Energy and life

1st law of thermodynamics:Law of Conservation of Energy.

Energy cannot be created or destroyed

Then why do we talk about the “energy crisis?”What does it mean to be phototrophic vs chemotrophic?

(Light as energy source vs chemical energy source)What does ATP synthetase or photosynthetic reaction center do?

Chapter 8: Energy, enzymes, and regulation

Energy transduction

Enzymes can convert one form of energy into another form.* Examples?

Myosin in muscle:

ATP synthase:

Flagellum:

Photosyntheticreaction center:

Electron transfer chainin mitochondria:

chemical to mechanical energy

transmembrane gradient into chemical energy

transmembrane gradient into motion

light into transmembrane gradient

chemical energy into transmembrane proton gradient

2nd law of thermodynamics: entropy (disorder) of an isolated system always increases

Is a living organism in a relatively low or high state?How to grow from a seed or an embryo to an adult organism? Decrease in entropy?

Entropy:

A measure of the randomness or disorder of a system

The greater the disorder the greater the entropy

Energy = The capacity to do work or to cause particular changes.

Chemical work

The synthesis of complex biological molecules from simpler precursors

Mechanical work

Changing the location of organisms (e.g., flagellum), cells and structures within cells

Transport work

The ability to transport molecules against a concentration gradient (uptake of nutrients, elimination of waste, maintenance of ion balance)

Efficiency of energy conversion?

Less than 100%. Question: Where does the rest go?

Heat: thermal motion of molecules without (strong) thermal gradient. It is often difficult to capture this form of energy for doing work

Idea: Eventual thermal death of the universe. Is being debated.

Bottom line for biology: living systems need input of energy to keep functioning. Question: what is the overall energy source driving the biosphere on earth?

Sun light: photosynthesis

G = H - TS

G = change in free energy (amount of energy available to do work)

Describes direction of spontaneous processes. Reactions with a negative G value will occur spontaneously

H = change in enthalpy (heat content)

T = temperature in Kelvin (C + 273)

S = change in entropy

Free energy G and chemical reactions

Standard free energy (G )and the equilibrium constant

When G is determined under standard conditions of concentration, pressure, and temperature the G is called the standard free energy change (G)

If the pH is set to 7, the standard free energy change is indicated by the symbol G´

A + B ⇄ C + D Keq = [C] [D] / [A] [B]

G´ = -RT ln Keq

Reactions proceed in the direction of negative G´

Reaction will proceedto the right (downhill process)

Reaction will proceedto the left (uphill process)

Key issue: how can cells achieve essential reactions with a positive G´?

Examples:

Nutrient uptakeDNA replicationAmino acid biosynthesisCO2 fixationFlagellar motionATP synthesis

By coupling an uphill process to a downhill process

A major role of ATP is to drive otherwise endergonic reactions

This makes the overall reaction downhill, so it will proceedFree energy input is needed to sustain life and growthMain downhill processes? ATP hydrolysis and proton motive force

Energy cycle

Note: this is simplification, because it ignores coupling of proton motive force to all three forms of work

Adenosine 5´-triphosphate (ATP)

ATP serves as the major energy currency of cells

“Contains 2 high energy bonds”. Note: there is nothing particularly special about these two bonds except that cells happen to use them.

ATP ADP + Pi + Energy

Pi = orthophosphate

Note: ATP is complexed to Mg2+

Oxidation-reduction reactions

Oxidation-reduction reactions are key in almost all energy metabolism of life (respiration, photosynthesis, and also fermentation, glycolysis):

Coupled to the generation of ATP, proton motive force.

Loss of electrons is oxidation (LEO)

Gain of electrons is reduction (GER)

Aerobic respiration is when O2 acts as the final electron acceptor (O2 H2O)

Acceptor + ne- donor, n = number of electrons transferred⇄

Quantifying redox reactions1. Split redox reactions into two half reactions involving two redox pairs.Example: Fe3+ + Cu+ Fe2+ + Cu2+

Fe3+ + e- Fe2+ (electron acceptor)Cu+ Cu2+ + e- (electron donor)

2. Redox potential E (similar to G) = EA - ED The equilibrium constant of a redox reaction is called the standard

reduction potential (E). G = -nFE F=constant of Faraday

2. Define hydrogen half reaction as the absolute reduction reduction potential: 2H+ + 2e- H⇄ 2

The reference standard for reduction potentials is the hydrogen system with an E´ of - 0.42 volts (at pH 7).

Note: a positive E corresponds to a negative G: electrons will flow to the compound with the most positive E

In our mitochondria:NADH + H+ NAD⇄ + + 2H+ + 2e- -0.32 VO2 + 2H+ + 2e- ⇄ H2O 0.82 V

E = EA - ED so: 0.82 - - 0.32 = 1.14VG = -nFEG = -2*23*1.14 = -54.4 kcal/molATP hydrolysis: -7.3 kcal/mol

Respiration in our mitochondria yields 1.14V of driving force to convert into other forms of energy (pmf)

Electrons flow to more positive redox potential

Electrons flow from donors with more negative redox potential to acceptors with more positive redox potential.

Key electron carriers

Electron carriers serve to transport electrons between different chemicals

Example - Nicotinamide adenine dinucleotide (NAD)

NADH + H+ + 1/2 O2 H2O + NAD+

NAD+/ NADH is more negative than 1/2 O2/ H2O, so electrons will flow from NADH (donor) to O2 (acceptor)

Structure of NAD

Water soluble electron carrier

Photosynthesis

Flavin adenine dinucleotide (FAD)

Proteins bearing FAD (or FMN) are referred to as flavoproteins

FAD is usually bound to proteins

Coenzyme Q (CoQ) or ubiquinone

Transports electrons and protons in respiratory electron transport chains.

Residues in membrane (hydrophobic molecule)

Note:

* One-versus two-electron processes

* In some cases electron transfer is coupled to protonation/deprotonation

Cytochromes

Cytochromes are redox proteins that bind a heme.

They use the iron atoms in the heme to reversibly transport a single electron

Iron atoms in cytochromes are part of a heme group

Nonheme iron proteins carry electrons but lack a heme group (e.g. Ferrodoxin)

EnzymesEnzymes are protein catalysts

* Enzymes catalyze an astonishing array of different reactions

* Enzymes speed up reactions without altering their equilibrium position. Note: they can couple down-hill and uphill reactions

* Enzymes are permanently chemically altered during catalysis

* Enzymes tremendously speed up reactions: typically 109

*Enzymes are highly specific

Reacting molecules = substrates

Substances formed = products

Enzymes can have cofactors

Some enzymes are composed purely of protein)

Some enzymes contain both a protein and a nonprotein component: a cofactor (like FAD)

The protein component = apoenzyme

The nonprotein component = cofactor

Apoenzyme + cofactor = holoenzyme

Cofactor tightly attached to apoenzyme = prosthetic groupLoosely bound cofactor = coenzyme

Classification of enzymes

Enzymes can be placed in six classes and are usually named in terms of substrates and reactions catalyzed.

Mechanisms of enzyme activity

Central effect: enzymes speed up the rate at which a reaction proceed to equilibrium by lowering the activation energy

Activation energy required to from the transition state (AB‡)

Lock-and-key model

Some enzymes are rigid and shaped to precisely fit the substrate(s)

Binding to substrate positions it properly for reaction

Referred to as the lock-and-key model

Induced fit model

Some enzymes change shape when they bind their substrate so that the active site surrounds and precisely fits the substrate

This is referred to as the induced fit model

Glucose binding to hexokinase

Describing enzyme activity: Km and Vmax

* Add various concentrations of substrate [S] to a constant amount of enzyme and measure the initial rate V0 (or v) of the reaction.

Question: why the initial rate?

* Repeat this for various substrate concentrations and plot V0 versus [S].

Question: what will the curve look like?

And: Where have we seen this curve before?

Michaelis-Menten kinetics: Km and Vmax

Hyperbolic dependence of V0 on [S]Saturation behavior: why?

Effect of temperature on enzyme activity

Enzymes are most active at optimum temperatures; deviation from the optimum can slow activity and damage the enzyme

Question: Where have we seen this before?

Effect of pH on enzyme activity

Enzymes often have pH optimium.Question: how to explain this?

Active site of serine protease

Change in protonation state of active site residues. Here: Asp and His. pKa values

Enzyme inhibition

Many poisons and antimicrobial agents are enzyme inhibitors

Can be accomplished by competitive or noncompetitive inhibitors

Competitive inhibitors - compete with substrate for the active site

Noncompetitive inhibitors - bind at another location

Usually resemble the substrate but cannot be converted to products

Malonate is competitive inhibitor of succinate dehydrogenase

Competitive inhibitors

Noncompetitive inhibitors

Bind to the enzyme at some location other than the active site

Do not compete with substrate for the active site

Binding alters enzyme shape and slows or inactivates the enzyme

Heavy metals often act as noncompetitive inhibitors (e.g. Mercury)

Metabolic regulation

Important to conserve energy and resources

Cell must be able to respond to changes in the environment

Changes in available nutrients will result in changes in metabolic pathways

Control of enzyme activity

* Allosteric control

* Covalent modification

Allosteric enzymes

Activity of enzymes can be altered by small molecules known as effectors or modulators

Effectors bind reversibly and noncovalently to the regulatory site

Binding alters the conformation of the enzyme

Positive and negative effectors

Example: regulation of aspartate carbamyltransferase

Regulation of aspartate carbamyltransferase is a well studied example of allosteric regulation

CTP inhibits activity and ATP stimulates activity

ACTase regulation

Binding of effectors cause conformational changes that result in more or less active forms of the enzyme

Top view

T stateLess active

R stateMore active

Side view

ACTase regulation

CTP inhibits activity and ATP stimulates activity

Binding of substrate also increases enzyme activity (more than one active site)

Velocity vs. substrate curve is sigmoid

Covalent modification of enzymes

Attachment of group to enzyme can result in stimulation or inhibition of activity

Attachment is covalent and reversible

Example: phosphorylase b from Neurospora crassa

Question: where have we seen this?

Feedback inhibition

Metabolic pathways can contain a pacemaker enzyme (rate-limiting step)

Usually catalyzes the first reaction in the pathway

Activity of the enzyme determines the activity of the entire pathway

Feedback inhibition occurs when the end product interacts with the pacemaker enzyme to inhibit its activity