CAPE 2 - Photosynthesis: Structure of the leaf, Photophosphorylation & The Calvin Cycle

The structure of leaf

¢In flowering plants, the major photosynthetic organ is the leaf.

¢ The functions of a leaf are best achieved by containing chlorophyll, absorbing carbon dioxide (and disposing of oxygen) and have a water and solute supply/transport route.

¢has a large surface area and arrangement such that it can absorb as much light as possible.

Shape and position

¢Large surface area of the lamina

¢Large surface area-to-volume ratio for maximum exposure to light and efficient gas exchange

¢Arrangement of leaves (leaf mosaic) helps the plant to absorb as much light as possible

¢Blade held at right angles to incident light

¢Thinness minimises diffusion pathway for gaseous exchange

Stomata

¢many stomata in the lower epidermis, which are pores in the epidermis through which gaseous exchange occurs.

¢Each stomata is bounded by two guard cells, and

¢changes in the turgidity of theses guard cells cause them to change shape

¢so that they open and close the pore. If the guard cells gain water, the pore is open, and vice-versa.

Mesophyll

¢main site of photosynthesis - have many more chloroplasts than spongy mesophylls, and also have several adaptions to maximise photosynthetic efficiency;

¢Large Vacuole - Restricts chloroplasts to a layer near the outside of the cell where they can be reached by light more easily.

¢Cylindrical Arrangement - They are arranged at right angles to the upper epidermis, reducing the number of light-absorbing cross walls preventing light from reaching the chloroplasts. This also allows long-narrow air spaces between them, providing a large surface area for gaseous exchange.

¢Thin cell walls - to allow gases to more easily diffuse through them.

Vascular System

¢Supplies water and mineral salts (xylem)

¢Removes products of photosynthesis (phloem)

¢As supporting skeleton together with lignified collenchyma and sclerenchyma

Chloroplasts: The Sites of Photosynthesis in Plants

¢In eukaryotes, photosynthesis takes place in organelles called chloroplasts.

¢Approximately 3 – 10 µm in diameter and are visible with a light microscope

¢Surrounded by two membranes, which form the chloroplast envelope.

¢Contain chlorophyll and other photosynthetic pigments located on a system of membranes

¢The membranes run through a ground substance called stroma.

¢The membrane system is the site of the light-dependent reactions in photosynthesis.

¢The membranes are covered with chlorophyll and other pigments, enzymes and electron carriers.

¢The system contains of many flattened, fluid-filled sacs called thylakoids which form stacks called grana.

¢The stroma is the site of the light independent reactions of photosynthesis.

¢The structure is gel-like containing soluble enzymes for the Calvin cycle and other chemicals such as sugars and organic acids.

Trapping Light Energy

¢Light energy is trapped by photosynthetic pigments

¢Different pigments absorb different wavelengths of light.

¢The photosynthetic pigments of higher plants form two groups: chlorophylls and carotenoids.

A Photosystem: A Reaction Center Associated with Light-Harvesting Complexes

¢ A photosystem

—Is composed of a reaction center surrounded by a number of light-harvesting complexes

¢ The light-harvesting complexes

—Consist of pigment molecules bound to particular proteins

—Funnel the energy of photons of light to the reaction center

¢ When a reaction-center chlorophyll molecule absorbs energy

—One of its electrons gets bumped up to a primary electron acceptor

Light-dependent reactions - Photophosphorylation

CLICK HERE FOR: Cyclic and Noncyclic Photophosphorylation animation

¢Include ATP synthesis in photophosphorylation and photolysis to give hydrogen ions

¢The hydrogen ions combine with a carrier molecule NADP to make reduced NADP

¢Photophosphorylation of ADP to ATP can be cyclic or non-cyclic depending on the pattern of electron flow.

¢NADP - nicotinamide adenine dinucleotide phosphate.

—It is a coenzyme that serves as an electron carrier in a number of reactions, being alternately oxidised.

¢NADPH – reduced nicotinamide adenine dinucleotide phosphate (NADP) carrying electrons and bonded with a hydrogen (H) ion; the reduced form of NADP.

Non-cyclic Photophosphorylation

Chemiosmosis

CLICK HERE FOR: Chemiosmosis animation

The Light Independent Reaction: Cyclic Photophophorylation - Cyclic Electron Flow

¢Occurs under certain conditions

—. Photoexcited electrons take an alternative path

—. Only photosystem I is used

—. Only ATP is produced

The Calvin cycle uses ATP and NADPH to convert CO2 to sugar

CLICK HERE FOR: Calvin Cycle animation

¢The Calvin cycle

—Is similar to the citric acid cycle

—Occurs in the stroma

¢The Calvin cycle has three phases

—Carbon fixation

—Reduction

—Regeneration of the CO2 acceptor

Photorespiration:

¢Concept 10.4: Alternative mechanisms of carbon fixation have evolved in hot, arid climates

¢On hot, dry days, plants close their stomata

—Conserving water but limiting access to CO2

—Causing oxygen to build up

¢In photorespiration

—O2 substitutes for CO2 in the active site of the enzyme rubisco

—The photosynthetic rate is reduced

C4 & CAM Plants

¢C4 plants minimize the cost of photorespiration

—By incorporating CO2 into four carbon compounds in mesophyll cells

¢These four carbon compounds

—Are exported to bundle sheath cells, where they release CO2 used in the Calvin cycle

¢CAM plants

—Open their stomata at night, incorporating CO2 into organic acids

¢During the day, the stomata close

—And the CO2 is released from the organic acids for use in the Calvin cycle

CAPE 1 - Water: Properties

PROPERTIES OF WATER

CLICK HERE FOR: tutorial on properties on water

CLICK HERE FOR: salt vs. sugar dissolving in water animation

CLICK HERE FOR VIDEO ON: Cohesion and Adhesion

 CLICK HERE FOR ANIMATION: interactions in the phases of water

CAPE 1 - Water: Introduction

WATER

A water molecule consists of one oxygen atom covalently bonded to two hydrogen atoms. 

• the electrons are not shared perfectly evenly: the oxygen atom is capable of pulling them towards itself and further away from the hydrogen atoms. 
• The result is that the oxygen part of the molecule becomes slightly negatively charged, and the hydrogen atoms slightly positively charged. 

Water is therefore described as a polar molecule (polar means charged internally).

Two atoms, connected by a covalent bond, may exert different attractions for the electrons of the bond. In such cases the bond is polar, with one end slightly negatively charged and the other slightly positively charged.

HYDROGEN BONDS

• Because they are polarized, two adjacent H2O molecules can form a linkage known as a hydrogen bond. 
• Hydrogen bonds have only about 1/20 the strength of a covalent bond.
• Hydrogen bonds are strongest when the three atoms lie in a straight line.

WATER STRUCTURE

• Molecules of water join together transiently in a hydrogen-bonded lattice. 
• Even at 37oC, 15% of the water molecules are joined to four others in a short-lived assembly known as a “flickering cluster.”
• The cohesive nature of water is responsible for many of its unusual properties, such as high surface tension, specific heat, and heat of vaporization.

HYDROPHILIC MOLECULES

Substances that dissolve readily in water are termed hydrophilic. 

• They are composed of ions or polar molecules that attract water molecules through electrical charge effects. 

• Water molecules surround each ion or polar molecule on the surface of a solid substance and carry it into solution.

HYDROPHOBIC MOLECULES

Molecules that contain a preponderance of non-polar bonds are usually insoluble in water and are
termed hydrophobic. 
This is true, especially, of hydrocarbons, which contain many C–H bonds.

• Water molecules are not attracted to such molecules and so have little tendency to surround them and carry them into solution. 

• This is known as formation of micelles. One very good example is shown below.

Feeding Relationships - pyramids

Population sizes

Now you have started thinking about the numbers of animals, the population sizes.

A population is a group of animals of the same species living in an area.

These are never exactly the same but over time they fluctuate about a constant level. There are six factors that can affect the population size, these are shown in the following diagram:

If the birth rate increases the population size will increase.

If the death rate increases due to an increase in predators the population size will decrease.

If competition increases the population will decrease.

Competition occurs when another species that eats the same food (or occupies the same space) comes into an area.

The other two factors are less common. They arise if animals move from one area to another, usually in migration.

You need to be able to answer questions that suggest a factor and ask what effect it would have on population size. Other factors might be the effects of a disease, or of changes in available light, or space, among other factors.

Now lets look at how two populations interact.

How do the numbers of a predator effect the numbers of its prey?

You can see that as the number of herbivores increases it is followed slightly later by a rise in the population size of the carnivores. There is a time lag between the two. This is due to the time it takes for carnivores to adjust to the presence of more food i.e. to produce baby carnivores.

If too many herbivores are eaten and their numbers drop, what happens?

There is a time lag and then the numbers of carnivores also falls. This is because there are too few herbivores for all the carnivores to eat and so some starve.

It's a hard life!

Pyramids

A nice way to show the size of different populations of organisms is by building a pyramid.

If you count up how many of each type of organism you have you can set up a pyramid of numbers like this:

The width of each trophic level tells you how many there are of each type. As you go up the pyramid there are fewer individuals on each trophic level.

It can be done for an individual food chain such as the one we had originally. Although it looks a little odd since there are only a few pea plants.

This is because when food chains or webs include plants such as trees there are only a few but they are very large.

A different way to show these food webs is to do a pyramid of biomass.

To do this you take the total masses of the individuals at each trophic level. So you need to go round and weigh each plant or animal.

Have you tried to weigh a tiger?

The final pyramid of biomass looks similar to the pyramid of numbers.

Tricky!

The main difference between them is that pyramids of numbers can look 'wrong' as there might only be one tree on the bottom trophic level. Pyramids of biomass always look right, since a tree will weigh much more than anything else.

So in an exam always be careful that you know which pyramid is which!

Energy flows

All this talk of food!

But why do we need food?

We only eat because we need fuel for respiration.

Respiration gives us energy which we use for growth, activity and so on.

The Sun is the ultimate source of all the energy in the environment. However the producers can only capture a small fraction of it using photosynthesis.

When plants get eaten by an animal what happens to any of that energy stored in them?

It is passed on to the animal - the consumer. The same happens if that animal is then eaten by another.

However not all the energy is available, some is lost at each stage.

The reasons for this include the energy for staying alive and growing. Any extra energy is stored, usually in the form of fat.

The amount of energy and biomass lost at each stage is about 90%.

In a fully grown animal 90% of the biomass it eats is lost in the faeces - that's why you can burn them for fuel. Try it sometime!

So the amount of energy that gets to the top carnivore is a fraction of that given out initially by the sun. By the time the hawk gets its energy there is only about 0.01% of the energy present in the pea plants. Not much!

This explains why pyramids of biomass have the expected shape. The amount of biomass (or energy) gets less each time you move up to the next trophic level.

Efficient food

So little energy is left by the end of a food chain that they cannot get too long. In fact the shorter they are the better. That's why on those survival programmes they spend so much time eating worms!

A better idea is to eat plants yourself, like vegetables, fruit and grains. They will provide you with more energy than you would get from raising a herd of cows on the same piece of land.

Losing one trophic level means that you get more energy at the end. It is more efficient.

Before you become a total vegetarian you do need to remember about vitamins and minerals. Deciding on such a diet needs careful thought to avoid malnutrition.

Intensively reared livestock are kept in restricted conditions so that they do not 'waste' energy moving around. However, apart from the ethical questions, they still end up wasting energy from their food.

Land can feed more people if used for crops. However some land such as hillsides and marshy areas are not suitable for crops and so rearing animals on it is the most efficient use.

Any organism has to keep up with any changes in their environment. They have to adapt in order to survive.

Adaptation means making changes in what you do or how you do it. Without the necessary changes you will fail to compete and die.

A favourite exam question is to ask you to think why a particular characteristic helps an animal or plant survive. Each has to adapt to its own niche - the place where it lives and fits into the local environment.

For example: a rabbit has the following adaptations to its life as a prey animal:

Adaptation	Survival advantage
Large ears	To hear predators
Thick brown fur	Good camouflage and for warmth
White tail	To act as a warning flag to other rabbits when its running away!
Fast and agile running	To avoid predators
Eyes on side of head	Allows all-round vision to watch for predators

Food webs and the size of populations has probably made you realise how interconnected things are in the environment.

This is not just true about the plants and animals but it is also the case for all the chemical molecules present on the Earth. The atoms that make them up cannot be destroyed, they just get moved around and around.

So if you look at a particular type of chemical you can follow it as it goes through a cycle in the environment. The best known are the carbon and nitrogen cycles.

First of all the chemicals need to get out of the animals or plants that they are in, this occurs through the process of decomposition.

Decomposition

All things die, sadly. But their molecules go marching on!

The cells and bodies of plants and animals decay by the action of soil bacteria and fungi. They are often called the decomposers. (There's a joke about Beethoven there somewhere).

The molecules released during decay are absorbed by the bacteria, fungi and also back into the soil from where plants can draw them up through their roots.

The decomposers work best at their optimum conditions since they use enzymes. The kind of conditions needed are shown nicely by the humble compost heap.

There are five necessary conditions or factors for good decomposition:

1. Organic material: plant or animal material to decay
2. Water: the right amount of moisture
3. Oxygen: air must be able to get to the material
4. Warmth: the temperature cannot be too hot or too cold
5. Decomposers: bacteria or fungi are needed to do the job

You would not get decomposition if one of these was missing.

The molecules released by this decay process include the most important elements carbon and nitrogen which have their own environmental cycles.

thanks to www.s-cool.co.uk

Feeding Relationships - chains and webs

Living in the wild is pretty dangerous!

You spend all the time trying to find your dinner and avoid ending up as someone else's.

We can look at who eats whom in the environment by setting up food chains and food webs. They help us by breaking up the environment into understandable bits.

Food Chains

With a food chain you always start off with a plant as they produce all the energy in the environment from photosynthesis. A plant is therefore called a producer.

Herbivores are animals that eat plants and they are placed next in the food chain. They consume the plants and so are also the primary consumers.

To show that the herbivore eats the plant in our chain we use an arrow.

The example food chain below shows this:

The direction of the arrow is very important. It shows who is eaten by who.

So in our example the maize is eaten by the locust, which are in turn eaten by the lizard, and so on.

If the locust are the primary consumers here, or the herbivores, the lizard is the secondary consumer. Then the snake is the next (tertiary) consumer, and so on.

The snake does not just eat other animals but will sometimes also eat fruit and nuts. Therefore you could actually call it an omnivore.

The animal that occupies the other trophic level is the top carnivore as nothing else will eat it.

Food Webs

Our example was very simple. Usually in natural ecosystems they are more complex, this is because one predatory species will usually eat more than one prey species.

What would happen if you were an animal that only ate one animal or plant?

If that food source ran out, you would starve to death. Not a good idea.

Another good idea for eating up your greens!

Animals tend to eat food from a variety of sources, different plants and animals.

Therefore our food chain is not very accurate, it does not cover all the connections.

In order to obtain a more accurate idea of what is going on we need to construct a food "web":

The food web attempts to show which organisms eat any other animal. They can get pretty complicated but are still as easy to read as a food chain. Just remember the arrows.

Now think about what happens if one animal species gets wiped out.

What do the snakes and the kingfishers do if all the frogs disappear?

The snakes will die out but the kingfishers will just start eating more trough and carp