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Biology 205 5.13.08 Reading Assignments: Chapter 3 Energy, Catalysis and Biosynthesis pgs. 83-94; 106-116 (Note the various roles of nucleotide based carrier molecules); work questions 3-2 and 3-3 Chapter 13 How Cells Obtain Energy from Food pgs. Pg 428-43; 434 -441; 447 and Figure 13-23 Browse through Panel 13-1; work question 13-2 HTTP://WWW.SCIENCE.SMITH.EDU/DEPARTMENTS/BIOLOGY/BIO231/GLYCOLYSIS.HTML

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What does a cell need to do? • propagate itself (and its genetic program)

reproduction • transform energy • communicate with other cells and with the

environment • maintain an ordered, stable system: growth

and development • evolve

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The Arabidopsis thaliana (weedy plant) genome project was recently completed. Here is a breakdown of the functional analysis of the genes discovered in the genome of this organism. Note that a large proportion of the genes are unclassifed -- meaning no one knows yet what they do for the organism.

Nature 408: 796 Dec. 14, 2000

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The Cell’s impressive metabolic feat: • An chemist carrying out an organic synthesis

rarely runs more than one reaction in a single reaction vessel

• This procedure is essential to prevent side reactions and to optimize the yield of the desired product

• A living cell carries out thousands of reactions simultaneously

• Each reaction sequence is precisely controlled by the cell so that intermediates and products accumulate to the desired levels (see also pg 83 of text)**

• Reactions of great mechanistic complexity and stereochemical selectivity proceed smoothly under mild conditions

• These mild conditions: 1 atm pressure, moderate temperature and a pH near neutrality

** The cell controls its metabolism by controlling the level of activity of enzymes that participate in each reaction or reaction sequence

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A QUICK REVIEW OF FREE ENERGY The molecules of a living cell possess • kinetic energy in their vibrations, rotations, and

movement through space • chemical energy stored in the bonds between

individual atoms Free energy (G) measures the energy of a molecule that could in principle be used to do useful work at constant temperature (as in a living cell)

The first law of thermodynamics says ?

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The first law of thermodynamics says that the energy of the universe is constant: energy can be transferred or transformed, but it can neither be created or destroyed We will spend the next two weeks discussing how cells interconvert chemical, electromagnetic, mechanical and osmotic (electropotential gradient) forms of energy

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The second law of thermodynamics says ?

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OLDer VERSION The second law of thermodynamics says that the disorder of the universe can only increase: every energy transfer or transformation increase the entropy of the universe

NEWer VERSION The second law of thermodynamics says that The total entropy of a system and its surroundings always increases for a spontaneous (energetically favorable) process TEXT VERSION The second law of thermodynamics says that in the universe, or in any isolated system*, the degree of disorder (entropy) can only increase [*a collection of matter thatt is completely isolated from the rest of the universe] TEXT RESTATEMENT Systems will change spontaneously towards those arrangements that have the greatest probability (disorder more probably than order) (see coin example on pg 85 of text)

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http://entropysite.com/students_approach.html What Is Entropy, REALLY? Entropy measures the spontaneous dispersal of energy: how much energy is spread out in a process, or how widely spread out it becomes — at a specific temperature. In chemistry the energy that entropy measures as dispersing is “motional energy”, the translational and vibrational and rotational energy of molecules [Figure 1 of http://www.2ndlaw.com/entropy.html ]

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Consider the reaction A → B ΔG = the free energy of the product B minus the free energy of the reactant A If ΔG is negative, the product B has less free energy than the reactant A • the reaction is exergonic and therefore will occur

without input of energy • in other words, a negative ΔG means that the

reaction is energetically favorable (or spontaneous)

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ΔG depends on the intrinsic character of the reacting molecules

ΔG of a chemical reaction is determined by two forces: 1. the tendancy to achieve the most stable bonding

state (number and kinds of covalent and non-covalent bonds broken and formed)

2. the tendancy to achieve the highest degree of randomness aka energy distribution (entropy)

A chemical reaction occurring in an isolated cell at constant temperature and volume can produce disorder in two ways: 1. Changes of bond energy of the reacting molecules

can cause heat to be released (heat disorders the environment)

2. The reaction can decrease the amount of order in the reacting molecules such as:

• breaking a polymer into monomer units • disrupting an interaction that prevents bond

rotations

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Consider the reaction D → F If ΔG is positive, the product (F) has more free energy than the reactant D • the reaction is endergonic or energetically

unfavorable (and will not occur spontaneously) • because the second law of thermodynamics states

that a chemical reaction will only proceed if it results in a net increase in the disorder of the universe, the cell uses exergonic reactions to drive endergonic reactions by coupling the two types of reactions

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What example of a coupled reaction

have we seen already?

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KNOW THIS WELL AND FOREVER • SPONTANEOUS MEANS ENERGETICALLY

FAVORABLE • SPONTANEOUS DOES NOT MEAN THAT

THE REACTION WILL OCCUR WITHOUT A CATALYST

ΒΟΤΗ ΤYPES OF REACTIONS

REQUIRE CATALYSTS

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KINETICS • How fast a reaction occurs is independent of the ΔG: note the activation energy required for both reaction ((previous page)

• In the cell catalysts are required for both exergonic

and endergonic reactions to proceed • The free energy change for a reaction is

independent of the pathway by which the reaction occurs

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• Metabolism • sum total of all chemical reactions in the cell • from the Greek word for change (meta) Metabolism serves two fundamentally different purposes: 1. the transformation of energy to drive vital functions 2. synthesis of biological molecules

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Catabolism • oxidative degradation of complex nutrient molecules

such as carbohydrates, lipids and proteins • characteristically exergonic or energy yielding • energy is often captured in the form of ATP Anabolism • the synthetic processes in which the varied and complex

biomolecules (including the macromolecules) are assembled from simpler precursors

• involves energy requiring or endergonic reactions • the precursors needed for anabolic reactions are found

among the products of catabolism

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☞ Cells use enzymes to catalyze the controlled oxidation of organic molecules in small steps through a sequence of reactions that allows useful energy to be harvested HUH? What does this mean?

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Cells harvest energy from organic compounds via a series of redox reactions REDOX REACTIONS OXIDATION/REDUCTION: any reaction in which electrons are transferred from one substance to another OXIDATION: removal of electrons REDUCTION: addition of electrons ELECTON DONOR [REDUCING AGENT]: a substance that can donate electrons to other substance, becoming oxidized in the process ELECTON ACCEPTOR [OXIDIZING AGENT]: a substance that can accept electrons from other substance, becoming reduced in the process When a molecule picks up an electron (e-), it often picks up a proton (H+) at the same time (protons are freely available in water) A + e- + H+ = AH This reduction is a hydrogenation reaction Dehydrogenation reactions are oxidation reactions

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COMPARISON OF THE STATE OF REDUCTION IN CARBON ATOMS WHAT IS THE MOST OXIDIZED FORM OF CARBON THE MOST REDUCED FORM?

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The carbon atom of methane can be converted to that of carbon dioxide by successive removal of its hydrogen atoms. With each step, electrons are shifted away from the carbon and the carbon becomes progressively more oxidized. Each of these steps is energetically favorable inside a cell.

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REDOX REACTIONS ARE EXERGONIC (RELEASE ENERGY) WHEN ELECTRONS MOVE CLOSER TO ELECTRONEGATIVE ATOMS ELECTRONS LOSE POTENTIAL ENERGY WHEN THEY MOVE CLOSE TO ELECTRONEGATIVE ATOMS

A reduction is occurring if the number of C-H bonds increases An oxidation is occurring if the number of C-H bonds decreases In the presence of O2, the most energetically stable form of carbon is CO2 In the presence of O2, the most energetically stable form of hydrogen is H2 O

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☞ Cells use enzymes to catalyze the controlled oxidation of organic molecules in small steps through a sequence of reactions that allows useful energy to be harvested

The controlled, stepwise oxidation of sugar in a cell, compared with ordinary burning (re: toasting marshmellows). In the cell, enzymes catalyze oxidation via a series of small steps in which free energy is transferred to carrier molecules -- most often ATP and NADH. At each step, an enzyme controls the reaction by reducing the activation energy barrier.

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ATP = ADENOSINE TRIPHOSPHATE The removal of one phosphate requires the breaking of one bond (purple) and results in a large release of energy The phosphate bonds in ATP are said to be “high energy” because they have a large negative ΔG of hydrolysis The formation of ATP from ADP and Pi is an endergonic process that is coupled to the exergonic oxidation of glucose

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ATP is an example of a metastable compound: • thermodynamically favored to break down

(hydrolysis of phosphates is exergonic) but does so only very slowly unless the reaction is catalyzed

• this is important because the cell needs to be able to control the release of energy from ATP

• biological polymers are also metastable compounds

• there is nothing chemically unusual about the bonds between the phosphates in ATP: they are considered high energy because the large negative delta G of hydrolysis

• we will discuss why hydrolysis of ATP releases lots of energy in a later lecture

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NADH (reduced form) is a carrier molecular The part of the molecular that participates in redox reaction is shown in purple This is one of a number of “electron couriers” that you will meet: these molecules pick up and carry electrons around -- always want to unload them on somebody else” NAD = nicotine adenine dinucleotide

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The reduced NADH is at a higher potential energy state than NAD+ because the pyrimidine ring is less stable when it is reduced The reduction of NAD+ to NADH is an endergonic process that is coupled to the exergonic oxidation of glucose

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This flowchart shows the major steps involved in breaking down glucose and converting its chemical energy into the chemical energy in the phosphate bonds of ATP in aerobic organisms red= source of carbon atoms (originally from glucose) blue= redox agents green = energy-currency molecules

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GLYCOLYSIS : a series if chemical reactions that oxidize glucose to produce pyruvate and ATP: used by all organisms (eukaryotic and prokaryotic) as part of fermentation or cellular respiration It is probably the most ancient of metabolic processes, having evolved prior to the appearance of abundant O2 in the atmosphere (more about that later) All organisms are capable of glucose degradation and ATP synthesis via glycolysis

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AT EACH EXERGONIC STEP, ENERGY IS TRANSFERRED TO EITHER ATP OR NADH OR FADH2 Basic steps in glycolysis • adding phosphates to energize the sugar • oxidation to make the high energy molecules NADH and ATP • note: pyruvate end-product is more oxidized than glucose, but

not fully oxidized: glycolysis does not efficiently harvest the energy in glucose

GLYCOLYSIS ANIMATOIN HTTP://WWW.SCIENCE.SMITH.EDU/DEPARTMENTS/BIOLOGY/BIO231/GLYCOLYSIS.HTML

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ENERGY RELEASED BY OXIDATIVE, EXERGONIC (EXERGONIC) STEPS IN GLYCOLYSIS IS CAPTURED IN THE FORM OF THE HIGH ENERGY MOLECULES NADH AND ATP The formation of ATP from ADP and Pi is an endergonic process that is coupled to the exergonic oxidation of glucose The reduction of NAD+ to NADH is an endergonic process that is coupled to the exergonic oxidation of glucose

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AEROBIC AND ANAEROBIC ORGANISMS One basic metabolic distinction among organisms is whether or not they can use O2 as an electron acceptor in energy producing pathways AEROBES: CAN USE O2 Obligate Aerobe: O2 is obligatory for life ANAEROBES: CAN SUBSIST WITHOUT O2 Facultative Anaerobe: can adapt to anaerobic conditions by substituting other electron acceptors for O2 (E. coli) Obligate Anaerobe: cannot use O2 and are poisoned by it

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FERMENTATION: an anaerobic biological reaction process FERMENTATION: THE ANAEROBIC FATE OF PYRUVATE The three common metabolic fates of pyruvate generated by glycolysis: 1. Under aerobic conditions, the pyruvate is completely oxidized via

the citric acid cycle to CO2 and H2O [NADH acts as a high energy compound]

2. Under anaerobic conditions, pyruvate must be converted to a reduced end product in order to reoxidize the NADH produced by the GAPDH reaction

• alcoholic fermentation: in yeast, pyruvate is converted to ethanol + CO2 [free energy of NADH oxidation is dissipated as heat]

• in muscle cells, under anaerobic conditions, pyruvate is reduced to lactate [free energy of NADH oxidation is dissipated as heat]

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