Biology Chapter 6

First law of thermodynamics (principle of conservation of energy)

Energy can be transferred or transformed, but not created or destroyed

Second Law of thermodynamics

Every energy transfer or transformation increases entropy (disorder) of the universe

How do the laws of thermodynamics relate to biological processes? (1st law)

Light energy → Chemical energy in organic molecules.

Metabolism

• Defined by the totality of an organism’s chemical reactions.

• Is an emergent property that arises from orderly interactions between molecules.

Metabolic Pathway

• Begins with a specific molecule and ends with a product

• each step is catalyzed by a specific enzyme.

Catabolic pathways

• Releases energy by breaking down complex molecules into simpler compounds

• Energy is then available to do cellular work

• EX: Cellular respiration, where glucose and other organic fuels are broken down into carbon dioxide and water.

Anabolic pathways

• Also called biosynthetic pathways

• Consume energy to build complex molecules from simpler ones.

• Example: proteins are synthesized from simpler molecules called amino acids.

Bioenergetics

The study of how energy flows through living organisms.

Energy

Capacity to cause change

Work

The movement of matter against opposing forces, such as gravity and friction.

Kinetic energy

Energy associated with motion

Thermal energy

Kinetic energy associated with random movement of atoms or molecules

Heat

Thermal energy in transfer from one object to another

Potential energy

Energy that matter possesses because of its location or structure

Chemical energy

potential energy available for release in a chemical reaction.

Potential vs KE

Catabolic reactions and biological systems

• The catabolic reaction of food molecules with oxygen provides chemical energy to power life processes in biological systems

• This transformation can be compared to that observed when hydrocarbons in gasoline react with oxygen in the engine of a car to power the pistons

Thermodynamics

Study of energy transformations

Entropy

Measure of molecular disorder, or randomness

The more randomly arranged a collection of matter is, the greater its entropy

Energy transfers does what to entropy?

increases entropy because some energy is always lost ot the surroundings as heat.

Heat does what to the surroundings?

Heat increases the disorder of the surroundings

Spontaneous processes

• Occurs without energy input; it can happen quickly or slowly

• For a process to occur spontaneously, it must increase the entropy of the universe

Nonspontaneous processes does what to entropy

Leads to a decrease in entropy; energy must be supplied

Evolution and organisms and thermodynamics

• The evolution of complex organisms does not violate the second law of thermodynamics

• Entropy (disorder) may decrease in a system, but the total entropy of the universe increases

• Organisms are islands of low entropy in an increasingly random universe

Free energy

Portion of a system’s energy that can do work when temperature and pressure are uniform throughout, as in a living cell.

Change in free energy

• ΔG = G _{final state} — G _{initial state}

• Spontaneous reactions can be harnessed to perform cellular work

ΔG → when does it show reaction is spontaneous

Only reactions with a negative ΔG are spontaneous

What can spontaneous reactions be used for

Spontaneous reactions can be harnessed to perform cellular work

What does free energy measure?

Free energy is a measure of a system’s instability, its tendency to change to a more stable state

Spontaneous change → what effect on stability?

During a spontaneous change, free energy decreases and the stability of a system increases

High G and low G systems -→ what tends to happen?

Unstable systems (higher G) tend to change such that they become more stable (lower G)

When is a process spontaneous and can perform work?

A process is spontaneous and can perform work only when it is moving toward equilibrium

Exergonic reaction

An exergonic reaction proceeds with a net release of free energy and is spontaneous; ΔG is negative.

Ex: Overall reaction for cellular respiration:

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O; ΔG = —686 kcal/mol

What does the magnitude of ΔG represent?

The maximum amount of work the reaction can perform.

Free energy changes (G) in exergonic and endergonic reactions

Endergonic reaction

Absorbs free energy from its surroundings and is nonspontaneous; ΔG is positive

• The magnitude of ΔG is the quantity of energy required to drive the reaction

EX: Photosynthesis, the reverse process of cellular respiration, is an example of an endergonic reaction → Energy is consumed to convert carbon dioxide and water to glucose and oxygen

Are cells in equilibrium?

Cells are not in equilibrium; Cells are open systems experiencing a constant flow of materials in and out.

What about metabolism is one of the defining features of life?

The fact that metabolism as a whole is never at equilibrium is one of the defining features of life.

Equilibrium and metabolism

• A catabolic pathway in a cell releases free energy in a series of reactions.

• Each reaction's product becomes the next reaction's reactant, preventing the system from reaching equilibrium.

ATP

• Adenosine triphosphate is composed of a ribose (a sugar) adenine (a nitrogenous base) and a chain of three phosphate groups

• ATP also used to make RNA

ATP and hydrolysis

• Bonds between phosphate groups in ATP can be broken by hydrolysis, the addition of a water molecule

• ATP hydrolysis releases energy and produces ADP (adenosine diphosphate) and inorganic phosphate

• Energy released comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves.

Why does ATP hydrolysis release a lot of energy?

•A T P hydrolysis releases a lot of energy due to the repulsive force of the three negatively charged phosphate groups

•The triphosphate tail of A T P is the chemical equivalent of a compressed spring

How is the chemical work in a cell powered?

• The chemical work in a cell is powered by A T P hydrolysis

• The energy released by the exergonic reaction of A T P hydrolysis is used to power endergonic reactions

Phosphorylated Intermediate

•A T P hydrolysis is coupled to endergonic reactions by phosphorylation, the transfer of a phosphate group from A T P to another molecule, such as a reactant

•The recipient molecule, now called a phosphorylated intermediate, is more reactive than the original unphosphorylated molecule

Overall, the coupled reactions are exergonic

ATP and proteins

• Transport and mechanical work in the cell are also powered by A T P hydrolysis

• ATP hydrolysis leads to a change in a protein’s shape and often its ability to bind to other molecules

• This can occur via a phosphorylated intermediate or noncovalent bonding between A T P and a protein

Regeneration of ATP

• Body needs a HUGE amount of ATP that cells can’t keep on producing, therefore ATP gets regenerated

• ATP is a renewable resource that is regenerated by addition of a phosphate group to ADP

• The A T P cycle functions as a revolving door through which energy passes during its transfer from catabolic to anabolic pathways

Enzyme

• An enzyme is a macromolecule that acts as a catalyst; most enzymes are proteins

  • For example, the enzyme sucrase catalyzes the hydrolysis of sucrose

Catalyst

A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction

Activation Energy

• (E_A ) The energy required to start a reaction by contorting reactant molecules so the bonds can break

• Activation energy is often supplied by heat that reactant molecules absorb from the surroundings

Activation energy - processes

• When reactant molecules have absorbed enough energy to break chemical bonds, they are in an unstable condition called the transition state

• After the bonds are broken, new, more stable bonds form and energy is released

• The activation energy provides a barrier that determines the rate of reactions

Energy profile of an exergonic reaction

Products - reactants = ΔG < 0

How Enzymes catalyze reactions

• Enzymes catalyze reactions by lowering the E_A barrier

• This enables reactant molecules to reach the transition state at moderate temperatures

• Enzymes do not affect the change in free energy ΔG for a reaction; they only speed up reactions that would eventually occur without them.

Substrate

The substrate is the reactant molecule on which an enzyme acts

Enzyme-substrate complex

The enzyme binds to its substrate, forming an enzyme-substrate complex

Enzyme suffix

• The enzyme binds to its substrate, forming an enzyme-substrate complex

• Most enzyme names end in -ase

  • For example, the enzyme sucrase catalyzes the hydrolysis of sucroe

Active site

The region on the enzyme to which the substrate binds

Induced fit

• Enzymes change shape due to chemical interactions with the substrate

• This induced fit of the enzyme to the substrate brings chemical groups of the active site together

Active site and substrates

• Substrates are held to an enzyme’s active site by weak interactions, such as hydrogen bonds and ionic bonds

• •The active site lowers the activation energy (E_A) and convert substrate to products

• After releasing the products, the active site is available to bind with more substrate molecules.

Four fundamental contributions by the active site

• Orienting substrates correctly

• Straining substrate bonds

• Providing a favorable microenvironment

• Covalently bonding to the substrate

How to speed up enzyme catalysis

• The rate of enzyme catalysis can usually be sped up by increasing the substrate concentration

• When all enzyme molecules in a solution are bonded with substrate, the enzyme is saturated

• At enzyme saturation, reaction speed can only be increased by adding more enzyme

Two things an enzyme’s activity can be affected by

• General environmental factors, such as temperature and p H

• Chemicals that specifically influence the enzyme

Enzymes and temperatures

• Each enzyme has an optimal temperature and p H at which its reaction rate is the greatest

• The reaction rate increases with increasing temperature until the optimal temperature is reached

• Beyond the optimal temperature, the reaction rate drops and the enzyme will eventually begin to denature

Optimal temperature depends on

•The optimal temperature of an enzyme is dependent on the environment in which it typically functions

–For example, the optimal temperature for human enzymes is typically 37 degrees C, whereas the optimal temperature for thermophilic bacteria is 75 degrees C.

Optimal pH of an enzyme is dependent on?

• The optimal temperature of an enzyme is dependent on the environment in which it typically functions

  • For example, the optimal temperature for human

Cofactors

• Cofactors are nonprotein molecules that help carry out processes that are difficult for amino acids

Coenzyme

• Cofactors may be inorganic (such as a metal in ionic form) or organic

• An organic cofactor is called a coenzyme

• Most vitamins act as coenzymes or as the raw materials from which coenzymes are made

Competitive inhibitors

Bind to the active site of an enzyme and prevent the substrate from binding

Noncompetitive inhibitors

Bind to an alternate site on the enzyme, causing the active site to change shape and become less effective

Different types on enzyme inhibitors

• Reversible enzyme inhibitors bind to enzymes by weak interactions; irreversible inhibitors form covalent bonds

• Toxins and poisons are often irreversible enzyme inhibitors

• Many antibiotics function as enzyme inhibitors in bacteria

— For example, penicillin blocks the active site of an enzyme many bacteria use to make cell walls