Learning objectives:

1. To know the importance of chemical energy in biological processes

2. To understand the role of ATP3. To draw the structure of ATP4. To understand the stages in aerobic

respiration: glycolysis, link reaction, Kreb’s cycle and the electron transport chain

What processes do cells need energy for?1. Movement e.g.

movement of cilia and flagella, muscle contraction

2. Maintaining a constant body temperature to provide optimum internal environment for enzymes to function

3. Active transport – to move molecules and ions across the cell surface membrane against a concentration gradient

6. Secretion – the packaging and transport of secretory products into vesicles in cells e.g. in the pancreas

5. Bioluminescence – converting chemical energy into light e.g. ‘glow worms’

4. Anabolic processes e.g. synthesis of polysaccharides from sugars and proteins from amino acids

(16)

(1)

(14)

(5)

(12)

(8)

(10)(9) (11)

(7)(6)

(13)

(4)(3)(2)

(15)

In pairs: Draw this grid on one Miniw’board. Put or on different sides of a second mwb

(16) Exocytosis uses ATP

(1) Active transport uses carrier proteins

(14) Facilitated diffusion uses

channel proteins

(5) Phagocytosis is a type of endocytosis

(12) Diffusion stops when

equilibrium is reached

(8) Facilitated diffusion uses

carrier proteins

(10) Endocytosis involves bulk

transport into a cell

(9) Simple diffusion uses

ATP

(11) Pinocytosis is a type of exocytosis

(7) Active transport occurs

from lower to higher conc.

(6) Facilitated diffusion needs

ATP

(13) Endocytosis involves bulk

transport out of a cell

(4) Passive transport methods use ATP

(3) Osmosis occurs from

lower to higher water potential

(2) Active transport needs

ATP

(15) Diffusion occurs up a

concentration gradient

(14) Facilitated diffusion uses

channel proteins

Why is energy needed within cells?Allows chemical reactions to take place

BUILD UP (synthesis) or BREAKDOWN of molecules

In order to do this, energy is required to make and break bonds

Where does the energy come from?

The SUN is the ultimate source of energy for nearly all living organisms (the exceptions being a few deep sea chemosynthetic bacteria)

Autotrophs make their own food (organic compounds) using carbon dioxide

Heterotrophs assimilate energy by consuming plants or other animals

Autotroph

Organisms that can synthesise complex organic molecules from simple ones. There are two types of autotroph, depending on how they obtain their energy:

i. Phototrophs: Autotrophs that use light energy e.g. Plants.

ii. Chemotrophs: Autotrophs that use inorganic chemical energy e.g. sulphur bacteria

ATP

What provides the energy within cells?

ATP…Adenosine Tri PhosphateCommon to ALL living thingsAny chemical that interferes with the

production or breakdown of ATP is fatal to the cell and therefore the organism

• Chemical energy is stored in the phosphate bonds

The role of ATP (adenosine triphosphate)The short term energy store of the cellOften called the ‘energy currency’ of the cell

because it picks up energy from food in respiration and passes it on to power cell processes.

ATP made up of:Adenine (a base)Ribose (a pentose sugar)3 phosphate groups

ATP is a nucleotidemade from:

1. The nitrogenous baseAdenine

2. A pentose sugarRibose 3. Phosphate groups

ATP Structure

2. It is the major energy currency of cells entrapping or releasing energy in most metabolic pathways.

1. It is a coenzyme involved in many enzyme reactions in cells.

5. It is one of the monomers used in the synthesis of RNA and, after conversion

to deoxyATP (dATP), DNA.

ATP: Function

4. It is a small molecule so will diffuse rapidly around the cell to where it is needed.

3. The energy is released from ATP in a single step and in a small manageable amount.

* Hydrolysis: Decomposition of a substance by the insertion of water molecules between certain of its bonds. Food is digested by hydrolysis)

*Free energy: The energy that can be harnessed to do work.

When the third phosphate group of ATP is removed by hydrolysis, a substantial amount of free energy is released, the exact amount depends on the conditions. For this reason, this bond is known as a "high-energy" bond. The bond between the first and second phosphates is also "high-energy". But note that the term is not being used in the same sense as the term "bond energy". In fact, these bonds are actually weak bonds with low bond energies.

ATP + H2O -> ADP + PiADP is adenosine diphosphate. Pi is inorganic phosphate.

ATP: and energy

How does ATP provide the energy?Chemical energy is stored in the

phosphate bonds, particularly the last oneTo release the energy, a HYDROLYSIS

reaction takes place to break the bond between the last two phosphate molecules

Catalysed by ATP-aseATP is broken down into ADP and PiFor each mole of ATP hydrolysed, about

34kJ of energy is releasedSome is lost, but the rest is useful and is

used in cell reactions

How ATP releases energyThe 3 phosphate groups are

joined together by 2 high energy bonds

ATP can be hydrolysed to break a bond which releases a large amount of energy

Hydrolysis of ATP to ADP (adenosine diphosphate) is catalysed by the enzyme ATPase (ATPase)

ATP ADP + Pi + 30 KJ mol-1

(H2O)

The 2nd phosphate group can also be removed by breaking another high energy bond.

The hydrolysis of ADP to AMP (adenosine monophosphate) releases a similar amount of energy

(ATPase)

ADP AMP + Pi + 30 KJ mol-1

(H2O)AMP and ADP can be converted back to ATP by

the addition of phosphate molecules

The production of ATP – by phosphorylation

- Adding phosphate molecules to ADP and AMP to produce ATP

Phosphorylation is an endergonic reaction – energy is used

Hydrolysis of ATP is exergonic - energy is released

Advantages of ATPInstant source of energy in the cell

Universal energy carrier and can be used in many different chemical reactions

It is mobile and transports chemical energy to where it is needed IN the cell

Releases energy in small amounts as needed

What does this have to do with photosynthesis?ATP is both synthesised and broken

down during photosynthesis!

6CO2 + 6H2O = C6H12O6 + 6O2Light energy is requiredChlorophyllStored within chloroplasts10-50 chloroplasts per plant cell

Biochemistry of Photosynthesis

An introduction…

Plant leaves are flattened to maximise the surface area for the absorption of light. The upper and lower surfaces are covered by a waxy cuticle which slows the loss of water from the leaf. Beneath the cuticle lies the epidermis which provides some support for the leaf. The lower epidermis has small pores called stoma that allow for gaseous exchange. During the day CO2 diffuses in and O2 out, during the night CO2 diffuses out and O2 in. Water vapour also escapes from the stomata and it is this loss that creates the transpiration stream drawing mineral nutrients from the soil and up into the plant.

The Leaf

The exchange of gases through the stomata is regulated by the guard cells which lie on either side of it. The palisade mesophyll cells are elongated and contain many chloroplasts, this is the main photosynthetic area of the plant. The spongy mesophyll has large air spaces to allow for the rapid diffusion of gases in and out of the leaf. The veins in the leaf contain vascular tissue, the xylem and phloem. The xylem provides support as well as carrying water and mineral nutrients. The phloem carries away the products of photosynthesis, primarily sucrose, to the rest of the plant.

The Leaf

Upperepidermis

Palsademesophyll

VeinVascular bundle

LowerEpidermis

Spongymesophyll

The Leaf

Cuticle

Upperepidermis

Chloroplasts

Air spaceIn spongymesophyll

Palisademesophyll

Stoma

Lowerepidermis

Guard Cells

Guard Cells and Stomata

http://www.sciencephoto.com/images/download_wm_image.html/B110036-Chloroplasts_in_plant_cells-SPL.jpg?id=661100036

“Life is bottled sunshine”

Wynwood Reade, Martyrdom of Man, 1924

Photosynthesis – what we know (or should know!!...)“Building from light”Converts carbon dioxide into organic

compoundsCarried out by autotrophsAll life either depends on it directly as a

source of energy, or indirectly as the ultimate source of the energy in their food

6CO2 + 6H2O = C6H12O6 + 6O2

So how do we know all this?...

The story starts a long time ago…Aristotle (384-

322BC)Greek philosopherHe proposed that

plants, like animals, require food

He concluded that green plants obtained their nourishment from the soil

Aristotle’s theory was widely accepted until the 1600’s…

Nicholas of Cusa (1401-1464)

Cardinal of the Catholic Church

Philosopher, mathematician, jurist and astronomer

He planned but never carried out an experiment to determine whether or not plants consume the soil

He proposed they did not

Revolutionary!!

Jean Baptiste van Helmont (1579-1644)Flemish physician and

chemist Identified carbon dioxide,

carbon monoxide, nitrous oxide and methane

He was a doctor. He married a wealthy noblewoman and her inheritance enabled him to retire early from medical practice and concentrate on his chemical experiments

Over 5 years, he carried out experiment originally planned by Nicholas of Cusa and concludes the increase in mass of the plant came from water. He does, however, ignore a slight decrease in soil mass

Robert Hooke Invented the light

microscopeObserved both plant

and animal cells‘Stoma’- from the

Greek word for mouthFirst observed by

MalphighiStoma were so named

by Heinrich Link because of their appearance

Their function was unknown to him though

Edme Mariotte (1620-1684) French physicist

and priestIn 1660 he

discovered the eye’s blind spot!

In 1676 he hypothesised that plants synthesise their food from air and water

Stephen Hales (1677-1791)Physiologist, chemist

and inventorHe studied the roles of

air and water and their importance to plant and animal life

He wrote that plant leaves “very probably“ take in nourishment from the air and that light may also be involved

Charles BonnetObserved the emission of

gas bubbles by a submerged illuminated leaf (clearly his pondweed was healthier than the pondweed we have in school!)

Joseph Priestley and his experiments…1733-1804Theologian, philosopher,

clergyman, scholar and teacher

One of the scientists credited with discovering "dephlogisticated air“ – oxygen

Finds out that air which has been made ‘noxious’ by the breathing of animals or burning of a candle can be restored by the presence of a green plant

Carried out a very famous experiment using bell jars, candles, plants and mice…

Antoine Lavoisier1743-1794Investigated and later

named oxygenRecognises it is used up

in both combustion and respiration

His work discredits “phlogiston”, a hypothetical substance previously believed to be emitted during respiration or combustion

One of the fathers of modern day chemistry

Jan Ingenhousz1730-1799Physicist, chemist and

plant physiologistDiscovered

photosynthesis (and Brownian motion!)

Showed that light is essential for photosynthesis and that only the green parts of the plants release oxygen

1782 – Jean Senebier demonstrates that green plants take in carbon dioxide from the air and emit oxygen under the influence of sunlight

1791 – Comparetti observes green granules in plant tissues, later identified as chlorophyll

Nicolas de Saussure1767-1845Chemist and plant

physiologistProved that the carbon

assimilated from atmospheric carbon dioxide cannot fully account for the increase of dry weight in a plant

The basic equation for photosynthesis was therefore established

The Biochemistry begins…

So scientists had now worked out that Carbon Dioxide was taken in and Oxygen was given out, and that the green pigment (named chlorophyll in 1818) played a part in this process, but what actually went on inside the leaf?...

1842 – Schleiden states that he believes the water molecule is split during photosynthesis

1844 – Hugo von Mohl makes detailed observations about the structure of chloroplasts

1845 – Julius Robert von Mayer proposes that the Sun is the source of energy used by living organisms and introduces the concept that photosynthesis converts light energy into chemical energy

1862 – Julius von Sachs demonstrates that starch formation in chloroplasts is light dependent

The discoveries continue…1864 – We have the balanced equation for

photosynthesis after accurate quantitative measurements of carbon dioxide uptake and oxygen production are made…

6CO2 + 6H2O C6H12O6 + 6O2

1873 – Emil Godlewski proves that atmospheric CO2 is the source of carbon in photosynthesis by showing that starch formation in illuminated leaves depends on the presence of CO2

Not just any old light..In 1883, Engelmann

illuminated a filamentous alga with light that had been dispersed using a prism

He discovered that aerobic bacteria in the water all congregated around the portions iluminated with red and blue wavelengths

This was the first action spectrum!

Thin layer chromatogram (TLC) of an extract of thylakoid membranes from the leaf of annual meadow grass Poa annua. TLC plastic sheets are coated with a 60 F254 silica gel which measures 0. 2 millimetres thick. A drop of extract, corresponding to the column here, was laid at the bottom of the sheet. The sheet was then placed in a beaker of solvent (75% acetone & 25% petroleum ether). The picture shows the solubility of the extract in solvent. Six bands are seen; top (orange) is carotene; 2 (green) pheophytin; 3 (green) chlorophyll A; 4 (green) chlorophyll B; 5 (yellow) & 6 (mere trace) are carotenoids. The line across the top of image is the solvent line

Plant Pigments and Chromatography

Carotene

Pheophytin

Chlorophyll A

Chlorophyll B

Carotenoids

Solvent line

Chlorophyll

Chlorophyll + Light = Chlorophyll+ + Electron-

ChlorophyllFound within chloroplastsAbsorb and capture lightMade up of a group of five pigments Chlorophyll aChlorophyll bCarotenoids; xanthophyll and carotenePhaetophytinChlorophyll a is the most abundantProportions of other pigments accounts for

varying shades of green found between species of plants

Photosystem I and Photosystem IIThese are distinct chlorophyll complexesEach contains a different combination of

chlorophyll pigmentsPSI absorbs light at 700nm and PSII at 680nmPSI particles are found on the intergranal

lamellaePSII particles are found on the grana

Plants have a variety of different plant pigments. Each of these have a different absorption spectra enabling the plant to harvest a wide variety of different wavelengths of light. Chlorophyll a has two peaks of absorption in the blue and red end of the spectrum, it does not absorb strongly in the green wavelengths and as a result these wavelengths are reflected and the plant will appear green. The pigments are found in the grana of the chloroplast and arranged to maximise the absorption of light

Photosynthetic Pigments

1905 – Limiting FactorsF.F. Blackman develops

the concept of limiting factors

He shows that photosynthesis consists of two stages…

A rapid light dependent process and a slower temperature dependent process

These become known as the ‘light’ and ‘dark’ reactions

1941 – Ruben and KamanThey set out to discover the

path of carbon dioxide during photosynthesis but end up discovering something different…

They experiment using heavy isotopes to discover whether the oxygen produced during photosynthesis comes from the splitting or water or carbon dioxide

They discover water is split during the first, light-dependent stage of photosynthesis

Daniel Arnon1910-1994Plant physiologist1954 – he

demonstrates light dependent ATP formation in chloroplasts

1955 – he demonstrates that isolated chloroplasts are capable of carrying out complete photosynthesis

Chloroplasts

Chloroplasts

{Thylakoids

Cytoplasm

Cell wall

Stroma

Grana

Intergranallamellae

Vacuole

False-colour transmission electron micrograph (TEM) of a stack of grana (black threads) in a plant chloroplast. The chloroplast is the unit within the leaf, which manufactures the food supply (starch) of the plant during photosynthesis. The granal stacks (flattened vesicles) contain the photosynthetic pigments (chlorophylls), which are active in the conversion of the sun's energy into chemical energy. The grana are connected at points called frets (the central conglomeration of black threads), which are embedded in the matrix of the chloroplast.

Grana

The Light Dependent phaseIs the first stage of photosynthesis.

Where? The Thylakoid membrane (photosystems)Why? This is where chlorophyll and accessory pigments are.

Photosystems. Purpose of the Photosystems is to trap light energy and convert it into Chemical energy in the form of ATP.

Photosystem I was the first to be isolated but is actually the second stage. It is located mainly in the intergranal Lamella.

Photosystem II was the second to be isolated but is the first stage of the reaction. It is located in the Granal lamella.

Equation for photosynthesis. 6H2O + CO2 C6H12O6 +6 O2

Water is needed for photosynthesis but why?Photosystem II (granal) contains enzymes which split water into H+ ions (Protons), electrons and O2. This is

known as photolysis.

2H2O + 4H+ + 4e- + O2

The ions which are produced are used for the Light Independent phase

(Dark reaction)

Some O2 is used for respiration

PSI (P700)

When light hits the chlorophyll molecule the light energy is transferred to the two electrons. These electrons become excited, and break their bonds.The electrons are captured by Electron acceptors and passed along a series of electron carriers.

As electrons pass along this chain energy is released.This energy is used to pump protons across the thylakoid membrane into the Thylakoid space where they build up. As protons build up a gradient is created the protons flow down this gradient. This Process is known as Chemiosmosis.This process enables ADP and Pi to make ATP, which is used in the Light Independent Phase. (It could also be used by the guard cells to bring in K+ causing water to flow into the cell via osmosis and the stoma to open). The production of ATP via this method is known as Cyclic Photophosphorylation.

Non Cyclic Photophosphorylation takes place in both the photosystems. It includes the production of ATP and NADP.

Plant biologists are prize winners!1956 – Melvin Calvin and his coworkers are

awarded the Nobel Prize in 1961 after they use radioactively labelled CO2 to show the pathway of carbon assimilation during photosynthesis. The second stage of photosynthesis is also known as the Calvin Cycle!

1960 – Robert Woodward synthesises chlorophyll and is awarded the Nobel prize in 1965

1984 – Deisenhofer, Michel and Huber crystallise the photosynthetic reaction centre from a purple bacterium and use x-ray diffraction techniques to determine its detailed structure. They are awarded the Nobel Prize in 1988.

Chloroplast

2. Oxidation and reduction

OIL RIG = “Oxidation Is Loss (of electrons), Reduction Is Gain (of electrons)

Any chemical which gives away electrons (e-) is said to be oxidised, and any chemical which accepts electrons is said to be reduced.

2. Oxidation and reduction

In addition:

Any chemical which gives away protons (H+) is oxidised, and any chemical which accepts protons is reduced

Chemical XH+

reduction

Chemical X e-

Chemical XH+

oxidation

Chemical X e-

NAD

Nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP) are two important cofactors found in cells. NADH is the reduced form of NAD+, and NAD+ is the oxidized form of NADH. It forms NADP with the addition of a phosphate group to the 2' position of the adenosyl nucleotide through an ester linkage. NAD is used extensively in glycolysis and the citric acid cycle of cellular respiration. The reducing potential stored in NADH can be converted to ATP through the electron transport chain or used for anabolic metabolism. ATP "energy" is necessary for an organism to live. Green plants obtain ATP through photosynthesis, while other organisms obtain it by cellular respiration.

NAD Function

Photosynthesis

1. Light stage 2. Light Independent stage

I. Takes Place in the Grana.

II. Uses light energy.III. It makes ATP and

reduced NADP.IV. Water is split in

photolysis.V. Oxygen is released as a

waste product.

I. Takes Place in the Stroma.

II. Uses ATP and reduced NADP from the light stage.

III. It uses CO2

IV. It makes organic molecules such as sugars.

Complicated diagram

Less Complicated diagram

elec

tron

s

elec

tron

s

Lightharvestingantennae

Ene

rgy

Pot

entia

l

Low

High

NADP

ReducedNADP

Photophosphorylation

ATP

ADP

Electron transfer chain

H2O = OH- + H+

4OH = 2H2O + O2

Excretion

1. The light stage of photosynthesis takes place in the grana of the chloroplast. Light energy is absorbed by pigments which are arranged into structures called the light harvesting antennae. These funnel the energy towards a central core called photosystem II.

The Light Stage

2. Electrons in the chlorophyll of photosystem II are excited by the light energy and the chlorophyll oxidised. The excited electron is passed to a series of carriers and the energy is used to generate ATP, the process is called photo-phosphorylation.

PSII

PSI

Lightharvestingantennae

3. Photosystem II is now oxidised and to replace the electron lost by the chlorophyll water is split in the process of photolysis. This releases an electron and a Hydrogen ion (H+). This electron reduces the chlorophyll in PSII. Oxygen is released from the water as a waste product of the process and some of this will diffuse out of the plant.

4. Having given up some of its energy the electron that passed down the electron transfer chain to photosystem I is excited again by light energy giving energy. The electron and the hydrogen ion from the photolysis of water combine to reduce NADP.

Therefore two products of the light stage are ATP and reduced NADP. Oxygen is a waste product.

Photolysis

Light Independent stageEnergy from ATP, hydrogens and electrons

from reduced NADP are used to reduce carbon dioxide to produce carbohydrate.

This happens in the stroma.

Complicated diagram 2

Light independent stage

light independent

reaction

Reduced NADP

NADP

Carbon dioxide

ATPADP + Pi

glucose

Ribulose Biphosphate

2X Glycerate-3-Phosphate

2X Triose Phosphate

Glucose

(1C)

(5C)

(3C)

(3C)

(6C)

NADPH

ATP

ATP

CO2

Regeneration

ATPADP

1. The C3 cycle takes place in the stroma of the chloroplast. The cycle has three important stages. Carboxylation: The pentose sugar ribulose 1:5 bisphosphate combines with carbon dioxide to form x2 of the three carbon sugar Glycerate phosphate (GP). This is done with the help of the enzyme Rubisco.

Carbo

xyla

tio

n

Reduction

RUBP

ReducedNADP

NADP

ATP

ADP + Pi

The Light IndependentStage

C3 Cycle

CO2

5c

GP3c

TP3c

Glucose6c

Sucrose

2. Reduction: The reduced NADP is oxidised and Glycerate phosphate reduced and converted to another triose sugars (GALP). In this step ATP is converted to ADP and phosphate, the ATP providing activation energy for the process.

RUBISCo

3. Regeneration: The triose sugars are converted in several steps back to RUBP. This process requires the triose sugars to be phosphorylated by ATP.

Every three times the cycle goes around three carbons will be added and one surplus triose sugar will be made. The surplus triose sugars are used to make other organic molecules. It will take six turns of the cycle to produce one completely new molecule of glucose and twelve for the disaccharide sucrose.Amino acids also require the addition of nitrogen.

GALP

Light Dark

RUBP

GP

ATPReduced NADP

ATP

Glucose

CO2

RUBP GP

TP1

Glucose

Light Stage

The Light IndependentStage

ATPReduced NADP

ATP

Glucose

CO2

RUBP GP

TP1

Glucose

Light Stage

The Light IndependentStage

What happens without light?

Which stages can still continue when the light is turned off?

Which molecules will build up when the light is turned off?

Exam question

Suggest why after the light was switched off the amount of GP...a) Increased immediatelyb) levelled out after a time

Sketch the curve to show what happens to the amount of RuBP after the light has been switched off,

Explain your answer.

Sketch what would happen if CO2 was removed with the light left on.

The light dependent reaction takes place on the...

This is so that...

The reaction needs ...., ...., .... and ....

The reaction produces .... and ...

.... is also produced.

The ... and ...pass into the ... for the second stage in photosynthesis.

Learning objectives:

1. To understand the stages in aerobic respiration: glycolysis, link reaction, Kreb’s cycle and the electron transport chain

2. To link the stages3. To explain the link between ATP production

and energy levels

RespirationEnergy is released in respirationA series of oxidation reactions taking place

inside living cells which releases energy to drive the metabolic activities that take place in cellsAerobic respiration – takes place in the

presence of oxygen

Anaerobic respiration – takes place in absence of oxygen

Aerobic respiration –– to release energy 4 main stages

glucose

pyruvate

Acetyl coenzyme A

Hydrogen atoms

Glycolysis

Link reaction

Krebs cycle

Electron transport chain

oxygen water

NADH FADH2

CO2

1. Glucose (6C) phosphorylated to Glucose phoshate (6C)

The phosphate comes from ATP

Glycolysis -the splitting of glucose

3. Glucose phosphate (6C) phosphorylated to fructose biphosphate (6C)

4. Fructose biphosphate (6C) is split into two molecules of glycerate 3 phosphate

5. Each Glycerate 3 –phosphate (3C) is converted to pyruvate (3C)

6. H+ is removed and transferred to the hydrogen acceptor NAD (nicotinamide adenine dinucleotide)7. 2 x 2 ATP produced

Glycolysis in detail

Takes place in cytoplasm of cells

Does not need oxygen – first stage of aerobic respiration and only stage of anaerobic respiration

Although glycolysis yields energy it does need an input of energy to get the reaction started

Glycolysis – overview

Glycolysis produces from 1 molecule of glucose:

2 molecules of ATP in total (4 ATP are produced but 2 are used at the start)

2 molecules of NADH2 (reduced NAD)2 molecules of pyruvate to enter the link

reaction

The link reaction in mitochondria in presence of oxygen

Pyruvate (3C)

Acetate (2C)

Coenzyme A

Acetyl coenzyme A

NAD+

NADH + H+CO2

1. Pyruvate decarboxylated - CO2 removed

2. Pyruvate dehydrogenated – hydrogen removed

3. Acetate (2C) combines with coenzyme A

Don’t forget this happens TWICE as 2 molecules of pyruvate are formed from each glucose molecule

Krebs cyclein matrix of mitochondria