1

Biology 205 5.10.06 Reading Assignment: Chapter 9 in textbook HTTP://WUNMR.WUSTL.EDU/EDUDEV/LABTUTORIALS/CYTOCHROMES/CYTOCHROMES.HTML

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

2

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

3

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 controlled so that intermediates and products accumulate to the desired levels

• 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

4

Example of an impressive feat: N2 fixation Fixation of N2-- • the vital function of taking nitrogen gas from

the atmosphere and converting it to ammonia • which is then incorporated into amino acids

and nucleotides and other organic compounds N2 converted to NH3 by nitrogen-fixing bacteria • requires a lot of energy Industrial N2 fixation requires • very high pressure (300X normal atmospheric) • very high temp. (500o C) german chemist who worked out industrial N2 fixation also developed the poisonous gas used in WWI • No plant or animal is capable of this feat • Neither are most bacteria • Currently all life on earth is dependent on a few

species of nitrogen-fixing bacteria to make ammonia from gaseous nitrogen

5

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

translations • 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 ?

6

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

7

The second law of thermodynamics says ?

8

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 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 ]

9

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)

10

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

11

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) • the cell uses exergonic reactions to drive

endergonic reactions by coupling the two types of reactions

12

Note on 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

13

• 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

14

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

15

16

☞ 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?

17

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

18

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

19

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.

20

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

21

☞ 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.

22

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

23

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

24

NADH (reduced form) 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”

25

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

26

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

27

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

28

AT EACH EXERGONIC STEP, ENERGY IS TRANSFERRED TO EITHER ATP OR NADH OR FADH2

29

REVIEW STRUCTURE OF GLUCOSE AND OTHER CHOS 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

ENERGY RELEASED BY OXIDATIVE, EXERGONIC (EXERGONIC) STEPS IN GLYCOLYSIS IS CAPTURED IN THE FORM OF THE HIGH ENERGY MOLECULES NADH AN 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

30

31

32

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

33

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]

34