Overview: energy of life

Ch8: Introduction to Metabolism Living cell is miniature chem. factory where thousands of reactions occur Cell extracts energy to perform, work (=Cellular respiration) Some convert energy to light, as in bioluminescence Some concert light to chemical energy (carbohydrates) that can be used in cellular respiration 8.1: An organisms metabolism transforms matter and energy, subject to the laws of thermodynamics 8.2: free-energy change of a reaction tells us whether or not the reaction occurs spontaneously 8.3: ARP powers cellular work by coupling exergonic reactions to endergonic rxns 8.4: Enzymes speed up metabolic rxns by lowering energy barriers 8.5: regulation of enzyme activity helps control metabolism Metabolism is the totality of an organisms chemical reactions Metabolism is emergent property of life that arise from interactions of molecules in cell

Key Concepts

C 8.1: an organisms metabolism transforms matter and energy, subject to the laws of thermodynamics Organization of chemistry of life into metabolic pathways

metabolic pathway begin with specific molecule and end with product of each step being catalyzed by a specific enzyme - (tons of paths, like a map) Catabolic pathways release energy by breaking down complex molecules to simpler ones Anabolic pathways consume energy to build complex molecules from simpler ones - synthesis of protein from amino acid Bioenergentics is study of how organisms manage their cell resources Energy is capacity to cause change Energy in form of many that can perform work Kinetic energy ties in with motion Heat energy (thermal energy), kinetic associated with random movement of atom or mlcl. Potential energy is energy that matter possesses because of location or structure Chemical energy is potential energy available for release in a chemical rxn Thermodynamics- study of energy transformation An isolated system is one where closed of from its surroundings In open system energy and matter can be swapped from system and surrounding Organisms are open systems According to 1st law of thermodynamics, energy of universe is constant (principle of conservation of energy) - energy can be transferred and transformed, but it cannot be created or destroyed During every energy transfer or transformation, some energy is unusable, lost as heat - every energy transfer or transformation increases entropy (disorder) of universe in order to maintain order in cells, living cells transform energy and unavoidably converts organized form of energy to heat spontaneous processes occur without energy input; happens quickly or slowly for processes to occur without energy input, it must increase energy of universe

Basic Energetics

Energy transformation = Thermodynamics

The first law of thermodynamics Second law of Thermodynamics

Cells, organisms and thermodynamics

Biological order and disorder

cells create ordered structures from less ordered materials organisms also replaced ordered forms of matter and energy with less ordered forms energy flows into ecosystem as light, and exits as heat evolution of complex organisms dont violate thermodynamics -> entropy (disorder) may decrease in organism but the universes total entropy increases biologist want to know which rxn are spontaneous and which arent to do so, they need to determine energy change that occurs in chemical rxn

C 8.2: the free-energy change of a reaction tells us whether or not the reaction occurs spontaneously Free- Energy change, G

livings system free energy is energy that can do work when temp and pressure are uniform, as in a living cell changes in free energy identify spontaneous rxn from one energy requiring ones change of free energy (G) during a process is related to the change or enthalpy, or change in total energy (H), change in entropy (S), and temperature in Kelvin (T) G= H-TS Only processes with a negative G are spontaneous G<0 (-) rxn occurs spontaneously G0 (+) rxn occurs non-spontaneously Spontaneous processes can be harnessed to perform work Free energy is systems instability, its tendency to change to a more stable state -> during spontaneous change, free energy decreases and the stability of a system increases Equilibrium is a state of maximum stability Process is spontaneous and can perform work only when its moving towards equilibrium Concept of free energy can be applied to chemistry of lifes processes Exorgonic and endorgonic reactions in metabolism - an exorgonic (catabolic) reaction proceeds with a net release of free energy and is spontaneous - an endergonic (anabolic) rxn absorbs free energy from its surroundings and is nonspontaneous Rxt in a closed system eventually reach =brium and then do no work Cells arent in =brium; they are open system that have constant flow from surrounding Acatabolic pathways in a cell releases free energy in a series of reactions Closed and open hydroelectric systems can serve as analogies Cell does 3 main kind of work - chemical - transport - mechanical To do work, cells energy manage by energy coupling, use of exorgonic process to drive an endergonic one Most energy couplings in cells is mediated by ATP ATP (adenosine triphosphate) is cells energy shuttle (currency for energy of cell) ATP is composed of ribose(sugar), adenine( nitrogenous base)and three phosphate groups Bonds between phosphate group tail can break down by hydrolysis releasing energy Release of energy some from chemical change to a state of lower free energy, not from phosphate themselves

Free energy, stability, and equilibrium

Free energy and metabolism

Equilibrium and metabolism

C 8.3: ATP powers cellular work by coupling exorgonic reactions to endergonic reactions

How the Hydrolysis of ATP perform work

types of cellular work(mechanical, chemical, transport)are powered by hydrolysis of ATP Energy from exergonic reaction of ATP hydrolysis can drive an endergonic rxn Overall, coupled reactions are exergonic (-G), so how does this actually work?.... ATP used in proteins, motor proteins, transport, etc ATP is renewable resource that is regenerated by addition of phosphate group to diphosphate (ADS) using catabolic reaction in the cell ATP cycle is a revolving door through which energy passes during its transfer during its transfer from catabolic to anabolic pathways A catalyst is a chemical agent that speeds up a reaction without being consumed in rxt Enzyme is a catabolic rxt Hydrolysis of sucrose by the enzyme sucrose in example of enzyme-catalyzed rxt Every chemical reaction between molecules involves bond breaking and bond forming Initial energy to start rxn is called free energy of activations, or activation energy (EA) and is often supplied in the form of heat from surroundings

The regeneration of ATP

Enzymes speed up metabolic reactions by lowering energy barriers

Activation energy barriers

How enzymes lower the EA Enzymes catalyze reactions by lowering the EA barrier Enzymes dont affect change in free energy; instead they hasten reaction that would barrier eventually occur Substrate Specificity of Enzymes Reactant that enzyme acts on is called the enzymes substrate Enzyme binds to substrate, forming enzyme-substrate complex Active site is the region on the enzyme where the substrate binds Induced fit of a substrate brings chemical groups of active site into position that enhance their ability to catalyze reaction In enzymatic rxn, substrate binds to active site of enzyme Active site can lower an EA barrier by: - orienting substrates correctly - straining substrate bonds - providing a favorable microenvironment - covalently bonding to the substrate An enzymes activity can be affected by: - general environmental factors, such as temperature and pH - chemicals that specifically influenced the enzyme o Cofactors o Inhibitors Each enzyme has optical temp and idea pH that favor most active shape for enzyme mol. Cofactors are nonprotein enzyme helpers Cofactors may be inorganic (such as a metal in ionic form) or organic An organic cofactor is called a coenzyme Coenzymes include vitamins - vitamin A, vitamin B, etc. Competitive inhibitors bind to active site of an enzyme, competing with the substrate Noncompetitive inhibitors bind to other parts on enzyme, causing enzyme to change shape and making active site less effective -> toxins, poison, pesticides, and antibiotics

Catalysis in the enzymes active site

Effects of local conditions on enzyme activity

Cofactors

Enzyme Inhibitors

Evolution of enzymes

Enzymes are proteins encoded by genes Changes (mutations) in genes lead to change in amino acid composition of an enzyme Altered amino acids in enzymes may change what type of substrate they use Under new environmental conditions a novel form of an enzyme might be favored Chemical chaos would result if a cells metabolic pathways were not tightly regulated Possible by cells ability to turn on and off genes that encode specific enzymes Each enzyme has an active and inactive form - binding of activator stabilizes active form of enzyme - binding of inhibitor stabilizes inactive from of enzyme Allosteric regulation may inhibit or stimulate enzymes activity and occurs when regulatory molecule (like polypeptide subunit) bind to protein at one site and affects the proteins function at another site Cooperativity is a form of allosteric regulation that can amplify enzyme activity 1 substrate molecule primes an enzyme to act on additional substrate mol. more readily Cooperativity is allosteric bcc binding by a substrate to one active site affects catalysis in different active sites Allosteric regulator are attractive drug candidates for enzyme regulation bcc of specificity Inhibition of proteolyc enzymes called caspases may help management of inappropriate inflammatory responses End product of metabolic pathway shuts down pathway Feedback inhibition prevents cell from wasting chemical resources by synthesizing more product than is needed Structure within cell help bring order to metabolic pathways Some enzymes act as structural components of membrane In eukaryotic cells, some enzyme reside in specific organelles, for Ex, enzymes for cellular respiration are located in mitochondria

C 8.5: Regulation of enzyme activity helps control metabolism Allosteric regulation of enzymes

Identification of Allosteric Regulators

Feedback inhibition

Specific localization of enzymes within the cell

You should now be able to

1. Distinguish between the following pairs of terms: catabolic and anabolic pathways; kinetic and potential energy; open and closed systems; exergonic and endergonic reactions 2. In your own words, explain the second law of thermodynamics and explain why it is not violated by living organisms 3. Explain in general terms how cells obtain the energy to do cellular work 4. Explain how ATP performs cellular work 5. Explain why an investment of activation energy is necessary to initiate a spontaneous reaction 6. Describe the mechanisms by which enzymes lower activation energy 7. Describe how allosteric regulators may inhibit or stimulate the activity of an enzyme