energy and life 1 st law of thermodynamics: law of conservation of energy. energy cannot be created...
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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