BELLRINGER #1…Explain the 4 structures of a protein.

Where are proteins made?

Answers to Bellringer… Primary= amino acid structure Secondary = alpha helices and beta sheets;

HYDROGEN BONDING creates these folds and coils

Tertiary = forms 3D structure R groups (side chains) on amino acids bind together Ionic bonds, Van der Waals forces, Disulfide

bridges, Hydrogen bonding Quartnary = 2+ polypeptides bond together

(NOT ALL PROTEINS); different protein DOMAINS are created-each can do a different fxn (ex: hemoglobin protein)

Answers to Bellringer… (Part 2)

Proteins are made on ribosomes FREE RIBOSOMES= make proteins

that are used INSIDE cell ATTACHED RIBOSOMES (to Rough

ER) = make proteins that are shipped out of cell and used elsewhere in organism

BELLRINGER #2… How do you determine the rate

of reaction for this enzyme?

http://www.hippocampus.org/Biology;jsessionid=0F877174B8F739BC8C8FE629659CA510

How does HEAT affect an enzyme?

How does pH affect an enzyme?

http://www.phschool.com/science/biology_place/labbench/lab2/ph.html

Chapter 8: Part 1ENERGY

An Introduction to MetabolismAP BiologyMs. Gaynor

Metabolism An organism’s metabolism transforms

matter and energy follows the laws of thermodynamics

MetabolismSum of ALL of an organism’s

chemical reactions

Metabolic Pathways

A metabolic pathway has many stepsbegin w/ a specific molecule and

end with a producteach pathway catalyzed by

many different enzymes

Enzyme 1 Enzyme 2 Enzyme 3

A B C D

Reaction 1 Reaction 2 Reaction 3

Startingmolecule

Product

Metabolic Pathways and Enzyme Inhibition

Competitive inhibitors mimic the substrate and

compete for the active site.Non-competitive inhibitors

bind to enzyme away from active site cause a change in the active site

Regulation of Enzyme Activity

A cell’s metabolic pathways must be tightly regulatedRegulating enzymes help CONTROL

metabolism

Allosteric Regulationwhen a protein’s function at one

site is affected by binding of a regulatory molecule at another site

http://bcs.whfreeman.com/thelifewire/content/chp06/0602002.html

Allosteric Regulation & Enzymes

Regulatory molecules bind to enzyme’s allosteric site changing shape of enzyme.

Allosterically regulated enzymes have a quaternary protein structure

Each subunit of the enzyme has an active site and an allosteric site.

Allosteric activators stabilizes active site

Allosteric inhibitors deactivates active site.

Negative Feedback inhibition

Active siteavailable

Isoleucineused up by

cell

Feedbackinhibition

Isoleucine binds to allosteric

site

Active site of enzyme 1 no longer binds

threonine;pathway is switched off

Initial substrate(threonine)

Threoninein active site

Enzyme 1(threonine)

Intermediate A

Intermediate B

Intermediate C

Intermediate D

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

End product(isoleucine)

The end product of a metabolic pathway shuts down the pathway

2 Types Metabolic Pathways

Catabolic pathways Break down complex molecules into

simpler compounds Release energy

Ex: Cellular Respiration Anabolic pathways (“add”)

Build complicated molecules from simpler ones

Sometimes called “biosynthetic pathways”

Consume energyEx: Building protein from amino acids

Forms of Energy

Energythe capacity to cause changeExists in various forms

thermal (heat)Chemical (potential)kinetic

2 Main Types of Energy

Kinetic energythe energy of movementType of energy that can do work

Potential energyenergy of position (stored energy)Ex: chemical energy energy stored in

a [ ] gradient, membrane potential *Energy can be converted from one form to

another

The Laws of Energy Transformation

Thermodynamics study of energy transformations (changes)

Closed vs. open systems Closed isolated from surroundings Open (i.e-organisms) energy can be

transferred from organism to surroundings

Absorb energy (light or chemical from organic molecules) release heat and metabolic waste products (CO2)

2 laws of thermodynamics

The 1st Law of Thermodynamics

According to the 1st law of thermodynamicsEnergy cannot be created or destroyed

ONLY transferred and transformed

Also known as the principle of energy conservation

An example of energy conversion

Figure 8.3 

First law of thermodynamics: Energy can be transferred or transformed but NeitherNeither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b).

ChemicalenergyEating

food food has stored

potential energy!

The 2nd Law of Thermodynamics

According to the 2nd law of thermodynamics With every energy transfer,

entropy is increasedEntropy = disorder (or

randomness) Some energy becomes unusable

released as heat

An example of 2nd Law of Thermodynamics

Second law of thermodynamics: Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, disorder is added to the cheetah’s surroundings in the form of heat and the small molecules that are WASTE of metabolism.

Heatco2

H2O+

DECOMPOSITION also increases enthropy

How is this connected to the 10% rule?

No chemical rxn is 100% efficient b/c not all energy is

converted into work

2nd Law of ThermodynamicsTOTAL ENERGY =

usable energy + unusable energyPotential/Kinetic+ Heat

Entropy = increase in disorderThe unusable energy

Enthalpy = increase in orderThe usable energyWhen energy is converted from one form to

another, some is becomes unusable!

Unusable energy usually equal

THERMAL energy (heat)

Free-Energy known as “G”Free-Energy known as “G”A living system’s free energy

Usable energy that can do work Known as Gibb’s Free Energy

Needed to maintain healthy cell growth, division, etc.

The change in free energy, ∆G during a biological processIs related directly to the

enthalpy change (∆H) and the change in entropy

∆H= total energy (usable + unusable energy)

∆S = change in entropyT = absolute temp (K)

∆G = ∆H – T∆S

Cellular Respiration

& Metabolism

INPUT OF ENERGY

(ATP)…MORE ORDER!

WASTE AND HEAT

OUTPUT… MORE

DISORDER!!!

COMPACT/ STORED

ENERGY = ORDERED

INCREASE INENTHALPY

INCREASE INENTROPY

USED ENERGY = LESS ORDERED

Why is ∆G helpful? It tells us if a chemical rxn will

occur spontaneously without input of energyNegative ∆G occurs

spontaneously (loses free energy)

+ or zero ∆G rxn never spontaneous

Free Energy and Metabolism

• 2 types of Reactions in Metabolism

1.Exergonic (Exothermic)

2.Endergonic (Endothermic)

Exergonic and Endergonic Reactions in Metabolism

An exergonic reaction (- ∆G )Proceeds with a net release of

free energy and IS spontaneous

Reactants

ProductsEnergy

Progress of the reaction

Amount ofenergyreleased (∆G <0)

Fre

e e

ner

gy

(a) Exergonic reaction: energy released

Endergonic reactions (+ ∆G )absorbs free energy from its surroundings and is NOT

spontaneousStores free energy in molecules

Figure 8.6

Energy

Products

Amount ofenergyreleased (∆G>0)Reactants

Progress of the reaction

Fre

e e

ner

gy

(b) Endergonic reaction: energy required

Madnitude of GRepresents amt of energy

needed to drive rxn

Real Life Examples… Exergonic (Exothermic)

Cellular Respiration Energy (ATP) is released when

glucose is broken down Endergonic (Endothermic)

Photosynthesis Energy (ATP) is NEEDED

(consumed) to put together glucose from CO2, H20 and sunlight

http://flightline.highline.edu/jbetzzall/BI100/animations/energy_changes.html

Coupled Reactions

http://www.hippocampus.org/AP%20Biology%20IIWatch Central Catabolic Pathways (Metabolism)

A cell does three main kinds of workMechanical = ex: movementTransport = ex: active cell

membrane transportChemical = ex: the pushing of

endergonic rxn’s

ATP powers cellular work by coupling exergonic rxns to

endergonic rxns

The Structure and Hydrolysis of ATP

ATP (adenosine triphosphate) Is the cell’s energy shuttle (molecule) Provides energy for cellular functions It is renewable RNA nucleotide

O O O O CH2

H

OH OH

H

N

H H

O

NC

HC

N CC

N

NH2Adenine

Ribose3 Phosphate groups

O

O O

O

O

O

-- - -

CH

Energy is released from ATP When the terminal phosphate bond is broken Exergonic rxn (G= -7.3 kcal/mol) PO4

-3 create instability

P

Adenosine triphosphate (ATP)

H2O

+ Free Energy given off

Inorganic phosphate + Adenosine diphosphate (ADP)

PP

P PP i

Sometimes referred to as “high energy”

phosphate bonds

ATP an “energy currency”

Example of Energy Coupling

ATP hydrolysis (splitting of ATP) Can be coupled to other reactions

Endergonic reaction: ∆G is positive, reaction is not spontaneous

∆G = +3.4 kcal/molGlu Glu

∆G = + 7.3 kcal/molATP H2O+

+ NH3

ADP +

NH2

Glutamicacid

Ammonia Glutamine

Exergonic reaction: ∆ G is negative, reaction is spontaneous

P

Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous ∆G = –3.9 kcal/mol

How ATP Performs Work ATP drives endergonic reactions

By phosphorylation, which is transferring a phosphate (PO4

3-) to other molecules (reactant becomes “phosphorylated”)More reactive (less stable) with PO4

3- on it acts as an intermediate in many rxns