biological concepts bmz 116 section b

Biological ConceptsBMZ 116 Section B

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Converting the Suns Nuclear Fusion Energy to Human Flesh

You should have read Chapter 8 Introduction to Metabolism Before Coming to Class

•Overview: The Energy of Life

•The living cell

– Is a miniature factory where thousands of reactions occur

– Converts energy in many ways

http://plantsinmotion.bio.indiana.edu/usbg/toc.htm

•Some organisms

•Convert light to energy, as in photosynthesis

http://earthobservatory.nasa.gov/Library/OzoneWeBreathe/Images/flourescence.jpg




• Some organisms

• Convert energy to light, as in bioluminescence

http://www.shoarns.com/Luminous.html



Metabolism = All controlled, enzyme‑mediated chemical reactions by which cells acquire and use energy.

Transcription & Translation Control

An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics

Compartmentalization

Organization of the Chemistry of Life into Metabolic Pathways

• A metabolic pathway has many steps

– That begin with a specific molecule and end with a product

– That are each catalyzed by a specific enzyme

Enzyme 1 Enzyme 2 Enzyme 3

A B C DReaction 1 Reaction 2 Reaction 3

Startingmolecule

Product

• Types of metabolic pathways

• Energy

– Is the capacity to cause change

– Exists in various forms, of which some can perform work• Work = Distance X Force

Metabolism = All controlled, enzyme‑mediated chemical reactions by which cells acquire and use energy.

Kinds of Work

1. Mechanical eg. Controlled Fall down Mad River Mountain

Kinds of Work

2. Transport eg. heart

Kinds of Work

3. Electrochemical eg. Nerves

• Kinetic energy

– Is the energy associated with motion

• Potential energy

– Is stored in the location of matter

– Includes chemical energy stored in molecular structure

Forms of Energy

Climbing up converts kinetic

energy of muscle movement

to potential energy.

Energy can be converted from one form to another

Diving platform over sink hole,

Wakulla Springs FL

Higher up on the platform, a diver

has more potential energy


Diving converts potential

energy to kinetic energy.



In the water, a diver has less potential energy

having transferred kinetic energy to the

water.

Divers chemical potential energy could be transferred if the gators kinetic energy exceeds that of the

diver

The Laws of Energy Transformation

• Thermodynamics

– Is the study of energy transformations

The First Law of Thermodynamics

– Energy can be transferred and transformed

– Energy cannot be created or destroyed

www.flmnh.ufl.edu/cnhc/potm-jul01.html

The chemical (potential)

energy in food will be converted to the kinetic

energy of the alligators movement

http://www.smh.com.au/news/world/battle-of-the-giants-python-bursts-eating-gator/2005/10/06/1128191820927.html

Battle of the giants: python bursts eating gatorOctober 6, 2005 - 10:34AM

Unless you bite off

more than you can digest!

The Second Law of Thermodynamics

– Conversion of energy from one source to another source is never 100% efficient, some energy is always lost as heat

– No process can take place which results in a net decrease in the entropy of the universe

• Entropy = Degree of randomness or disorder in a system

www.saltgrassflats.com/wildlife/alligator.html

The Second Law of Thermodynamics– Spontaneous changes that do not require outside energy increase

the entropy, or disorder, of the universe

Every energy transfer or transformation

increasesthe disorder (entropy) of the universe. For example, disorder is added to the gator’ssurroundings in the form of heat and the small molecules that are the by-products

of metabolism.www.saltgrassflats.com/wildlife/alligator.html

•Living systems are highly ordered

Do living organisms violate the Second Law of Thermodynamics?

Do living organisms violate the Second Law of Thermodynamics?

Sun ‑ Ultraviolet image spanning about a month

Galileo image of Earth & Moon

Plants

Advanced Very High Resolution Radimeter image of Vegetation Index Aug 1987

Dark‑blue & green = Dense Vegetation Pink & dark red = Sparse Vegetation

Plants

Little more than 10% of old growth forest remains in Pacific Northwest Mt Hood National Forest

Dark red = Old Growth; Light Red = Regrowth; Pink= Young seedlings;

Blue = No timber due to logging

4. Chloroplasts (Photosynthesis)

5. Animals/Plants (Cellular Respiration)

Hertzsprung‑Russel Diagram depicting stellar evolution

Even the Sun is subject to the Laws of

Thermodynamics

Projected Life History of our Sun

Link to Discussion on Red Giants Link to Discussion on Stellar Evolution

All terrestrial life will be extinct 500 million years from now

• Which of the following represents the ∆G of the reaction? – a

– b

– c

– d

– e

Which of the following represents the ∆G of the reaction?

20% 20% 20%20%20%

1. a

2. b

3. c

4. d

5. e

• For a process to be spontaneous

• ∆G must be negative

– Either give up enthalpy, ∆H is negative

– Or give up order, ∆S is positve

– Or both

∆G = ∆H – T∆S

T = temperature

The free-energy change of a reaction tells us whether the reaction occurs spontaneously

• The change in free energy, ∆G during a biological process

– Is related directly to the enthalpy change (∆H) and the change in entropy (∆S)

∆G = ∆H – T∆S

The free-energy change of a reaction tells us whether the reaction occurs spontaneously

T = temperature

Free-Energy Change, G

•A living system’s free energy

– Is energy that can do work under cellular conditions

Ergonic = grk “work” En = “in” Ex = “out”

Free Energy, Stability, and Equilibrium

• Organisms live at the expense of free energy

• During a spontaneous change

– Free energy decreases and the stability of a system increases

• At maximum stability

– The system is at equilibrium

Chemical reaction. In a cell, a sugar molecule is broken down into simpler molecules.

.

Diffusion. Molecules in a drop of dye diffuse until they are randomly dispersed.

Gravitational motion. Objectsmove spontaneously from ahigher altitude to a lower one.

• More free energy (higher G)• Less stable• Greater work capacity

• Less free energy (lower G)• More stable• Less work capacity

In a spontaneously change • The free energy of the system decreases (∆G<0) • The system becomes more stable• The released free energy can be harnessed to do work

(a) (b) (c)

Figure 8.5

Free Energy and Metabolism

Endergonic and Exergonic Reactions in Metabolism

Energy

Products

Amount ofenergyreleased (∆G>0)

Reactants

Progress of the reaction

Fre

e e

ne

rgy

(b) Endergonic reaction: energy required Figure 8.6

Reactants

Products

Energy

Progress of the reaction

Amount ofenergyreleased

(∆G <0)

Fre

e e

ne

rgy

(a) Exergonic reaction: energy released

PHOTOSYNTHESIS CELLULAR RESPIRATION

∆G = +686 kcal/mol

Equilibrium and Metabolism

• Reactions in a closed system

– Eventually reach equilibrium

Figure 8.7 A

(a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium.

∆G < 0 ∆G = 0

• Cells in our body

– Experience a constant flow of materials in and out, preventing metabolic pathways from reaching equilibrium

Figure 8.7

(b) An open hydroelectric system. Flowing water keeps driving the generator because intake and outflow of water keep the system from reaching equlibrium.

∆G < 0


• An analogy for cellular respiration

Figure 8.7 (c) A multistep open hydroelectric system. Cellular respiration is analogous to this system: Glucoce is brocken down in a series of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for the next, so no reaction reaches equilibrium.

∆G < 0

∆G < 0

∆G < 0


The Structure and Hydrolysis of ATP

• ATP (adenosine triphosphate)

– Is the cell’s energy shuttle

– Provides energy for cellular functions

• ATP hydrolysis

– 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/molFigure 8.10

How ATP Performs Work

• ATP drives endergonic reactions

– By phosphorylation, transferring a phosphate to other molecules

• The three types of cellular work

– Are powered by the hydrolysis of ATP

(c) Chemical work: ATP phosphorylates key reactants

P

Membraneprotein

Motor protein

P i

Protein moved

(a) Mechanical work: ATP phosphorylates motor proteins

ATP

(b) Transport work: ATP phosphorylates transport proteins

Solute

P P i

transportedSolute

GluGlu

NH3

NH2

P i

P i

+ +

Reactants: Glutamic acid and ammonia

Product (glutamine)made

ADP+

P

Figure 8.11

I. Metabolism = All controlled, enzyme‑mediated chemical reactions by which cells acquire and use energy.


The active siteIs the region on the enzyme where the

substrate binds

Induced fit of a substrateBrings chemical groups of

the active site into positions that enhance their ability to

catalyze the chemical reaction

Active site

Specific orientation Temporary bonds

Changing shape Bond Strains

The activation energy, EAIs the initial amount of energy needed to start a chemical reaction Is often supplied in the form of heat from the surroundings in a system

An enzyme catalyzes reactions By lowering the EA barrier


• A metabolic pathway has many steps

– That begin with a specific molecule and end with a product

– That are each catalyzed by a specific enzyme

Enzyme 1 Enzyme 2 Enzyme 3

A B C DReaction 1 Reaction 2 Reaction 3

Startingmolecule

Product

• The catalytic cycle of an enzyme

Substrates

Products

Enzyme

Enzyme-substratecomplex

1 Substrates enter active site; enzymechanges shape so its active siteembraces the substrates (induced fit).

2 Substrates held inactive site by weakinteractions, such ashydrogen bonds andionic bonds.

3 Active site (and R groups ofits amino acids) can lower EA

and speed up a reaction by• acting as a template for substrate orientation,• stressing the substrates and stabilizing the transition state,• providing a favorable microenvironment,• participating directly in the catalytic reaction.

4 Substrates are Converted intoProducts.

5 Products areReleased.

6 Active siteIs available fortwo new substrateMole.

Figure 8.17


Competetive Inhibition Non-competetive Inhibition

Feed back Inhibition

• Each enzyme

– Has an optimal temperature in which it can function

Figure 8.18

Optimal temperature for enzyme of thermophilic

Rat

e o

f re

actio

n

0 20 40 80 100Temperature (Cº)

(a) Optimal temperature for two enzymes

Optimal temperature fortypical human enzyme

(heat-tolerant) bacteria

Effects of Local Conditions on Enzyme Activity

– Has an optimal pH in which it can function

Figure 8.18

Rat

e o

f re

actio

n

(b) Optimal pH for two enzymes

Optimal pH for pepsin (stomach enzyme) Optimal pH

for trypsin(intestinalenzyme)

10 2 3 4 5 6 7 8 9

Effects of Local Conditions on Enzyme Activity

Cofactors

• Cofactors

– Are nonprotein enzyme helpers

• Coenzymes

– Are organic cofactors

Allosteric Regulation of Enzymes

• Allosteric regulation

– Is the term used to describe any case in which a protein’s function at one site is affected by binding of a regulatory molecule at another site

Allosteric Activation and Inhibition

• Many enzymes are allosterically regulated

– They change shape when regulatory molecules bind to specific sites, affecting function

Stabilized inactiveform

Allosteric activaterstabilizes active fromAllosteric enyzme

with four subunitsActive site

(one of four)

Regulatorysite (oneof four)

Active formActivator

Stabilized active form

Allosteric activaterstabilizes active form

InhibitorInactive formNon-functionalactivesite

(a) Allosteric activators and inhibitors. In the cell, activators and inhibitors dissociate when at low concentrations. The enzyme can then oscillate again.

Oscillation

Figure 8.20

Allosteric Activation and Inhibition

• Cooperativity

– Is a form of allosteric regulation that can amplify enzyme activity

Figure 8.20

Binding of one substrate molecule toactive site of one subunit locks all subunits in active conformation.

Substrate

Inactive form Stabilized active form

(b) Cooperativity: another type of allosteric activation. Note that the inactive form shown on the left oscillates back and forth with the active form when the active form is not stabilized by substrate.

Feedback Inhibition

The end product of a metabolic pathway shuts down the pathway

Active siteavailable

Isoleucineused up bycell

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(threoninedeaminase)

Intermediate A

Intermediate B

Intermediate C

Intermediate D

Enzyme 2

Enzyme 3

Enzyme 4

Enzyme 5

End product(isoleucine)

Figure 8.21

Specific Localization of Enzymes Within the Cell

• Within the cell, enzymes may be

– Grouped into complexes

– Incorporated into membranes

– Contained inside organelles

1 µm

Mitochondria,sites of cellular respiraion

Figure 8.22

biological concepts bmz 116 section b

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