TOPIC 8: Metabolism, Cell Respiration, Photosynthesis

Cell Respiration

is the controlled release of energy from organic compounds (principally glucose) to produce ATP within cells

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Organic molecules

**store** energy within their chemical bonds 

* The energy is **not** easily accessible for use within the cell

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ATP functions as

an immediate source of energy within cells

* The energy is readily accessible for use within the cell
* ATP is considered to be the *energy* currency of all cells

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ATP consists of

nucleoside linked to 3 phosphates via high energy bonds

* When ATP is hydrolysed to ADP (+P), the energy contained is released for use

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the two types off cell respiration

* **Anaerobic** respiration
* **Aerobic** respiration

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Anaerobic respiration

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The **partial** breakdown of organic compounds for a small ATP yield. (net gain = 2 x AATP)

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***Also takes place in the presence of oxygen***

Via glycolysis:

* Glucose is converted into pyruvate ( x2)
* There is a net gain of **two ATP**
* Oxidized carrier molecules (NAD+) are reduced to form two hydrogen carrier molecules (NADH)

Aerobic respiration

The **complete** breakdown of organic compounds for a large ATP yield. (net gain = 36 x ATP)

* ***Takes place in the absence of oxygen***

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Via aerobic respiration:

* Hydrogen carriers are made in large quantities
* These hydrogen carriers (NADH) are used to produce significant amounts of ATP (net = 36) via the process of oxidative phosphorylation

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Compare and contrast anaerobic and aerobic cell respiration

Oxidation

* Addition of oxygen atoms
* Removal of hydrogen atoms
* Loss of electrons from a substance

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Reduction

* Removal of oxygen atoms
* Addition of hydrogen atoms
* Addition of electrons to a substance

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Glycolysis

 occurs in the cytosol and does not require oxygen (it is an anaerobic process)


1. Phosphorylation
2. Lysis
3. Oxidation
4. ATP Formation

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1. Phosphorylation

1. A hexose sugar (typically glucose) is phosphorylated by two molecules of ATP (to form a hexose bisphosphate)
2. This phosphorylation makes the molecule less stable and more reactive, and also prevents diffusion out of the cell 

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2. Lysis

1. The hexose bisphosphate (6C sugar) is split, with water, into two triose phosphates (3C sugars)

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3. Oxidation

1. Hydrogen atoms are removed from each of the 3C sugars (via oxidation) to reduce NAD+ to NADH (+ H+)
2. Two molecules of NADH are produced in total (one from each 3C sugar)

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4. ATP Formation

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1. Some of the energy released from the sugar intermediates is used to directly synthesise ATP
2. This direct synthesis of ATP is called *substrate level phosphorylation*
3. In total, 4 molecules of ATP are generated during glycolysis by substrate level phosphorylation (2 ATP per 3C sugar)

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At the end of glycolysis, the following reactions have occurred:

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* Glucose (6C) has been broken down into two molecules of pyruvate (3C)
* Two hydrogen carriers have been reduced via oxidation (2 × NADH + H+)
* A **net** total of two ATP molecules have been produced (4 molecules were generated, but 2 were used)

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Fermentation

__**(occurs in cytoplasm)**__

releases energy from food molecules by producing ATP

* Follows glycolysis when **oxygen is not available** (anaerobic)
* By passing high-energy electrons back to pyruvic acid, NADH turns into NAD+ →allowing glycolysis to produce a steady supply of ATP

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Alcoholic Fermentation

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* Used by yeasts and other microorganisms 
* Produces ethyl alcohol and CO2
* Pyruvic Acid + NADH → Alcohol + CO2 + NAD+

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Lactic Acid Fermentation

* Most organisms carry out  fermentation by converting **pyruvic acid** to **lactic acid** 
* Doesn’t give out CO2
* Regenerates NAD+ so glycolysis can continue
* NADH + Pyruvic Acid → Lactic Acid + NAD+

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Explain the relationship between the structure and function of the mitchondria

* having two membranes(the inner and outer) → creates separate compartments within the mitochondrion
* Having these separate compartments also allows for a concentration gradient to occur(where the higher H+ concentration shifts to the area with the lower H+ concentration)
* this allows for diffusion to occur to power phosphorylation of ADP→ ATP
* Cristae increases the surface area of the inner membrane → this allows for more proteins that make up ETC→ this increases ATP molecule production

Where does the krebs cycle occur

in the matrix of the mitochondria

What is the general goal of the krebs cycle

over a series of reactions, the 6C compound is broken down to reform the original 4C compound(hence, a cycle)

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Per glucose molecule, the Krebs cycle produces:  4 × CO2  ;  2 × ATP  ;  6 × NADH + H+  ;  2 × FADH2

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Steps of the krebs cycle

* Two carbon atoms are released via decarboxylation to form two molecules of carbon dioxide (CO2)
* Multiple oxidation reactions result in the reduction of hydrogen carriers (3 × NADH + H+; 1 × FADH2)
* One molecule of ATP is produced directly via substrate-level phosphorylation
* As the link reaction produces **two** molecules of acetyl CoA (one per each pyruvate), the Krebs cycle occurs *twice*

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Where does the electron transport chain occur

the inner mitochondrial membrane

What is the general goal of the electron transport chain(ETC)

it releases the energy stored within the reduced hydrogen carriers in order to synthesize ATP → oxidative phosphorylation

Steps of the electron transport chain

1. NAD →NAD+ + e- + H+ 


1. Gets oxidized→ loses electron and H+
2. Electrons are used to pump H+ from matrix to intermembrane space
2. FADH2 → FAD + e+ + H+


1. Gets oxidized → loses electrons and H+
2. Electrons are used to pump H+ from matrix to intermembrane space
3. High concentration of H+ in intermembrane space; Low H+ concentration in matric →**concentration gradient (proton gradient)**
4. Oxygen is final electron acceptor; H2O is formed as waste product 
* ADP + P → ATP


1. H+ flows down concentration gradient, diffusing through ATP synthase

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Metabolism definition

describes the sum total of all reactions that occur within an organism in order to maintain life.

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Pathways

are a series of reactions that result in most chemical changes in a cell.

* each step is controlled by a specific enzyme

Metabolic Pathways

allow for a greater level of regulation, as the chemical change is controlled by numerous intermediates

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they are typically organized into chains or cycles of enzyme catalyzed reactions.

* examples of chains: glycolysis (in cell respiration), coagulation cascade (in blood clotting)

Examples off cycles

the krebs cycle (in cell respiration) and the calvin cycle (in photosynthesis)

Anabolism

the *building up* - desscribes the set of metabolic reactions that build up complex molecules from simpler ones

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* **Synthesizes complex molecules from simpler ones** 
* **Uses energy to construct new bonds (endergonic)**
* **Typically involves reduction reactions**

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Condensation reactions occur when

monomers are covalently joined and water is produced as a by-product

monosaccharides are joined via

glycosidic linkage to form disaccharides and polysaccharides(via condensation)

amino acids are joined via

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peptide bonds to make polypeptide chains

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glycerol an fatty acids are joined via

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ester linkage to create triglycerides

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nucleotides are joined by

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phosphodiester bonds to form polynucleotide chains

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Condensation

smaller molecules are assembled into larger ones AND water is produced

Catabolism

*breaking down;* describes the set of metabolic reactions that break complex molecules down into simpler molecules

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* **Breaking down complex molecules into simpler knees**
* **Releases energy when bonds are broken (exergonic)**
* **Typically involves oxidation reactions**

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Hydrolysis reactions require

the consumption of water molecules to break the bonds within the polymer

Chlorophyll

* Main pigment in green plants
* Needed for photosynthesis
* Capture light
* Intakes red + blue/violet light
* Reflects green light


* 2 Forms: chlorophyll A & B 

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Xanthophyll

can be seen on leaves in the autumn; reflects yellow light

Carotene

can be seen on leaves in the autumn; reflects orange light

Light Dependent Reactions

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* occurs in thylakoids
* uses light energy to make ATP and NADPH
* splits H2O in photolysis to replace electrons and H+ release O2 into the atmosphere
* 2 e- transport chains, Photosystems 2 and 1

use light energy to produce ATP and to split water (photolysis), making H+ ions

Photolysis: 6H2O → O2 + H+

Light independent reactions

* occurs in stroma
* uses ATP and NADH to form triose phosphate
* returns ADP, inorganic phosphate and NADP to light-dependent reactions
* involves calvin cycle

Some O2 is a waste product

use ATP and H+ ions to “fix” CO2, making glucose

6CO2 + 6H2O → C6H12O6 + 6O2

→ ADP → ATP

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electromagnetic energy

* energy for photosynthesis, comes from light
* travels in wavelengths
* visible light spectrum is important for photosynthesis
* shorter wavelengths = higher energry
* specific pignments absorb light more efficiently within certain wavelengths

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Spectrophometer

device to measure absorption at various light wavelengths

* produces absorption spectrum

Absorption spectrum

combination of all absorption spectra of all pigments in chloroplasts

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Action spectrum

* the rate of photosynthesis at particular wavelengths of visible light
* Produce action spectrum by measuring oxygen production → high oxygen = high rate of photosynthesis
* Light energy drives photosynthesis, the wavelength of the light absorbed by chloroplasts partly determines photosynthetic rate

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The __**action spectrum**__ of photosynthesis and __**absorption spectrum**__ of chlorophyll…

overlap each other - this tells us that chlorophyll is the most important of the photosynthetic pigments (there are others). 

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* __Blue light__ and __red light__ → __greatest absorption__ & peak in rate of photosynthesis
* __Green light__ → __Low absorption__ corresponds to lower rate of photosynthesis

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The chloroplast

where photosynthesis takes place

has:

* extensive membrane surface area of thylakoids
* small space(lumen) within thylakoids
* grana
* chlorophyll
* Stroma
* double membrane(inner and outer)
* isolates working parts and enzymes from surrounding cytoplasm

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Thylakoids

internal structure of chloroplasts

* allows greater absorption of light by photosystems
* their lumen allows for faster accumulation of protons to create a concentration gradient

grana

flattened disk shaped structure formed from thylakoids

chlorophyll

photosynthetic pigment embedded in thylakoids

stroma

colorless substance containing enzymes, RNA, DNA, and ribosomes that surrounds the thylakoids

* allows area for enzymes necessary for the calvin cycle

Light dependent reactions

light energy is absorbed and converted into chemical energy

* occur in the thylakoids of grana
* one stack of thylakoids=1 granum
* plants during this phase absorb sunglight (photons) using pigments such as chlorophyll and cartenoids

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The photosystems

* photosystem 1: most efficient at wavelength 700 nm
* photosystem 2: most efficient at wavelength 680 nm
* work together during non-cyclic electron transfer → non-cyclic phosphorylation

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Steps for Light dependent reactionS

1. photoactivation of PS2
2. electron capture by primary electron acceptor of reaction center in PS2
3. replacing lost electrons
4. Electron transport chain
5. phosporylation of ADP to produce ATP
6. photon absorbed by pigments in PS1
7. high energy e- travel down second ETC


1. NADP enzyme catalyzes transfer of e- → NADPH and ATP are the final products

Step 1 of light dependent reactions

Photoactivation of PSII

* Photon absorbed by pigment in photosystem II and transferred to other pigment molecules until it reaches chlorophyll a (P680) in the reaction center
* Photon excites electrons to higher energy state → high energy electron

Step 2 of light dependent reactions

* Electron captured by primary electron acceptor of reaction center in photosystem II

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Step 3 of light dependent reactions

Replacing Lost Electrons

* Water split by enzyme →generates more **electron, hydrogens ions** (H+) and **oxygen**
* Process powered by energy in light → **photolysis**
* Electrons supplied to chlorophyll a molecules in the reaction center

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Step 4 of light dependent reactions

* High energy electrons go down electron transport chain →lose energy
* 1st carrier = **plastoquinone (PQ)**
* 2nd (middle) carrier = **cytochrome complex (cytochrome C)**

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Step 5 of light dependent reactions

* Energy lost as electrons move down ETC drives **chemiosmosis** → **phosphorylation** of **ADP to produce ATP**
* H ions are pumped into **thylakoid space** to create gradient 
* H ions diffuse through ATP synthase→ providing energy to produce ATP

Step 6 of light dependent reactions

* Photon absorbed by pigments in photosystems I
* Energy transferred until reaches chlorophyll (P700)
* High energy electrons produced
* De-energized electrons from photosystem II resupply the electrons needed in photosystem I

Step 7 of light dependent reactions

* High energy electrons travel down second ETC
* Carrier = ferredoxin

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Step 8 of light dependent reactions

* NADP enzyme catalyzes transfer of the electron from ferredoxin to the energy carrier NADP+ → NADPH
* 2 electrons required to fully reduce NADP+ → NADPH
* **NADPH & ATP are final products of light reactions**
* **Supply energy needed to power the light-independent reactions**

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Light- Independent Reactions

* Occurs within stroma or cytosol-like region of chloroplast
* ATP and NADPH provide energy to power these reactions
* Glucose produced


* Involves **Calvin cycle** (begins and ends with same substance - hence cycle)

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The Calvin Cycle

outlines the events that result in the formation of organic molecules from inorganic sources (CO2)

* Ribulose bisphosphate (RuBP) is carboxylated by carbon dioxide (CO2) to form a hexose biphosphate compound
* The hexose biphosphate compound immediately breaks down into molecules of glycerate-3-phosphate (GP)
* The GP is converted by ATP and NADPH into molecules of triose phosphate (TP)
* TP can be used to form organic molecules or can be recombined by ATP to reform stocks of RuBP

Calvin cycle compounds

Step 1 of the calvin cycle

* **Ribulose bisphosphate (RuBP) - 5 carbon compound binds to CO2 from the air → carbon fixation**
* This step is catalyzed by **RuBP carboxylase** (**Rubisco**)
* Results in **6 carbon compound**

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Step 2 of the calvin cycle

* Unstable 6 carbon compound breaks down into 3-carbon compounds → **glycerate-3-phosphate**

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Step 3 of the calvin cycle

* Glycerate-3-phosphate acted on by ATP and NADPH to form triose phosphate (TP)
* Reduction Reaction

Step four of the calvin cycle

* Molecules of **TP** (triose phosphate) have two options
* 1. Some leave cycle to become sugar phosphates, may become more complex carbohydrates
* 2. Continue in the cycle to reproduce origination compound of the cycle, RuBP

Step 5 of the calvin cycle

* To regain RuBP from TP, ATP is used

Cyclic Phosphorylation

* is another way to produce ATP during the light-dependent reactions
* proceeds only when light is not a limiting factors
* and when there is an accumulation of NADPH

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Occurs in three steps

Step 1 of cyclic phosphorylation

light energized electrons from photosystem 1 flow back to cytochrome c

Step 2 of cyclic phosphorylation

electrons flow down the remaining ETC. allowing ATP synthesis via chemiosis

* electrons do NOT go down a secondd ETC - that would produce NADPH

Step 3 of cyclic phosphorylation

additional ATPs sent to calvin cycle so it can go faster

Factors limiting photosynthesis

* light intensity
* CO2 levels
* temeprature

Light intensity on photosynthesis

CO2 concentration on photosynthesis

Temperature on photosynthesis