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
March April May June 7. 3. 4. 4. 2. 5. 6. 6. 14. 3. 11. 4. 9. 5. 13. 6. 18. 4. 23. 5. 20. 6. 25. 4. 30. 5. 27. 6.
Principle issues of Biochemistry 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 Biochemistry reveals the working mechanisms of the natural world
Life and Cells
Biogenic elements Simple inorganic compounds form more complex molecules, that are the basic of live forms in molecules as ions B, F, Al, Si, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Mo, Cd, I, W
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
Spontaneity of biochemical reactions Gibbs free energy ΔG = ΔH TΔS ΔG = ΔG o + RT lnk (ΔG o = RT lnk eq ) ΔH Enthalpy - heat at constant pressure (exothermic, endothermic) T temperature in Kelvins S Entropy R gas constant K reaction quotient K eq equilibrium constatnt G o Standard free energy
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 + P i ATP = 2.25 mm ADP = 0.25 mm P i = 1.65 mm T = 37 o C (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
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 ~ 70 % of human body mass is 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 O H.. :N O H.. :O N H.. :N N H.. :O 155 kj/mol 1.13 Å 29 kj/mol 2.88 Å 21 kj/mol 2.70 Å 13 kj/mol 2.93 Å 8 kj/mol 3.04 Å
Noncovalent - weak forces are the principal interactions in biological molecules the whole life is based on weak interactions
Learning objectives 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
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 FADH 2 Stage 3: electrons are funneled into a chain of electron carriers reducing O 2 to H 2 O. 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 O 2 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 AH 2 + 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 (Fe 3+, oxidized) or ferric(fe 2+, 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 P i transfer 2) Resonance stabilization of free P i 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
The Role of Magnesium in ATP Reactions Mg 2+ 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
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
Learning objectives 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