Basic Metabolism
BASIC METABOLISM...................................................................................................................................... 1
MAJOR CONCEPTS........................................................................................................................................ 3
WHAT IS METABOLISM?..........................................................................................................................................3
METABOLIC DIVERSITY............................................................................................................................................3
ANABOLISM AND CATABOLISM.................................................................................................................................3
Catabolism:.....................................................................................................................................................3
Anabolism:......................................................................................................................................................3
Adenosine Triphosphate (ATP):......................................................................................................................3
NAD/NADH:....................................................................................................................................................4
NADP/NADPH:................................................................................................................................................4
METABOLISM IS HIGHLY REGULATED..........................................................................................................................4
METABOLISM IS COMPARTMENTALIZED......................................................................................................................4
Prokaryotes (no organelles):..........................................................................................................................4
Eukaryotes:.....................................................................................................................................................4
THERMODYNAMICS OF BIOLOGICAL SYSTEMS............................................................................................... 5
TYPES OF SYSTEMS.................................................................................................................................................5
1ST LAW OF THERMODYNAMICS:................................................................................................................................5
INTERNAL ENERGY (E), HEAT AND WORK....................................................................................................................5
ENTHALPY AND HEAT EXCHANGE...............................................................................................................................5
2ND LAW OF THERMODYNAMICS AND ENTROPY (S)......................................................................................................6
Gibbs free energy (G):.....................................................................................................................................6
STANDARD STATE REACTIONS...................................................................................................................................6
SPONTANEOUS REACTIONS......................................................................................................................................6
High energy compounds:................................................................................................................................7
Coupled Reactions:.........................................................................................................................................7
GLYCOLYSIS.................................................................................................................................................. 7
FUNCTION............................................................................................................................................................7
PHASE 1: ENERGY REQUIRING..................................................................................................................................7
Part A:.............................................................................................................................................................7
Reaction 1: ( -kinase = adds phosphate group)..........................................................................................................7
Hexokinase regulation:..............................................................................................................................................9
Reaction 2:................................................................................................................................................................ 9
Reaction 3:................................................................................................................................................................ 9
Phosphofructokinase Regulation...............................................................................................................................9
Part B (of Phase 1):.......................................................................................................................................10
Reaction 4:..............................................................................................................................................................10
Reaction 5:..............................................................................................................................................................10
Phase 1 summary:........................................................................................................................................10
PHASE 2: ENERGY GENERATING..............................................................................................................................10
Reaction 6:....................................................................................................................................................10
Reaction 7:....................................................................................................................................................11
Reaction 8:....................................................................................................................................................11
Reaction 9:....................................................................................................................................................11
Reaction 10:..................................................................................................................................................11
Pyruvate kinase Regulation:....................................................................................................................................12
ENERGETIC ELEGANCE OF GLYCOLYSIS......................................................................................................................12
ANAEROBIC VS AEROBIC METABOLISM....................................................................................................... 12
ALCOHOLIC FERMENTATION...................................................................................................................................12
LACTIC ACID FERMENTATION..................................................................................................................................12
PYRUVATE DECARBOXYLATION................................................................................................................................13
ACETYL-COENZYME A...........................................................................................................................................13
KREBS CYCLE:.............................................................................................................................................. 13
1
, Basic Metabolism
REACTION 1:...................................................................................................................................................... 13
REACTION 2:...................................................................................................................................................... 13
REACTION 3:...................................................................................................................................................... 14
REACTION 4:...................................................................................................................................................... 14
REACTION 5:...................................................................................................................................................... 14
REACTION 6:...................................................................................................................................................... 14
REACTION 7:...................................................................................................................................................... 14
REACTION 8:...................................................................................................................................................... 14
SUMMARY OF KREBS CYCLE:..................................................................................................................................15
REGULATION OF KREBS CYCLE..................................................................................................................... 15
ANAPLEROTIC REACTIONS......................................................................................................................................15
GENERAL REGULATION.........................................................................................................................................15
REGULATION OF PYRUVATE DEHYDROGENASE COMPLEX..............................................................................................15
THE ELECTRON TRANSPORT CHAIN.............................................................................................................. 16
SUMMARY..........................................................................................................................................................16
REDUCTION POTENTIAL.........................................................................................................................................16
MITOCHONDRIA STRUCTURE..................................................................................................................................16
COMPLEX I:........................................................................................................................................................16
COMPLEX II:.......................................................................................................................................................17
COMPLEX III: THE Q CYCLE....................................................................................................................................17
1st Cycle:........................................................................................................................................................17
2nd Cycle:.....................................................................................................................................................17
Summary:.....................................................................................................................................................17
COMPLEX IV: CYTOCHROME C OXIDASE...................................................................................................................18
OXIDATIVE PHOSPHORYLATION.................................................................................................................. 18
CHEMIOSMOTIC COUPLING....................................................................................................................................18
TOTAL ATP PRODUCED:.......................................................................................................................................18
ATP SYNTHASE...................................................................................................................................................18
Structure:......................................................................................................................................................18
Mechanism:..................................................................................................................................................19
DISRUPTIONS OF ELECTRON TRANSPORT AND ATP SYNTHESIS.......................................................................................19
RECYCLING NAD+ FOR GLYCOLYSIS..........................................................................................................................19
2
, Basic Metabolism
Major Concepts
What is metabolism?
- Chemical changes within cells
- Breakdown of raw materials/nutrients to energy and complex cell products
Metabolic diversity
Classifications of organisms by energy and carbon source
Classifications Energy Carbon Source Examples
Source
H, Sulfur, Fe, N, Carbon
Chemoautotrophs Chemical Inorganic
monoxide oxidizing bacteria
Chemotrophs
Chemoheterotroph Organic All animals, most fungi,
Chemical
s compounds protozoa, bacteria
All plants, algae,
Photoautotrophs Light Inorganic cyanobacteria,
Phototrophs green/purple sulfur bacteria
Organic Green/purple non-sulfur
Photoheterotrophs Light
compounds bacteria, heliobacteria
Anabolism and Catabolism
- 2 broad process in metabolism:
Catabolism:
- Energy generating process
o Energy used in anabolism
- Break-down/degradation of complex molecules
- Oxidative
Anabolism:
- Energy requiring process
- Synthetic process which produces complex molecules
- Reductive
Adenosine Triphosphate (ATP):
- Links anabolism & catabolism
- Phototrophs: light energy converted to ATP
- Heterotrophs: chem energy converted to ATP
- Stored in energy-rich phosphoric anhydride bonds of ATP
- Energy currency of the cell
3
BASIC METABOLISM...................................................................................................................................... 1
MAJOR CONCEPTS........................................................................................................................................ 3
WHAT IS METABOLISM?..........................................................................................................................................3
METABOLIC DIVERSITY............................................................................................................................................3
ANABOLISM AND CATABOLISM.................................................................................................................................3
Catabolism:.....................................................................................................................................................3
Anabolism:......................................................................................................................................................3
Adenosine Triphosphate (ATP):......................................................................................................................3
NAD/NADH:....................................................................................................................................................4
NADP/NADPH:................................................................................................................................................4
METABOLISM IS HIGHLY REGULATED..........................................................................................................................4
METABOLISM IS COMPARTMENTALIZED......................................................................................................................4
Prokaryotes (no organelles):..........................................................................................................................4
Eukaryotes:.....................................................................................................................................................4
THERMODYNAMICS OF BIOLOGICAL SYSTEMS............................................................................................... 5
TYPES OF SYSTEMS.................................................................................................................................................5
1ST LAW OF THERMODYNAMICS:................................................................................................................................5
INTERNAL ENERGY (E), HEAT AND WORK....................................................................................................................5
ENTHALPY AND HEAT EXCHANGE...............................................................................................................................5
2ND LAW OF THERMODYNAMICS AND ENTROPY (S)......................................................................................................6
Gibbs free energy (G):.....................................................................................................................................6
STANDARD STATE REACTIONS...................................................................................................................................6
SPONTANEOUS REACTIONS......................................................................................................................................6
High energy compounds:................................................................................................................................7
Coupled Reactions:.........................................................................................................................................7
GLYCOLYSIS.................................................................................................................................................. 7
FUNCTION............................................................................................................................................................7
PHASE 1: ENERGY REQUIRING..................................................................................................................................7
Part A:.............................................................................................................................................................7
Reaction 1: ( -kinase = adds phosphate group)..........................................................................................................7
Hexokinase regulation:..............................................................................................................................................9
Reaction 2:................................................................................................................................................................ 9
Reaction 3:................................................................................................................................................................ 9
Phosphofructokinase Regulation...............................................................................................................................9
Part B (of Phase 1):.......................................................................................................................................10
Reaction 4:..............................................................................................................................................................10
Reaction 5:..............................................................................................................................................................10
Phase 1 summary:........................................................................................................................................10
PHASE 2: ENERGY GENERATING..............................................................................................................................10
Reaction 6:....................................................................................................................................................10
Reaction 7:....................................................................................................................................................11
Reaction 8:....................................................................................................................................................11
Reaction 9:....................................................................................................................................................11
Reaction 10:..................................................................................................................................................11
Pyruvate kinase Regulation:....................................................................................................................................12
ENERGETIC ELEGANCE OF GLYCOLYSIS......................................................................................................................12
ANAEROBIC VS AEROBIC METABOLISM....................................................................................................... 12
ALCOHOLIC FERMENTATION...................................................................................................................................12
LACTIC ACID FERMENTATION..................................................................................................................................12
PYRUVATE DECARBOXYLATION................................................................................................................................13
ACETYL-COENZYME A...........................................................................................................................................13
KREBS CYCLE:.............................................................................................................................................. 13
1
, Basic Metabolism
REACTION 1:...................................................................................................................................................... 13
REACTION 2:...................................................................................................................................................... 13
REACTION 3:...................................................................................................................................................... 14
REACTION 4:...................................................................................................................................................... 14
REACTION 5:...................................................................................................................................................... 14
REACTION 6:...................................................................................................................................................... 14
REACTION 7:...................................................................................................................................................... 14
REACTION 8:...................................................................................................................................................... 14
SUMMARY OF KREBS CYCLE:..................................................................................................................................15
REGULATION OF KREBS CYCLE..................................................................................................................... 15
ANAPLEROTIC REACTIONS......................................................................................................................................15
GENERAL REGULATION.........................................................................................................................................15
REGULATION OF PYRUVATE DEHYDROGENASE COMPLEX..............................................................................................15
THE ELECTRON TRANSPORT CHAIN.............................................................................................................. 16
SUMMARY..........................................................................................................................................................16
REDUCTION POTENTIAL.........................................................................................................................................16
MITOCHONDRIA STRUCTURE..................................................................................................................................16
COMPLEX I:........................................................................................................................................................16
COMPLEX II:.......................................................................................................................................................17
COMPLEX III: THE Q CYCLE....................................................................................................................................17
1st Cycle:........................................................................................................................................................17
2nd Cycle:.....................................................................................................................................................17
Summary:.....................................................................................................................................................17
COMPLEX IV: CYTOCHROME C OXIDASE...................................................................................................................18
OXIDATIVE PHOSPHORYLATION.................................................................................................................. 18
CHEMIOSMOTIC COUPLING....................................................................................................................................18
TOTAL ATP PRODUCED:.......................................................................................................................................18
ATP SYNTHASE...................................................................................................................................................18
Structure:......................................................................................................................................................18
Mechanism:..................................................................................................................................................19
DISRUPTIONS OF ELECTRON TRANSPORT AND ATP SYNTHESIS.......................................................................................19
RECYCLING NAD+ FOR GLYCOLYSIS..........................................................................................................................19
2
, Basic Metabolism
Major Concepts
What is metabolism?
- Chemical changes within cells
- Breakdown of raw materials/nutrients to energy and complex cell products
Metabolic diversity
Classifications of organisms by energy and carbon source
Classifications Energy Carbon Source Examples
Source
H, Sulfur, Fe, N, Carbon
Chemoautotrophs Chemical Inorganic
monoxide oxidizing bacteria
Chemotrophs
Chemoheterotroph Organic All animals, most fungi,
Chemical
s compounds protozoa, bacteria
All plants, algae,
Photoautotrophs Light Inorganic cyanobacteria,
Phototrophs green/purple sulfur bacteria
Organic Green/purple non-sulfur
Photoheterotrophs Light
compounds bacteria, heliobacteria
Anabolism and Catabolism
- 2 broad process in metabolism:
Catabolism:
- Energy generating process
o Energy used in anabolism
- Break-down/degradation of complex molecules
- Oxidative
Anabolism:
- Energy requiring process
- Synthetic process which produces complex molecules
- Reductive
Adenosine Triphosphate (ATP):
- Links anabolism & catabolism
- Phototrophs: light energy converted to ATP
- Heterotrophs: chem energy converted to ATP
- Stored in energy-rich phosphoric anhydride bonds of ATP
- Energy currency of the cell
3
