Catalyst (10/31)

You are eating pumpkin bread with cream cheese frosting and sipping on some cider….mmmmm! Look at the ingredients below and write the name of at least 3 macromolecules and their monomers that you’re eating.

--sugar (in the cider, bread and frost…SUGAR!)--butter --reduced fat cream cheese (cholesterol, milk fat, protein)--whole wheat flour--pumpkin (protein)--smart balance vegetable oil--baking soda OR sodium bicarbonate NaHCO3 (this isn’t a

macromolecule but something else we learned about)

BONUS: what reaction will your body use to break the macromolecules down?

ENERGY & METABOLISM

AP Biology-Chapter 8

I. Biological Work Requires Energy

A. All life depends on a continuous input of energy

1. Metabolism: the totality of an organism’s chemical processes.

a) Concerned with managing the material and energy resources of the cell.

B. Energy: the capacity to do work (cause change)

I. Biological Work Requires Energy

A. Organisms carry out conversions between potential energy and kinetic energy

1. Kinetic Energy: energy of motiona) Moving objects perform work by

causing other matter to move2. Potential Energy: stored energy

a) Objects that are not actively moving but have the capacity to do so.

I. Biological Work Requires Energy

Examples:A. Boulder perched on a hilltop=POTENTIA

L

I. Biological Work Requires Energy

Examples:A. Child at the top of a slide= POTENTIA

L

I. Biological Work Requires Energy

Examples:A. Child sliding down the slide=KINETI

C

I. Biological Work Requires Energy

Examples:A. Stretched rubber band=POTENTIA

L

I. Biological Work Requires Energy

Examples:A. Waterfall=BOTH!

I. Biological Work Requires Energy

4. Energy can take many formsa) Mechanicalb) Heatc) Soundd) Electric currente) Lightf) Radioactive radiation

I. Biological Work Requires Energy

5. Energy is measured as heat (all other forms of energy can be converted to heat)

a) Kilocalorie (Kcal): unit of heat used in biology

i. 1 kcal=1000 cal

II. Two laws of thermodynamics govern energy transformations

A. First Law of Thermodynamics: law of conservation of energy

1. The total energy of a closed system remains constant

a) Closed system does not exchange energy with its surroundings

2. Organisms are open systemsa) Open systems exchange matter and

energy with their surroundings.b) Explains why organisms must

continually capture energy from surroundings.

Energy is neither created or destroyed….it can only

be transferred and transformed!! (write this

in the margin!)

II. Two laws of thermodynamics govern energy transformations

3. Organisms can only convert energy to other forms

4. Examples:a) Plants: take in light energy and release

heat and oxygenb) Animals: take in organic molecules and

release heat, carbon dioxide and metabolic waste

II. Two laws of thermodynamics govern energy transformations

B. Second Law of Thermodynamics: energy cannot be changed from one form to another w/o the loss of usable energy

1. Law states that disorder (entropy) in the universe is continuously increasing.

2. Explains why no process requiring energy is ever 100% efficient.

a) In every energy transaction, some energy is dissipated as heat, which contributes to entropy

i. Heat is the most random form of energy or lowest grade.

II. Two laws of thermodynamics govern energy transformations

II. Two laws of thermodynamics govern energy transformations

C. How can we reconcile the second law of thermodynamics—the unstoppable increase in the entropy of the universe—with the orderliness of life, which is one of biology’s themes?

1. Organisms are open systems (another theme)a) Organisms exchange energy and materials

with surroundingsb) Cells create ordered structures from less

organized starting materialc) Does not violate the second law—the

entropy of a particular system, such as an organism, may actually decrease, so long as the total entropy of the universe increases

Organisms are islands of low entropy in a random universeorder entropy stability

III. Metabolic reactions involve energy transformations

A. Metabolism is the sum of all chemical activities that take place in an organism

B. Two main pathways of metabolism1. Anabolism: the various pathways in which

complex molecules are synthesized from simple substances (BUILD) monomerspolymersExample:

2. Catabolism: the pathways in which larger molecules are broken into smaller ones. Example:

Dehydration, photosynthesis

Digestion, hydrolysis, cellular respiration

(put in margin)--Cannibals eat things and break them

into smaller pieces

IV. Organisms live at the expense of free energy

A. Spontaneous Processes: a change that can occur without outside help

1. Can be harnessed to perform worka) Example: downhill flow of water can be used to turn

a turbine in a power plant2. When a spontaneous process occurs in a

system, the stability of that system increasesa) Unstable systems tend to change to more stable

forms.i. Examples:• A body of elevated water is less stable than

that same water at sea level• A system of charged particles are less stable

when they are apart than when they are together

(put in margin)—no energy input needed

Spontaneous stabilityentropyfree

energy

III. Organisms live at the expense of free energy

3. A process can only occur spontaneously if it increases the entropy (disorder) of the universe

a) This principle is good in theory but can not readily be applied to a biological system, because we must measure changes in the surroundings.

b) Free energy: a measurement that is based on the system alone and gives a standard for predicting stability (or spontaneity)

Equilibrium=max stability

III. Organisms live at the expense of free energy

B. Free Energy: A criterion for spontaneous change

1. Free energy: is the portion of a system’s energy that can perform work when temperature is uniform throughout the system

a) G=system’s free energyb) H=system’s total energyc) S=system’s entropyd) T=absolute temperature (in Kelvin units)

2. Free energy, G, can be thought of as a measure of a system’s instability—tendency to change to a more stable state.

a) G is the change in free energy as a system goes from a starting state to a different state.

G=H-TS

ΔG=Gfinal state-Gstarting state

more free energy stable capacity to do work

SPONTANEOUS CHANGE

free energy stable capacity to do work

III. Organisms live at the expense of free energy

3. For a process to occur spontaneously a system must either

a) Give up energy (decrease in H)b) Give up order (a decrease in S)c) Or both

4. Chemical reactions involve changes in free energy

a) Exergonic rxn (reaction) ΔG is negative Occurs spontaneously Free energy decrease

b) Endergonic reaction ΔG is positive Energy must be supplied Free energy increases

ΔG=ΔH-TΔSClosed system evens out, open system has a

negative ΔG b/c energy is harnessed.

III. Organisms live at the expense of free energy

5. Coupling reactionsa) Coupling occurs when the energy released by an

exergonic reaction is used to drive an endergonic reactionexample: ATP proteinamino acids

Breakdown of ATP is exergonic Muscle contraction is endergonic

Muscle contraction is coupled to ATP breakdown and the overall process is exergonic and now muscle contraction can occur.

IV. ATP is the energy currency of the cell

A. ATP=energy currency of the cell1. Nitrogen containing base (adenine)2. Ribose (a pentose)3. 3 phosphate groups (PO4) in a series

Release energy

Catalyst (11/2)

The breakdown of ATP ADP + Pi is1. ANABOLISM or CATABOLISM?2. ENDERGONIC or EXERGONIC?

IV. ATP is the energy currency of the cell

A. ATP donates energy through the transfer of a phosphate group

1. The bonds linking the three phosphate groups may be broken by hydrolysis

a) Rxn has a large –ΔG (-7.6kcal/mole)b) ATP is hydrolyzed to form ADP +Pic) Rxn may be coupled with endergonic rxnsd) It is the last P group that is removes from ATP

• ATP live charges repelling each other (O-)• Slightly negative charges on double bonded O repel each

other• So breaking of bond is easier due to instability• Break the bond, release energy• Only a little energy is released so it is the aggregate (many

ATP’s broken) that gets things done• The ease of getting energy out of ATP is built into the

structure.

Inorganic phosphate

IV. ATP is the energy currency of the cell

2. Cell maintains a high ratio of ATP to ADP (10:1).

a) ATP cannot be stockpiledb) Resting human uses 100 lbs of ATP per dayc) Approximately 10 million molecules of ATP are made

and recycled per second per cell.3. Catabolic pathways (exergonic) provide the

energy for the endergonic process of making ATP

a) Cellular respiration (regenerates the bulk of the ATP)

b) Photosynthesis

Catalyst (11/7)

What is one thing you did to sculpt your brain to prepare for the midterm?

What is one thing you would have done better this past quarter? How can you be superior to your former self this upcoming quarter?

COUPLED RXNS AND ATP

AP Biology-Chapter 8

I. Coupled Reactions

A. ATP powers cellular work by coupling exergonic rxns to endergonic rxns.

1. Cellular work:a) Mechanical Work:

• Beating of cillia• Contraction of muscle cells• Chromosome movement

Coupling= energy (E) from exergonic rxns to push endergonic rxns

I. Coupled Reactions

b) Transport Work:• Transport of materials across plasma

membranesEx. Sodium potassium pump

I. Coupled Reactions

b) Chemical Work: • “pushing” of nonspontaneous

endergonic reactionsEx. Synthesis of polymers from monomers

I. Coupled Reactions

B. How ATP performs work1. In a test tube, the hydrolysis of ATP (the release of free

energy), just heats the surrounding water.

2. In a cell:a) Specific enzymes “help” couple the energy of ATP

hydrolysis to endergonic reactions.• Transfer the terminal phosphate group from ATP to

some other molecule• The recipient molecule is said to be phosphorylated.• Phosphorylated intermediate is more reactive (less

stable) than the original molecule.b) Examples: (see back of your sheet)

ATP + H2O ADP + Pi

I. Coupled ReactionsEndergonic Rxn(nonspontaneous)

Enzyme

Inorganic phosphate

Phosphorylated intermediate

Phosphorylation=capture E in bond to Pi

Exergonic Rxn(spontaneous)

ENZYMES

AP Biology-Chapter 8

I. Enzymes are chemical regulators

A. Enzymes are protein catalysts that speed the rate of chemical rxns.

1. Enzymes are not altered permenantly or used up in the reaction

a) May catalyze the same rxn repeatedly, as long as substrate is available.

I. Enzymes are chemical regulators

2. Do not make anything happen that would not happen on its own just speed it up

3. Enzymes are substrate specific4. New research shows that not all organic

catalysts are enzymesa) Certain nucleic acids (e.g. Riboxyme) function

as enzymes.

Lock & key!!

Lock=enzyme

Key=substrate

I. Enzymes are chemical regulators

B. All rxns have a required activation energy1. The energy required to break the existing bonds and

begin the rxnC. Enzymes lower the activation E necessary to

get a rxn going.

I. Enzymes are chemical regulators

D. Steps in the process1. Binding the substrate (the molecule acted on by the

enzyme)2. Catalyst (chem rxn)3. Release of product.

I. Enzymes are chemical regulators

E. STEP 1: Binding of the substrate1. Enzymes have at least one three dimensional area, known as

the active sitea) Active site: is the few amino acid R-groups that are arranged

in a specific way to interact with a bound substrate.b) Active site is always on the surface (looking at three

dimensional structure)• Can be on a smooth surface or in pits and clefts on the glob

I. Enzymes are chemical regulators

2. Induced Fit Model is the current model of how the enzyme substrate complex forms.

a) Binding site has a shape & amino acid R-groups that in some way are rougly complementary to the properties of the substrate.

b) Substrate actually induces a change in shape of the binding site so the substrate gets “grabbed” and is held firmly.

• Analogy: baseball and glove.

Catalyst (11/7)

Explain in 3-5 sentences what an enzyme is and how it works.

I. Enzymes are chemical regulators

F. STEP 2: Catalysis or Catalytic Mechanism1. Hydrophobic enzyme interior

a) Interior of the enzyme is hydrophobic, so H2O is excludedb) Hydrophobic parts of the substrate are more soluble in this

H2O excluded environment2. Conformational strain

a) Bends the substrate out of shape allowing the rxn to occur3. Disturb the electron configuration of the substrate

a) Enzyme might have an oxidized group associated with it that can pull an e- (electron) away from the substrate temporarily (conversely reduced state and donates an e-)

b) R-group may get involved w/the substrate creating a “transition state” that makes the substrate less stable

Redox Rxn:LEO goes GER(Lose Electrons Oxidized, Gain Electrons Reduced)

I. Enzymes are chemical regulators

G. STEP 3: product is released and enzyme can be reused.

I. Enzymes are chemical regulators

H. Most enzyme names end in –ase. Older named enzymes end in –zymeExamples: Sucrase

ATP ase1. Exceptions: pepsin and trypsin

give no clue to their function (digestive enzymes)

I. Enzymes are chemical regulators

I. Enzymes are specific because of the binding at the active site

1. But not all enzymes are specific (e.g. lipases react with variety of fats).

I. Enzymes are chemical regulators

I. Most enzymes require cofactors

1. Some enzymes (e.g. pepsin) consist on of a protein

2. Others have two components—and both must be present for catalytic activity to take place.

a) Protein—the enzymeb) Cofactor—an additional chemical component

I. Enzymes are chemical regulators

a) Cofactor—an additional chemical component• Inorganic cofactors include elements such as Mg,

Ca, Fe, Cu, Zn, Mn (trace elements)• Coenzyme: organic, nonpolypeptide, compound

that binds to the enzyme Most are carrier molecules that transfer e- or part of

a substrate from one molecule to the other

Examples: NADH, NADPH, ATP, Coenzyme A, and FADH2. Most vitamins are or are part of coenzymes.

b) Neither the apoenzyme or the cofactor has catalytic activity.

I. Enzymes are chemical regulators

K. Enzymes are most effective at optimal conditions1. Each enzyme has an optimal temperature

a) Velocity of an enzymatic rxn increases with increasing temperaturei. Substrates collide w/active sites more frequently when the

molecules move more rapidlyb) Rxn in fastest at optimal temperaturec) Optimal temperature allows the greatest number of collisions

without denaturing the enzymesd) Beyond the optimal temperature the speed of the enzymatic rxn

drops sharplye) Thermal agitation disrupts the hydrogen bonds, ionic bonds, and

other weak interactions that stabilize active conformationi. Protein molecule (enzyme) denatures

f) Most human enzymes optimal temperature is around body temperature

I. Enzymes are chemical regulators

2. Each enzyme has an optimal pHa) Optimal pH for most enzymes falls between pH 6-8.

i. Exceptions: pepsin (digestive stomach enzyme) has an optimal pH of 2

b) Suboptimal pH denatures protein enzymesc) Alteration in pH alters charges on the enzymed) Changes in charge affect the ionic bonds that

contribute to tertiary/ quarternary structure.e) Change in the protein’s conformation changes

activity.f) Most enzymes become inactive and usually

irreversibly denatured, when the medium is made very acidic or very basic

I. Enzymes are chemical regulators

3. Salinity can also alter enzyme structure and therefore function

a) Increase in salt concentration increases ion concentration in the medium (increase in the number of charges in the medium)

b) Increase in charges affects the ionic bonds that contribute to tertiary and quartenary structure

I. Enzymes are chemical regulators

4. Enzyme Inhibitors:a) Can be irreversible, but can

be reversible when the inhibitor binds by weak bonds.

b) Competitive Inhibitors: mimic the normal substrate molecule and compete for admission into active site

i. Reduce the productivity of enzymes by blocking the active site

ii. Temporary bindingiii. Reversibleiv. Increase in the amount of

substrate and there are more substrate molecules than inhibitors

I. Enzymes are chemical regulators

c) Noncompetative Inhibitors: impede enzyme action by binding to another site on the enzyme causing the enzyme to change shape, rendering the active site unreceptive to substrate

i. Do not directly compete with the substrate at the active siteii. Reversible when the inhibitor unbinds the enzyme returns

to its active shape.

I. Enzymes are chemical regulators

d) Irreversible Inhibitors: permanently inactivate the enzyme

i. Examples: nerve gases, heavy metalsii. Some drugs are enzyme inhibitors

Examples: sulfa drugs and penicillin which are used to combat bacterial infections

Catalyst (11/10)

Explain in how the three types of inhibition work.

I. Enzymes are chemical regulators

L. Enzymes are organized into teams in metabolic pathways working in sequence

M. The cell regulates enzymatic activity—controls metabolism

1. Cell controls when and where various enzymes are active

a) Pathways are controlled by either switching on or off the genes that encode specific enzymes

b) Regulate the activity of enzymes once they are made

BEFORE THE ENZYME IS MADE

I. Enzymes are chemical regulators

2. Allosteric control: controls enzyme activity by either activating or inhibiting an enzyme

a) Some enzymes have an allosteric site, non catalytic sites to which a substance can bind, changing the enzymes activity

i. Allosteric activator: molecule that can bind to the allosteric site of an enzyme

ii. Example of allosteric control: Allosteric activator binds to allosteric site Enzyme’s shape is chagned Substrate binds with enzyme Rxn takes place

AFTER ENZYME IS MADE

I. Enzymes are chemical regulators

b) Allosteric enzymes are subject to feedback inhibition, in which the formation of an end product inhibits an earlier reaction in the sequence

i. Feedback inhibiton: the switching off of a metabolic pathway by its end product, which acts as an inhibitor of an enxyme within its pathway

I. Enzymes are chemical regulators

I. Enzymes are chemical regulators

b) Feedback inhibition