondary

13.3kJ
(can be oxidized)

elimination then addition

Isocitrate Dehydrogenase
O HO O O O

C CH HC C CH2 C
O O

NAD

NADH

CO2

C C O CH2 CH2 C
O

isocitrate dehydrogenase

isocitrate

alpha ketoglutarate

All dehydrogenase reactions make NADH or FADH2 Oxidative decarboxylation -20.9kJ Energy from increased entropy in gas formation

-ketoglutarate dehydrogenase
O

C C O CH2 CH2 C
O

SCoA

CoASH

CO2

NAD

NADH

C CH2 CH2 C
O O

alpha ketoglutarate
dehydrogenase

alpha ketoglutarate

succinyl CoA

Same as pyruvate dehydrogenase reaction Formation of thioester

endergonic driven by loss of CO2
increases entropy exergonic

-33.5kJ

Succinyl CoA synthetase

SCoA O

O GDP GTP CoASH

C CH2 CH2 C
O O
succinyl CoA

O C CH2

succinyl CoA synthetase

CH2 C O O succinate

Hydrolysis of thioester

Coupled to synthesis of GTP

-2.9kJ

Releases CoASH Exergonic

Endergonic GTP very similar to ATP and interconverted later

Succinate dehydrogenase
O C CH2 O FAD FADH2
H
succinyl CoA
dehydrogenase

C C C C

CH2 C O O succinate

fumarate

Dehydrogenation Uses FAD

NAD used to oxidize oxygen-containing groups
Aldehydes alcohols

FAD used to oxidize C-C bonds 0kJ

Fumarase
O O O

O C HC OH CH2 C
O O

C C
H O

H2O
H
fumarase

C C
O

fumarate

malate

Addition of water to a double bond -3.8kJ

Malate Dehydrogenase
O

O C HC OH CH2 C
O O
malate
dehydrogenase

O
NAD
NADH

O C C O CH2 C O

malate

oxaloacetate

Oxidation of secondary alcohol to ketone Makes NADH Regenerates oxaloacetate for another round 29.7 kJ

Net From Krebs

Oxidative process
3 NADH FADH2 GTP

X 2 per glucose
6 NADH 2 FADH2 2 GTP

All ultimately turned into ATP (oxidative phosphorylationlater)

INHIBITOR OF TCA CYCLE

1. Fluoroacetate Condensation with CoA Fluoroacetyl-CoA Condensation FluoroacetylCoA with Oxaloacetate Fluorocitrate inhibit Akonitase enzyme accumulation of citrate Fluoroacetate pesticide 2. Malonate suksinat dehydrogenase enzyme 3. Arsenite -ketoglutarate dehydrogenase enzyme

REGULATION OF TCA CYCLE

REGULATION OF TCA CYCLE

Electron Transport System

The electrons released from glycolysis and the Krebs cycle are carried to the electrontransport system (ETS) by NADH and FADH2. The electrons are transferred through a series of oxidation-reduction reactions until they are ultimately accepted by oxygen atoms forming oxygen ions. 32 molecules of ATP are produced.

What is the electron transport chain?

A chain of protein complexes embedded in the inner mitochondrial membrane. Transports electrons and pumps hydrogen ions into the intermembrane space to create a gradient.

Components of the electron transport chain (ETC)

NADH dehydrogenase Ubiquinone (Q) Succinate dehydrogenase Cytochrome b-c1 Cytochrome c Cytochrome oxidase

Arranged in order of increasing

electronegativity (weakest to strongest)

NADH produced from glycolysis

VS
NADH produced from Krebs cycle

VS

NADH produced in the cytoplasm by glycolysis: CAN diffuse from outer mitochondrial membrane to intermembrane space. CANNOT diffuse from inner membrane to matrix.
NADH produced from Krebs cycle: Already in the matrix.

What to do?
Cytosolic NADH (NADH that are produced by glycolysis) pass electrons to shuttles

Glycerol-phosphate shuttle: Transfers electrons from cytosolic NADH to FAD to produce FADH2
Aspartate shuttle: Transfers electrons from cytosolic NADH to NAD+ to produce NADH

Complex I: NADH dehydrogenase

NADH dehydrogenase oxides NADH back to NAD+ NADH + H+ NAD+ + 2H+ + 2e The electrons are transferred to flavin mononucleotide (FMN) which reduces to FMNH2

FMN + 2H+ + 2e- FMNH2

The electrons are then passed to iron-sulphur proteins (FeS) located in NADH dehydrogenase

Complex I Continued
Electrons are accepted by Fe3+ which is reduced to Fe2+

2Fe3+ + 2e- 2Fe2+

These two electrons are then given to ubiquinone (Q) The two hydrogen ions are pumped into the intermembrane space

*One hydrogen ion is pumped per electron transferred

Ubiquinone (Q)
A mobile electron carrier

2Fe2+ gives 2e- to Q Q is reduced to QH2 (ubiquinol) and 2Fe2+ is oxidized 2Fe3+
Carries electrons to complex III, cytochrome b-c1

Interactive Animation:
http://www.brookscole.com/chemistry_d/ templates/student_resources/shared_re sources/animations/oxidative/oxidativep hosphorylation.html

Complex II: Succinate Dehydrogenase

oxidation of succinate from Krebs cycle to fumarate
Succinate + FAD Fumarate + FADH2
FADH2 then tries to oxidize back into FAD by passing its electrons to 2 Fe2+

2Fe3+ + 2e- 2Fe2+

Complex II Continued...
These electrons from 2Fe2+ are then stolen by ubiquinone (Q), which carries them to complex III. 2+ 3+

Q + 2Fe

2Fe + QH2

Unlike complex I, complex II doesnt have enough free energy for active transport of the hydrogen ions (protons) from FADH2 across the intermembrane . This is why oxidation of FADH2 only yields 2 ATP molecules instead of 3 ATP molecules like NADH.

Complex III: cytochrome b-c1

Contains cytochrome b, cytochrome c1, and FeS proteins. QH2 passes two electrons to cytochrome b causing Fe3+ to reduce to Fe2+ Same way from cyt b to FeS protein and then to cyt c1

Cytochrome C (c)
Im a protein and like Q...
I am also a water soluble mobile electron carrier. I transport electrons one at a time from complex III to complex IV.

Complex IV: Cytochrome Oxidase

(The End of the Line)

This is the end of the line for electrons from NADH or succinate. Oxygen (breathed in) is reduced and when combined with these electrons, they form...

O2 (g) + 2H+ + 2e- H2O (l)

WATER

THIS REACTION IS EXPLOSIVE! Its highly exergonic, releasing large amounts of energy.

Electrochemical gradient
A concentration gradient created by pumping ions into a space surrounded by a membrane that is impermeable to the ions. Two components: electrical and chemical Proton-motive force (PMF) moves protons through an ATPase complex on account of the free energy stored in the form of an electrochemical gradient of protons across a biological membrane.

Chemiosmosis
Peter Mitchell Nobel Prize in Chemistry in 1978 A process for synthesizing ATP using the energy of an electrochemical gradient and the ATP synthase enzyme. osmosis After chemiosmosis, ATP molecules are transported through both mitochondrial membranes.

Connections!
Electrons from NADH and FADH2 were passed down the ETC As the electrons move down, energy released moves protons to create electrochemical gradient Protons move through proton channels, and release energy to synthesize ATP from ADP and Pi The many processes of ATP synthesis are all continuous

Fermentation
Fermentation describes anaerobic pathways that oxidize glucose to produce ATP. An organic molecule is the ultimate electron acceptor as opposed to oxygen. Fermentation often begins with glycolysis to produce pyruvic acid.

Anaerobic Cellular Respiration

Anaerobic respiration does not require oxygen as the final electron acceptor. Some organisms do not have the necessary enzymes to carry out the Krebs cycle and ETS. Many prokaryotic organisms fall into this category. Yeast is a eukaryotic organism that performs anaerobic respiration.

 First step in anaerobic respiration is also glycolysis

Diagram Cytoplasm
C6H12O6 glucose

Anaerobic Respiration glycolysis

Alcoholic fermentation Bacteria, Yeast 2 ATP Lactic acid fermentation Muscle cells 2 ATP

Aerobic Respiration

Krebs Cycle

ETC

Mitochondria

Alcoholic Fermentation
Alcoholic fermentation is the anaerobic pathway followed by yeast cells when oxygen is not present Pyruvic acid is converted to ethanol and carbon-dioxide. 4 ATPS are generated from this process, but glycolysis costs 2 ATPs yielding a net gain of 2 ATPs.

 Alcoholic fermentationoccurs in bacteria and yeast

Process used in the baking and brewing industryyeast produces CO2 gas during fermentation to make dough rise and give bread its holes glucose ethyl alcohol + carbon dioxide + 2 ATP

ALCOHOL FERMENTATION

Lactic Acid Fermentation

In Lactic acid fermentation, the pyruvic acid from glycolysis is converted to lactic acid. The entire process yields a net gain of 2 ATP molecules per glucose molecule. The lactic acid waste products from these types of anaerobic bacteria are used to make fermented dairy products such as yogurt, sour cream, and cheese.

 Lactic acid fermentationoccurs in muscle cells Lactic acid is produced in the muscles during rapid exercise when the body cannot supply enough oxygen to the tissuescauses burning sensation in muscles glucose lactic acid + carbon dioxide + 2 ATP

LACTIC ACID FERMENTATION