A LEVEL: Biology (F214), Respiration

BIOLOGY: UNIT 1

Respiration

Respiration is the process in which energy stored in complex organic molecules are used to make ATP.

Energy is potential energy and kinetic energy. Moving molecules can generate this kinetic energy.

To drive a biological process, cells require energy. Metabolism is the word for all processes that occur in the cells. 

• Synthesis of large molecules from smaller ones = ANABOLIC REACTIONS
• Hydrolysis of large molecules into smaller ones = CATABOLIC REACTIONS

Energy comes from PHOTOAUTOTROPHS such as plants and bacteria, they create chemical potential energy which consumers such as humans will eventually use for their own biological processes. Such as RESPIRATION to create their own energy as ATP.

ATP is a phosphorylated nucleotide. 

•  HIGH ENERGY INTERMEDIATE COMPOUND
• ADENINE + RIBOSE + 3 PHOSPHATE GROUPS 
• HYDROLYSED = ADP + inorganic P
• This released 30.6 KJ mol-1
• It is the universal energy currency 
• The energy released from ATP hydrolysis, due to the splitting of the bonds is an immediate source of energy 

(Note: Remember the structure of ATP, it has appeared in a previous past paper question)

COENZYMES

To remove hydrogen atoms, oxidation needs to occur and these reactions are catalysed by dehydrogenase enzymes. Or coenzymes!

NAD: Nicotinamide Adenine Dinucleotide 

Can be extracted from Vitamin B3

A molecule of NAD needs to accept two hydrogen atoms and only then does it become reduced. 

However, to become oxidised it loses electrons. 

CoA: Coenzyme A

• it carries ethanoate or the acetate group during the link reaction into the Krebs cycle. 

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GLYCOLYSIS REACTION

Occurs in the CYTOPLASM and has four stages:

1. Phosphorylation
2. Splitting of hexose, 1,6 bisphosphate
3. Oxidation of Triose phosphate 
4. Conversion of Triose phosphate to pyruvate

1. PHOSPHORYLATION

Glucose is a hexose sugar (6C sugar)

• One ATP molecule is hydrolysed and the released phosphate group joins to the glucose molecule.

• Glucose 6 phosphate becomes Fructose 6 phosphate. -> Isomerisation

• Another ATP molecule is hydrolysed and the phosphate group bonds to the to Fructose 6 phosphate to form a Hexose 1,6 bisphosphate. 

2. SPLITTING OF HEXOSE, 1,6 BISPHOSPHATE

• Each molecule of Hexose 1,6-bisphosphate is split into two new molecules called triose phosphate. This is because a molecule such as Hexose, 1,6-bisphosphate is unstable. A triose phosphate is a 3-Carbon sugar molecule with one phosphate group. 

3. OXIDATION OF TRIOSE PHOSPHATE

• An oxidation process.

• Two hydrogen atoms are removed from each triose phosphate.

• Involves dehydrogenase enzymes.

• Helped by coenzyme NAD, the two hydrogen atoms bond with the NAD to form REDUCED NAD. NAD is a hydrogen acceptor. 

• Two reduced NAD per molecule of glucose. 

• Two molecules of ATP are also produced = SUBSTRATE LEVEL PHOSPHORYLATION. 

4. CONVERSION OF TRIOSE PHOSPHATE TO PYRUVATE 

• 4 enzyme catalysed reactions convert each triose phosphate molecule to a molecule of pyruvate. 
• 2 molecules of ADP are phosphorylated to 2 molecules of ATP 

PRODUCTS OF GLYCOLYSIS 

• Net gain of: 2 ATP
• 2 Molecules of Reduced NAD
• 2 Molecules of Pyruvate

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STRUCTURE AND FUNCTION OF THE MITOCHONDRIA

 Mitochondria in the muscle cells tend to be longer with more densely packed cristae and more ETC and ATP synthase. 

Matrix: The Link Reaction & Krebs Cycle 

It contains:

• Enzymes that catalyse these stages of the reaction
• Molecules of Coenzyme NAD
• oxaloacetate: 4C compound that accepts acetate from the link reaction
• Mitochondrial DNA/Eve DNA
• Mitochondrial ribosomes (stalked particles)

Outer Membrane: Similar to other membranes around the organelles, and contains proteins.

Inner Membrane:

• it is impermeable to most small molecules, including hydrogen ions
• folded into many cristae for a larger surface area
• has electron carriers and ATP synthase enzymes

Electron carriers:

• is a enzyme, it also has cofactors, that are not proteins and contain a haem-group and iron
• cofactors can donate and accept electrons
• oxireductase enzymes
• some have coenzymes that help pump the protons from the matrix to the inter membrane space.
• protons accumulate in the inter membrane space, because the inner membrane is impermeable. 

ATP Synthase enzymes: 

• protrude from the inner membrane to the matrix
• stalked particles
• allow protons to pass through (H+ ions)

Chemiosmosis: flow of hydrogen ions through ATP synthase enzymes. The force of this flow allows the production of ATP. Occurs across the thylakoid membranes during the light dependent stage of photosynthesis. Also occurs across the inner mitochondrial membrane during oxidative phosphorylation (in respiration)

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THE LINK REACTION & THE KREBS CYCLE

Pyruvate made during glycolysis is transported across the inner membrane and outer mitochondrial membrane into the matrix. 

oxidation: loss of hydrogen

reduction: is gain of hydrogen 

Pyruvate is changed into a 2-Carbon compound during the link reaction, acetate is then oxidised during krebs cycle. 

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THE LINK REACTION

Pyruvate dehydrogenase: removes hydrogen atoms from pyruvate

Coenzyme NAD accepts the hydrogen atoms to become reduced NAD

Pyruvate decarboxylase: removes carboxyl group from pyruvate - makes CO2

Coenzyme A accepts acetate to become acetyl coenzyme A. The point of CoA is to transport the acetate to the Krebs cycle.

The equation for the Link Reaction:

2pyruvate + (2NAD+) + 2CoA —> 2acetyle coenzyme A + 2CO2 + 2NADH 

(NAD+) - NAD in its oxidised state. 

2 molecules of pyruvate because they are the products from glucose, two pyruvate molecules are made for every single glucose. 

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THE KREBS CYCLE

Takes place in the matrix,

 1. Acetate is offloaded from CoA and binds with oxaloacetate to form a 6C compound called  citrate.

 2. Citrate is decarboxylated and releases a CO2 and reduced NAD. Forms a 5C compound.

 3. 5-C compound is decarboxylated and dehydrogenated to form a 4C compound and reduced NAD.

4. 4C compound undergoes isomerisation, and a ADP molecule is phosphorylated to ATP. = SUBSTRATE LEVEL PHOSPHORYLATION. 

5. The second 4C is changed to another 4C compound and a pair of hydrogen atoms are remove and accept by the coenzyme FAD, which becomes reduced

6. The 4C compound is further dehydrogenated and regenerates oxaloacetate, another molecule of NAD is reduced. 

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OXIDATIVE PHOSPHORYLATION

(the formation of ATP by adding inorganic phosphate to ADP, in the presence of Oxygen, the final electron acceptor) 

ETC: Electron transport chain

Oxidative phosphorylation is the FINAL STAGE.

Reduced FAD and NAD are

re-oxidised and release FAD and two electrons and H+ions.

First Electron carrier acceptor: NADH dehydrogenase.

• The protons go into the solution in the matrix
• The electrons are passed along the ETC in the inner membrane space before being donated to the final electron acceptor: OXYGEN

Chemiosmosis

1. Electrons pass through the ETC.
2. Energy is released
3. Energy used by co-enzymes
4. Co-enzymes pump the protons across into the inter membrane space
5. A chemical gradient is formed, as well as a electrochemical gradient
6. Potential energy builds up in the inter-membrane space
7. Protons diffuse through channel proteins
8. The ion channels are associated with the enzyme ATP-Synthase

Oxidative Phosphorylation

1. ATP is formed by ADP and P(i)
2. Protons flow through the ion channels
3. Drive the rotation of ATP Synthase 
4. Joins ADP and P(i)
5. Electrons pass through final electron acceptor: Oxygen
6. Hydrogen also joins: 4H+ + 4e- + O2 ————> 2H2O

ATP NET GAIN:

2 molecules of ATP: Glycolysis (substrate level phosphorylation)

2 molecules of ATP: Krebs Cycle (substrate level phosphorylation)

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ATP Production during Oxidative Phosphorylation.

Reduced NAD and FAD provide electrons for the ETC, in oxidative phosphorylation.

Reduced NAD provides hydrogen ions to produce an accumulation of ions, resulting in a proton gradient for chemiosmosis. Hydrogen from FAD, remain in the matrix but combine with oxygen to form water. 

• 10 molecules of reduced NAD can theoretically produce 26 molecules of ATP, during oxidative phosphorylation. 
• For each reduced NAD it produced 2.6 molecules of ATP
• Total yield of ATP is around 30. 

However this does not occur because:

• Some protons leak across the mitochondrial membrane resulting in reducing the number of protons to generate proton motive force, 

• Some ATP produced is used to actively transport pyruvate into the mitochondria.

• Some ATP is used to shuttle hydrogen from reduced NAD made during glycolysis, in the cytoplasm into the mitochondria. 

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Anaerobic Respiration: The release of energy in the absence of oxygen

Glycolysis: 

• 2 molecules of ATP
• 2 molecules of reduced NAD
• 2 molecules of Pyruvate

reduced NAD

Pyruvate ——————————> Lactate

(lactate dehydrogenase)

1. reduced NAD becomes reoxidised
2. Pyruvate becomes a hydrogen acceptor
3. Accepts the hydrogen and Reduced NAD becomes NAD
4. NAD is then recycled back for use in glycolysis 
5. Generates more ATP
6. Enzyme = Lactate dehydrogenase

extra: lactate is then carried to the liver. when more oxygen is available it gets broken down back into pyruvate and used again in the kerbs cycle or broken down into glucose or glycogen. 

it is the reduction in pH that affects enzyme activity in the muscles.

Anabolic Respiration 

1. pyruvate molecule loses a CO2 molecule through a process of carboxylation it produces ethanal
2. the reaction is catalysed by Pyruvate decarboxylase
3. Ethanal receives a hydrogen from reduced NAD (Hydrogen acceptor) 
4. reduced NAD has been re-oxidised into NAD
5. The dehydrogenation reaction makes it reduced into ethanol 
6. NAD can then be recycled in the glycolysis reaction and more ATP can be produced.

(CO2)                                        (reduced NAD ——> NAD)

Pyruvate ————————————> Ethanal ————————————> Ethanol

(pyruvate decarboxylase)                          (ethanol dehydrogenase)

                                                     (This reaction is irreversible)

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Respiratory Substrates: an organic substance that can be used for respiration

Carbohydrates:

Rule: Cn(H2O)n

Carbohydrates are made of glucose and monosaccharides or polysaccharides can be broken down into glucose or glycogen for storage and later used in respiration. 

most commonly used respiratory substrate

stored as glycogen

• Max. energy for glucose, 2870KJ mol-1
• 30.6 KJ for 1 mol ATP
• 1 mol of glucose = 94 mol ATP
• 30 mol ATP = 32% efficiency
• remaining energy is lost as heat - so that the optimum conditions are retained for enzymes

Protein

Amino acids are deaminated 

removes amine group and converted to urea

rest of the molecule is converted into glycogen and fat and then stored or respired.

protein is hydrolysed -> amino acids

• can be converted into pyruvate or acetate and moved into the krebs cycle
• or it can enter krebs cycle directly
• slightly more H atoms than glucose are accepted by NAD

Lipids 

Triglyceride: Glycerol and 3 Fatty acids

Glycerol -> Glucose

Fatty Acids combine with CoA using energy released by ATP being hydrolysed into AMP

Fatty acid CoA complex taken to matrix, broken down not 2 acetyl group. 

Reduced NAD and FAD formed 

Acetyl grops released from CoA, into the Krebs cycle: 3 NADH, 1 FADH, 1 ATP. Coenzymes enter the electron transport chain.  

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Respiratory Quotient:

CO2 eliminated

  O2 consumed