Chapter 3 Bioenergetics, Enzymes, Metabolism Bioenergetics Energy transformations in living organisms Necessary to fuel life processes

Thermodynamics Study of changes in energy in various events/ reactions/ processes in the universe Can indicate the direction and likelihood of a reaction occurring Energy Capacity to do work Based on availability of energy

First law of thermodynamics Law of conservation of energy Energy neither created or destroyed Can be converted into different forms

System Energy changes Change in heat content Performance of work

Any loss or gain balanced out in the surroundings E= Q-W Change in internal energy (E) equals heat energy (Q) minus work energy (W)

Change in internal energy can be positive or negative or zero Exothermic

Heat loss (negative)

Endothermic Heat gain (positive)

Second law of thermodynamics Events have direction High to low energy Decreasing availability of energy for additional work Ex. Rock fall, Olympic jump, heat flow. Food chain

Events are spontaneous Thermodynamically favorable Occuring without input of external energy

Enthropy Tendency toward disorder or randomness

TS T= absolute temperature (K), S = change in entropy between initial and final states

Cells release heat Glucose oxidation, friction of blood cells in blood vessels, Entropy zero at absolute zero temperature (0 K)

Living organisms can decrease their own entropy by increasing the entropy of their surroundings

Entropy decreased by the ordered structures of macromolecules

Amino acids- peptide chains- folded tertiary or quarternary structures

Need metabolism to be able to form these structures In metabolism, there is a breakdown of glycogen and release of heat as well as H2O and CO2 There is an increase of entropy in the environment

Maintaining a state of high information content requires the input of energy High information is a low entropy state Specific sequences of DNA and proteins

Free energy J. Willard Gibbs H= G +TS H (enthalpy), G (free energy), TS Enthalphy Total energy content of a system

Free energy Change in energy available to do work

TS Energy unavailable to do work

H= G +TS Spontaneity G Indicates maximum amount of available energy for next reactions If negative Predict direction and extent of reaction

 H= G +TS Same with E G

Proceeded toward a lower energy state Thermodynamically favored

Exergonic Negative Thermodynamically favored Spontaneous

Endergonic Positive Thermodynamically unfavored

H Positive if heat is gained

S Positive is more disordered

Free energy changes in chemical reactions A + B <-> C + D Rates of reaction proportional k1 [A][B] = k2 [C][D] k1/ k2= [C][D]/ [A][B] ki/k2= equilibrium constant (Keq)

For a given set of reactions, can predict the concentration of products to concentration of reactants

Free energy changes in metabolic reactions ATP hydrolysis

ATP + H2 -> ADP + Pi Standard free energy difference -7.3 kcal/ mol

G negative Spontaneous/ favorable Exergonic

Endergonic and Exergonic reactions Glutamic acid + NH3 -> glutamine Endergonic G = + 3.4 kcal/mol

Equilibrium vs. Steady State Metabolism Reaction Towards equilibrium Free energy available decreases Entropy increases

Cellular metabolism Non-equilibrium Ratio of products and reactants Some reactions are irreversible and go in one direction

Equilibrium A + B <-> C + D

Steady state Can have continuous influx of nutrients from outside the system Can include dynamic nonequilibrium Rates of forward and reverse reactions can change depending on the needs of the organism

Enzymes Hans and Eduard Buchner Fermentation utilized enzymes James Sumner Structure Most are conjugated proteins Have cofactors (non-protein components) Inorganic Organic Properties of Enzymes 1. Required in small amounts 2. Not reversibly altered in the reaction 3. Do not directly affect reaction thermodynamics Does not supply energy Does not affect ratio of products and reactants Called coenzymes Enzyme urease from Jackbeans Enzymes: proteins and ribozymes (RNA) Yeast juice With sugar Produced ethanol and CO2

4. Enzymes are catalysts 5. Inorganic catalysts 100-1000x faster

6. Enzymes 10^8 - 10^13 x faster Highly specific 1. Reactants (substrates) Activation energy Activation energy barrier Must be overcome so that the reaction may proceed

Reactants must have sufficient kinetic energy to break covalent bonds Transition state fleeting, activated complex in which bonds are being formed and broken

Enzymes bind to the transition state Stabilizes the activated complex Lower the activation energy

Transition state studies Proteins with similar structure can act as inhibitors Bind to catalytic region of enzymes

Antibodies Found to act as enzymes/ catalysts Bind to molecules with high affinity

The Active site

Enzyme Substrate Complex May form covalent or non covalent bonds Active site Directly involved in substrate binding Complementary shape with substrate

Active site Buried in a cleft Substrates enter, undergo desolvation Hydrophobic environment More reactive

Amino acids distant in the polypeptide chain

Mechanisms of enzyme catalysis Changes in the physical and chemical components of the substrate due to binding in the enzyme substrate complex Substrate orientation Correct orientation lower enthalpy

Changing substrate reactivity Substrate with sidechains Affect electron distribution Make more reactive and give a more stable transition state

Shifts in the position of atoms during binding Induced fit Complementary position

Substrate may be in an unstable state

(Review: Energy, Thermodynamics First law Law of conservation of energy E= Q-W

Second law Entropy Systems tend towards entropy TS To decrease entropy in a system, must increase entropy in the environment Metabolism: release heat to synthesize organic molecules

Free energy H= G +TS G= H -TS Free energy is total energy minus entropy loss Sponteneity - G A loss of free energy after the process Release of heat

Snowflake forming from water Need more energy input to get into this more ordered state Heat absorbed, not released Endergonic Change in G is positive, not spontaneous

Water hydrolysis Need some energy to start the reaction, but the bonds between atoms have more energy Release of heat Exergonic Change in G is negative, spontaneous

Steady state and equilibrium state Equilibrium state: No energy transfer Equal rate of making products and reactants

Steady state: Energy constantly put into the system, high free energy Maintain higher order Processes tend to be irreversible, toward one set of products)

Enzyme kinetics Catalytic activity of enzymes Rate at which it catalyzes a reaction under different experimental conditions

Leonor Michaelis and Maud Menten Velocity of enzyme reactions Consider amount of product formed or substrates consumed.

[S]: substrate concentration Km: Michaelis constant

Michaelis- Menten equation When the substrate concentration [S] is equal to Km the reaction velocity [V] is equal to half of V max, thus

Km = [S]; V = Vmax At V max, Km= [S]

Michaelis constant (Km) Substrate concentration when the reaction velocity is half of V max Constant for a given enzyme Km Indirectly proportional to the affinity of an enzyme to the substrate Higher Km To generate the curve Used same amount of enzyme, increasing concentration of substrate Substrate molecules are rate limiting Enzymes work at max capacity state of saturation Turnover number Aka catalytic constant Maximum number of molecules that can be converted to a product by one enzyme molecule per unit time Initial velocity is V max Need higher substrate concentration to achieve Vmax Points to a lower affinity between enzyme and substrate independent of substrate or enzyme concentration

Enzyme inhibitors Bind to an enzyme to decrease its activity Regulates enzymes Can act as drugs Reversible or irreversible

Irreversible inhibitors Bind very tightly to an enzyme Often form a covalent bond with an amino acid Ex.nerve gases, pesticides acetylcholinesterase Reversible Inhibitors Bind loosely, readily displaced Competitive Reversible Compete with a substrate to access the active site of an enzyme Complementary to active site resemble the substrate Continued muscle contraction

Non-competitive Substrate and inhibitor do not compete for the same binding site Inhibitor acts at a site other than the active site

Metabolism Biochemical reactions in a cell Metabolic pathways Usually the product of one reaction is the substrate for the next Specific enzymes

Metabolic intermediates or metabolites Compounds formed at each step

Overview of metabolism Catabolism Breakdown of complex molecules Provide raw materials for synthesis of new molecules Provide chemical energy Anabolism Synthesis of more complex compounds Require input of energy high energy phosphates (ATP) high energy electrons ( NADPH)

Redox Reactions Refer to loss or gain of electrons Reversible reactions Oxidation Loss of electrons Becomes positive

Reduction Gain of electrons Becomes negative

Reducing agent: Fe Oxidation agent: Cu

Redox in organic compounds

Organic compounds involve carbon atoms with covalent bonds C-H bond reduced state electrons closer to C

C-O bond Oxidized state electrons closer to electronegative O

Capture and utilization of energy Energy released when compounds are burned with O2 More oxidized

Degree of reduction Relates with ability to perform chemical work in the cell The H atoms can be removed, the more ATP it can produce

Carbohydrates

Fats Which has more energy and why?

Glucose oxidation

 ADP to ATP conversion

One molecule of glucose can produce a lot of ATP Up to 36 molecules

Glucose catabolism Glycolysis In the cytosol Forms pyruvate

Tricarboxylic acid (TCA) cycle In mitochondria of eukaryotes In cytosol of prokaryotes Carbon atoms oxidized to CO2

Glycolysis Anaerobic Pathway of energy transfer Major anabolic pathway of organisms

Glycolysis and ATP Formation Harden and Young Glucose breakdown in yeast generates CO2 Eventually stopped releasing despite excess glucose

Added inorganic phosphates Needed in initial phase of glycolysis

Glycolysis Linkage of sugar to phosphate group Use one ATP

Phosphorylation activates the sugar Can have phosphate groups removed and transferred around to other acceptors

Glucose 6-phosphate converted to fructose 6-phosphate, then fructose 1,6-biphosphate Fructose 1,6-biphosphate split into 2 3-carbon monophosphates

ATP formation Needs coenzyme (NAD+) nicotinamide adenine dinucleotide

Redox reaction Forms NADH Dehydrogenase

Step 7 Substrate level phosphorylation Direct route of ATP formation Phosphate from substrate to ADP

Final step Substrate level phosphorylation

Free energy change in the cell Transfer potential

Any donor higher in the scale can phosphorylate something lower the scale Higher greater free energy less affinity for transferred parts

Less affinity better donor

Greater affinity better acceptor

Glycolysis Anaerobic

4 ATP molecules per molecule of glucose oxidized to pyruvate

Pyruvate Between anaerobic and aerobic pahtway Without oxygen Fermentation

With oxygen Aerobic respiration catabolism

One of the products is NADH Uses up NAD+ (short supply) NAD+ must be regenerated from NAPH Cannot be oxidized by the electron transport chain without oxygen Must generate by fermentation in the cytosol

Reducing power Synthesis of biomolecules requires a strong reducing agent Cells reserve of NADPH Photosynthesis: Measure of cells usable energy content

Metabolic regulation Always regulate the amount of available ATP Energy normally stored in carbohydrates and fats Cells can regulate by controlling key enzymes in metabolic pathways Can modify conformation Covalent modification Addition or removal of phosphates by protein kinases

Allosteric modification A compound on the allosteric site will inhibit or stimulate Feedback inhibition Enzyme inactivated when too much of product

Catabolic and Anabolic Pathways Glycolysis and Glyconeogenesis Glycolysis 3 irreversible reactions

Gluconeogenesis Thermodynamically favored steps