Metabolic Pathway- A series of small reactions controlled by enzymes
Phosphorylation- Adding a phosphate to a molecule
Photophosphorylation- Adding a phosphate to a molecule using light
Photolysis- The splitting of a molecule using light energy
Hydrolysis- The splitting of a molecule using water
Decarboxylation- removal of carbon dioxide from a molecule
Dehydrogenation- Removal of hydrogen from a molecule
Redox reactions- Reactions involving oxidation and reduction
Oxidised molecules- Have lost electrons and hydrogen and gained oxygen
Reduced molecules- Have gained electrons and hydrogen and lost oxygen
Plants are autotrophs- make their own food by photosynthesis
6C0 + 6H20 + energy --> 2C6H1206 + 602
Light energy converted to chemical energy in form of glucose. Energy stored in glucose until plants release it by respiration.
it Animals are heterotrophs- can't make their own food, so obtain glucose and respire it to release energy.
Two types of respiration= Aerobic (with oxygen) and Anaerobic (without oxygen)
C6H1206 + 602 --> 6C02 + 6H20 + energy
Properties that make it a good energy source:
* No energy wasted--> only releases or stores small amounts at a time *
* Small, soluble mlecule, easily transported around cell *
* Easily broken down, energy easily released *
* Can transfer energy to nother molecule by transferring a phosphate group *
* ATP can't pass out of the cell, so cell always has immediate supply *
ATP is an energy source for:
* Metabolic processes- DNA/RNA/ polypeptide synthesis *
* Movement/secretion- energy for muscle contraction/forms lysosomes *
* Active transport- changes shape of carrier proteins in plasma membranes *
* Activation of molecules- transferred phosphate lowers activation energies *
A cell can't get its energy directly from glucose, so in respiration the energy released is used to make ATP:
Adenosine triphosphate: Nucleotide adenine + Ribose sugar + 3 phosphates
1. ATP is synthesised from ADP and Pi (inorganic phosphate) using energy from energy-releasing reaction (e.g. brakdown of glucose in respiration).
2. Energy stored as chemical energy in phosphate bond.
3. Catalysed by ATP synthase. This is a hydrolysis reaction.
4. ATP diffuses to the part of cell where it is needed, and broken back down into ADP and Pi.
5. Chemical energy is released from phosphate bond and used by cell.
6. Catalysed by ATPase. This is a condensation reaction.
7. ADP and inorganic phosphate recycled, and process starts again.
A coenzyme is a molecule that aids the function of an enzyme.
They work by transferring a chemical group from one molecule to another.
A coenzyme in photosynthesis is NADP.
NADP transfers hydrogen- it can reduce (give hydrogen to) or oxidise (remove hydrogen from) a molecule.
Coenzymes in respiration are: NAD, coenzyme A, FAD
NAD and FAD transfer hydrogen,they can reduce (give H) or oxidise (remove H)
Coenzyme A transfers acetate between molecules
(When hydrogen is transferred so are electrons).
Useful process for energy I didn't mention...
Plants need energy for: Animals need energy for:
Photosynthesis Muscle contraction
Active transport Maintaining body temperature
DNA replication Active transport
Cell division DNA replication
Protein synthesis Cell division
FYI- photosynthesis is the process where energy from light is used to make glucose from water and carbon dioxide. The light energy is converted to chemical energy in the form of glucose.
1. Write down three biological processes in animals that need energy.
2. What is photosynthesis?
3. What is the overall equation for aerobic respiration?
4. How many phosphate groups does ATP have?
5. Give the name of the coenzyme involved in photosynthesis.
ATP is the immediate source of energy inside a cell. Describe how the synthesis and breakdown of ATP meets the energy needs of a cell. (6 marks)
Exam question answer
Any from the 8 points:
1. in the cell, ATp is synthesised from ADP and inorganic phosphate (Pi)
2. Using energy from an energy -releasing reaction e.g. respiration
3. Energy is stored as chemical energy in the phosphate bond
4. ATP synthase catalyses this reaction
5. Atp then diffuses to the part of the cell that needs energy
6. Here it's broken down back to ADP and Pi
7. THis is catalysed by ATPase
8. Chemical energy is released from the phosphate bond and used by the cell.
ATP synthase synthesises ATP, and ATPase breaks it down
Adaptations of the leaf
Large surface area to collect maximum sunlight
Arrangement of leaves minimises overlapping and shadowing
Thin to create short diffusion pathway
Transparent cuticle + epidermis so light through to photosynthetic mesophyll cells
Long narrow upper mesophyll cells packed with chloroplasts
Numerous stomata for gas exchange
Stomata open and close in response to light intensity
Air spaces in lower mesophyll allow diffusion of oxygen and carbon dioxide
Xylem brings water to leaf cells
Phloem carries away sugars produced in photosynthesis
Photosynthesis takes place in the chloroplasts...
Chloroplasts are small, flat organelles found in plant cells
Have double membrane called the chloroplast envelope
Thylakoids are stacked up into structures called grana (singular = granum)
Chloroplasts contain photosynthetic pigments that absorb the light energy:
Chlorophyll A, Carotene, Chlorophyll B
Pigments found in thylakoid membranes attached to proteins.
Protein + pigment = photosystem
Photosystem I (PSI) absorbs light best at wavelength 700nm
Photosystem II (PSII) absorbs light best at wavelength 680nm
Stroma (gel-like liquid) surrounds thylakoids. Contains enzymes, organic acids, and sugars
Carbohydrates produces by photosynthesis stored as starch grains in stroma
Site of the Light- Dependant Reaction
This takes place in the thylakoids of the chloroplasts:
Thaylakoid membranes provide large sufrace area for attachment of chlorophyll, electron carriers and enzymes
Proteins in the grana hold the chlorophyll so to allow maximum light absorption
Granal membranes have enzymes attached to help manufacture of ATP
Chloroplasts contain DNA and ribosomes so they can quickly and easily manufacture proteins needed for light-dependant reaction.
The Light-Dependant Reaction
Reaction needs light energy and takes place in thylakoid membranes of chloroplasts
Light energy absorbed by photosynthetic pigments in photosystems and converted to chemical energy
Light energy used to add a phosphate to ADP to form ATP and to reduce NADP to form reduced NADP.
ATP transfers energy and reduced NADP transfers hydrogen to light-independant.
During process, H20 oxidised to 02.
Light energy absorbed by photosystems is used for:
1. Phosphorylation of ADP to make ATP
2. Making reduced NADP from NADP
3. Splitting water into protons (H+ ions), electrons and oxygen - photolysis
Light-dependant reaction includes two types of phosphorylation: non-cyclic and cyclic, each producing different products
Non-cyclic Phosphorylation produces ATP reduced NA
Need to know- photosystems linked by electron carriers, which are proteins that transfer electrons. Photosystems and electron carriers form electron transport chain. (A chain of proteins through which excited electrons flow).
All these happen together, but splitting them up makes things easier:
- Light energy is absorbed by Photosystem II, and excites electrons in chlorophyll
- Electrons move to a higher energy level (more energy) and move along electron transport chain to PSI.
-Photolysis of water produces protons (H+), electrons and 02
- Electrons that have moved up chain must be replaced
- Light energy splits water H20 --> 2H+ + 1/2 02
Non-cyclic phosphorylation continued...
Excited electrons lose energy as they move along electron transport chain
This energy is used to transport protons into the thylakoid, so it has a higher concentration of protons than the stroma
Forms a proton gradient across the membrane
Protons move down gradient into stroma via the enzyme ATP synthase
Energy from this combines ADP and inorganic phosphate (Pi) to form ATP
The movement of H+ across a membrane to form ATP called chemiosmosis
Light energy absorbed by Photosystem I which excites electrons to an even higher level
Electrons are transferred to NADP along with a proton from the stroma to form reduced NADP.
Cyclic Phosphorylation- only produces ATP
Cyclic Phosphorylation only uses Photosystem I (PSI)
Called "cyclic" as electrons from chlorophyll molecule are not passed onto NADP
Instead they are passed back to PSI via electron carriers
Electrons are therefore recycled and repeatedly flow through PSI
Process doesn't produce any NADP or 02 and only produces small amounts of ATP.
So pretty much, from above, only steps 1 and 3 occur.
Summary of two the two reactions:
NADPH is just reduced NADP so don't panic (NADP with a hydrogen get it?)
Light- Independent reaction takes place in the stroma of the chloroplast
Also called the Calvin Cycle, doesn't use light but depends on products from previous reaction.
ATP and reduced NADP from light-dependant reaction supply energy and hydrogen to make glucose from C02.
Light-Independent Reaction / The Calvin Cycle
The Calvin Cycle is also called carbon fixation becuase the carbon from C02 is fixed into an organic molecule.
The cycle makes a molecule call triose phosphate from C02 and something called ribulose bisphosphate ( a 5-carbon compound).
Triose phosphate can be used to make glucose and other organic substances.
Needs ATP and H+ to keep it going, reactions linked in a cycle so ribulose bisphosphate is regenerated.
Steps of the Calvin Cycle
C02 enters leaf through stomata and diffuses into stroma of chloroplast
Here it combines with ribulose bisphosphate- RuBP, a 5 carbon compound to mke an unstable 6 carbon compound.
This quickly breaks down into two molecules of a 3 carbon compound called glycerate 3-phosphate- GP.
Ribulose bisphosphate carboxylase (rubisco) catalyses C02 and RuBP reaction
ATP from light dependent reaction provides energy to turn GP into a different 3-carbon compound called triose phosphate, TP.
Reaction also requires H+ ions that come from reduced NADP in light-dependent reaction. Reduced NADP is recycled to NADP.
Triose phosphate (also can be called GALP, glyceraldehyde 3-phosphate) is then converted into useful organic compounds e.g. glucose
Steps of Calvin Cycle continued...
Five out of every six molecules of TP produced in cycle aren't used to make hexose sugars but are are used to regenerate RuBP.
Regenerating RuBP uses the rest of the ATP produced by the light-dependent reaction.
TP and GP are converted into useful organic substances like glucose
- Calvin cycle is the starting point for making all organic substances a plant needs.
- TP and GP are used to make carbs, lipids, proteins and nucleic acids.
Carbs- made by joining two TP's together, larger- made by joining hexose sugars
Lipids- made using glycerol synthesised from TP and fatty acids, synthed by GP
Proteins- some amino acids are made from GP
Nucleic acids- sugar in RNA (ribose) is made using TP
Calvin Cycle- turns 6 times to make 1 hexose sugar
* 3 turns = 6 molecules of TP because 2 molecules TP made for every 1 C02 *
* 5/6 TP molecules used to regenerate RuBP- ribulose bisphosphate *
* So for every 3 turns, only 1 TP is produced thats used to make a hexose sugar *
* Hexose sugar has 6 carbons though,so 2 TP molecules needed to make 1 hexose sugar *
* So cycle must turn 6 times :) *
* 6 turns of the cycle need 18 ATP and 12 reduced NADP from light-dependent *
Optimum conditions for photosynthesis:
High light intensity- light needded to provide energy for light-dependent. HIgher the intensity= more energy it provides
Certain wavelength- Photosynthetic pigments chlorophyll a, chlorophyll b and carotene only absorb red nd blue in sunlight. Green is reflected (plants look it)
Temperature around 25 degrees- below 10 enzymes become inactive, over 45 enzymes become denatured. At high temperatures stomata close to void water loss, slows photosynthesis as less carbon dioxide enters the leaf.
Carbon dioxide at 0.4%- there is 0.04% of the gas in the atmosphere. Increasing to 0.4 gives higher rate of photosynthesis, but any higher and the stomata start to close.
Plants also need constant supply of water- too much and soil becomes waterlogged (reducing uptake of magnesium for chlorophyll a), too little and photosynthesis has to stop.
Light, temperature and C02 can all limit photosynt
Limiting factor= at any given moment, the rate of a physiological process is limited by the factor that is t its least favourable value.
On a warm, sunny day, C02 is usually the limiting factor. At night, its light intensity.
If one factor is too high or low, photosynthesis will be limited, even if the others are ok.
Saturation point= Where a factor is no longer limiting the reaction- something else has become the limiting factor.
Light- A graph would increase and then level off... as light intensity increases, so does photosynthesis. Levels off after the saturation point, as something else is limiting.
Temperature- Graph normally has two temps. Both level off when light intensity is no longer the limiting factor. and e.g. line at 25 degrees levels at a higher point than 15, showing temp was a limiting factor at 15 degrees.
C02 concentration- Two lines, both level off when light is not the limiting factor. graph at 0.4 levels off higher than 0.04 so co2 must have been a limiting factor at 0.04. Limiting factor wouldn't be temp as its the same for both graphs.
Commercial growers and greenhouses
Create optimum conditions in greenhouses to minimise limiting factor effects, and to increase plant growth and yield.
C02 concentration - C02 added to air by burnign propane in a generator
Light intensity - light can get in through glass and use lamps at night
Temperature- Glasshouses trap heat energy from sunlight. Heaters and coolers also used and sir circulation systems make sure temperature is even throughout.
Answer as to why more C02 is good:
Plants use C02 to produce glucose by photosynthesis. The more C02 they have, the more glucose they can produce, this means that they respire more and so have more ATP for DNA replication cell division and protein synthesis.
Four stages of aerobic respiration:
Glycolysis, link reaction, krebs cycle and oxidative phosphorylation
First 3 stages are a series of reactions, products from theses used in final stage to produce ATP.
First stage happens in the cytoplasm of cells and the other three stages take place in the mitochondria. (mitochondria has an outer membrane, inner membrane, folds called cristae in inner membrane for large SA and a matrix).
All cells use glucose to respire. But organisms can also break down other complex organic molecules (e.g. fatty and amino acids) which can then be respired.
Involves splitting one molecule of glucose ( 6 carbon) into two molecules of pyruvate (3 carbon).
1st stage of aerobic and anaerobic, doesn't need oxygen, so is anaerobic itself.
Stages of Glycolysis diagram
Stages of Glycolysis
ATP is used to phosphorylate glucose---> triose phosphate. This is then oxidised, releasing ATP. Overall the net = 2 ATP
Stage 1- Phosphorylation
Glucose is phosphorylated by adding 2 phosphates from 2 molecules ATP. This creates 1 molecule of hexose bisphosphate and 2 molecules ADP. Hexose bisphosphate then split into 2 molecules of triose phosphate
Stage 2- Oxidation
Triose phosphate is oxidised (loses hydrogen) forming two molecules pyruvate. NAD collects the hydrogen ions, forming 2 reduced NAD. 4 ATP are produced but 2 were used up in stage 1, so net gain = 2 ATP
What happens to the products:
The 2 molecules reduced NAD go to last stage, oxidative phosphorylation. The 2 pyruvate molecules are actively transported into matrix of mitochondria for link reaction.
Link reaction diagram
Takes place in the mitochondrial matrix
Pyruvate is decarboxylated- 1 carbon atom removed from pyruvate in form of C02
NAD is reduced- it collects hydrogen from pyruvate, changing pyruvate to acetate
Acetate is combined with coenzyme A (CoA) to form acetyl coenzyme A
No ATP is produced in this reaction
Link reaction occurs twice for every glucose molecule
2 pyruvate molecules are made for every glucose molecule that enters glycolysis.
Means the link reaction and Krebs cycle must happen twice for every glucose molecule, so for each glucose molecule:
2 molecules acetyl coenzyme A go into the Krebs cycle
2 C02 molecules are released as a waste product
2 molecules of reduced NAD are formed and go to final stage- oxidative etc.
Krebs cycle diagram
Krebs cycle produces Reduced Coenzymes and ATP
Involves a series of redox reactions. Takes places in the mitochondria. One cycle for every pyruvate molecule, so two cycles for every glucose molecule.
Step 1: Acetyl CoA from link reaction combines with oxaloacetate to form citrate. Coenzyme A goes back to the link reaction to be used again
Step 2: 6 carbon citrate molecule converted to a 5 carbon molecule by decarboxylation. Dehydrogenation also occurs (so hydrogen removed). Hydrogen is used to produce reduced NAD from NAD
Step 3: 5 carbon molecule converted to a 4 carbon molecule. Decarboxylation and dehydrogenation occur, producing 1 molecule reduced FAD and two of reduced NAD (reduced coenzymes). ATP is produced by direct transfer of a phosphate group from intermediate compound to ADP. This is called substrate-level phosphorylation.
Citrate has now been converted into oxaloacetate
Products of Krebs cycle used in Oxidative phosphor
Some products are reused, some released and some used for the next stage of respiration:
1 coenzyme A= used in the next link reaction
Oxaloacetate = Regenerated for use in the next Krebs cycle
2 C02 = Released as waste product 1 ATP= Used for energy
3 reduced NAD and 1 reduced FAD= To oxidative phosphorylation
1 reduced FAD= To oxidative phosphorylation
Produces lots of ATP (point of previous stages= make reduced NAD and FAD)
Energy carried by electrons, from reduced coenzymes (NAD/FAD) to make ATP
Involves two processes: electron transport chain and chemiosmosis
1. Hydrogen atoms released from reduced NAD and FAD as they're oxidised to NAD and FAD. Hydrogen splits into protons (H+) and electrons (e-). (regenerated coenzymes are then reused in the Krebs cycle)
2. Electrons move along electron transport chain (made up of electron carriers) losing energy at each carrier
3. Energy used by electron carriers to pump protons from the mitochondrial matrix into the intermembrane space (space between inner and outer mitochondrial membranes).
4. Concentration of protons is higher in intermembrae space than matrix, forms electrochemical grdient (concentrtion gradient of ions)
5. Protons move down gradient, into matrix via ATP synthase.
6. Movement drives synthesis of ATP from ADP and Pi - Chemiosmosis
7. In the matrix, at the end of the electron transport chain, the protons electrons and 02 (from the blood) combine to form water.
8. Oxygen is said to be the final electron acceptor.
32 ATP can be made from one glucose molecule
Oxidative phosphorylation makes ATP. Energy is used from reduced coenzymes- 2.5 ATP from reduced NAD and 1.5 ATP from reduced FAD.
Stage Molecules produced No. of ATP molecules
Glycolysis 2 ATP 2
Glycolysis 2 reduced NAD 2 x 2.5 = 5
Link reaction (x2) 2 reduced NAD 2 x 2.5 = 5
Krebs cycle (x2) 2 ATP 2
Krebs cycle (x2) 6 reduced NAD 6 x 2.5 = 15
Krebs cycle (x2) 2 reduced FAD 2 x 1.5 = 3
Total ATP ------------------> 32
Actual yield is lower because inner mitochondrial membrane is leaky, protons leak into matrix. Some reduced NAD formed in first 3 stages get used in those reactions instead of last one. Some ATP used in active transport of ADP, phosphate and pyruvate into mitochondria.
Doesn't use oxygen
Doesn't involve the link reaction, Krebs cycle or oxidative phosphorylation
2 types of anaerobic respiration: Alcoholic fermentation and Lactate fermentation
Both take place in the cytoplasm
Both produce 2 ATP per molecule of glucose
Both start with glycolysis which produces pyruvate
Lactate fermentation happens in mammals and produces lactate
Alcoholic fermentation occurs in yeast cells and produces ethanol
1. Reduced NAD from glycolysis transfers hydrogen to pyruvate to form lactate and NAD
2. NAD can then be reused in glycolysis
Production of lactate regenerates NAD, so glycolysis can continue even with little oxygen, so small amount of ATP is produced to keep things going
1. C02 is removed from pyruvate to form ethanol
2. Reduced NAD from glycolysis transfers hydrogen to ethanol to form ethanol and NAD
3. NAD can then be reused in glycolysis- so again process can continue with little oxygen.
Some bacteria carry out lactate fermentation
Alcoholic fermentation occurs in plants.