chapter 8: metabolism metabolism metabolism – all of the chemical reactions in an organism - a...

Chapter 8: Metabolism

Metabolism

• Metabolism – all of the chemical reactions in an organism

- A metabolic pathway begins with a specific molecule and ends with a product

- Each step is catalyzed by a specific enzyme

Examples dehydration synthesis (synthesis)

hydrolysis (digestion)

+

H2O

+

H2O

enzyme

enzyme

Enzyme 1 Enzyme 2 Enzyme 3

DCBAReaction 1 Reaction 3Reaction 2

Startingmolecule

Product

• Catabolic pathways release energy by breaking down complex molecules into simpler compounds (ex: digestion)

- Ex: Cellular Respiration

• Anabolic pathways consume energy to build complex molecules from simpler ones

- The synthesis of protein from amino acids is an example of anabolism

Catabolic and Anabolic Pathways

Forms of Energy

• Energy is the capacity to do work

- Kinetic energy is energy associated with motion

- Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules

- Potential energy is energy that matter possesses because of its location or structure

- Chemical energy is potential energy available for release in a chemical reaction

* Energy can be converted from one form into another

Describe the E transformations that occur when you climb to the top of a stairway

Flow of energy through life• Life is built on chemical reactions

– transforming energy from one form to another

organic molecules ATP & organic molecules

organic molecules ATP & organic molecules

sun

solar energy ATP & organic molecules

Energy Transformation

• Thermodynamics is the study of energy transformations– 1st law of thermodynamics = conservation of

energy • Energy of universe is constant, energy CAN be

transferred and transformed, but NOT created/destroyed

– 2nd law of thermodynamics• Every energy transfer or transformation increases the

entropy (disorder or randomness) in universe

(a) First law of thermodynamics (b) Second law of thermodynamics

Chemicalenergy

Heat CO2

H2O

+

Exergonic and Endergonic Reactions in Metabolism

• An exergonic reaction releases free energy • An endergonic reaction absorbs free energy from its

surroundings• Cells manage energy resources and do work by energy coupling• EXERGONIC REACTIONS DRIVE ENDERGONIC REACTIONS

Energy & life• Organisms require energy to live

– where does that energy come from?

• coupling exergonic reactions (releasing energy) with

endergonic reactions (needing energy)

+ + energy

+ energy+

digestion

synthesis

ATP powers cellular work by coupling exergonic reactions to

endergonic reactions• A cell does three main kinds of work:

– Chemical– Transport– Mechanical

• To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one

• Most energy coupling in cells is mediated by ATP

The Structure and Hydrolysis of ATP• ATP (Adenosine tri phosphate) is composed

of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups

Phosphate groups Ribose

Adenine

• The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis (unstable bonds)

3 Things happen: WRITE THIS DOWN

1.A phosphate group is removed

2.ATP becomes ADP

3.Energy is released (exergonic reaction)

Inorganic phosphate

Energy

Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP)

P P

P P P

P ++

H2O

i

How ATP Performs Work

• The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP

• In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

• ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant

• The recipient molecule is now phosphorylated

Fig. 8-11

(b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzed

Membrane protein

Pi

ADP+

P

Solute Solute transported

Pi

Vesicle Cytoskeletal track

Motor protein Protein moved

(a) Transport work: ATP phosphorylates transport proteinsATP

ATP

The Regeneration of ATP

• ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)

• The energy to phosphorylate ADP comes from catabolic reactions in the cell

Fig. 8-12

P iADP +

Energy fromcatabolism (exergonic,energy-releasingprocesses)

Energy for cellularwork (endergonic,energy-consumingprocesses)

ATP + H2O

Enzymes speed up metabolic reactions by lowering energy barriers

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

• An enzyme is a catalytic protein• The reactant that an enzyme acts on is called the enzyme’s

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

substrate complex• The active site is the region on the enzyme where the

substrate binds

The Activation Energy Barrier

• The initial energy needed to start a chemical reaction is called the activation energy (EA)

• Enzymes catalyze reactions by lowering the EA barrier

• Enzymes do not affect the change in free energy (∆G); instead, they speed up reactions that would occur eventually

Activation energy• Breaking down large molecules

requires an initial input of energy– activation energy

– large biomolecules are stable

– must absorb energy to break bonds

energycellulose CO2 + H2O + heat

Progress of the reaction

Products

Reactants

∆G is unaffectedby enzyme

Course ofreactionwithoutenzyme

Fre

e en

erg

y

EA

withoutenzyme EA with

enzymeis lower

Course ofreactionwith enzyme

Properties of enzymes• Reaction specific

– each enzyme works with a specific substrate • chemical fit between active site & substrate

– H bonds & ionic bonds

• Not consumed in reaction– single enzyme molecule can catalyze thousands

or more reactions per second• enzymes unaffected by the reaction

• Affected by cellular conditions– any condition that affects protein structure

• temperature, pH, salinity

Induced fit model• More accurate model of enzyme action

– 3-D structure of enzyme fits substrate– substrate binding cause enzyme to change

shape leading to a tighter fit • “conformational change”• bring chemical groups in position to catalyze

reaction

Substrate Specificity of Enzymes

• Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

Fig. 8-16

Substrate

Active site

Enzyme Enzyme-substratecomplex

(b)(a)

Factors Affecting Enzyme Function

• Enzyme concentration

• Substrate concentration

• Temperature

• pH

• Salinity

• Activators

• Inhibitors

catalase

Cofactors

• Cofactors are nonprotein enzyme helpers

- Cofactors may be inorganic (zinc, iron, copper)

OR…

• An organic cofactor is called a coenzyme

- Coenzymes include vitamins

Enzyme Inhibitors

• Competitive inhibitors bind to the active site of an enzyme, competing with the substrate

• Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

• Examples of inhibitors include toxins, poisons, pesticides, and antibiotics

Competitive Inhibitor • Inhibitor & substrate “compete” for active site

– penicillin blocks enzyme bacteria use to build cell walls

– disulfiram (Antabuse)treats chronic alcoholism

• blocks enzyme that breaks down alcohol

• severe hangover & vomiting5-10 minutes after drinking

Allosteric Regulation of Enzymes

• Allosteric regulation may either inhibit or stimulate an enzyme’s activity

• Allosteric regulation occurs when a regulatory molecule binds to a protein at one site (not active site)– This binding changes shape of enzyme

Non-Competitive Inhibitor • Inhibitor binds to site other than active site

– allosteric inhibitor binds to allosteric site – causes enzyme to change shape

• conformational change• active site is no longer functional binding site

– keeps enzyme inactive

– some anti-cancer drugsinhibit enzymes involved in DNA synthesis

• stop DNA production

• stop division of more cancer cells

– cyanide poisoningirreversible inhibitor of Cytochrome C, an enzyme in cellular respiration

• stops production of ATP

Feedback Inhibition

• In feedback inhibition, the end product of a metabolic pathway shuts down the pathway

• Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed