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DISCLAIMER: This lecture outline is intended to help you take notes during lecture. It is
not a substitute for attending lecture, taking notes, and reading the textbook. Examination
questions will cover material presented in lecture that is not in this outline. You may only
use this outline if you have read and understood this disclaimer.
Biochemistry Lecture 19:
Summary
Summary
Introduction to metabolism.
Metabolism
- chemical reactions responsible for living state
- synthesis of new biomolecules for growth and repair
- production of energy for various activities
- metabolic strategies
- sources of starting materials for biomolecules
- autotrophic
- biomolecules from inorganic compounds
- e.g. CO2, H2O, NH3, NO3- heterotrophic
- biomolecules from complex organic molecules
- dependant on autotrophic organisms
- sources of energy
- phototrophic
- energy from light
- chemotrophic
- energy from chemical oxidation
- biochemical pathways
- sequences of chemical reactions
- perform particular function
- catabolic
- complex molecules ➞ simple molecules
- convergent
- oxidative
- exergonic
- anabolic
- simple molecules ➞ complex molecules
- divergent
- reductive
- endergonic
DISCLAIMER: This lecture outline is intended to help you take notes during lecture. It is
not a substitute for attending lecture, taking notes, and reading the textbook. Examination
questions will cover material presented in lecture that is not in this outline. You may only
use this outline if you have read and understood this disclaimer.
Biochemistry Lecture 20:
Bioenergetics.
Bioenergetics
- energy transfer in biochemical systems
- first law of thermodynamics
- total energy of universe remains constant
- no gain or loss of energy in transfer
- second law of thermodynamics
- systems tend towards disorder
- entropy increases
- reaction produces heat
- products more disordered than reactants
- ΔG = ΔH - TΔS
- A➞B
- if ΔG is negative forward reaction will occur
- B will be formed
- if ΔG is zero reaction is at equilibrium
- if ΔG is positive back reaction will occur
- A will be formed
- standard free energy change, ΔGo'
- standard conditions
- 1M concentration
- 298K
- 1 atmosphere
- pH 7.0
- non-standard conditions
- A+B➞C+D
- ΔG = ΔGo' + 2.303RT log([C][D]/[A][B])
- if reaction is at equilibrium
⇔ 0= ΔGo' + 2.303RT log([C][D]/[A][B])
⇔ ΔGo' = - 2.303RT log([C][D]/[A][B])
⇔ ΔGo' = -2.303RT log Keq
- reaction coupling
- if
A➞B
- if
C➞D
- then
A+C➞B+D
ΔGo'
ΔGo'
ΔGo'
=+16 kJ/mol
=-24 kJ/mol
=+16 kJ/mol – 24 kJ/mol
= -8 kJ/mol
- catabolism
- negative ΔGo' reactions coupled to ADP phosphorylation
- ADP + Pi ➞ ATP + H2O
- ΔGo' = +30.5 kJ/mol
- anabolism
- positive ΔGo' reactions coupled to ATP hydrolysis
- ATP + H2O ➞ ADP + Pi
- ΔGo' = -30.5 kJ/mol
- free energy in oxidation-reduction reactions
- Ared + Box ➞ Aox + Bred
- ΔGo = -nF(E°reduced - E°oxidized)
- e.g. NADH +H+ + 1/2 O2 ➞ NAD+ + H2O
- free energy in gradients across membranes
- A outside ➞ Ainside
- ΔG = ΔGo' + 2.303RT log([Ainside]/[A outside])
- free energy in membrane potentials
- ΔG = FΔΨ
DISCLAIMER: This lecture outline is intended to help you take notes during lecture. It is
not a substitute for attending lecture, taking notes, and reading the textbook. Examination
questions will cover material presented in lecture that is not in this outline. You may only
use this outline if you have read and understood this disclaimer.
Biochemistry Lecture 21:
Coenzymes.
Coenzymes
- organic molecules
- assist enzymes in catalysis
- provide functions not available in polypeptide chain
- association with enzyme
- tightly bound to enzyme
- prosthetic group
- bind only during catalysis
- transient carriers of chemical groups
- nicotinamide adenine dinucleotide (NAD+)
- transient binding
- electron acceptor in catabolism
- carries electrons to electron transport system
- ATP produced
- nicotinamide adenine dinucleotide phosphate (NADP+)
- electron donor in anabolism (NADPH)
- flavin adenine dinucleotide (FAD)
- tightly bound
- electron acceptor in catabolism
- carries electrons to electron transport system
- ATP produced
- coenzyme A (CoASH)
- transient binding
- carries acyl groups in catabolism and anabolism
- thiamine pyrophosphate (TPP)
- tightly bound
- removal of carboxyl groups from α-keto acids
- carries aldehyde groups
- pyridoxal phosphate
- tightly bound
- interconversion of amino acids and α-keto acids
- carrier of amino groups
- biotin
- tightly bound
- carboxylation reactions
- carries carboxyl groups
- lipoamide
- tightly bound
- carrier of electrons and acyl groups
Vitamins
- organic substances required in diet in small amounts
- water soluble
- precursors of coenzymes
- except ascorbate
- fat soluble
- various functions
- not coenzyme precursors
DISCLAIMER: This lecture outline is intended to help you take notes during lecture. It is
not a substitute for attending lecture, taking notes, and reading the textbook. Examination
questions will cover material presented in lecture that is not in this outline. You may only
use this outline if you have read and understood this disclaimer.
Biochemistry Lecture 22:
Interactive
Glycolysis.
Glycolysis
- glucose (C6) ➞ 2 pyruvate (C3)
- ten reactions
- in cytosol
- exergonic
- ATP formed
- oxidative
- NADH formed
- Stage 1
- glucose ➞ 2 glyceraldehyde-3-phosphate
- five reactions
- uses 2 ATP
- Stage 2
- 2 glyceraldehyde-3-phosphate ➞ 2 pyruvate
- five reactions
- produces four ATP, two NADH
Regulation of metabolism
- at committed step
- large negative ΔG
- irreversible reaction
- feed-back inhibition
- end products inhibit
- feed-forward activation
- starting materials activate
- regulation of glycolysis
- hexokinase
- irreversible reaction
- allosteric
- glucose-6-phosphate inhibits
- feed-back inhibition
- phosphofructokinase
- irreversible reaction
- committed step
- major point of regulation
- allosteric
- ATP inhibits
- AMP activates
- response to energy status
- citrate inhibits
- feed-back inhibition
- fructose-2,6-bisphosphate activates
- depends on fructose-6-phosphate level
- feed-forward activation
- pyruvate kinase
- irreversible reaction
- allosteric
- ATP inhibits
- response to energy status
- alanine inhibits
- feed-back inhibition
- fructose-1,6-bisphosphate activates
- feed-forward activation
DISCLAIMER: This lecture outline is intended to help you take notes during lecture. It is
not a substitute for attending lecture, taking notes, and reading the textbook. Examination
questions will cover material presented in lecture that is not in this outline. You may only
use this outline if you have read and understood this disclaimer.
Biochemistry Lecture 23:
Glycolysis.
Glycolysis (continued)
- materials for glycolysis
- from diet
- polysaccharides
- glycogen ➞ maltose
- starch ➞ maltose
- disaccharides
- maltose ➞ glucose + glucose
- sucrose ➞ glucose + fructose
- lactose ➞ glucose + galactose
- monosaccharides
- glucose ➞ glucose-6-phosphate
- fructose ➞ fructose-6-phosphate
- fructose ➞ dihydroxyacetone phosphate + glyceraldehyde-3-phosphate
- galactose ➞ glucose-6-phosphate
- from glycogen reserves
- glycogen phosphorylase
- releases glucose-1-phosphate
- converted to glucose-6-phosphate
- transferase and debranching enzyme
- release branch monomer as glucose
- converted to glucose-6-phosphate
- regulation
- glycogen phosphorylase
- allosteric
- reversible covalent modification
- normal conditions
- glycogen phosphorylase b
- glucose-6-phosphate inhibits
- ATP inhibits
- AMP activates
- inactive
- energy status poor
- glycogen phosphorylase b
- AMP increased
- active
- hormone stimulation
- glycogen phosphorylase a
- phosphorylation of serine
- fully active
Uses of pyruvate
- anaerobic metabolism
- oxygen not involved
- pyruvate used to regenerate NAD+
- pyruvate ➞ ethanol + CO2
- bacteria and yeasts
- pyruvate ➞ lactate
- bacteria and complex animals (oxygen limited)
- aerobic metabolism
- oxygen used to regenerate NAD+
- electron transport system
- pyruvate enters citric acid cycle
Transition reaction
- pyruvate ➞ acetyl-CoA + CO2
- one reaction
- in mitochondria (eukaryotes)
- five steps
- decarboxylation
- hydroxyethyl on TPP
- oxidation-reduction
- acetyl and electrons to lipoamide
- formation of acetyl CoA
- oxidation-reduction
- electrons to FADH2
- oxidation-reduction
- electrons to NADH
- regulation
- allosteric
- acetyl-CoA inhibits
- NADH inhibits
- feed-back inhibition
- GTP inhibits
- AMP activates
- response to energy status
- reversible covalent modification
- phosphorylation inactivates
- ATP, acetyl-CoA, NADH stimulate phosphorylation
DISCLAIMER: This lecture outline is intended to help you take notes during lecture. It is
not a substitute for attending lecture, taking notes, and reading the textbook. Examination
questions will cover material presented in lecture that is not in this outline. You may only
use this outline if you have read and understood this disclaimer.
Biochemistry Lecture 24:
The citric acid cycle.
Citric acid cycle
- acetyl-CoA (2C) ➞ 2 CO2 (1C)
- eight reactions
- in mitochondria (eukaryotes)
- aerobic metabolism only
- exergonic
- GTP (= ATP) formed
- oxidative
- NADH, FADH2 formed
- functions
- aerobic energy production
- anabolic starting material production
- amphibolic pathway
- regulation of the citric acid cycle
- citrate synthase
- allosteric
- ATP inhibits
- response to energy status
- isocitrate dehydrogenase
- allosteric
- NADH inhibits
- feedback inhibition
- ATP inhibits
- ADP activates
- response to energy status
- α-ketoglutarate dehydrogenase
- allosteric
- NADH inhibits
- succinyl-CoA inhibits
- feedback inhibition
- materials for the citric acid cycle
- mono-, di-, and polysaccharides
- enter via glycolysis and transition reaction
- Glucose
➞ 2 pyruvate
(2 ATP, 2 NADH)
- 2 Pyruvate
➞ 2 acetyl-CoA + 2 CO2 (2 NADH)
- 2 Acetyl-CoA ➞ 4 CO2
(2 ATP, 6 NADH, 2 FADH2)
- total = 4 ATP, 10 NADH, 2 FADH2
- fatty acid catabolism
- amino acid catabolism
- production of anabolic starting materials
- must replace intermediates
- anaplerotic reactions
- pyruvate carboxylase
- allosteric
- acetyl-CoA activates
DISCLAIMER: This lecture outline is intended to help you take notes during lecture. It is
not a substitute for attending lecture, taking notes, and reading the textbook. Examination
questions will cover material presented in lecture that is not in this outline. You may only
use this outline if you have read and understood this disclaimer.
Biochemistry Lecture 25:
The electron transport system.
Electron transport system
- NADH/FADH2 oxidized to NAD+/FAD
- O2 reduced to H2O
- at inner mitochondrial membrane (eukaryotes)
- exergonic
- ATP formed (indirectly)
- functions
- regeneration of NAD+ and FAD
- aerobic energy production
- electron carriers
- NAD+
- nicotinamide carries electrons
- NADH ➞ NAD+ + H+ + 2e- FAD
- flavin carries electrons
- FADH2 ➞ FAD + 2H+ + 2e- FMN
- flavin carries electrons
- FMNH2 ➞ FMN + 2H+ + 2e- iron-sulphur clusters
- iron ions carry electrons
- Fe2+ ➞ Fe3+ + e- ubiquinone
- quinone derivative carries electrons
- CoQH2 ➞ CoQ + 2H+ + 2e- cytochromes
- haem groups
- iron ion carries electron
- Fe2+ ➞ Fe3+ + e- copper ions
- copper ion carries electron
- Cu1+ ➞ Cu2+ + e-
Movie
Quiz
- reactions
- complex I
- NADH + H+ + CoQ ➞ NAD+ + CoQH2
- electrons transferred via FMN, Fe-S clusters
- four H+ pumped
- complex II
- succinate + CoQ ➞ fumarate + CoQH2
- electrons transferred via FAD, Fe-S clusters
- no H+ pumped
- complex III
- CoQH2 + 2 cyt c (Fe3+) ➞ CoQ +2 cyt c (Fe2+)
- electrons transferred via Fe-S cluster, cytochromes b, c1
- two H+ pumped
- complex IV
- 2 cyt c (Fe2+) + 2H+ + 1/2 O2 ➞ 2 cyt c (Fe3+) + H2O
- electrons transferred via cytochromes a, a3, 2 copper ions
- four H+ pumped
- coupling of gradient and ATP formation
ADP + Pi + 3H+outside ➞ ATP + H2O + 3H+inside (ATP synthase)
- free energy change of hydrogen ion movement
- from concentration gradient
ΔG = ΔGo' + 2.303RT log([H+ inside]/[H+ outside])
= 0 + 2.303RT log (1/25)
= 2.303 x 0.0083 x 298 x (-1.4)
= -8.0 kJ/mol
- from membrane potential
ΔG = FΔΨ
= 96.5 x -0.14
= -13.5 kJ/mol
- total
= -8.0 + (-13.5)
= -21.5 kJ/mol
- three hydrogen ions per ATP formed
- transport of ATP into cytosol
ATPinside + ADPoutside ➞ ATPoutside + ADPinside
- one hydrogen ion per ATP transported
- total cost
- four hydrogen ions per ATP
NADH + H+ + 1/2O2 + 21/2ADP + 21/2Pi ➞ NAD+ + 21/2ATPoutside + 31/2H2O
FADH2 + 1/2O2 + 11/2ADP + 11/2Pi ➞ FAD + 11/2ATPoutside + 21/2H2O
DISCLAIMER: This lecture outline is intended to help you take notes during lecture. It is
not a substitute for attending lecture, taking notes, and reading the textbook. Examination
questions will cover material presented in lecture that is not in this outline. You may only
use this outline if you have read and understood this disclaimer.
Biochemistry Lecture 26:
Triacylglycerol catabolism.
Electron transport system (continued)
- materials for the electron transport system
- NADH and FADH2
- glycolysis
- cytosol
- transition reaction and citric acid cycle
- matrix
- triacylglycerol catabolism
- cytosol and matrix
- shuttle electrons from cytosolic NADH into matrix
- glycerol-3-phosphate shuttle
- malate-aspartate shuttle
- ADP and inorganic phosphate
- ADP by ATP-ADP translocase
- Pi by other transport protein
- aerobic catabolism of glucose
- glucose ➞ 2 pyruvate
- uses
2 ATP
- produces 4 ATP
2 NADH (cytosol)
- 2 pyruvate ➞ 2 acetyl-CoA + 2 CO2
- produces 2 NADH (matrix)
- 2 acetyl-CoA ➞ 4 CO2
- produces 2 GTP
6 NADH (matrix)
2 FADH2
- total
- uses
2 ATP
- produces 4 ATP, 2 GTP
2 NADH (cytosol)
8 NADH (matrix)
2 FADH2
- yield = 30 ATP (glycerol-3-phosphate)
- yield = 32 ATP (malate-aspartate)
Triacylglycerol catabolism
- function
- aerobic energy production
- triacylglycerol + 3 H2O ➞ glycerol + 3 fatty acids
- three reactions
- extracellular (mostly)
- glycerol ➞ dihydroxyacetone phosphate
- two reactions
- in cytosol
- oxidative
- NADH formed
- fatty acid ➞ acetyl-CoA
- repeated cycle of four reactions
- β-oxidation
- in mitochondria (eukaryotes)
- oxidative
- NADH, FADH2 formed
- odd-carbon fatty acids
- last cycle gives propionyl-CoA
- propionyl-CoA + CO2 + ATP ➞ ➞ succinyl-CoA + AMP + PPi
- unsaturated fatty acids
- cycle starts at second reaction
- additional enzymes required
- energy yield (three palmitic acid chains)
- glycerol ➞ dihydroxyacetone phosphate
- uses
1 ATP
- produces 1 NADH (cytosol)
- dihydroxyacetone phosphate ➞ 3 CO2
- produces 2 ATP
- produces 1 GTP
- produces 1 NADH (cytosol)
- produces 4 NADH (matrix)
- produces 1 FADH2
- 3 palmitic acid ➞ 24 acetyl-CoA
- uses
6 ATP (3 ATP ➞ 3AMP)
- produces 21 NADH (matrix)
- produces 21 FADH2
- 24 acetyl-CoA ➞ 48 CO2
- produces 24 GTP
- produces 72 NADH (matrix)
- produces 24 FADH2
- total
- uses
7 ATP
- produces 2 ATP
- produces 25 GTP
- produces 2 NADH (cytosol)
- produces 97 NADH (matrix)
- produces 46 FADH2
- regulation
- lipases (adipose tissue)
- reversible covalent modification
- phosphorylation on hormonal signal increases activity
- carnitine acyltransferase I
- allosteric
- malonyl-CoA (from acetyl-CoA) inhibits
- feed-back inhibition
- two β-oxidation enzymes
- allosteric
- acetyl-CoA inhibits
- NADH inhibits
- feed-back inhibition
DISCLAIMER: This lecture outline is intended to help you take notes during lecture. It is
not a substitute for attending lecture, taking notes, and reading the textbook. Examination
questions will cover material presented in lecture that is not in this outline. You may only
use this outline if you have read and understood this disclaimer.
Biochemistry Lecture 27:
Protein catabolism.
Protein catabolism
- proteins ➞ amino acids
- proteases and peptidases
- extracellular
- functions
- amino acids for protein synthesis
- conversion to other metabolic intermediates
- energy production
- amino acid catabolism
- removal of amino groups
- transamination
- one reaction
- all parts of cell
- ΔGo' ≈ 0 (reversible)
- aminotransferases (or transaminases)
- specific for α-ketoglutarate
- less specific for amino acid
- oxidative deamination
- one reaction
- in mitochondria
- glutamate dehydrogenase
- allosteric
- GTP inhibits
- ADP stimulates
- response to energy status
- disposal of excess amino groups
- as urea (most terrestrial vertebrates)
- formed in liver
- transport amino groups to liver
- as glutamine
- as alanine
- urea cycle
- two amino groups + carbon dioxide ➞ urea
- five reactions
- two reactions in mitochondria
- three reactions in cytosol
- endergonic
- uses ATP
- as ammonia (bacteria, most aquatic animals)
- as uric acid (insects, terrestrial reptiles, birds)
- conversion of carbon skeleton
- formation of acetyl-CoA, pyruvate, citric acid cycle intermediates