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Higher Biology

Unit 1 Revision

Name: ________________________

Cell Ultrastructure

Introduction and Revision

Cells are the basic units that make up nearly all living things. Most cells have certain

features in common. Cells can easily be identified as plant or animal in origin as there

are basic differences in their structures.

Unicellular Organisms

Some microscopic living things consist of only one cell. These are called Unicellular or

Single-celled organisms. To survive, such organisms must possess all the structures

needed to perform all the functions essential to life, all in the one cell.

Some unicellular organisms have the characteristics of animal cells. These belong to a

group of animals called protozoans. Others are like single plant cells, and these all

belong to the group of plants called algae. However there are some types that cannot

easily be classified, as they possess some characteristics of both animals and plants.

Multicellular Organisms

A single cell cannot grow indefinitely. When it reaches a certain size it either stops

growing or divides into 2 smaller cells that then grow. Indefinitely growth appears to be

limited by the nucleus. It seems that any one nucleus can only exert control over a

certain volume of cytoplasm. In terms of evolution this means for an organism to

increase in size it must become multicellular.

Becoming multicellular, then allows an increase in size. With this comes the possibility of

specialisation. Instead of every cell carrying out every task, certain cells become

specialised for one function. This division of labour permits greater efficiency and

enables the organism to exploit environments that are denied to simpler forms.

With increased size and cell specialisation come all sorts of other advantages. For

example, better muscles and skeleton can be developed. These give an animal

greater strength and allow it to tackle larger prey or withdraw faster from predators.

Having specialised cells also means that more sophisticated physiological mechanisms

can be developed that allows constant body temperature to be maintained

independent of the surrounding temperature.

Cell Variety and Function

A group of similar cells working together and carrying out a specific function are known

as a ‘Tissue’, e.g muscle. A group of different tissues make up an ‘organ’, e.g. stomach.

A group of related tissues and organs, e.g. stomach and intestines make up a ‘System’,

e.g. digestive system.

Cells are specialised to perform particular tasks. e.g. red blood cells have no nucleus so

they can carry more oxygen.

Plant Cells Revision

Answer the following questions on plant cells and tissues.

1) What function do the palisade mesophyll cells have?

2) The shape of the spongy mesophyll cells aid their function, describe this shape and

function.

3) Xylem are described as ‘… dead hollow tubes…’, how does this allow them to carry

out their job?

4) Xylem vessels contain lignin, what is the function of lignin?

5) What is the function of the phloem?

6) Another cell is associated with the phloem cell, what is it and what does it do?

Animal Cell Revision

1. What is the function of a Red Blood Cell (RBC)?

2. How does the shape of the RBC aid its function?

3. Describe the function of the ciliated epithelium tissue.

4. How does the structure of nerve tissue aid its function?

Cell Structure

Under very powerful electron microscopes it is possible to see many tiny structures

suspended in the cytoplasm. These tiny, sub-cellular structures are called organelles.

These organelles carry out various chemical processes which are called the cell’s

metabolism.

Animal Cell

Plant Cell

Absorption and Secretion of Materials

Diffusion Revision

This is the movement of molecules or ions from a region of high concentration to a

region of low concentration of that molecule along a concentration gradient, until

evenly spread.

For example: movement of oxygen and glucose into a cell and carbon dioxide out of a

cell.

Osmosis Revision

This is the movement of water molecules from a region of High Water Concentration

(HWC) to a region of Low Water Concentration (LWC) along a concentration gradient,

through a selectively permeable membrane.

Solutions

If a solution is of a higher water concentration than the cell, the solution is said to

be Hypotonic.

If a solution is of a lower water concentration than the cell, the solution is said to

be Hypertonic.

When the solution and cell concentration are equal, it is known as an Isotonic

solution.

Effect of Osmosis on Cells

The Plasma (Cell) Membrane

As you know, Osmosis is the movement of water through a selectively permeable

membrane. Below is a simplified diagram of these membranes. It is known as a

Phospholipid Bilayer, due to it’s double layer of phospholipids. It is often referred to as

the ‘Fluid Mosaic Model’ due to the ‘movement’ of the bilayer.

Label the diagram

Proteins can either be partly embedded or extend right across to the other side. Some

of these also contain channel, which gives the cell surface membrane its selectively-

permeability.

The other proteins on the membrane have other functions such as

Support

Channels for transport of

molecules

Carriers, e.g. Sodium/Potassium

pump (see next page)

Enzymes

Receptors for hormones, etc

Active Transport

As mentioned on the last page, some of the proteins embedded in the plasma

membrane can act as Carriers.

Active Transport is the movement of molecules or ions from a low concentration to a

high concentration against a concentration gradient through a plasma (cell)

membrane (this is the opposite movement from diffusion & osmosis which are passive

processes).

This process requires energy, which is supplied through respiration. Active transport

carriers are often known as ‘pumps’.

Some carriers exchange one ion for another, e.g. Sodium/Potassium Pump. Sodium is

pumped out while potassium is pumped in.

Label the diagrams below

The Cell Wall

As you know, Plant cells have an additional cell boundary compared to animal cells –

the Cell Wall.

This wall gives plant cells their rigid structure. It is a non-living layer, which is composed of

cellulose. This cellulose is made up of chains of glucose molecules grouped into fibres.

The cell wall is freely permeable.

Moving Larger Particles

Membrane transport systems can transport relatively small particles easily, involving the

proteins, however, sometimes cells need to take in or pass out larger particles. These

involve gross movements of the whole membrane – Endocytosis (taking particles into

the cell) and Exocytosis (Removing particles from the cell).

Endocytosis

Generally the substance is packaged up in a vesicle which is formed by part of the cell

membrane.

This process requires energy and an example of it is ‘Phagocytosis’ which you study in

‘Cellular Defence’.

Exocytosis

This is the reverse of endocytosis. It is a process by which a substance passes out of cells

while keeping the plasma membrane intact. The substance is enclosed in a vesicle. You

will study this in Protein Synthesis and Secretion.

Cell Variety and Function

Learning Outcome I can

find this

in my

notes

I can

do this

Label a drawing to show the Name and Function of the following cell

organelles:

Cell wall

Cell (plasma) membrane

Chloroplast

Golgi apparatus (body)

Lysosome

Mitochondrion

Nucleus

Nucleolus

Ribosome

Rough E-R

Smooth E-R

Define the term ‘tissue’

Name and state the function of different plant cells

Identify the specific features of each example and explain how they

enable the cell to function

Name and state the function of different animal cells

Identify the specific features of each example and explain how they

enable the cell to function

Give example of unicellular organisms

Absorption and Secretion of Materials

Learning Outcome

I can find this in

my notes

I can do

this

Give a definition of osmosis

Give examples of osmosis in plants and animals

Give a definition of diffusion

Give examples of diffusion in plants and animals

State that the cell wall is freely permeable

Describe the structure of the cell wall

State that the cell membrane is selectively permeable

Describe the structure of the cell membrane by referring to

the fluid-mosaic model, phospholipids and proteins

Draw and label a diagram of the fluid-mosaic model of the

cell membrane to show phospholipids & proteins

State two features of the cell membrane which give it special

properties and describe those properties

Give a definition of the term active transport

Describe the process of active transport by referring to carrier

molecules in the cell membrane

Give examples of active transport occurring in plants and

animals

Structure of Adenosine Triphosphate (ATP)

Adenosine triphosphate (ATP) is the energy molecule of the cell.

A molecule of ATP is composed of a complex organic molecule, adenosine, to which

three inorganic phosphates are attached.

Chemical energy is stored in the bonds between the inorganic phosphate molecules.

This stored energy is released when the bond attaching the last phosphate is broken by

enzyme action. This results in the formation of Adenosine Diphosphate (ADP) and

inorganic phosphate (Pi).

+

Energy is needed to regenerate ATP from ADP and inorganic phosphate.

During an energy releasing reaction ATP is generated from ADP and an

inorganic phosphate molecule using the energy released by that reaction.

Phosphorylation

There are 3 types of energy releasing reactions in which a cell can produce ATP from

ADP and Pi (phosphorylation): These are: Photophosphorylation (light energy to

chemical), substrate level phosphorylation (chemical energy to chemical energy),

Oxidative phosphorylation (chemical energy to chemical energy)

Use the words/phrases below to complete the passage: Phosphorylation; terminal

phosphate; adenosine; phosphates; reduced; glucose ; oxidised; adenosine diphosphate

(ADP); broken.

ATP is a molecule composed of____________________ and three _______________. Energy

is fixed into the molecule when the bond joining the ____________ ___________ to the rest

of the molecule is made. Energy is released when the bond is _____________. The

synthesis of ATP by the making of the bond is called ______________________ and is

achieved by the linking of inorganic phosphate to____________ ____________. This bond-

making process occurs in cells when an energy rich compound such as

_________________ is broken down by enzymes during respiration.

The Importance of ATP

ATP is found in all living cells. ATP was originally found in muscle fibres. Since then it has

been shown to fuel many processes such as transmission of nerve impulses, muscle

contraction, synthesis of new molecules and luminescence (fire fly).

Pi Adenosine Pi Pi

Metabolism

It takes a lot of energy to make large molecules e.g. fats from fatty acids and glycerol.

Metabolism has two parts:

Synthesis reactions requiring energy: The process of synthesising large molecules from

smaller ones is called anabolism. The energy comes from ATP.

Breakdown reactions releasing energy: The energy stored in the ATP molecule came

from energy releasing reactions called catabolic reactions.

Metabolism can be defined as the sum of all the chemical reactions both anabolic

and catabolic that take place in a cell.

ATP is the molecule which transfers energy from breakdown to synthesis reactions.

Oxidation and Reduction

Oxidation: The molecule is oxidized when it loses a hydrogen.

Reduction: The molecule is reduced when it gains a hydrogen.

NB. Remember: OIL RIG (oxidation is loss, reduction is gain)

Mitochondrion Structure

The mitochondrion is a sausage shaped organelle. It is the site of aerobic respiration.

The mitochondrion has a double membrane, the outer one is smooth whilst the inner

one is greatly folded into cristae which project into the fluid filled cavity called the

matrix.

The energy used for the synthesis of ATP from ADP plus inorganic phosphate (Pi)

becomes available during tissue respiration. Throughout this process glucose is

gradually oxidised during a series of enzyme controlled reactions. Such a series of

reactions is referred to as a metabolic pathway. Each reaction in such a series of

reactions is catalysed by its own enzyme. Respiration is an example of a metabolic

pathway which occurs in all living cells at all times. For the complete oxidation of

glucose, aerobic respiration must occur, this requires the presence of oxygen.

Aerobic Respiration

During respiration, glucose is broken down (oxidised) in a series of steps. Each of these

steps is under the control of a different enzyme.

Some of these steps involve the release of hydrogen. Each of these steps is controlled

by a dehydrogenase enzyme. There are many different types of dehydrogenase

depending on the substrate.

Other reactions in the respiration pathway involve the removal of carbon in the form of

carbon dioxide. These reactions are controlled by a series of enzymes called

decarboxylases.

Respiration can be divided into THREE major stages that can be studied individually.

1. Glycolysis 2. Krebs cycle 3. Cytochrome system

Stage 1: Glycolysis (breakdown of glucose)

Glycolysis is the name given to the first stage in the breakdown or oxidation of glucose.

In animals this glucose, if not already present in the blood, can be derived from the

breakdown of stored glycogen. In plants the equivalent food store is starch.

1. During glycolysis, Glucose (a 6 carbon molecule) is broken down to 2 molecules

of Pyruvic acid (a 3 carbon molecule)

2. Glycolysis takes place in the cytoplasm of the cell.

3. Oxygen is not required to be present for Glycolysis to occur.

4. During Glycolysis enough energy is released for the production of 4 molecules of

ATP. However, as 2 ATP molecules are used up to start the process the net

production of ATP from Glycolysis is only 2 ATP molecules for each glucose

molecule broken down.

5. Two hydrogen ions are released. These immediately combine with one of the

hydrogen carriers in the cell (a co-enzyme) called NAD (Nicotinamide adenine

dinucleotide). NAD = hydrogen carrier/acceptor, NADH2 = reduced hydrogen

acceptor.

Stage 2: The Krebs Cycle OR Citric Acid Cycle

After glycolysis, the process can only proceed if there is a supply of oxygen. The cycle

of reactions by which citric acid is gradually converted back to a 4-carbon compound

is called the Krebs cycle.

1. If oxygen is present, pyruvic acid molecules diffuse into the mitochondria, where

they are converted into a 2-carbon Acetyl group.

2. These Acetyl groups then join with Co-enzyme A molecules to form Acetyl Co-

enzyme A (Acetyl CoA).

3. These compounds then become involved in a cyclical sequence of reactions

known as the Krebs Cycle or Citric Acid Cycle.

4. In the Krebs Cycle Acetyl CoA reacts with a 4 carbon compound to form citric acid

(6 carbon compound).

5. This 6C compound is converted, by enzyme controlled reactions, to a 5C

compound, this is then converted into a 4C compound. This 4C compound is then

converted into two further 4C compounds. Two molecules of carbon dioxide are

released.

6. At certain stages of the cycle hydrogens are released. These hydrogens are

immediately picked up by the carrier NAD and taken to the cytochrome system.

7. The Krebs Cycle occurs in the matrix of the mitochondria.

Stage 3: The Cytochrome System

During both Glycolysis and the Krebs Cycle many compounds are oxidised by the

removal of hydrogen. This hydrogen never occurs as free atoms or molecules but is

immediately picked up by the carrier NAD.

1. The NAD transports the hydrogen to the Cytochrome System as NADH2.

2. The Cytochrome System occurs on the Cristae of the mitochondria.

3. As hydrogen passes along the carrier molecules of the cytochrome system

enough energy is released for the production of ATP. At the end of the

cytochrome system the hydrogen combines with oxygen to form water. Oxygen

is often referred to as the final hydrogen acceptor.

The total number of ATP molecules generated during the Cytochrome System is 36ATP,

making the over all ATP production for 1 glucose molecule 38ATP.

Cytochrome (Hydrogen Transfer) System

If oxygen is not present to act as the terminal hydrogen acceptor, hydrogen cannot pass

through the system so the cytochrome system and the Krebs Cycle cannot work.

Alternative Respiratory Substrates

Glucose is the normal substrate which is broken down by enzymes in tissue respiration to

release energy. Sometimes however, there is not enough starch or glycogen to provide

sufficient glucose to meet the energy requirements. In these cases other substrates

must be used. The diagram below shows how fats and proteins are converted into

substances which can enter the respiratory pathway. Carbohydrates, fats and proteins

can all be oxidised to produce ATP in respiration.

Anaerobic Respiration

Absence of Oxygen

Glycolysis occurs when oxygen is absent, but krebs cannot proceed. The pyruvic acid

has an alternative fate.

In Plants

In Animals

Due to the only partial breakdown of glucose, little energy is derived. There are only

2ATP molecules released during anaerobic respiration – these are those produced

during Glycolysis.

(Acetyl Co-A)

Respirometers

Another way of studying respiration is to measure the rate of uptake of oxygen using

devices known as respirometers. These can be set up in various ways but nearly all

work on the same principles. The idea is that a substance, usually soda lime or a strong

alkali (like potassium hydroxide) is placed in a sealed container along with a living

organism. The alkali absorbs any carbon dioxide produced by the organism.

The oxygen used up by the organism causes a reduction of volume and pressure of

gas inside the container, this is measured in one of a number of different ways. If the

time lapsed during the experiment is also measured, then a value for the quantity of

oxygen absorbed per unit of time can be obtained.

The apparatus below was set up to investigate rate of oxygen consumption in a small

animal.

1. What is the purpose of tube B?

2. Complete the diagram to show the missing contents of tube B.

3. Why is the soda lime included?

4. What is the purpose of the stopcocks?

5. How can the effect of room temperature be reduced?

Energy Release

Learning Outcome I can find

this in my

notes

I can

do this

State that ATP is the energy source for cells

Write the equation for the formation of ATP

State two examples of the use of ATP in a cell

State that ATP is formed during respiration

Name the three stages of aerobic respiration

List the names of the main compounds in aerobic respiration and

give the numbers of carbon atoms in each (glucose, pyruvic acid,

acetyl-Co-A and citric acid)

State that Glycolysis takes place in the cytoplasm

State that Glycolysis is the breakdown of glucose into pyruvic acid

with a net gain of 2ATP

State that pyruvic acid breaks down into acetyl-CoA with the

release of carbon dioxide

Draw the Krebs cycle

Identify the stages at which carbon dioxide is released

Identify the stages at which hydrogen is released

Name the carrier (NAD) which accepts the hydrogen

State that the Krebs cycle takes place in the matrix of the

mitochondrion

Describe the Hydrogen Transfer System (Cytochrome System) by

referring to oxidation, reduction, carriers, hydrogen, ADP, Pi, ATP,

oxygen and water

State that for complete oxidation to take place oxygen must be

present

State that the Hydrogen Transfer System takes place in the cristae

of the mitochondrion

State that energy may be released from a few individual steps in

the overall process, but most of the energy is made available by

the cytochrome system

Compare Aerobic and Anaerobic respiration (mention products,

conditions required, energy released, and the difference

between anaerobic respiration in plants and animals

Equation for Photosynthesis

This can be summarised as:

Chlorophyll

6CO2 + 6H2O C6H12O6 + 6O2

Light Energy

This is misleading because

It suggests that photosynthesis is a single reaction when it is in fact a complex

series of reactions

It suggests that oxygen could come from carbon dioxide when it in fact comes

from water

Raw materials needed for photosynthesis

Water from the soil

Carbon Dioxide from the air

In addition

Magnesium for chlorophyll production

The site of photosynthesis

Photosynthesis takes place in Chloroplasts. The different stages of photosynthesis take

place in the different parts of the Chloroplasts.

Chloroplast Structure

The light trapping pigments are located in the chloroplasts of the cell.

The chloroplast is bound by a double membrane

Grana appear like stacks of coins. Each granum contains chlorophyll, has a

large surface area and is arranged to absorb the maximum volume of light for

photosynthesis

The lamellae

are tubular

extensions

which link the

stacks of Grana.

They do not

contain

chlorophyll

A chloroplast is

approximately 5

microns in

length

Photosynthesis and light

What is white light?

White light is a form of radiant energy. This means that it travels from place to place as

waves. These waves always travel in straight lines. If a beam of white light is passed

through a glass prism, it is split into coloured components - the rainbow colours, red,

orange, yellow, green, blue, indigo and violet. These colours are known as the

spectrum of white light. Each colour of the spectrum has a different wavelength with

red having the longest wave and the blue, indigo and violet (the blue end) having the

shortest wave.

Visible white light from the sun is the source of energy for photosynthesis. When it strikes

a green leaf a lot of light is absorbed and a small percentage of this is used in

photosynthesis. The remainder of the light is either reflected or transmitted through the

leaf. Most leaves are green in colour and this is because they transmit green light.

Absorption of light

Different colours of light have different wavelengths. Chlorophyll does not absorb

different wavelengths evenly. The main colours absorbed are red and blue. The leaf

contains other pigments which can absorb different wavelengths of light. These

accessory pigments, xanthophylls and carotene transfer absorbed energy to the

chlorophyll molecule used in photosynthesis.

The different colours of white (visible) light form a spectrum if passed through a prism.

The absorption spectrum is the spectrum produced when white light is first passed

through a leaf extract. This shows the colours of light which the leaf extract has

absorbed.

Absorption spectrum of

extracted pigments

The absorption spectrum is the

spectrum produced when white

light is passed through a leaf

extract. This shows the colours

of light which the leaf extract

has absorbed.

Light is absorbed by chlorophyll. Chlorophyll does not consist of one pigment but a

range of pigments. By making a separate solution of each pigment the absorption

spectrum of each can be determined.

The Action Spectra

The action spectrum is a measure of the effectiveness with which the plant uses the

different wavelengths of light for photosynthesis. This can be measured either as the

gain in dry mass by plants grown in a particular wavelength or as the rate of

photosynthesis of plants growing in a particular wavelength.

The shapes of the absorption and action spectra graphs are almost the same.

Note: Some photosynthesis does occur in colours of light not absorbed by chlorophyll a,

this is because the accessory pigments absorb other wavelengths of light and pass the

energy onto the chlorphyll.

The Chemistry of Photosynthesis

In the process of photosynthesis, raw materials are assembled to make organic food

molecules according to this simple equation.

Light energy

Carbon dioxide + Water Glucose + Oxygen

Photosynthesis consists of two separate stages:

1. The first stage is light dependent and includes Photolysis

2. The second stage is a temperature dependent series of enzyme controlled reactions

called Carbon fixation or the Calvin cycle, or the light-independent reaction.

The two separate reactions occur in the chloroplast. The first is called the light reaction.

This stage occurs in the granum where the chlorophyll is found and is dependant on

light energy.

The second is called the Calvin cycle or Carbon Fixation. This stage occurs in the

stroma, this process is dependant on temperature because it is an enzyme catalysed

reaction.

Stage 1: Light dependent stage

During this reaction:

Water is split (photolysis)

Hydrogen is accepted by NADP to form NADPH2

Oxygen is released as a by-product

ATP is generated (photophosphorylation)

This production of ATP is known as photophosphorylation.

Chlorophyll

The ATP and NADPH2 are essential for the second stage of photosynthesis. They transfer

from the Grana to the Stroma.

Photolysis (the splitting of water)

Photophosphorylation

This is the generation of ATP using light energy. ATP is a source of energy which is

essential for the dark reaction to occur.

Stage 2: The temperature-dependent stage (Calvin Cycle)

Carbon fixation was discovered by Melvin Calvin and is also known as the Calvin Cycle.

The reactions of carbon fixation use hydrogen (NADPH) and ATP produced in

Photolysis, to reduce carbon dioxide to form a carbohydrate - glucose. It occurs in the

stroma of the chloroplast. This is the temperature-dependent stage.

CO2 C6H12O6

reduction

The events occurring in the Calvin Cycle

A molecule of CO2 enters the chloroplast by diffusion

The CO2 combines with a 5-carbon molecule of Ribulose Biphosphate (RuBP) to

form a 6-carbon unstable compound. This process is known as Carbon Fixation

The unstable 6-carbon compound rapidly splits into 2 molecules of 3-carbon

Glycerate Phosphate (GP)

3-carbon Glycerate Phosphate is converted to 3 carbon Triose Phosphate (TP).

This process requires energy and H+ ions.

The energy is provided by the breakdown of ATP into ADP + Pi. The H+ ions are

provided by the reduced hydrogen carrier NADPH2

N.B. Remember ATP and NADPH2 were generated during Photolysis

Glucose is then synthesised from a pair of Triose Phosphate molecules

These glucose molecules may then be used in respiration or joined together to

produce polysaccharides such as starch or cellulose. Other biochemical

reactions can convert the simple molecules produced in photosynthesis into

protein, fats and nucleic acids.

The remaining Triose Phosphate molecules not used to make glucose are

recombined to regenerate the carbon dioxide acceptor, RuBP. This process also

requires energy which is again obtained from the breakdown of ATP into ADP +

Pi.

REMEMBER!

Ribulose Biphosphate (RuBP) has 5 Carbons

Glycerate phosphate (GP) has 3 Carbons

Triose phosphate (TP) has 3 Carbons

Glucose has 6 Carbons

Limiting Factors in Photosynthesis

Chemical reactions such as photosynthesis can be speeded up and slowed down by

the prevailing conditions. A condition which is able to hold back the rate of a reaction

is called a limiting factor. For example, when baking a cake, a limiting factor might be

the temperature of the oven.

The main limiting factors in photosynthesis are light, temperature and carbon dioxide

concentration.

Although water is needed for photosynthesis it is rarely in short supply and need not be

considered as one of the limiting factors for photosynthesis.

The apparatus shown was set up to investigate the effect of light intensity on the rate of

photosynthesis in Elodea at a constant temperature of 20C. The rate was measured by

averaging the number of bubbles of oxygen gas evolved from the cut stem over three

periods of one minute. The light intensity was varied by altering the distance between

the lamp and the Elodea.

The principal of limiting factors is illustrated by the following graph:

Light can be seen to be limiting each graph A – D when the rate of photosynthesis

increases as the light intensity increases.

When the graph

levels off, another

factor is limiting the

rate.

A and B are slower

than C and D

because they

have a greater

concentration of

carbon dioxide.

learning Objectives

Photosynthesis

I can find this

in my notes

I can do

this

State that light is absorbed, transmitted and reflected by

a leaf

Name the four photosynthetic pigments and state their

function

Identify the wavelengths of light absorbed by a plant as

shown in an absorption spectrum

State that absorption occurs primarily in the blue and

red regions

State that accessory pigments absorb some light from

other regions of the spectrum and pass the energy onto

the chlorophyll

Describe the difference between an absorption

spectrum and an action spectrum

State that the chloroplast is the site of photosynthesis

Label a drawing of a chloroplast to show the grana,

stroma and starch grains

State the function of the grana and stroma

Name the two stages of photosynthesis

State that photolysis is the splitting of water using light

energy

Name the two products of photolysis

State that carbon fixation (Calvin Cycle) is needed for

the production of glucose

State that these reactions which require ATP and

Hydrogen which is provided by Photolysis, involves the

reduction of CO to form a carbohydrate

Name the three main compounds found in the Calvin

Cycle and the number of Carbon atoms in each

Draw a Calvin Cycle showing RuBP, GP, TP, glucose,

NADPH , ATP and CO in the correct place

State that photosynthesis derives major biological

molecules in plants (e.g. proteins, fats, carbohydrates,

nucleic acids, etc,

Name the environmental factors which can affect the

rate of photosynthesis

Give a definition of the term ‘Limiting factor’

RNA, DNA and PROTEIN SYNTHESIS

The type of protein produced by a cell depends on the primary structure of the protein.

This is determined by a gene located on the chromosome of a cell. The gene is the

code for a particular characteristic. The code is carried in the structure of the genetic

material known as Deoxyribonucleic acid or DNA. The DNA is held in place by

structural proteins.

Enzymes are proteins which catalyse all the reactions that take place in a cell. By

switching on or off the gene to produce an enzyme, a cell can control all the reactions

taking place in the cell.

An important part of your diet is protein. Protein is used in growth, in repair of wounded

tissues and for enzymes which control the chemical reactions in the body. It is our

genetic make up which allows us to use digested dietary protein to make the specific

human proteins we need.

The aim of this unit is to introduce the variety of protein molecules, to describe how they

are synthesised in cells according to the genetic instructions on DNA and try to explain

how they can be released from the cells by secretion.

Structure of proteins

Proteins are organic molecules i.e. they contain carbon. Cells contain 4 groups of

organic molecules. These are proteins, carbohydrates, lipids and nucleic acids. These

all contain carbon, hydrogen and oxygen. In addition proteins contain nitrogen and

some may contain sulphur or phosphorus.

Complete the table below:

Carbohydrate Fat Nucleic acid Protein

Elements

present

Carbon (C)

Hydrogen (H)

Oxygen (O)

Nitrogen (N)

Phosphorous (P)

Each protein is made from building blocks called amino acids. These are joined

together by peptide bonds to make polypeptides which link to form larger proteins.

There are 20 different types of naturally occurring amino acids. Nine of these are

essential amino acids. Essential amino acids must be included in an animal’s diet as

they cannot be synthesised by cells.

Variety of Proteins

Proteins are important molecules in biology and you will already be familiar with their

role as enzymes in cells. In this unit this idea is developed and the widely different

functions of proteins as regulators and hormones are introduced, along with their roles

as structural components of tissue.

Properties of Proteins

Fibrous Proteins

Are insoluble

They are structural proteins and are often able to contract e.g. keratin in hair,

collagen in bone, myosin and actin in muscle.

They consist of long polypeptide chains which are cross linked and the whole

structure resembles a long rope made up of strands of string.

Globular Proteins

Are not truly soluble. They make colloidal suspension in water.

These proteins consist of polypeptide chains tightly folded to make a spherical

shape resemblimg a ball of string.

Globular proteins include cell membrane proteins, enzymes, hormones and

antibodies.

The table below relates different proteins to their function in cells and tissues. With the

aid of the function list below, complete the table, Torrance pages 59-62 (old) pages 66-

69 (new) will also help you.

Protein Fibrous or Globular Function

Pepsin

Actin

Fibrinogen Protection – involved in blood

clotting

Insulin

Lipase

Myosin

Haemoglobin Transport – carries O2 within

blood

Collagen

Growth Hormone

Structure of DNA

Cell proteins are made according to inherited information held in the nucleus. The

information is packaged as chromosomes. Chromosomes are thread-like structures

which contain Deoxyribonucleic Acid (DNA).

A chromosome contains a chain of regions called genes. The gene is the unit of

heredity and it contains the information to code for the production of proteins.

The theoretical scientists who worked out the structure of DNA were Watson and Crick

(1953). A DNA molecule is made up of two strands these are made from structural units

called nucleotides. Each nucleotide consists of a 5 carbon sugar called Deoxyribose,

an organic base and an inorganic phosphate.

Label the diagram of a nucleotide.

There are four bases, what are they called?

1)_____________ 2) _____________ 3) _____________4) ______________

Four different types of nucleotides exist. These nucleotides can link by strong chemical

bonds forming between the sugar group of one nucleotide and the phosphate group

of the next. The linked phosphate and sugar molecules form a strand.

On the diagram on the left add the

phosphate bonds to these nucleotides to

form a chain and add the missing bases.

Base Pairing

Weak hydrogen bonds form between the bases. Base pairing only occurs between

certain bases.

Two nucleotide strands are linked by weak hydrogen bonds between opposing bases.

Adenine bonds to thymine and guanine bonds to cytosine, this is called complimentary

base pairing.

The two linked strands coil into a double helix.

To allow the projecting nucleotides to fit together the two sugar-phosphate backbones

must run in opposite directions. The two strands must fit together and coil into a double

helix.

DNA Replication

When cells divide each daughter cell must contain identical chromosomes to those

found in the parent cell. Therefore an essential property of the genetic material is that it

should be able to replicate accurately.

Before a cell divides by mitosis or meiosis DNA must replicate exactly. This ensures that

each new cell that is formed contains an exact copy of all the genetic information

possessed by the parent cell.

Adenine pairs with _______________

Cytosine pairs with _______________

Steps in Replication

DNA double helix uncoils

Hydrogen bonds break

between the bases (DNA

unzips)

Free DNA nucleotides join with

the complementary

nucleotide on the open strand

(T-A, G-C)

Hydrogen bonds form

between a base on the strand

and a base on the nucleotide

Strong chemical bonds form

between sugar of one

nucleotide and phosphate of

the next. This gives each

strand it’s ‘sugar-phosphate’

backbone. This linking of

nucleotides is controlled by an

enzyme called DNA

Polymerase.

Newly formed daughter DNA

molecules can now coil up to

form a double helix.

In order to replicate DNA the cell must have:

Free DNA nucleotides

ATP

Enzymes

A template DNA strand

This form of replication is called semi-conservative as one strand in each new molecule

comes from the original molecule and the other is newly synthesised.

Each new DNA molecule formed gets one nucleotide chain from the parental DNA

and one from newly inserted nucleotides.

The Genetic Code

The sequence of bases along one strand of a DNA molecule is anything but random.

The order of the bases and the way in which they are arranged is called the genetic

code. The code is actually a recipe for the production of protein. Protein as you know

is made up of a chain of amino acids. There are about 20 different amino acids in

nature.

The Structure of RNA

Proteins are made in the ribosomes which are found in the cytoplasm of the cell. DNA

is only found in the nucleus of the cell. A messenger molecule called messenger RNA

(mRNA) carries the genetic code from the nucleus of the cell to the cytoplasm.

RNA (Ribonucleic acid) is similar to DNA except for the following:

It contains the sugar ribose not deoxyribose

It is single stranded not a double helix

It contains the base uracil instead of thymine

It is found in both the nucleus and cytoplasm

Differences between DNA and RNA

Label the diagram below which compares a DNA nucleotide and a RNA nucleotide.

DNA nucleotide: RNA nucleotide

Feature DNA RNA

Number of types

Where found

Number of strands

Name of sugar

Bases present

Base pairing

There are two types of RNA:

1. mRNA (messenger RNA) is made against the DNA and then moves from the

nucleus to the cytoplasm where it attaches to the ribosome.

2. tRNA (transfer RNA) found in the cytoplasm. It carries amino acids.

NB: Ribosomes are found either free in the cytoplasm or attached onto the

endoplasmic reticulum.

Protein Synthesis

DNA is the "Genetic Code", but how does this code control the production of a wide

range of proteins, each made up of a different sequence of amino acids?

The answer is in two stages:

1. Transcription

2. Translation

Transcription of the Code - Formation of mRNA

The method of copying the DNA code onto mRNA is called transcription. In a similar

way to DNA replication, DNA acts as a template for the mRNA. When a protein is

required by the cell the gene for that protein is switched on.

Events occurring in transcription of mRNA

the DNA uncoils at the appropriate point

the weak hydrogen bonds between the bases break (DNA unzips), exposing the

bases

free RNA nucleotides in the nucleus join to the appropriate bases on the template

DNA strand

the RNA nucleotides join together by strong chemical bonds to form a single

stranded mRNA molecule

In mRNA synthesis only one of the DNA strands is used and uracil pairs with adenine

instead of thymine.

Complete the base pairing below

Translation of a protein from the base sequence on mRNA

once synthesised the mRNA separates from the DNA and leaves the nucleus

through a nuclear pore (a gap in the nuclear membrane)

once in the cytoplasm it attaches to a ribosome and starts to synthesise protein.

Ribosomes are the site of protein synthesis. The process of synthesising protein

using the information on mRNA is called translation.

The mRNA consists of a line of bases copied from the DNA in the nucleus. These

are read as a triplet code (3 bases). Each triplet codes for one amino acid and is

known as a codon.

Translation of Protein from mRNA

Another form of RNA is needed for the process of translation. This is called transfer

RNA (tRNA) and it’s function is to carry the correct amino acid to its position on

the mRNA strand (in ribosome).

At one end of the tRNA molecule is a bases triplet called an anticodon which is

complementary to the codon on the mRNA strand. At the other end of the

molecule it carries a specific amino acid. Each of the 20 amino acids have at

least one tRNA molecule assigned to them and some may have several.

As the ribosome moves along the mRNA strand it provides the skeletal

attachment for the tRNA/amino acid complex and the mRNA to correctly attach

together. Other tRNA/amino acid complexes will also align on the mRNA strand.

Peptide bonds then form between the amino acids and the tRNAs are released into the

cytoplasm and are free to pick up another amino acid and start the process again.

It takes about 20 seconds to make a protein containing 400 amino acids.

Nucleic Acid Name of the three bases

DNA Triplet code

mRNA Codon

tRNA Anticodon

The role of the Endoplasmic Reticulum and Golgi Apparatus

Ribosomes are found in the cytoplasm of the cell closely associated with the

Endoplasmic Reticulum (ER).

The endoplasmic reticulum is a system of flattened sacs and tubules which are

continuous with the nuclear membrane and extend through the cytoplasm. Its function

is to act as a transport system for substances (e.g. proteins) to pass quickly throughout

the cell.

Transcription Translation

DNA mRNA Protein

Endoplasmic Reticulum with ribosomes attached, is referred to as Rough Endoplsmic

Reticulum (RER)

In the case of the Rough Endoplasmic Reticulum, the newly synthesised polypeptide

passes through the cell to another system of flattened sacs called the Golgi Apparatus.

It is in the Golgi Apparatus that the different

components of the protein are assembled

ready to be used in the cell itself or pinched

off in a vesicle and discharged from the cell.

The Secretion Of Protein

Many of the enzymes and other proteins

made by the cell have to be secreted from

the cell.

The Golgi Apparatus has the important

function of modifying, processing and packaging the protein.

The Endoplasmic Reticulum and Golgi Apparatus are involved when we are packaging

proteins that will be secreted from the cell.

Processing and Packaging Proteins

The synthesised protein moves into Endoplasmic Reticulum

Polypeptide is transported to Golgi Apparatus in vesicles pinched off from ER

Golgi modifies and packages protein

Vesicle pinches off Golgi and moves to Plasma Membrane

Vesicle attaches to membrane and protein is expelled.

Synthesis and Release of Proteins

Activity I can find this

in my notes

I can do this

State that DNA carries genetic information

State that DNA is found in nuclei as chromosomes

Describe the DNA molecule as double stranded, made

of repeating units called nucleotides and twisted into a

helix

Draw and label a nucleotide

Name the four bases found on nucleotides

Draw and label a single strand of DNA to show the

sugar-phosphate bonds

Draw and label a double strand of DNA to show weak

hydrogen bonds between bases

Explain the term ‘complementary base pairing’

State that it is the order of the bases on DNA that

determine the genetic information of an organism

Describe the process of replication by referring to:

Site in the cell

Unravelling and splitting of double helix

Free nucleotides, ATP, enzymes

Daughter molecules with 1 original & 1 new strand

The importance of replication

Compare DNA with RNA (strands, bases, sugars)

Describe the process of protein synthesis by referring to

the following:

Translocation

Role of mRNA

Ribosome’s on rough ER

Triplets of bases (codons)

Translation

tRNA and free amino acids

Anticodons

Resulting chain of amino acids

Describe the structure of proteins with reference to

peptide bonds and sequence of amino acids

Describe the role of proteins in a cell by referring to their

occurrence in cell membranes and by giving examples

of:

enzymes

hormones

antibodies

carriers

Describe the packaging and export of proteins from the

cell by referring to the role played by: rough ER, vesicles,

Golgi apparatus, secretory vesicles

VIRUSES

Both animals and plants have mechanisms to defend themselves against disease.

Some operate at the level of the whole organism, i.e. having a tough outer skin or

epidermis. Others operate at the cellular level.

Defence

Our body has a very complicated Defence system which operates all the time and is

usually very successful. Even when we do become ill our body fights back and we

recover, showing that our defence system has been successful.

Disease Causing Organisms:

a) Viruses

b) Bacteria

c) Fungi

d) Protozoa

Viruses

Viruses are particles which can only be seen with the aid of an electron microscope.

They consist of a coat made of protein surrounding a core of nucleic acid. (This nucleic

acid contains the viruses genetic information.) In certain viruses the nucleic acid is DNA

whilst in others it is RNA. Viruses cannot reproduce on their own; they can only

reproduce inside a living host cell (animal, plant or bacteria).

The Nature of Viruses

Viruses are infectious particles. They do not possess all the characteristics of living

organisms. They can only reproduce inside the cells of another living organism such as

a plant, animal or micro-organism.

Since the viral invasion of another cell causes the destruction of that cell, viral infections

are always associated with disease.

Viruses are specific to a particular cell. They are much smaller than bacteria and

contain one type of nucleic acid, DNA or RNA surrounded by a protective coat called

a capsid which is made of protein.

Examine the diagram on the right of a virus which attacks

bacteria. Label it with: head containing DNA; hollow tail;

protein coat.

Invasion of cells by a virus

A virus attaches to a host cell

The viral nucleic acid is injected into the host cell.

Once inside the virus takes over the host cell

The host cell is then instructed to make new viral nucleic acid and new protein

coats

The viral nucleic acid and new protein coats are assembled to make complete

viral particles.

Viral particles are released, destroying the host cell in the process. This process is

called cell lysis.

The many hundreds of viruses released from each cell then go onto infect other

cells.

Viral Replication

Viruses invade cells and affect the metabolism of the host cell.

Viral DNA is injected into bacterial wall.

New viruses released from the cell.

Virus attaches to the surface of the cell.

Virus DNA replicates inside the cell.

Virus approaches cell.

New viruses assembled.

Virus penetrates cell surface.

Viral protein coats are produced.

Viral nucleic acid switches off the host cell’s normal nucleic acid replication and

protein synthesis.

The host cell must provide a number of things to enable the virus to replicate, these are:

ATP

Amino Acids

Nucleotides

Retroviruses and HIV

Retroviruses contain RNA and therefore need to copy the RNA to DNA before

multiplication can occur in the host cell. This is called reverse transcriptase.

Retroviruses are implicated in serious diseases such as leukaemia and AIDS. The HIV

virus infects a type of white blood cell called a helper T Cell. These cells are essential for

the immune system to function correctly. The destruction of these T cells by the HIV virus

allows a person to be susceptible to diseases such as pneumonia and some cancers.

Approach

Attachment

Injection of

Nucleic Acid

DNA Replication

Protein Synthesis

Assembly

Release

Defence Mechanisms

Our body has a number of different strategies to defend itself against pathogens

(disease causing organisms). There is a first line of defence which involves both physical

and chemical barriers. If this defence is breached then there is a second line of

defence which involves white blood cells and antibodies.

First Line Defence Mechanisms

This is concerned with the prevention of the entry of micro-organisms into the body. The

bodies of plants and animals are constantly under attack from micro-organisms. If they

penetrate an organism’s outer defences these organisms may cause disease. There

are a number of strategies known as first line defence mechanisms which prevent

invasion by micro-organisms.

Second Line of Defence (cellular defence in mammals)

This involves active processes which destroy the micro-organisms if they

manage to overcome the first line of defence. Once a micro-

organism has penetrated the body’s outer defences, conditions are

ideal for microbial growth. In order to prevent disease i.e. uncontrolled

replication by the micro-organism there are other defence

mechanisms used by an animal.

Two of these mechanisms (phagocytosis and antibody production) are

brought about by the white blood cells. These white blood cells are

called phagocytes and lymphocytes.

Phagocytosis

You should already know that phagocytosis is a general term for the

engulfing of material through the cell membrane into a vacuole. The

material is digested by lysosomes. White blood cells known as

phagocytes engulf any foreign body including pathogenic micro-

organisms that penetrate the outer defences. There is therefore a non-

specific immune response.

Carried out by white blood cells called Phagocytes

Phagocytes are made in the lymph nodes.

Phagocytes can move out of blood vessels into the

spaces between cells.

Each one can engulf and destroy any bacteria or

viruses which have entered the body

Antibody Production

As already mentioned, phagocytosis is a non-specific form of immune response. It gives

general protection against a wide range of invading micro-organisms. There is also a

specific form of immune response involving the production of antibodies. It is said to be

specific because each antibody works on only one invading organism.

Antibodies are T-shaped globular proteins produced by lymphocytes in response to

chemicals called antigens on the surface of invading foreign organisms.

An antigen is any substance which triggers antibody production. E.g. viral coat. The

antibody has receptor sites which are specific to a particular antigen.

These organisms are recognised as foreign since their surface antigens are different

from the surface antigens on the host cells. The body has thousands of different

lymphocytes whicha re produced in the bone marrow, each one capable of

recognising one antigen. Each type of lymphocyte releases antibodies specific to

that antigen.

Antibody production unlike phagocytosis is a specific response since lymphocytes

make antibodies targeted to each invading antigen.

Primary Response

The first time a person is infected by a certain antigen, it is known as the ‘Primary

Response’. It takes a period of time for the body to produce the correct antibodies, so

the person often becomes ill.

Secondary Response

A second exposure to the same antigen at some later point, results in a ‘Secondary

Response’, usually the person does not become ill. This is because:

Antibody production is more rapid

Concentration of antibodies produced is higher

Higher concentration of antibodies is maintained for longer

How is this possible?

During the Primary response, lymphoctyes specific to the antigen are produced, known

as ‘Memory Cells’. When the person is exposed a second time, these mempry cells

produce a clone of antibody forming lymphocytes and fight it off.

The person is said to have ‘Natural Acquired Immunity’

Rejection of Transplanted Tissue

When a living tissue is transplanted the lymphocytes think this new tissue is foreign and

attempt to destroy it.

This ‘tissue rejection’ always occurs and successful transplants are only possible by

choosing a donor who is as genetically similar as possible to the patient and then giving

them ‘immunosuppressor drugs’.

Immunosuppressor Drugs

These greatly inhibit the patient’s immune system to stop rejection, but it means that

they are susceptible to serious diseases. New drugs are now being developed that stop

rejection but do not reduce the immune system as much.

Essay: Describe the basic structure and way of life of viruses and discuss the ways in

which animals defend themselves from attack by viruses or other infections.

Plant Defences

Plants are also susceptible to invasion by micro-organisms such as bacteria, fungi and

viruses. They are also at risk of being eaten by herbivores.

Plants do not have an immune system but as with animals they have methods of

preventing entry of micro-organisms and also methods of dealing with the intruder

once it has penetrated the first line of defence.

Attack is often through a wound and the plant’s response tends to be at or around the

damaged surface. Entry occurs also through the stomata.

The cell wall in plant cells acts as a barrier against pathogenic micro-organisms.

Bacteria and viruses usually only gain access via the biting or piercing mouth parts of

insects.

Fungal pathogens can penetrate the cell wall by secreting digestive enzymes.

Plants can respond to attack by pathogens by:

1. producing barriers to isolate infected areas

2. Producing a variety of toxic compounds.

Isolating barriers in plants

Galls & (Tannins)

On infection by an insect or fungus, the plant often produces a gall in response to a

chemical stimulus by the insect or fungus.

A gall is an abnormal swelling of plant tissues at the site of injury. It is due to the cells

undergoing mitosis.

Galls contain acidic chemicals called tannins which play a protective role as they

denature the parasitic proteins.

The extra layers of cells and rich deposits of tannin in a gall form a protective barrier

around the parasite thus isolating it and preventing further damage.

Resin

A sticky substance which blocks off wounds and also blocks infected xylem and

phloem.

Toxic compounds in plants

Tannins

A group of acidic chemicals which are toxic to many microbes. They protect by

inhibiting enzymes which an invading pathogen secretes and interferes with it’s

metabolism.

Cyanide

Hydrogen-cyanide is a poison which blocks an organism’s cytochrome system. Some

plants produce a non-toxic chemical that can be hydrolysed to hydrogen cyanide

when the plant is damaged, e.g. when it is nibbled by a herbivore – this is known as

Cyanogenesis.

Nicotine

A poisonous substance which disrupts the nervous system of insects. It can be

extracted and added to insecticides.

Cellular Response in Defence

Activity I can find

this in my

notes

I can do

this

State that viruses have a protein coat surrounding a

core of either DNA or RNA

State that a virus can only reproduce in living cells

Describe the steps involved when a virus infects a living

cell

Define ‘antigen’ as a foreign particle or organism which

will set-off an immune response

Describe phagocytosis by referring to the type of cell

responsible and steps involved including the role of

lysosomes

Describe antibody production by referring to: type of

cell responsible, specific nature of antibodies, the fate of

the antigen-antibody complex, immunity from future

infections

Explain pros and cons of immuno-supressor drugs

State that plants can protect themselves by producing

a variety of toxic compounds, these include: tannins,

cyanide and nicotine

State that plants can also protect themselves by

isolating injured areas by means of substances such as

resin