Foundations of Biochemistry Piamsook Pongsawasdi Piamsook Pongsawasdi Kanoktip Packdibamrung Kanoktip Packdibamrung August 2016 Physical Foundations and Genetic Foundation

Living Organisms Exist in a Dynamic Steady State They are never at equilibrium with their surroundings Molecules and ions within living organism are different in kinds and concentration from those in the surroundings Constant characteristic composition at maturity but population changes Continuous synthesis and breaking down of small molecules, macromolecules, and supramolecular complexes, therefore maintaining a constant concentration – Dynamic Steady State Involve constant flux of mass and energy through the system 2

Living Organisms Need Energy A living organism is an open system Exchanges both matter and energy with its surroundings Extract, channel and consume energy Organisms derive energy in two ways Take up chemical fuels (e.g. glucose) from the environment and extract energy by oxidizing them Absorb energy from sunlight 1 st Law of Thermodynamics: Energy Conservation In any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change Cells are consummate transducer of energy, capable of inter- converting chemical, electromagnetic, and osmotic energy with great efficiency 3

Energy Conversion (a) Energy extracted from surroundings (b) Energy conversion to produce work 4

(c) Return energy to surroundings (d) Release end-products (e) Macromolecule formation Energy Conversion 5

Entropy – Randomness & Disorder Oxidation of Glucose C 6 H 12 O 6 + 6O 2 6CO 2 + 6H 2 O Increase in number of molecules, solid changes into liquid and gas more freedom of movement, more molecular disorder, entropy increases 6

The Flow of Electrons Provides Energy All energy transduction in cells can be traced to a flow of electrons from one molecule to another, in a downhill flow from higher to lower electrochemical potential Photosynthetic cells absorb the sun's radiant energy and use it to drive electrons from water to carbon dioxide, forming energy-rich products such as starch and sucrose 6CO 2 + 6H 2 O C 6 H 12 O 6 + 6O 2 Non-photosynthetic organisms obtain energy by oxidizing the energy-rich products of photosynthesis, passing electrons to atmospheric oxygen to form water, carbon dioxide, and other end products, which are recycled in the environment. C 6 H 12 O 6 + 6O 2 6CO 2 + 6H 2 O 7 Light energy Light-driven reduction of CO 2 Energy-yielding oxidation of glucose

Creating & Maintaining Order Requires Energy Energy is required for formation of covalent bond between monomeric subunits and for ordering subunits into correct sequence of macromolecules According to 2 nd law of Thermodynamics: the total entropy of the universe is continually increasing To synthesize macromolecules, free energy must be supplied to the cells 8

Energy Changes during Chemical Reaction When a chemical reaction occurs at constant temperature (T in Kelvin) :  G =  H – T  S Free energy change Enthalpy change Entropy change numbers and kinds of chemical bonds and non-covalent interaction broken and formed  H is –ve for a reaction that releases energy  S is +ve for a reaction that increases the system’s randomness  G is –ve for a spontaneous reaction (exergonic) 9

Coupled Biological Reactions A process occurs spontaneously if  G is –ve (free energy released – exergonic ) For energy requiring reactions (endergonic), cells couple them with other exergonic reactions to make sum of  G –ve 10

K eq and  G o Both measure reaction tendency to proceed spontaneously If high equilibrium constant K eq,, the reaction proceeds until almost reactants converted to products Free energy  G – a measure of the distance of a system from its equilibrium position Standard free energy change,  G o, a constant characteristic for each reaction From Gibbs:  G =  G o + RT ln K eq At equilibrium,  G = 0, then  G o = – RT ln K eq 11

Enzymes – Biological Catalysts Enhance the rate of specific reactions without being consumed in the process Change of reactants (substrates) to products Distortion of substrate’s existing bonds create a transition state (TS) of higher free energy Energy difference between reactant in its ground state and in its TS =  G ‡ (activation energy) Binding of E to TS is exergonic; energy released by binding reduces  G ‡ and increases the reaction rate 12

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14 Release of Ordered Water Favors Formation of an Enzyme-Substrate Complex

Pathways Enzyme-catalyzed reactions are organized into many sequences of consecutive reactions (pathways) Catabolism: degradative pathways - change organic nutrients into simple end products and release chemical energy to drive the synthesis of ATP Anabolism: synthetic pathways – change small precursors to larger and more complex molecules Metabolism: overall network of enzyme-catalyzed pathways, interconnected and interdependent, regulated to achieve balance and economy (save energy) Pathways acting on the main constituents of cells (proteins, fats, sugars and nucleic acids) are identical in all living organisms 15

Central Roles of ATP and NAD(P)H ATP links energy releasing (exergonic) and energy consuming (endergonic) cellular processes Cofactor - NAD(P) + - collects electrons from oxidative reactions NAD(P)H which donates electrons in reduction reactions in biosynthesis * Nicotinamide adenine dinucleotide phosphate 16

Summary – Physical Foundations (1) Living cells are open systems, exchanging matter and energy with their surroundings, extracting and channeling energy to maintain themselves in a dynamic state, distant from equilibrium Energy is obtained from sunlight or fuels by converting the energy from electron flow into the chemical bonds of ATP The tendency for a chemical reaction to proceed toward equilibrium can be expressed as the free energy change,  G, which =  H – T  S 17

Summary – Physical Foundations (2) When  G of a reaction is –ve, the reaction is exergonic and tends to go toward completion; when it is +ve, the reaction is endergonic and tends to go in the reverse direction. When 2 reactions are summed, the overall  G is the sum of  G of 2 separate reactions. The reactions converting ATP to P i + ADP or to AMP + PP i are highly exergonic. Many endergonic cellular reactions are driven by coupling them, through a common intermediate to these highly exergonic reactions. 18

Summary – Physical Foundations (3) The standard free-energy change,  G o, is related to the equilibrium constant:  G o = – RT ln K eq Most cellular reactions proceed at useful rates via enzyme catalysis. Enzymes act by stabilizing the transition state, reducing the activation energy,  G ‡ and increasing the reaction rate. Metabolism - interconnected reaction sequences that interconvert cellular metabolites. Each sequence is regulated to provide what the cell needs at a given time and to expend energy only when necessary. 19

Genetic Foundations Living cells and organisms can reproduce themselves for countless generations Continuity of inherited traits implies constancy in the structure of molecules containing genetic information DNA - sequence of deoxyribonuclotide subunits encodes the instructions for forming all other cellular components Effective storage, expression and reproduction of genetic messages define individual biological species 20

DNA – linear polymer of covalently joined deoxyribonucleotides Deoxyadenylate (A) Deoxyguanylate (G) Deoxycytidylate (C) Deoxythymidylate (T) Two complementary strands held together by hydrogen bond between A – T, G – C Twist about each other to form DNA double helix Complementarity in Double-stranded DNA 21

Two DNA strands separate Each serves as a template for synthesis of a new complementary strand Generating two identical double helical molecules, one for each daughter cell If one strand is damaged, the other strand acts as a template for repair of the damage Fidelity of DNA Replication 22

23 Concept of Central dogma

From 1- to 3-Dimensions Expression of linear sequence of deoxyribonucleotide subunits in DNA mRNA protein (corresponding linear sequence of amino acids) 24

Protein folds into particular 3-D shape, stabilized primarily by non-covalent interaction Precise 3-D structure “native conformation” is important for its function From 1-D to 3-D 25

Summary – Genetic Foundations Genetic information is encoded in the linear sequence of 4 types of deoxyribonucleotides in DNA The double-helical DNA molecule contains an internal template for its own replication and repair The linear sequence of amino acids in a protein, which is encoded in the DNA of the gene for that protein, produces a protein’s unique 3-D structure – a process also dependent on environmental conditions Individual macromolecules with specific affinity for other macromolecules self-assemble into supramolecular complexes 26