Introduction to Metabolism

Metabolism is the sum of an organism’s chemical reactions Metabolism is an emergent property of life that arises from interactions between molecules within the cell

BIOCHEMICAL PATHWAY VIDEO A metabolic pathway begins with a specific molecule and ends with a product The product of one reaction is substrate of the next Each step is catalyzed by a specific enzyme BIOCHEMICAL PATHWAY VIDEO

ENZYMES THAT WORK TOGETHER IN A PATHWAY CAN BE Concentrated in specific location Covalently bound in complex Soluble with free floating intermediates Attached to a membrane in sequence

CATABOLIC PATHWAY (CATABOLISM) Release of energy by the breakdown of complex molecules to simpler compounds EX: digestive enzymes break down food ANABOLIC PATHWAY (ANABOLISM) consumes energy to build complicated molecules from simpler ones EX: linking amino acids to form proteins

Krebs Cycle connects the catabolic and anabolic pathways

Forms of Energy ENERGY = capacity to cause change Energy exists in various forms (some of which can perform work) Energy can be converted from one form to another

KINETIC ENERGY – energy associated with motion HEAT (thermal energy) is kinetic energy associated with random movement of atoms or molecules POTENTIAL ENERGY = energy that matter possesses because of its location or structure CHEMICAL energy is potential energy available for release in a chemical reaction

Diving converts potential energy to kinetic energy. On the platform, the diver has more potential energy. In the water, the diver has less potential energy. Climbing up converts kinetic energy of muscle movement to potential energy.

THERMODYNAMICS = the study of energy transformations CLOSED system (EX: liquid in a thermos) = isolated from its surroundings OPEN system energy + matter can be transferred between the system and its surroundings Organisms are open systems

The First Law of Thermodynamics = energy of the universe is constant Energy can be transferred and transformed Energy cannot be created or destroyed The first law is also called the principle of CONSERVATION OF ENERGY

The Second Law of Thermodynamics During every energy transfer or transformation entropy (disorder) of the universe INCREASES some energy is unusable, often lost as heat

ORGANISMS are energy TRANSFORMERS! Second law of thermodynamics First law of thermodynamics Chemical energy Heat CO2 H2O ORGANISMS are energy TRANSFORMERS! Spontaneous processes occur without energy input; they can happen quickly or slowly For a process to occur without energy input, it must increase the entropy of the universe

Free-Energy Change (G) can help tell which reactions will happen ∆G = change in free energy ∆H = change in total energy (enthalpy) ∆S = change in entropy T = temperature ∆G = ∆H - T∆S Only processes with a negative ∆G are spontaneous Spontaneous processes can be harnessed to perform work

Free Energy, Stability, and Equilibrium Free Energy- a measure of a systems instability Unstable systems (higher G) tend to change in such a way that they become more stable (lower G) A process is spontaneous and can perform work only when it is moving toward equilibrium Equilibrium is a state of maximum stability

More free energy (higher G) Less stable Greater work capacity In a spontaneous change The free energy of the system decreases (∆G < 0) The system becomes more stable The released free energy can be harnessed to do work Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change Less free energy (lower G) More stable Less work capacity

Exergonic and Endergonic Reactions in Metabolism EXERGONIC reactions (energy outward) (- ∆G) Release energy are spontaneous

Exergonic and Endergonic Reactions in Metabolism ENDERGONIC reactions (energy inward) (+ ∆G) Absorb energy from their surroundings are non-spontaneous

Mechanical Transport Chemical Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work: Mechanical Transport Chemical In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic

ATP provides energy for cellular functions ATP (adenosine triphosphate) is the cell’s renewable and reusable energy shuttle ATP provides energy for cellular functions Energy to charge ATP comes from catabolic reactions Adenine Phosphate groups Ribose

Adenosine triphosphate (ATP) + P P + Energy i Inorganic phosphate Adenosine diphosphate (ADP)

Energy for cellular work provided by the loss of phosphate from ATP Energy from catabolism (used to charge up ADP into ATP ADP + P i

Glutamic acid Ammonia Glutamine ATP H2O ADP Endergonic reaction: DG is positive, reaction is not spontaneous NH2 + NH3 DG = +3.4 kcal/mol Glu Glu Glutamic acid Ammonia Glutamine Exergonic reaction: DG is negative, reaction is spontaneous ATP + H2O ADP P + DG = –7.3 kcal/mol i Coupled reactions: Overall DG is negative; Together, reactions are spontaneous DG = –3.9 kcal/mol

Reactants: Glutamic acid P i P Motor protein Protein moved Mechanical work: ATP phosphorylates motor proteins Membrane protein ADP ATP + P i P P i Solute Solute transported Transport work: ATP phosphorylates transport proteins P NH2 + NH3 Glu + P i Glu Reactants: Glutamic acid and ammonia Product (glutamine) made Chemical work: ATP phosphorylates key reactants

Every chemical reaction between molecules involves bond breaking and bond forming ACTIVATION ENERGY = amount of energy required to get chemical reaction started Activation energy is often supplied in the form of heat from the surroundings Free energy animation IT’S LIKE PUSHING A SNOWBALL UP A HILL . . . Once you get it up there, it can roll down by itself

The Activation Energy Barrier D Transition state A B EA Free energy C D Reactants A B DG < O C D Products Progress of the reaction

CATALYST = a chemical agent that speeds up a reaction without being consumed by the reaction ENZYMES = biological catalysts Most enzymes are PROTEINS Exception = ribozymes (RNA)

ENZYMES work by LOWERING ACTIVATION ENERGY; Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Free energy Course of reaction with enzyme DG is unaffected by enzyme Products Progress of the reaction ENZYMES work by LOWERING ACTIVATION ENERGY;

ENZYMES LOWER ACTIVATION ENERGY BY: Orienting substrates correctly Straining substrate bonds Providing a favorable microenvironment Enzymes change ACTIVATION ENERGY but NOT energy of REACTANTS or PRODUCTS

ENZYMES Most are proteins Lower activation energy Specific Shape determines function Re-usable Unchanged by reaction

The REACTANT that an enzyme acts on = SUBSTRATE Enzyme + substrate = ENZYME-SUBSTRATE COMPLEX Region on the enzyme where the substrate binds = ACTIVE SITE Substrate held in active site by WEAK interactions (ie. hydrogen and ionic bonds)

TWO MODELS PROPOSED LOCK & KEY Active site on enzyme fits substrate exactly INDUCED FIT Binding of substrate causes change in active site so it fits substrate more closely

Enzyme Activity can be affected by: General environmental factors, such as temperature, pH, salt concentration, etc. Chemicals that specifically influence the enzyme See a movie Choose narrated

TEMPERATURE & ENZYME ACTIVITY Each enzyme has an optimal temperature at which it can function (Usually near body temp)

Increasing temperature increases the rate of an enzyme-catalyzed reaction up to a point. Above a certain temperature, activity begins to decline because the enzyme begins to denature.

pH and ENZYME ACTIVITY Each enzyme has an optimal pH at which it can function

COFACTORS = non-protein enzyme helpers EX: Zinc, iron, copper COENZYMES = organic enzyme helpers Ex: vitamins

SUBSTRATE CONCENTRATION & ENZYME ACTIVITY ← V MAX Adding substrate increases activity up to a point

REGULATION OF ENZYME PATHWAYS GENE REGULATION cell switches on or off the genes that code for specific enzymes

REGULATION OF ENZYME PATHWAYS FEEDBACK INHIBITION end product of a pathway interacts with and “turns off” an enzyme earlier in pathway prevents a cell from wasting chemical resources by synthesizing more product than is needed FEEDBACK INHIBITION

NEGATIVE FEEDBACK An accumulation of an end product slows the process that produces that product B A C D Enzyme 1 Enzyme 2 Enzyme 3 Negative feedback Example: sugar breakdown generates ATP; excess ATP inhibits an enzyme near the beginning of the pathway

POSITIVE FEEDBACK (less common) The end product speeds up production W X Y Z Enzyme 4 Enzyme 5 Enzyme 6 Positive feedback EXAMPLE: Chemicals released by platelets that accumulate at injury site, attract MORE platelets to the site.

REGULATION OF ENZYME ACTIVITY ALLOSTERIC REGULATION protein’s function at one site is affected by binding of a regulatory molecule at another site Allosteric regulation can inhibit or stimulate an enzyme’s activity Allosteric enzyme inhibition

SOME ALLOSTERIC ENZYMES HAVE MULTIPLE SUBUNITS Each enzyme has active and inactive forms The binding of an ACTIVATOR stabilizes the active form The binding of an INHIBITOR stabilizes the inactive form

Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. Substrate Inactive form Stabilized active form COOPERATIVITY another type of allosteric activation

COOPERATIVITY = form of allosteric regulation that can amplify enzyme activity Binding of one substrate to active site of one subunit locks all subunits in active conformation

Enzyme Inhibitors COMPETITIVE inhibitor REVERSIBLE; Mimics substrate and competes with substrate for active site on enzyme ENZYME ANIMATION

Enzyme Inhibitors NONCOMPETITIVE inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective ENZYME ANIMATION