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Thermodynamics of Life II: Bioenergetics, Metabolism, and Order

Attitude survey due Wed 1/30 (15 pts) at the link in the announcements

HW1. Expectations due Wed 1/30 (15 pts) download to Canvas HW2. Thermo NOW due Wed 2/6 (15 pts) paper copy

General features and operating rules of biological energy flow

1. Group discussion identify general features and operating rules.

2. Write down features and rules in your in-class worksheet, and share them in class discussion

The complete pdf posted after class on Mon will include the 3 missing slides based on your descriptions of the operating rules for the energy flow diagrams. 1) Energy in the form of

light flows into the biological world, does physical and chemical work, and ultimately leaves as heat. 2) Matter is ultimately recycled in the biological world. 3) The balance of P/R cycle has profound effects on Earths climate

Biological energy flow General features

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1) Organisms do not create energy, they transform it. 2) Global Light energy flowing into the biological world is ultimately equal to heat energy leaving it. 3) Each step the energy of the initial conditions is equal to the energy of the final conditions.

Biological energy flow Energy balance rules 1) Light is highly usable

energy as it can do biological work. 2) Heat can not be used as metabolic energy in biological systems. 3) Global: energy flows in the biological world in the direction of usable to unusable forms. 4) Each step: energy flows in the direction of usable to unusable forms. 5) Energy is not equivalent to biological work!

Biological energy flow Reaction direction rules

Biological energy flows in organisms Joe the Physicist says, Thermodynamics specifies the rules for converting energy and molecules available in the environment into useful forms for sustaining life.

Energy balance rules = First Law of Thermodynamics Reaction direction rules = Second Law of Thermodynamics

Genomes - store the solutions (i.e., molecular mechanisms) that different lineages have evolved to harness thermodynamic laws.

First Law of Thermodynamics - bioenergetics Joe the Physicist says: The physics is actually quite easy, but it takes some effort to figure out that its easy.

! refers to difference between final state and initial state of a process

First Law H refers to enthalpy (total energy)

!H = 0 (in the universe) Total energy in the universe is neither created nor destroyed in any process, but it can be transformed from one form to another.

OR Total energy of the initial state of a biological process is equal to the total energy of its final state.

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2nd Law of Thermodynamics - bioenergetics Second Law "H = "G + T"S "H = change in total energy (enthalpy) "G = change in chemical energy (Gibbs free energy) the ability to do chemical work T = temperature "S = change in entropy (randomness/disorder)

Biochemistry closed system functioning at STP (standard temp and pressure); ignores physical work (pV work) Then the 2nd Law is: !G < 0 (in the system)

Free energy of final state (Gf) < free energy of initial state (Gi)

2nd Law of Thermodynamics - metabolism Second Law "H = "G + T"S !G < 0 (in the system)

Spontaneous reactions (requiring no additional energy) proceed in the direction that reduces free energy (G), or the useful energy available to do chemical work.

OR In biological systems, spontaneous bioenergetic and metabolic reactions tend to proceed in the direction that releases unusable heat into the environment.

C & R Fig 9.1

First Law !H = 0 Second Law !G < 0

Initial state absorbed light E Final state - ATP, plus heat

Which state has more H? Which state has more G? If you add ATP plus heat to the mitochondria, can they produce light? Why or why not?

Bioenergetics Example Thermodynamic efficiency

www.niquette.com/certainb/chapt06/6text.htm

Another expression of the Second Law is: no real process can be 100% efficient

Efficiency (%) = free energy of final statefree energy of initial state X 100%

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Metabolism

Thermodynamics - direction vs. kinetics - rate

Activation energy - energy needed to initiate the reaction

Joe the Physicist says, We need to focus on !G < 0 again, but it has a new twist called activation energy.

!G < 0

Metabolism - the role of catalysts Potential Catalysts

inorganic catalysts (often metallic ions)

enzymes with metallic ion cofactors

enzymes lacking cofactors

Thermodynamics - molecules for free - metabolism Lifes challenge - to transform available molecules into useful molecules at the right sites and the right times. Genome encodes the enzymes for meeting this challenge.

1. Metal ions were probably used as the catalysts for some metabolic reactions in early protolife. 2. Evolutionary relics: Metallic co-factors at the active sites of many enzymes of ancient origin, e.g.,

Cytochrome c - Fe heme protein (oxidative phosphorylation)

Chlorophyll a - Mg tetrapyrrole

(photosynthetic pigment)

fig.cox.miami.edu/~cmallery/255/255phts/gk6x5.chlorophyll.gif www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3CYT www.rcsb.org/pdb/molecules/pdb26_3.html

Nitrogenase - MoFeS and FeS metaloprotein (nitrogen fixation)

A plausible evolutionary scenario

3. Most enzymes of more recent origin use only amino acids in their active sites.

2nd Law of Thermodynamics - order Second Law "H = "G + T"S "H = change in total energy (enthalpy) "G = change in chemical energy (Gibbs free energy) T = temperature "S = change in entropy (randomness/disorder)

Physics ignores chemical energy, but uses open systems with the ability to exchange energy and matter between the system and its surroundings (= the universe) Another expression !S > 0 (in the universe) Entropy of final state (Sf) > entropy of initial state (Si) Spontaneous processes (requiring no additional energy) proceed in the direction that increases entropy in the universe.

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2nd Law of Thermodynamics - order Second Law "H = "G + T"S !S > 0 (in the universe)

Spontaneous processes (requiring no additional energy) proceed in the direction that increases entropy in the universe.

Entropy - a measure of the randomness or the disorder

Entropy correlates with heat loss in biological systems.

Organisms can use entropy increases to drive physical processes, in particular self-assembly.

How does life spontaneously organize itself if all processes proceed in the direction

that increases universal entropy?

Membrane formation in early life

Protein folding from polypeptide to active protein

adam.steinbergs.us/images/books/lodish/protein-folding.jpg

Hydrophobic interactions Non-polar molecules tend to neither attract or repel each other.

But polar water molecules (and charged ions) tend to attract or repel each other.

Polar and/or charged molecules tend to squeeze hydrophobic regions together.

www.uic.edu

Entropy-driven order !S>O

Polypeptide Adjacent water molecules Unfolded state

Various configurations with exposed hydrophobic amino acids (Intermediate S)

Ice-like shells around exposed hydrophobic amino acids

(Low S)

Folded state

Active protein with hydro- phobic amino acids inside (Low S)

Water molecules freely moving

(Very high S)

Spontaneous biological order at the expense of universal disorder

Self-folding of small polypeptides

Alberts et al. Fig 6.81

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Some examples of entropy-driven order - self-assembly

Virus assembly Self-folding of small polypeptides

Alberts et al. Fig 6.81

C & R 18.3

Bacterial ribosomes composed of 54 proteins and 3 rRNAs - self-assembly in vitro!

www.wadsworth.org

Other macromolecular complexes - scaffolding proteins often called chaperones

T4 bacteriophage

Lesson: simple systems - physics is generally sufficient complex systems - often additional biological control

www.vetmed.iastate.edu

Chaperonins facilitate the correct folding of polypeptides in isolation

Campbell Biology, Fig 5.23

Phospholipids - major components of biological membranes

F Fig. 6.4

Membranes - biological boundaries maximizing hydrophobic interactions

F Fig. 6.5

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First membranes the separation of life from non-life

F Fig. 6.7

Hydrophobic interactions drive formation of lipid vesicles for bounding early life forms - Spontaneous local order maximizes universal disorder.

www.ashland-city.k12.oh.us/.../sunflower.jpgs/

Thermodynamic Definition of an Organism Organisms are open systems that: 1) use thermodynamically favored processes to transform available energy and matter into lifes forms, 2) use high quality free energy for carrying out lifes processes, 3) release low quality energy (heat), and 4) maintain ordered structures at the cost of increased universal disorder.

www.evolutionhappens.net

Alberts et al. Fig 2.38

Genomes ! All the hereditary information in an organism

! Prokaryotes chromosome and plasmid(s) ! Eukaryotes nucleus, mitochondrion (most),

chloroplast (some) ! Record of evolutionary history of the organism ! Molecular mechanisms for lifes processes for example, human genome encodes

! Operating system - DNA replication, RNA transcription, protein synthesis (~29% of the genes)

! Metabolism, bioenergetics, transport (~17%) ! Structure and development (~20%) ! Signal transduction (~14%) ! Miscellaneous (~20%)

DNA sequencing gel - fluorescent tags at the ends of DNA fragments

Summary=Learning objectives=Study guide

Homework problems Obtain HW2. Thermodynamics of Life from HW assignments link in course menu Due Monday 2/4

Work on these assignments in your study group, but then write the answers on your own.

1. In organisms, energetics and metabolism depend on two sets of instructions: thermodynamics specifies the general operating rules, whereas genomes encode the molecular mechanisms for carrying out those transformations.

2. Energy flows through the biological world, whereas matter is recycled in and out of the biological world. 3. Organisms do not create or destroy energy and matter, but they can transform them.

4. Each biological energy transformation tends to result in a decrease in useful energy and an increase in heat energy. 5. Organisms maintain local order at the cost of increased universal disorder

Depending on the topic, students should be able to explain the meaning of each statement, organize relevant knowledge into a conceptual model, refer to appropriate examples, apply appropriate equations, and/or solve problems: