Enzymes and Energy

Thermodynamics and Biology

Metabolism: The totality of an organism’s chemical processes; managing the material and energy resources of the cell

Catabolic pathways: degradative process such as cellular respiration; releases energy

Anabolic pathways: building process such as protein synthesis; photosynthesis; consumes energy

Energy and Enzymes

Almost all energy for life is derived from the sun.

Life requires energy.Life requires energy

The sun is the ultimate source of all energyEnergy ~ Capacity to do work Kinetic energy~ energy of motion; Potential energy~ stored energyChemical energy~ potential energy

stored within the bonds of a molecule

Thermodynamics~ study of energy flow through living and non-living systems i.e. energy transformations

System ~ a process under study in relations to the rest of the universe

Closed System~ a system isolated from its environment

Open System ~ a system that has relationship with its environment

Energy can neither be created, nor destroyed, but can be transformed from one form to another

First Law of thermodynamics

Free Energy: portion of system’s energy that can perform work e.g. building the molecules in a cell

Total Energy = Free Energy + Lost Energy Free Energy < Total Energy

Free energy

Exergonic reaction: net release of free energy to surroundings

Endergonic reaction: absorbs free energy from surroundings

Second Laws of Thermodynamics

Energy cannot be transformed from one form to another without a loss of useful energy

i.e. every energy transformations increases the entropy (disorder, randomness) of the universe

A measure of the tendency of a system to become organized is called entropy.

The Direction of Spontaneous Reactions (and what it takes to go the other way)

Activation energy ~ the initial input of energy to start a chemical reaction

Energy and Chemical Reactions

Activation Energy

Classification of chemical reaction based on whether it releases or uses energy

Exothermic Reaction ~Is accompanied by release of energy

Reactants Products + Energy 10 energy = 8 energy + 2 energy

Reactants

Products

-DH

Ene

rgy

Energy of reactants

Energy of products

Reaction Progress

C6H12O6 +6O2→6CO2 + 6H2O + Energy (Useful and waste)

An example of exothermic reaction is cellular respiration

Endothermic Reaction~ involves an input of energy

Energy + Reactants Products

+DH Endothermic

Reaction progress

Ene

rgy

Reactants

ProductsActivation Energy

6CO2 + 6H2O + Sun Energy → C6H12O6 + 6O2

An example of endothermic reaction is photosynthesis

Enzymes as Catalysts

Enzymes ~Catalysts for biological reactions Increase the rate of reactions without being

consumed or permanently altered in the process

They are mostly proteins and certain class of RNA (ribozymes)

Increase the rate of chemical reaction by lowering the activation energy

2.2

Enzymes Lower a Reaction’s Activation Energy

Effect of Catalyst on Reaction Rate

reactants

products

Ene

rgy

activation energy for catalyzed reaction

Reaction Progress

No catalyst

Catalyst lowers the activation energy for the reaction.

Name of Enzymes

Ends in –ase Identifies a reacting substance

sucrase- reacts with sucrose

lipase reacts with lipid Describes functions of enzyme

oxidase -catalyzes oxidation

hydrolase - catalyzes hydrolysis

Classification of Enzymes

Class Reactions catalyzed Oxidoreducatase oxidation-reduction Transferases transfers group of atoms Hydrolases hydrolysis Lyases add/remove atoms to

form a double bonds Isomerases rearrange atoms Ligases combine molecules

using ATP

Table 2.2

Mode of Action of Enzymes

Substrate: enzyme reactant An enzyme binds a substrate in a region

called the active site Active site is a hollow depression (pocket or

groove on enzyme)

Two main Models Induced fit Model

Lock and Key Model

Induced Fit Model

Enzymes structure flexible, not rigid Enzyme and active site adjust shape to bind

substrate Increase range of substrate specificity Shape change also improve catalysis during

reaction

See Figure 2.5 and 2.6 on page 43 of your textbook

Lock and Key Model

• An enzyme binds a substrate in the active site

• Only certain substances can fit the active site

• Amino acid R-groups in the active site help substrate bind

• Enzyme-substrate complex forms

• Substrate reacts to form product

• Product is released

• The enzyme is available to repeat the cycle

Enzymes speed biochemical reactions

Figure 4-8: Two models of enzyme binding sites

The active site of an enzyme is where substrate is bound.

Many Enzymes Work by Altering

the Shape of Their Substrates

Enzyme Activity-Temperature

Low activity at low temp Rate increases with temp Activity lost with

denaturation at extreme temperatures

Enzyme Activity- pH

Maximum activity at optimum pH R group of amino acid have proper charge to interact

with the substrate Tertiary structure of enzyme is correct Narrow range of activity Most lose activity in low or high pH

Enzyme Activity- Concentration of Substrate

Increasing substrate concentration increases the rate of reaction (enzyme concentration is constant)

Max activity reached when all of enzyme combines with substrate

Enzyme Inhibitors

Irreversible (covalent); reversible (weak bonds)

Competitive: competes for active site (reversible); mimics the substrate

Noncompetitive: bind to another part of enzyme (allosteric site) altering its conformation (shape); poisons, antibiotics

Enzyme Inhibitors and Allosteric Regulation

A competitive inhibitors• Has a structure similar to substrate• Occupies the active site• Competes with substrate for active site• Has effects reversed by increasing substrate

concentration

A Noncompetitive Inhibitor Does not have a structure like substrate Binds to the enzyme but not active site Change the shape of enzyme and active site Substrate cannot fit altered active site No reaction occurs Effect is not reversed by adding substrate

Feedback inhibition

Control of Metabolic Pathways

ATP and Coupled Reactions

Adenosine Triphoshate (ATP) is the energy currency of the cell

Cellular respiration converts energy stored in the chemical bonds of food substances into chemical energy stored in ATP

ATP is made up of Adenine (nitrogenous base), a ribose sugar (Carbohydrate) and 3 phosphates groups

Ribose sugar+ Adenine → Adenosine

Adenosine + PO4 → Adennosine Monophosphate (AMP)

AMP is a component of electron carrier and coenzyme NAD+

Adenosine +2 PO4 → Adenosine Diphosphate (ADP)

Energy Coupling & ATP

Energy coupling: use of exothermic reaction to drive an endothermic reaction

Adenosine triphosphate ATP tail: high negative charge ATP hydrolysis: release of free E Phosphorylation (phosphorylated

intermediate)~ enzymes

ATP - Life’s Energy Currency

Energy is released when ATP is hydrolyzed (broken down) to ADP.

ATP is restored from ADP and an input of energy.

ATP’s energy is used to drive endergonic (energy-requiring) reactions.

ATP

Chemical work-ATP supplies the energy needed to the macromolecules that comprise the cell

Mechanical work- ATP supplies the energy needed to permit muscles to contract, cilia and flagella to beat

Transport work- ATP supplies the energy the cells need to pump substances e.g. active transport

Enzymes

Catalytic proteins: change the rate of reactions w/o being consumed

Free E of activation (activation E): the E required to break bonds

Substrate: enzyme reactant Active site: pocket or groove on

enzyme that binds to substrate Induced fit model