bioenergetics

Bioenergetics

Graphing Tuesday• Create a line graph with 2 y axes.• These are fake numbers @ hunting in

Summer Shade!Year # Hunters

2000 150

2001 200

2002 125

2003 100

2004 300

2005 350

2006 355

Year # Deer

2000 8,000

2001 7,800

2002 3,000

2003 2,500

2004 3,000

2005 3,250

2006 4,500

Stem Cell Review• 1. What is a stem cell? _____________

________• 2. List the 2 types of stem cell: ______

________• 3. Which stem cell is controversial? Why?• 4. Where do they get adult stem cells from?

Review• Potential vs. Kinetic Energy• List 4 macromolecule types• How are these made/destroyed?• Functions of Each Macromolecule.

Metabolism• The sum of all chemical reactions occurring

in an organism.• Catabolism- breaking down. EXERGONIC.

Releases stored potential energy/heat.• Anabolism- building up. ENDERGONIC.

Absorbs energy/heat from environment.

• Anabolism and Catabolism are an example of ENERGY COUPLING…2 different processes united by common energy.

Energy (E)• Kinetic- energy of movement, usually e- or

protons in Biology.• Potential- energy of position, usually in the

chemical bonds of e-/p in Biology.• Cell Respiration releases energy (KE),

Photosynthesis allows capture of E from great E source (PE)

Potential Energy vs. Kinetic Energy

Thermodynamics• Study of heat and its properties.• First Law of Thermodynamics: energy

cannot be created/destroyed just transformed/transferred.

• Second Law of Thermodynamics: every energy transfer increases entropy (disorder).• Most organized at conception, as you move

towards death you become more organized…evolution?

Thermodynamics

LE 8-3

Chemical energy

Heat CO2

First law of thermodynamics Second law of thermodynamics

H2O

Sunlight is high quality E, Heat is low quality E

Gibbs “Free” Energy- ability to work (make ATP/GTP)

• Δ G = ΔH – TΔ S• G- Gibbs “free” energy• H – Enthalpy (Total usable energy in the system)• T – Temperature in Kelvin (273 + C )⁰• S- Entropy (Disorder created by something being

broken down)• Δ – Change in a variable over time

Unstable (Capable of work)=LIVINGvs.

Stable (no work)=DEAD

G = 0

A closed hydroelectric system

G < 0

LE 8-6a

Reactants

EnergyProducts

Progress of the reaction

Amount ofenergyreleased(G < 0) Final-initial E

Free

ene

rgy

Exergonic reaction: energy released

Catabolism if G is negative, e.g. cell respiration. There is free energy to do work

LE 8-6b

ReactantsEnergy

Products

Progress of the reaction

Amount ofenergyrequired(G > 0)

Free

ene

rgy

Endergonic reaction: energy required

Anabolism if G is positive, then it cannot do work, energy is bound up (photosynthesis=endergonic)

Remember• Not all energy can be used…• Lots is lost to heat, some to waste

(defacation)

Types of work performed by living cells

NH2

Glu

P i

P i

P i

P i

Glu NH3

P

P

P

ATPADP

Motor protein

Mechanical work: ATP phosphorylates motor proteins

Protein moved

Membraneprotein

Solute

Transport work: ATP phosphorylates transport proteins

Solute transported

Chemical work: ATP phosphorylates key reactants

Reactants: Glutamic acidand ammonia

Product (glutamine)made

+ +

+

ATP

ATP• The 3 PO4 make it very unstable. This

instability allows it to do lots of work.

Phosphorylation

ATPADP +Pi G=-13J ADP +Pi ATP G=13J

Exergonic, can do workEndergonic, can’t do work

Phosphorus Cycle

Initially in rocks, rocks weather, P then in soil or inwater to be used by producers to make phospholipids, DNA/RNA, proteins.

Data Set 1 PictureU2,D1

Enzyme Review• Protein function is caused by structure…

sequence of _ _ and how they are _.• All major processes in cells involve

proteins.• Suffix of most proteins:_• Proteins are catalysts: speed up and control

rate of reactions.

Enzyme Review• Enzymes are not consumed in the reaction.

Benefit?• Enzymes used to be described as “lock and

key” now they are said to be “induced fit” or “fits like a glove”

• H bonds responsible for induced fit

Enzymes Lower EA

• Energy of Activation is the energy required to get the molecules lined up and ready for a reaction to take place (metabolism).

• Because the molecules are sitting in the enzyme in position, it reduces all the time and energy of them “naturally” coming together.

• Enzymes also eliminate the need for heat to move the molecules faster…we won’t incinerate ourselves during metabolism

.

Course ofreactionwithoutenzyme

EA

without enzyme

G is unaffectedby enzyme

Progress of the reaction

Free

ene

rgy

EA withenzymeis lower

Course ofreactionwith enzyme

Reactants

Products

.

Substrate

Active site

Enzyme Enzyme-substratecomplex

Enzymatic Process• Active Site- location of chemical reactions

between enzyme and substrate.• Enzyme Substrate Complex- caused by

induced fit. Held together by H bonds, ionic bonds, and Van der Waals.

• The amino acid R groups perform the reaction.

R groups of Amino Acids

.

Enzyme-substratecomplex

Substrates

Enzyme

Products

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

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

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.

Substrates areconverted intoproducts.

Products arereleased.

Activesite is

availablefor two new

substratemolecules.

3 Factors that Affect Enzymes• 1. Temperature• 2. Salinity• 3.pH• *They all affect the 2*structure of proteins

by altering the H bonds.• If a protein unwinds it is said to be __• Type of protein that prevents misfolding_

Enzyme Inhibitors• These will slow or stop the rate of

reactions• 1. Competitive Inhibitors- compete with

substrate for active site, bind to active site, and SLOW reactions down.

• 2. Non-competitive Inhibitors- bind somewhere to the enzyme, change the active site completely, and STOP reactions.

• Inhibitors can be classified as reversible (Antabuse) or irreversible (Sarin-nerve gas)

.

Substrate

Active site

Enzyme

Competitiveinhibitor

Normal binding

Competitive inhibition

Noncompetitive inhibitor

Noncompetitive inhibition

A substrate canbind normally to the

active site of anenzyme.

A competitiveinhibitor mimics thesubstrate, competing

for the active site.

A noncompetitiveinhibitor binds to the

enzyme away from theactive site, altering the

conformation of theenzyme so that its

active site no longerfunctions.

Allosteric Enzymes “Allo” different, “stery” shape

• Enzymes that will change shape, thus being turned off or on.

• Inhibitor molecules turn the enzyme off• Feedback Inhibition or Negative Feedback

Loop-prevents wasting energy• Activator molecules turn the enzyme on

Feedback Inhibition or

Negative Feedback Active siteavailable

Initial substrate(threonine)

Threoninein active site

Enzyme 1(threoninedeaminase)

Enzyme 2

Intermediate A

Isoleucineused up bycell

Feedbackinhibition Active site of

enzyme 1 can’tbindtheoninepathway off

Isoleucinebinds toallostericsite

Enzyme 3

Intermediate B

Enzyme 4

Intermediate C

Enzyme 5

Intermediate D

End product(isoleucine)

Cooperativity• One active site helps other active sites on

the same molecule.• RBC-4 part molecule, each part carries O.

When Part 1 fills with O the next part does …and RBC deliveer O in the same way.

• This is an example of cell efficiency/specializatino, conservation of E, and regulation.

Proteins involved in constructing a

red blood cellQuaternaryStructure b Chains

a ChainsHemoglobin

IronHeme

CollagenPolypeptide chain

Polypeptidechain

Bioenergetics• Enzymes are needed in all efficient energy

reactions.• Two energy reactions we will focus on:

• Photosynthesis- anabolic, endergonic, +G• Cell Respiration-catabolic, exergonic, -G

Remember• Electrons are a source of E• CHOs come from H20 and CO2 by plant’s

chloroplast• E in a molecule is directly related to # H

present.• Autotrophs =• Heterotrophs =

Autotroph - Plants

Autotroph - Algae

Autotroph - Phytoplankton

Autotroph - Bacteria

Heterotroph - Animal

Heterotroph - Fungus

Photosynthesis• Chlorophyll- light absorbing protein

pigment that reflects green light. Found in plants, algae, and blue-green bacteria.

• Chloroplast- organelle that contains grana (thylakoids) and stroma

Chloroplast

Chloroplast Parts• Thylakoids- contain chlorophyll. Site of

Light reaction. Purpose is to make ATP & NADPH.

• Grana- stacks of thylakoids• Stroma- watery area @ thylakoids. Site of

light independent (Calvin Cycle). Purpose is to use ATP & NADPH to make glucose using CO2

Photosynthesis chemical reaction(Remember… conservation of matter.)

• 6 CO2 + 6 H2O C6H12O6 + 6 O2 + Heat

Photosynthesis• Take radiant energy and convert into

chemical energy (ATP & NADPH)• Take chemical energy (ATP & NADPH)

and turn it into potential chemical energy (carbohydrate). Sugar creation is done by catabolism.

Photosynthesis Light Reaction

Photosynthesis Calvin Cycle

Sunlight Terminology

Electromagnetic Spectrum

Absorption vs. Reflection

Sunlight• High quality E• Sunlight travels in waves.• Each color has a wavelength• Red light has the longest wavelengths

• Least energy of the white light• Blue light has the shortest wavelengths

• Most energy of the white• Units of light are called photons

Chloroplasts REFLECTINGGreen Light

Whitelight

Refractingprism

Chlorophyllsolution

Photoelectrictube

Galvanometer

The high transmittance (low absorption) reading indicates that chlorophyll absorbs very little green light.

Greenlight

Slit moves to pass light of selected wavelength

0 100

Chlorophyll ABSORBINGBlue light to power

photosynthesis

Whitelight

Refractingprism

Chlorophyllsolution

Photoelectrictube

The low transmittance (high absorption) reading indicates that chlorophyll absorbs most blue light.

Bluelight

Slit moves to pass light of selected wavelength

0 100

Chloroplasts absorbing the blue and the red light waves. The green

is NOT being absorbed.

Light Absorption vs. Reflection• Absorbed light = used light (red and blue0• Reflected light- unused light (green light)

in plants

Chlorophyll Molecule(How many electrons are in Mg’s outer shell?)

Hint: Look at the Periodic Table.

Absorbed Light• Light is absorbed by pigments:

• Chlorophyll A-main one• Chlorophyll B- help A• Carotenoids- reflects orange, red, yellow,

help A• Photosystems- groups of pigments in the

thylakoid membrane• Photosystem I: makes ATP & NADPH• Photosystem II: makes ATP

Photosystem and collecting sunlight energy.

Where are the photosystems located?

Synthesis Question (U2, D6)• Question: The word “photosynthesis”

means the “the process of using light to make”. What is made in the process is the organic macromolecule sugar (carbohydrate). In no more than three sentences, justify the meaning of photosynthesis by briefly telling what colors of light are involved in the process, what the light is converted into, and what are those molecules purpose. (5 Points)

• 1pt. Discussion of the red and blue colors of white light being absorbed by plants.

• 1pt. Discussion of converting the light energy into ATP and NADPH or chemical

• energy molecules 1pt. Discussion of ATP and NADPH (Chemical energy molecules) being used to make sugar.

• 1pt. Correct use of scientific terms.• 1pt. Answer has no more than three

sentences. (Following Directions.)

Remember• Cells have a high SA:V ratio. Why? SA:V

ratio also high for mitochondria and chloroplast.

• Valence electrons involved in bonding.

Light Dependent Reactions of Photosynthesis

• * Turns radiant energy into chemical energy __ & __.

• Takes place in the light, on thylakoid membrane.

• Uses photosystems either in a cyclic electron flow or a non-cyclic electron flow.

• There are 1000s of photosystems per each thylakoid. Benefit? SA:V?

Non-cyclic electron flow

Cyclic electron flow

Photosynthesis• 1. Sunlight strikes the Photosystem II, 2

H2O enters Photosystem II.• 2. O2 is released from PII as waste, and

2H+, 2 E- are left.• 3. H+ is in the stroma, and the e- move

using a carrier protein, Cytochrome C, down the primary electron transport chain.

• 4. Light also strikes Photosystem I causing it to lose electrons and move down another primary electron transport chain.

• 5. e-from PI, move towards enzyme, to NADP+ Reductase this enzyme reduces NADP+ into NADPH.• Redox Reactions- 2 molecules exchanging e-

• 6. Redox reactions cause e- to move down ETC

• 7. As e- move down the ETC, they power proton pumps (H+) with their kinetic energy.

• 8. H+ actively pumped from stroma into the thylakoid which causes a change in pH, and the concentration gradient is established. (air in balloon)

• 9. This [gradient] is the potential energy that will make ATP using the enzyme ATP Synthetase Complex (complex=many proteins) through anabolic phosphorylation. (air leaving balloon)

• The quantities are mind boggling. A hectare (e.g. a field 100 m by 100 m) of wheat can convert as much as 10,000 kg of carbon from carbon dioxide into the carbon of sugar in a year, giving a total yield of 25,000 kg of sugar per year.

• There is a total of 7000 x 109 tonnes of carbon dioxide in the atmosphere and photosynthesis fixes 100 x 109 tonnes per year. So 15% of the total carbon dioxide in the atmosphere moves into photosynthetic organisms each year.

H+ (protons) being pumped into the thylakoid to “build” potential energy.

Photosynthesis

Energy Coupling• Using energy from the proton pump to

make energy in the form of ATP.• Active transport sets up [gradient],

diffusion creates the ATP• Making ATP in photosynthesis is called

chemiosmosis.

Data set 2 picture (U2,D7)

Review

Remember• 1. Law of Conservation of Mass- Matter is

neither created or destroyed…just transferred/ transformed.

• CHO are energy storage molecules for quick release.

• C is the backbone of the 4 biomolecules. • Primary source of C is CO2 from air.

Light Independent Reactions- Calvin Cycle

• Uses ATP and NADPH to perform carbon fixation (make sugar from CO2).

• 1. CO2 enters through the stomata, CO2 diffuses through c.m. and membrane of chloroplast into the stroma.

• 2. 3CO2 molecules will be added to RuBP- a five carbon molecule.

• 3. Immediately the 6C molecule breaks into 2 3C molecules (6 3C molecules total).

Calvin Cycle step 1

• 4. Use 6 ATP & 6 NADPH to bend each 3C sugars. (6 3C sugars).

• The bent 3C sugars are then 6 molecules of G3P.

• 5. 1G3P goes into making glucose, the other 5 G3Ps go back into the Calvin Cycle.

• 6. Using 3 ATP they are converted into 3 molecules of RuBP

Making Glucose• One G3P per turn of the cycle.• Takes 2 turns to make one glucose.• Takes 9 ATP and 6NADPH per turn…

18 ATP and 12 NADPH per glucose.

• The glucose is used for food, and excessis stored in starch to be used in cell respiration or making cell walls.

Photorespiration• Uses O2 to fix carbon instead of CO2.• This is a last resort to stay alive, when the

stomata are closed off to prevent H20 loss.• In C3 plants this will quickly lead to death.• In C4 plants there is extra enzymes to grab

CO2, and photosynthesis occurs in the inner leaf cells. These plants are adapted for hot weather…corn, cotton, summer flowers.

CAM Plants• Crussulacean Acid Metabolism- utilize

CO2 stored as Crussulacean Acid because stomata only open at night. The C. acid is broken down in the day, and releases CO2 for Calvin Cycle.

• Desert plants, succulents, bromeliads, etc.• CAM Plants prevent transpiration.

Transpiration• Transpiration dictates available energy…• Deserts have lots of transpiration …

minimal photosynthesis…minimal E.

• Rainforests have little transpiration…lots of photosynthesis…lots of E…bigger food webs.

Competition vs. Evolution• Each plant type (C3, C4, CAM) have its

own niche.• A niche prevents competition thus

conserving E.• The more E conserved the more spent of

reproducing, thus highly populating the area.

• Is this competition or evolution? Justify in 3 sentences.

Remember…• Law of Conservation of Matter…• Second Law of Thermodynamics- all E

initiates from the sun (high quality), and ends up in entropy (low quality/disorder).

• Carbon skeletons for 4 biomolecules

Energy Flow and Matter Cycling

Microorganismsand other

detritivores

Tertiaryconsumers

Secondaryconsumers

Detritus Primary consumers

Sun

Primary producers

Heat

Key

Chemical cycling

Energy flow

Carbon Cycle

Cellularrespiration

Burning offossil fuelsand wood

Carbon compoundsin water

Photosynthesis

Primaryconsumers

Higher-levelconsumers

Detritus

Decomposition

CO2 in atmosphere1. All C starts in atm.2. Photosynthesis fixes CO2 to

sugar.3. Sugars used by consumers

in cell respiration and release CO2.

4. Fossil fuel burning also releases CO2 into atm.

Ecosystems• All the interacting communities is a given

area, also involves abiotic factors.• Important Abiotic factors:

• Temp.• Water• Nutrient cycling• Energy flow

Trophic Structure “troph=feed”• These are feeding relationships.• Second Law- with each level E is lost to

entropy.• All E eventually lost to heat.• Matter also flows through the trophic

levels, never created/ destroyed…think geochemical cycles

Food Web vs. Chain

Energetic Hypothesis/ Pyramid of Numbers

• Energetics Hypothesis- there are short food chains because of the 10% rule.

• 90% of all energy consumed by the organisms is lost to heat/ maintenance before eaten by the next trophic level.

Food chains and the 10% Rule of Energy

10% Rule

Growth (new biomass)

Cellularrespiration

Feces100 J

33 J

67 J

200 J

Plant materialeaten by caterpillar

Primary Productivity• Total amount of sunlight turned into

chemical energy by photosynthesis.• Global Energy Budget- amount of sunlight

used for photosynthesis.• Photosynthesis produces 170 billion tons of

sugar annually.• Using only 1% of solar energy.

Productivity of the Earth(Based on Chlorophyll Density)

Red And Yellow areas have the highest productivity…so where are they located?

Net Primary Productivity• Gross Primary Productivity- total E

produced• R- E used by autotrophs• NPP usually = 10%. It is the E available to

next trophic level.

• NPP = GPP - R

Data Set 3 picture U2,D9