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BIOCHEMISTRY
František Vácha
http://www.prf.jcu.cz/~vacha/
JKU, Linz
Recommended reading:
D.L. Nelson, M.M. Cox
Lehninger Principles of Biochemistry
D.J. Voet, J.G. Voet, C.W. Pratt
Principles of Biochemistry
L. Stryer
Biochemistry
April
4. 4.
11. 4.
18. 4.
25. 4.
May
2. 5.
9. 5.
23. 5.
30. 5.
June
6. 6.
13. 6.
20. 6.
27. 6.
March
7. 3.
14. 3.
1. What are the chemical and three-dimensional structures of biological molecules
2. How do biological molecules interact with each other
3. How does the cell synthesize and degrade biological molecules
4. How is the energy conserved and used by the cell
5. What are the mechanisms for organizing biological molecules and coordinating
their activities
6. How is genetic information stored, transmitted and expressed
Principle issues of Biochemistry
Biochemistry reveals the working mechanisms of the natural world
Life and Cells
B, F, Al, Si, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Mo, Cd, I, W
Simple inorganic
compounds form
more complex
molecules, that are
the basic of live
forms
• in molecules
• as ions
Biogenic elements
Living organisms are
based on various complex
molecules consisting of
simple atoms
Combining different functional groups
in a single large molecule increases the
chemical versatility of such molecule
Different macromoleculs with
complementary arrangements of
functional groups can associate with
even greater range of functional
possibilities
Thermodynamics
and
Spontaneity of biochemical reactions
Gibbs free energy
ΔG = ΔH – TΔS
ΔG = ΔGo + RT lnK
(ΔGo = – RT lnKeq)
ΔH – Enthalpy - heat at constant pressure (exothermic, endothermic)
T – temperature in Kelvins
S – Entropy
R – gas constant
K – reaction quotient
Keq – equilibrium constatnt
Go – Standard free energy
Spontaneity of biochemical reactions
Equilibrium constant measures the
direction of spontaneous processes
At biochemical standard conditions (1M, pH 7, 298 K, 101.3 kPa)
the free-energy change of a biochemical reaction is simply an
alternative expression of the equilibrium constant
Actual free-energy changes depend
on reactant and product
concentrations
Standard equilibrium (K’eq) – initial concentrations of each
component is at 1M
This is not the case of living organism
Different concentrations of metabolites can affect the
reaction direction
In human erythrocytes
ATP = ADP + Pi
ATP = 2.25 mM
ADP = 0.25 mM
Pi = 1.65 mM
T = 37 oC (310 K)
DG’o = - 30.5 kJ/mol
DG = - 52 kJ/mol
Adenosin nucleotide and inorganic
phosphate concentrations in some cells
• Large negative value of ΔG does not ensure that a
process will proceed at measurable rate
• The rate depends on the detailed mechanism of the
reaction and not on the ΔG
• Nearly all molecular components of an organism can
react with each other and many of these reactions are
thermodynamically favored
• Organism can regulate the reactions by altering their
mechanisms
• Enzyme catalysis
Life Needs Energy
• The ultimate source of this energy on the Earth is
the sunlight
Organisms can be classified according to the
source of energy and carbon
Water
and
noncovalent weak forces
~ 70 % of human body mass is water
• medium for majority of biochemical reactions
• water itself actively participates in many biochemical
reactions
• nearly all biological molecules acquire their shape,
and therefore their functional properties, in an
interaction with water
• the unique physical and chemical properties of
water enables the present life forms on the Earth
Water
Hydrogen bonds – key feature of water for biology
Water is polar molecule: - 0.66 e on oxygen and + 0.33 e on each hydrogen
Hydrogen bond in water is ~ 1.9 Å
Energy of H-bond ~ 20 kJ . mol-1
—F—H…..:F— 155 kJ/mol 1.13 Å
—O—H…..:N— 29 kJ/mol 2.88 Å
—O—H…..:O— 21 kJ/mol 2.70 Å
—N—H…..:N— 13 kJ/mol 2.93 Å
—N—H…..:O— 8 kJ/mol 3.04 Å
Noncovalent - weak forces are the principal
interactions in biological molecules
the whole life is based on weak interactions
• Biogenic elements are part of complex molecules or
appear as ions
• Chemical versatility of macromolecules with different
functional groups
• Gibbs free energy as a measure or reaction spontaneity
• Water as a basic environment for biochemical reactions
• Noncovalent – weak forces are the key interactions in
biomolecules
• H-bonds
Learning objectives
Introduction to metabolism
Metabolism
• Sum of all chemical reactions in an
organism
• Complex and highly coordinated
• The core parts are similar in all living
organisms
• Reactions in sequence form
metabolic pathways
• Some pathways are primarily
targeted to produce energy
• catabolism
• Some pathways are primarily
targeted to synthetize new
substances (on the cost of energy)
• anabolism
Catabolism of proteins, fats,
and carbohydrates in the
three stages of cellular
respiration
• Stage 1: oxidation of fatty acids, glucose, and
some amino acids yields acetyl-CoA.
• Stage 2: oxidation of acetyl groups in the citric
acid cycle to form NADH and FADH2
• Stage 3: electrons are funneled into a chain of
electron carriers reducing O2 to H2O. This
electron flow drives the production of ATP.
Complete Oxidation of Reduced
Compounds is Strongly Favorable
• This is how chemotrophs obtain most of their energy
• In biochemistry the oxidation of reduced fuels with O2 is stepwise and controlled
• Thermodynamically favorable is not the same as being kinetically rapid – enzyme catalysis
Electron carriers
• A few types of coenzymes and proteins
serve as universal electron carriers
• Many biochemical oxidation-reduction
reactions involve transfer of two electrons
• In order to keep charges in balance, proton
transfer often accompanies electron
transfer
NAD and NADP as common
redox cofactors
• These are commonly called pyridine nucleotides
• They can dissociate from the enzyme after the reaction
• In a typical biological oxidation reaction, hydride(:H-) from an alcohol is transferred to NAD+ giving NADH
• AH2 + NAD(P)+ A + NAD(P)H + H+
NAD and NADP in metabolism
NAD+/NADH - catabolism, further in ATP
production
NADP+/NADPH – anabolism, biosynthetic
reactions
Flavin Cofactors allow Single
Electron Transfers
• Flavoproteins (FMN, FAD)
• May participate in one- or two-electron transfers
• Flavin cofactors are usually tightly bound to proteins, some covalently
• Variability in reduction potentials
Iron-Sulfur Centres
• Bound in proteins
• Transfer one electron i time
• Diferent types
Cytochromes
• Membrane or soluble heme-containing protein
• Heme – a tetrapyrrol binding an iron ion in a form
of either ferrous (Fe3+, oxidized) or ferric(Fe2+,
reduced)
• Single electron carriers
Principal role of ATP
in metabolism
• stores energy obtained in catabolic reactions
• transport the energy to compartments or parts of organism where it is needed
• provides the energy for anabolic biosynthetic processes
Chemical basis of large negative
free-energy of ATP
• Separation of negative charges on phosphate
oxygens upon ATP hydrolysis
• Resonance stabilization of phosphate products
• Ionisation of ADP product
• Better solvation of products
ATP provides energy by group transfer
Simple hydrolysis of ATP is not the
source of energy (only liberation of
heat)
• In most cases it is two-step
process:
1) Favorable ATP hydrolysis and Pi
transfer
2) Resonance stabilization of free Pi
• Some processes involve simple
hydrolysis:
- Binding ATP to a protein and its
hydrolysis – conformation change
of the protein – mechanical motion
Actual DG of ATP hydrolysis
depends on a type of tissue
The cellular concentration of ATP is usually above the equilibrium
constant making it even better source of energy
Actual DG of ATP hydrolysis
depends on a type of tissue
DG = -30.5 kJ/mol + [(8.315 kJ/mol.K)(310 K) ln((0.25x10-3)(1.65x10-3))/(2.25x10-3)
DG = -52 kJ/mol
Mg2+ binds to ATP and ADP to form complexes of Mg-ATP
and Mg-ADP
Regulatory role, shielding of negative charges of oxygen,
conformation changes of ATP and ADP molecules
The Role of Magnesium in ATP Reactions
Several Phosphorylated Compounds
Have Larger DG’° Than ATP
• Again, electrostatic repulsion within the reactant, molecule is relieved
• The products are stabilized via resonance, or by more favorable solvation
• Possible tautomerization product
Hydrolysis of phosphoenolpyruvate (PEP)
Hydrolysis of 1,3 bisphosphoglycerate
Hydrolysis of phosphocreatine
Substrate level phosphorylation
Phosphorylated molecules with higher ΔG°’ can be used to synthesize ATP
PEP + ADP = Pyruvate + ATP
ΔG°’ – 61,9 kJ/mol
Hydrolysis of Thioesters
• Acetyl-CoA
Hydrolysis of Thioesters
• Hydrolysis of thioesters, such as acetyl-CoA is
strongly favorable
• Acetyl-CoA is an important donor of acyl groups
– Feeding two-carbon units into metabolic pathways
– Synthesis of fatty acids
Hydrolysis of acetyl-coenzyme A
• Catabolism and Anabolism
• Stepwise oxidation as a source of energy
• Electron carriers in biological systems
• Principal role of ATP in metabolism
• Energy in ATP
• Substrate level phosphorylation
Learning objectives
Recommended