1. Unit 1 Communication, Homeostasis and Energy
Respiration

2. Test Yourself What is aerobic respiration?
What is anaerobic respiration?
Which organelle carries out most of the stages of respiration in eukaryotic cells?
What are the products of aerobic respiration?
What is the universal energy currency molecule?

3. Learning Outcome
Outline why plants, animals and microorganisms need to respire, with reference to active transport and metabolic reactions.

4. Energy in Living Organisms
In order to maintain life, organisms need a source of energy.
In most organisms this is provided by the oxidation of organic molecules.
Autotrophic nutrition
Synthesise organic materials from inorganic sources e.g. photosynthesis
Heterotrophic nutrition
Obtained in organic form

5. Energy Energy is the ability to do work Energy exists in two states
Kinetic energy
Energy of motion
Potential energy
Stored energy

6. Energy Facts Energy facts Cannot be created or destroyed
Can be converted from one form to another
Takes a variety of forms
Measured in joules or kilojoules

7. Metabolism Metabolism
All reactions that take place within the organism
Anabolism
Build up of larger, more complex molecules from smaller, simpler ones
Catabolism
Breakdown of complex molecules into smaller, simpler ones
Releases energy

8. Energy in Living Organisms
“Work”
Synthesis of complex substances
Active transport e.g. sodium-potassium pump
Movement
Bioluminescence
Maintenance of body temperature
Production of electricity
Maintenance, repair and division
Activation of chemicals

9. Testing your progress
Energy is defined as the ability to do ________________.
The energy of motion is known as ___________ energy, whereas _________ energy is stored energy.
Living organisms need energy for many reasons
__________ reactions in which simple molecules are built up into complex ones
The movement of material by __________ against a concentration gradient.

10. Progress questions
Fireflies can produce light in a process called bioluminescence. Outline the energy transformations that occur in fireflies as they use energy from their food to produce luminescence.
Comment on the statement below.
Respiration produces energy to form ATP.

11. Learning outcomes
Describe, with the aid of diagrams, the structure of ATP.
State that ATP provides the immediate source of energy for biological processes.

12. Structure of ATP ATP is a phosphorylated nucleotide. Adenosine
Adenine
Ribose sugar
Three phosphate groups

13. Structure of ATP

14. The structure of ATP
Covalent bonds between phosphate groups are unstable and easily broken releasing energy
ATP  ADP = 30.6kJmol-1 (energy)
ADP  AMP = 30.6kJmol-1(energy)
AMP  Adenosine = 14.2kJmol-1 (energy)

15. The role of ATP
As ATP is hydrolysed energy is immediately available to the cell in small, manageable amounts.
ATP is described as the universal energy currency.
ATP is continually being hydrolysed and resynthesised.

16. Think!! What type of base is adenine?
ATP is a nucleic acid / nucleotide derivative.
Is it derived from DNA or RNA nucleotides?
Give reasons for your answer
Explain why ATP is known as the universal energy currency.

17. Learning Outcomes
explain the importance of coenzymes in respiration, with reference to NAD and coenzyme A;
state that glycolysis takes place in the cytoplasm
outline the process of glycolysis;

18. Respiration The oxidation of food to obtain free energy (ATP)
Respiration of glucose can be summarised in four stages
Glycolysis
The link reaction
Krebs cycle
Oxidative Phosphorylation

19. Redox Reactions OIL RIG Oxidation Reduction
Loss of electrons
Loss of hydrogen atoms
Reduction
Gain of electrons
Gain hydrogen atoms
If one substrate becomes oxidised another becomes reduced.
OIL RIG

20. Coenzymes in Respiration
During respiration, hydrogen atoms are removed from substrate molecules in oxidation reactions.
This is catalyzed by dehydrogenase enzymes
Co enzymes are required to activate the oxidation reactions in respiration
Hydrogen atoms becomes attached to co enzymes e.g. NAD

21. NAD Nicotinamide adenine dinucleotide (NAD
Is reduced when it has accepted two hydrogen atoms with their electrons
Operates in glycolysis, link reaction, the Krebs cycle and the anaerobic pathways.

22. Coenzyme A
Function
To carry ethanoate (acetate) groups made in the link reaction, onto the Krebs cycle
To carry acetate groups made from fatty acids or amino acids onto the Krebs cycle

23. Glycolysis Ancient biochemical pathway
Glucose (6C) is broken down into two molecules of pyruvate (3C), with a net gain of 2 ATP molecules.
Occurs in the cytoplasm

24. Glycolysis Pathway can be outlined in four stages Phosphorylation
Splitting of hexose 1,6-bisphosphate
Oxidation of triose phosphate
Conversion of triose phosphate to pyruvate

25. Products of Glycolysis
Net gain of two ATP molecules
Two molecules of reduced NAD
Two molecules of pyruvate

26. Stretch and challenge 10 minutes – hand in answers
Enzymes that cause the shape of a molecule to change (without changing in proportions of atoms in that molecule) are called isomerases.
At which stage of glycolysis are isomerase enzymes involved?
How does the fact the nearly all living things use the glycolysis pathway support the theory of evolution?

27. Learning Outcomes recall the structure of a liver mitochondrion
identify inner and outer membranes and the inter membranal space
state that, during aerobic respiration in animals, pyruvate is actively transported into mitochondria;
explain, with the aid of diagrams and electron micrographs, how the structure of mitochondria enables them to carry out their functions;

28. Mitochondria
All mitochondria have an inner and outer phospholipid membrane (envelope)
Inner membrane is folded into cristae
Intermembrane space
Matrix
Contains looped DNA
Mitochondrial ribosomes
enzymes

29. Mitochondria

30. Mitochondria

31. Mitochondria

32. Mitochondrial matrix
This is where the link reaction and the Krebs cycle take place
It contains
Enzymes
Molecules of coenzyme NAD
Oxaloacetate
Mitochondrial DNA
Mitochondrial ribosomes

33. Outer Membrane It contains
Protein channels or carriers to allow pyruvate to pass through
Other proteins act as enzymes

34. Inner membrane
Has a different membrane structure and is impermeable to small ions (e.g. hydrogen ions)
Folded into cristae to give a large surface area
Contains electron carriers and ATP synthase enzymes

35. Questions
It has been suggested that mitochondria are derived from prokaryotes. What features of their structure support this suggestion?
Suggest how the structure of a mitochondria from a skin cell would differ from that of a mitochondrion from heart muscle tissue.

36. Learning Outcomes
state that the link reaction takes place in the mitochondrial matrix;
outline the link reaction, with reference to decarboxylation of pyruvate to acetate and the reduction of NAD;
explain that acetate is combined with coenzyme A to be carried to the next stage;

37. The Link Reaction
Pyruvate is actively transported into the matrix of the mitochondria.
Pyruvate is dehydrogenated and decarboxylated to acetate in a series of enzyme controlled reactions.
Enzymes
Pyruvate dehydrogenase
Pyruvate decarboxylase

38. The link reaction NAD accepts the hydrogen ions
Coenzyme A accepts acetate to form Acetyl CoA, to carry onto the Krebs cycle.
Carbon dioxide is released

39. Learning Outcomes
state that the Krebs cycle takes place in the mitochondrial matrix;
outline the Krebs cycle, with reference to the formation of citrate from acetate and oxaloacetate and the reconversion of citrate to oxaloacetate
explain that during the Krebs cycle, decarboxylation and dehydrogenation occur, NAD and FAD are reduced and substrate level phosphorylation occurs

40. Krebs Cycle Takes place in the mitochondrial matrix Main stages
Decarboxylation
Removal of Co2
Dehydrogenation
reduction of NAD
Substrate-level phosphorylation
Production of ATP

41. Krebs cycle
For each original glucose molecule there are two turns of the Krebs cycle.
Products
6 reduced NAD
2 reduced FAD
4 carbon dioxide
2 ATP
Although oxygen is not used up in these stages, they can not take place if it is absent – they are aerobic stages

42. Products of Aerobic respiration
Product per molecule of glucose
Glycolysis
Link reaction
Krebs cycle
Reduced NAD
Reduced FAD
CO2
ATP

43. Products of Aerobic respiration
Product per molecule of glucose
Glycolysis
Link reaction
Krebs cycle
Reduced NAD 2 6
Reduced FAD
CO2 4
ATP

44. Moving into the last stage of aerobic respiration
10 reduced NAD
2 reduced FAD

45. Stretch and challenge
Explain why mature erythrocytes cannot carry out the link reaction or Krebs cycle

46. Stretch and challenge
The inner mitochondrial membranes are impermeable to reduced NAD. For this reason a shunt mechanism moves hydrogen ions from reduced NAD made during glycolysis, to the matrix side of the inner mitochondrial membrane. The hydrogens are carried in by another chemical than then becomes reoxidised, reducing NAD that is already in the mitochondrial matrix.
Explain why such a shunt mechanism is not required for NAD reduced during the link reaction and Krebs cycle.

47. Stretch and challenge
Aerobic prokaryotes can carry out the link reaction, Krebs cycle and oxidative phosphorylation.
Suggest where in the prokaryotic cell these reactions take place.

48. Learning outcomes
outline the process of oxidative phosphorylation, with reference to the roles of electron carriers, oxygen and the mitochondrial cristae;
state that oxygen is the final electron acceptor in aerobic respiration;

49. Oxidative phosphorylation
Formation of ATP by adding a phosphate group to ADP
Takes place in the presence of oxygen
Oxygen is the final electron acceptor
Takes place across the inner mitochondrial membrane

50. Stage 1
Reduced NAD and reduced FAD are reoxidised when they donate the hydrogen, split into H+ and e-
Electrons are accepted by electron carriers
Protons go into solution in the matrix

51. Stage 2: Electron transport chain
Electrons passed along chain of carriers, energy released is used to pump protons across to intermembrane space
building up a proton/ pH / electrochemical gradient
Hydrogens diffuse through ion channels associated with ATPsynthase (chemiosmosis)

52. Stage 3 oxidative phosphorylation
As protons flow through ATP synthase
Drive the rotation of part of enzyme
This joins ADP and Pi to form ATP
Electrons and hydrogen ions combine with oxygen to form water.

53. Learning outcomes
outline the process of chemiosmosis, with reference to the electron transport chain, proton gradients and ATPsynthase
evaluate the experimental evidence for the theory of chemiosmosis

54. The synthesis of ATP
The complete oxidation of one molecule of glucose produces a net yield of 32 ATP’s.
Energy required to make ATP comes from:
Respiration – energy released by rearranging chemical bonds
The transfer of electrons by electron carriers in mitochondria
H+ ions create a concentration gradient through a protein channel;
this protein channel acts as the enzyme ATP synthase.
3 H+ ions provide the energy to make one ATP molecule, provided that ADP and Pi are available.

55. 1961 – Peter Mitchell chemiosmosis

56. Chemiosmosis
Build of hydrogen ions on one side of membrane is a source of potential energy
Movement of ions across the membrane down an electrochemical gradient – provides energy to form ATP from ADP and Pi.
Inner mitochondrial membrane = energy transducing membrane
Kinetic energy of the flow of ions = proton motive force

57. Evaluating evidence
On the hand out – write out how each piece of evidence supports the chemiosmosis theory put forward by Mitchell in 1961.

58. Compelling Evidence
pH gradient across the membranes in involved in ATP production
The pH on one side of the membrane is higher than the other
This suggests hydrogen ions are being actively moved across the membrane
Membranes make ATP even if there is no electron transport taking place, as long as a pH gradient is produced.

59. Evidence for chemiosmotic theory

60. Questions
Explain why was it important to keep the thylakoids in the dark?
Explain why the pH inside and outside the thylakoid membranes becomes equal when they are left in pH4 buffer for some time.

61. Questions
Does a pH4 buffer contain a greater or smaller concentration of H+ than a pH8 buffer?
In which direction was there a pH gradient when the thylakoids were place in the pH8 buffer?
Explain why and how the thylakoids were able to make ATP when they were placed in the pH8 buffer solution.

62. Compelling Evidence
Chemicals that prevent hydrogen ions being transported across the membrane also stop ATP being produced.
Dinitrophenol is a chemical that acts as a hydrogen carrier across membranes.
If Dinitrophenol is added – no hydrogen ion gradient is built up.

63. The evidence suggests
The hydrogen ion gradient is responsible for making ATP not the electron transport.

64. Learning outcomes
explain why the theoretical maximum yield of ATP per molecule of glucose is rarely, if ever, achieved in aerobic respiration;

65. How much ATP!! Summary aerobic respiration
Glucose is oxidised to pyruvate in glycolysis
Pyruvate is oxidised in Krebs Cycle
Hydrogen ions removed are passed along the electron transport chain
For every two hydrogen donated to the ETC by reduced NAD – 3 ATP molecules are made
For every two hydrogen donated to the ETC by reduced FAD – 2 ATP molecules are made

66. However…. Some energy has been put in to these processes.
For every two hydrogen donated to the ETC by reduced NAD – 2.5 ATP molecules are made
For every two hydrogen donated to the ETC by reduced FAD – 1.5 ATP molecules are made

67. Theoretical Maximum Yield
process
ATP used
ATP produced
Glycolysis
Phosphorylation of glucose
Direct phosphorylation of ADP
From reduced NAD
Link reaction
Krebs cycle
From reduced FAD
Totals
Net yield

68. Theoretical Maximum Yield
process
ATP used
ATP produced
Glycolysis
Phosphorylation of glucose 2
Direct phosphorylation of ADP 4
From reduced NAD 5
Link reaction
Krebs cycle 15
From reduced FAD 3
Totals 34
Net yield 32

69. Energy is used to: Transport ADP into mitochondria from the cytoplasm
Transport ATP from mitochondria into the cytoplasm
Protons could “leak” across membrane reducing the number to generate the proton motive force.
Active transport of pyruvate into mitochondria

70. Investigating the activity of dehydrogenase enzyme in yeast
Read the information supplied at the top of the practical sheet.
Set up the three test tubes as shown below.
10ml glucose
10ml yeast
5 ml dye

71. Investigating the activity of dehydrogenase enzyme in yeast
Shake tubes vigorously for 20 seconds, and place in a water bath set at 37oC.
Leave for a few minutes
Write up the experiment using the back of the sheet.

72. Investigating the activity of dehydrogenase enzyme in yeast
Tube A
Colour change from blue via pink to colourless.
Hydrogen has been rapidly released and has reduced the dye.
For this to happen – dehydrogenase enzymes present in yeast cells must have acted on the glucose, the respiratory substrate, and oxidised it.

73. Investigating the activity of dehydrogenase enzyme in yeast
Tube B
Change from blue – pink – colourless
Reaction is slower since no glucose was added.
Dehydrogenase could only act on any small amount of respiratory substrate already present in the yeast cells.
Tube C
Boiling has killed the yeast and denatured the dehydrogenase enzymes.

74. Learning Outcomes
explain why anaerobic respiration produces a much lower yield of ATP than aerobic respiration;
compare and contrast anaerobic respiration in mammals and in yeast;

75. Anaerobic Respiration
Occurs when free oxygen is not available
oxygen is no longer the final hydrogen acceptor
Reduced NAD cannot be recycled to NAD
The stages of respiration inside the mitochondrion can not take place

76. Alternative pathways
Two other pathways recycle the reduced NAD formed during glycolysis
Alcoholic fermentation
Conversion of pyruvate to ethanol
Lactate fermentation
Conversion of pyruvate to lactate
Both pathways are inefficient and provide a net gain of two ATP molecules per glucose molecule

77. Alcoholic fermentation
Pyruvate is decarboxylated to form ethanal
Ethanal accepts hydrogen from reduced NAD to form ethanol
The alcoholic fermentation pathway is irreversible

78. Alcoholic Fermentation

79. Lactate fermentation
Pyruvate accepts the hydrogen and is converted into lactate
The lactate pathway is reversible by the Cori cycle in the mammalian liver
Lactate causes a fall in pH which may stop the muscles from contracting.

80. Lactate Fermentation

81. Learning outcomes define the term respiratory substrate;
explain the difference in relative energy values of carbohydrate, lipid and protein respiratory substrates

82. Respiratory Substrates
Molecules from which energy can be liberated to produce ATP in a living cell.
Below are 3 respiratory substrates and their energy value
Glucose 16kJg-1
Lipid 39kJg-1
Protein 17kJg-1

83. Respiration of fatty acids and amino acids
Fatty acids enter the Krebs cycle after being broken down into two Acetyl CoA molecules
Amino acids are deaminated
Converted either into pyruvate and enter the link reaction or acetate and enter the Krebs cycle

84. Respiratory substrates
Glycogen or starch
Protein
Glucose
Lipid
Pyruvate
Amino Acids
fatty Acids
Acetylcoenzyme A
Krebs cycle

85. Energy values of respiratory substrates
The more hydrogens there are in the structure of a molecule, the greater the energy value
Revise the structure of glucose, amino acids and fatty acids from the AS course.

86. Respiratory Quotients (RQ)
The respiratory quotient (RQ) is the ratio of the volumes of oxygen absorbed and carbon dioxide given off in respiration.
RQ = Volume of carbon dioxide given off
Volume of oxygen taken in 

87. Calculate RQ Calculate the RQ for the aerobic respiration of Glucose.
Calculate the RQ for the fatty acid oleic acid, when respired aerobically.
C18H34O O2  18 CO H2O

88. Calculating RQ for Anaerobic respiration
C6H12O6  2C2H5OH + 2CO2
A high RQ value suggests that anaerobic respiration is taking place.
No RQ can be calculated for the lactate pathway as no carbon dioxide is given off.

89. Respiratory Quotients (RQ)
The respiratory quotients of different respiratory substrates are well documented from previous investigations.
Carbohydrate 1.0
Protein 0.9
Fat 0.7
It is possible to deduce which substrate is being used by the metabolism at a specific time.
NB if a mixture of substrates is being used then the figure will be different from those above.

90. The RQ (and oxygen uptake) can be measured using a respirometer.

91. Respirometer
Sodium hydroxide absorbs all CO2 from the air in the apparatus from the beginning.
As the germinating seeds use oxygen and the pressure reduces in tube A so the manometer level nearest to the seeds rises.
Any CO2 excreted is absorbed by the sodium hydroxide solution.

92. Respirometer
The syringe is used to return the manometer fluid levels to normal.
The volume of oxygen used is calculated by measuring the volume of gas needed from the syringe to return the levels to the original values
If water replaces the sodium hydroxide then amount of carbon dioxide given off can be measured

93. Measuring Respiratory Quotient
The respiratory quotient can be measured.
RQ = x + y or x - z x x
where
x is the oxygen consumption
y is the increase in volume of air (if more CO2 is produced than oxygen taken in)
z is the decrease in the volume of air (if less CO2 is produced than oxygen taken in) 

94. Simple Respirometers