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1 Characteristics and classification of living organisms

1.1.1 Characteristics of Living Organisms

 Movement: an action by an organism or part of an organism causing a change of


position or place
 Respiration: the chemical reactions that break down nutrient molecules in living
cells to release energy for metabolism
 Sensitivity: the ability to detect or sense stimuli in the internal or external
environment and to make appropriate responses
 Growth: a permanent increase in size and dry mass by an increase in cell number or
cell size or both
 Reproduction: the processes that make more of the same kind of organism
 Excretion: the removal from organisms of toxic materials, the waste products of
metabolism (chemical reactions in cells including respiration) and substances in
excess of requirements
 Nutrition: the taking in of materials for energy, growth and development; plants
require light, carbon dioxide, water and ions; animals need organic compounds, ions
and usually need water

1.1.2 Concept & Uses of Classification Systems


How Organisms are classified

 There are millions of species of organisms on Earth


 A species is defined as a group of organisms that can reproduce to produce fertile
offspring

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 These species can be classified into groups by the features that they share e.g. all
mammals have bodies covered in hair, feed young from mammary glands and have
external ears (pinnas)

The Binomial System

 Organisms were first classified by a Swedish naturalist called Linnaeus in a way that
allows the subdivision of living organisms into smaller and more specialised groups
 The species in these groups have more and more features in common the more
subdivided they get
 He named organisms in Latin using the binomial system where the scientific name
of an organism is made up of two parts starting with the genus (always given
a capital letter) and followed by the species (starting with a lower case letter)
 When typed binomial names are always in italics (which indicates they are Latin)
e.g. Homo sapiens
 The sequence of classification
is: Kingdom, Phylum, Class, Order, Family, Genus, Species

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Dichotomous Keys

 Keys are used to identify organisms based on a series of questions about their
features
 Dichotomous means ‘branching into two’ and it leads the user through to the name of
the organism by giving two descriptions at a time and asking them to choose
 Each choice leads the user onto another two descriptions
 In order to successfully navigate a key, you need to pick a single organism to start
with and follow the statements from the beginning until you find the name
 You then pick another organism and start at the beginning of the key again,
repeating until all organisms are named

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1.1.3 Concept & Uses of Classification Systems: Extended
Reflecting Evolutionary Relationships: Extended

 Classification systems aim to reflect evolutionary relationships between species


 Traditional biological classification systems grouped organisms based on
the features that they shared
 If organisms shared more similar features then they were said to be more closely
related
 In the past, scientists have encountered many difficulties when trying to determine
the evolutionary relationships of species based on this method
 Using the physical features of species (such as colour/shape/size) has many
limitations and can often lead to the wrong classification of species

Using DNA to Classify Organisms: Extended

 Organisms share features because they originally descend from a common


ancestor
 Example: all mammals have bodies covered in hair, feed young from mammary
glands and have external ears (pinnas)
 Originally, organisms were classified using morphology (the overall form and shape
of the organism, e.g. whether it had wings or legs) and anatomy (the detailed body
structure as determined by dissection)
 As technology advanced, microscopes, knowledge of biochemistry and
eventually DNA sequencing allowed us to classify organisms using a more scientific
approach
 Studies of DNA sequences of different species show that the more similar the base
sequences in the DNA of two species, the more closely related those two
species are (and the more recent in time their common ancestor is)
 This means that the base sequences in a mammal’s DNA are more closely
related to all other mammals than to any other vertebrate groups

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DNA sequences can show how closely related different species are

 The sequences above show that Brachinus armiger and Brachinus hirsutus
are more closely related than any other species in the list as their DNA sequences
are identical except for the last but one base (B.armiger has a T in that position
whereas B.hirsutus has an A)
 As DNA base sequences are used to code for amino acid sequences in proteins,
the similarities in amino acid sequences can also be used to determine how closely
related organisms are

1.1.4 Features of Organisms


The Five Kingdoms

 The first division of living things in the classification system is to put them into one
of five kingdoms. They are:
o Animals
o Plants
o Fungi
o Protoctists
o Prokaryotes
o
 Main features of all animals:
o they are multicellular
o their cells contain a nucleus but no cell walls or chloroplasts
o they feed on organic substances made by other living things

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 Main features of all plants:
o they are multicellular
o their cells contain a nucleus, chloroplasts and cellulose cell walls
o they all feed by photosynthesis

The Animal Kingdom

 Several main features are used to place organisms into groups within the animal
kingdom

Vertebrates

 All vertebrates have a backbone


o There are 5 classes of vertebrates

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Invertebrates

 Invertebrates do not possess a backbone


 One of the morphological characteristics used to classify invertebrates is whether
they have legs or not
 All invertebrates with jointed legs are part of the phylum Arthropods
 They are classified further into the following classes:

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Invertebrate Table

1.1.5 Features of Organisms: Extended

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The Five Kingdoms: Extended

 The first division of living things in the classification system is to put them into one
of five kingdoms
 They are:
o Animals
o Plants
o Fungi
o Protoctists
o Prokaryotes
 Main features of all fungi (e.g. moulds, mushrooms, yeast)
o usually multicellular
o cells have nuclei and cell walls not made from cellulose
o do not photosynthesize but feed by saprophytic (on dead or decaying
material) or parasitic (on live material) nutrition

A typical fungal cell

 Main features of all Protoctists (e.g. Amoeba, Paramecium, Plasmodium)


o most are unicellular but some are multicellular
o all have a nucleus, some may have cell walls and chloroplasts
o meaning some protoctists photosynthesise and some feed on organic
substances made by other living things

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Two examples of protoctist cells

 Main features of all Prokaryotes (bacteria, blue-green algae)


o often unicellular
o cells have cell walls (not made of cellulose) and cytoplasm but no nucleus
or mitochondria

A typical bacterial cell

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The Plant Kingdom: Extended

 At least some parts of any plant are green, caused by the presence of the
pigment chlorophyll which absorbs energy from sunlight for the process
of photosynthesis
 The plant kingdom includes organisms such as ferns and flowering plants

Ferns

 Have leaves called fronds


 Do not produce flowers but instead reproduce by spores produced on the
underside of fronds

Ferns reproduce by spores found in the underside of their fronds

Flowering plants

 Reproduce sexually by means of flowers and seeds


 Seeds are produced inside the ovary found at the base of the flower
 Can be divided into two groups – monocotyledons and dicotyledons

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Wheat plants are monocotyledons Sunflowers are dicotyledons

How do you distinguish between monocotyledons and dicotyledons?


1) Flowers

 Flowers from monocotyledons contain petals in multiples of 3


 Flowers from dicotyledons contain petals in multiples of 4 or 5

2) Leaves

 Leaves from monocotyledons have parallel leaf veins


 Leaves from dicotyledons have reticulated leaf veins (meaning that they are all
interconnected and form a web-like network throughout the leaf)

Comparing monocots and dicots

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Viruses: Extended

 Viruses are not part of any classification system as they are not considered living
things
 They do not carry out the seven life processes for themselves, instead they take
over a host cell’s metabolic pathways in order to make multiple copies of
themselves
 Virus structure is simply genetic material (RNA or DNA) inside a protein coat

Structure of a typical virus

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2. Organization of the Organism
2.1.1 Cell Structure

Animal & Plant Cells


Animals

 The main features of animals:


o They are multicellular
o Their cells contain a nucleus with a distinct membrane
o Their cells do not have cellulose cell walls
o Their cells do not contain chloroplasts (so they are unable to carry
out photosynthesis)
o They feed on organic substances made by other living things
o They often store carbohydrates as glycogen
o They usually have nervous coordination
o They are able to move from place to place

A typical animal cell

Plants

 The main features of plants:


o They are multicellular
o Their cells contain a nucleus with a distinct membrane
o Their cells have cell walls made out of cellulose
o Their cells contain chloroplasts (so they can carry out photosynthesis)
o They feed by photosynthesis
o They store carbohydrates as starch or sucrose
o They do not have nervous coordination

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A typical plant cell

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Cell Structures Found in Both Animal and Plant Cells Table

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An animal and plant cell as seen under a light microscope

Bacteria Cells

 Bacteria, which have a wide variety of shapes and sizes, all share the following
biological characteristics:
o They are microscopic single-celled organisms
o Possess a cell wall (made of peptidoglycan, not cellulose), cell
membrane, cytoplasm and ribosomes
o Lack a nucleus but contain a circular chromosome of DNA that floats in
the cytoplasm

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o Plasmids are sometimes present - these are small rings of DNA (also
floating in the cytoplasm) that contain extra genes to those found in the
chromosomal DNA
o They lack mitochondria, chloroplasts and other membrane-bound
organelles found in animal and plant cells
 Some bacteria also have a flagellum (singular) or several flagella (plural). These
are long, thin, whip-like tails attached to bacteria that allow them to move
 Examples of bacteria include:
o Lactobacillus (a rod-shaped bacterium used in the production of yoghurt
from milk)
o Pneumococcus (a spherical bacterium that acts as the pathogen causing
pneumonia)

A typical bacterial cell

Identifying Cell Structures & Function

 Within the cytoplasm, the following organelles are visible in almost all cells except
prokaryotes when looking at higher magnification (ie using an electron microscope):
o Mitochondria (singular: mitochondrion) are organelles found throughout the
cytoplasm

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o Ribosomes are tiny structures that can be free within the cytoplasm or
attached to a system of membranes within the cell known as Endoplasmic
Reticulum
o Endoplasmic reticulum studded with ribosomes looks rough under the
microscope; this gives rise to its name of Rough Endoplasmic
Reticulum (often shortened to R.E.R.)
o Vesicles can also be seen using a higher magnification - these are small
circular structures found moving throughout the cytoplasm

Structures in an animal cell visible under a light microscope and an electron


microscope

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Structures in a plant cell visible under a light microscope and an electron
microscope

Producing New Cells

 The cells in your body need to be able to divide to help your


body grow and repair itself
 Cells grow and divide over and over again
 New cells are produced by the division of existing cells

Specialised Cells
Specialised cells in animals

 Specialised cells are those which have developed certain characteristics in order
to perform particular functions. These differences are controlled by genes in the
nucleus
 Cells specialise by undergoing differentiation: this is a process by which cells
develop the structure and characteristics needed to be able to carry out their
functions

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Specialised Cells in Animals Table

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Ciliated cell

Nerve cell

Red blood cells

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Sperm cell

Egg cell

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Examples of specialised cells in plants:

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Diagrams of specialised cells in plants:

Root hair cell

Xylem structure

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Palisade mesophyll cell

Levels of Organisation in an Organism

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Levels of organisation

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 Your syllabus states that you should be able to identify the different levels of
organisation in drawings, diagrams and images of familiar material
 An example of this is shown in the exam question below:

Typical levels of organisation question

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2.1.3 Magnification Formula
Magnification Formula
Calculating magnification and specimen size using millimetres as units

 Magnification is calculated using the following equation:

Magnification = Image size ÷ Actual size

 A better way to remember the equation is using an equation triangle:

Magnification equation

 Rearranging the equation to find things other than the magnification becomes easy
when you remember the triangle - whatever you are trying to find, place your finger
over it and whatever is left is what you do, so:
o Magnification = image size / actual size
o Actual size = image size / magnification
o Image size = magnification x actual size

Remember magnification does not have any units and is just written as ‘x 10’ or ‘x 5000’

To find the actual size of the cell:

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Worked example using the magnification equation

2.1.4 Converting Between Units: Extended


Converting Between Units: Extended
Using millimetres and micrometres as units

 The table below shows how millimetres are related to two other measures of length
 What this basically means is that 1mm = 1000µm and 1cm = 10,000µm
 This usually comes up in questions where you have two different units and you need
to ensure that you convert them both into the same unit before proceeding with the
calculation
 For example:

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Example extended magnification question

 Remember 1mm = 1000µm


 2000 / 1000 = 2 so the actual thickness of the leaf is 2mm and the drawing thickness
is 50mm
 Magnification = image size / actual size = 50 / 2 = 25
 So the magnification is x 25 (NO UNITS)

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3. Movement into & out of Cells
3.1.1 Diffusion

 Diffusion is the movement of molecules from a region of its higher concentration to


a region of its lower concentration
 Molecules move down a concentration gradient, as a result of their random
movement

Diffusion across the cell membrane

 For living cells, the principle of the movement down a concentration gradient is the
same, but the cell is surrounded by a cell membrane which can restrict the free
movement of the molecules
 The cell membrane is a partially permeable membrane - this means it allows some
molecules to cross easily, but others with difficulty or not at all
 The simplest sort of selection is based on the size of the molecules
 Diffusion helps living organisms to:
o obtain many of their requirements
o get rid of many of their waste products
o carry out gas exchange for respiration

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Examples of diffusion in living organisms

 You will need to learn examples of substances that organisms obtain by diffusion
 Don’t forget that plants require oxygen for respiration at all times, as well
as carbon dioxide for photosynthesis when conditions for photosynthesis are right
(e.g. enough light and a suitable temperature)

Examples of Diffusion Table

Where does the energy for diffusion come from?

 All particles move randomly at all times


 This is known as Brownian motion
 The energy for diffusion comes from the kinetic energy of this random movement of
molecules and ions

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Brownian motion

3.1.2 Factors that Influence Diffusion


Factors that Influence Diffusion
Surface area to volume ratio

 The bigger a cell or structure is, the smaller its surface area to volume ratio is,
slowing down the rate at which substances can move across its surface
 Many cells which are adapted for diffusion have increased surface area in some
way - eg root hair cells in plants (which absorb water and mineral ions) and cells
lining the ileum in animals (which absorb the products of digestion)

Cell
adaptations for diffusion

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The highly folded surface of the small intestine increases its surface area

Distance

 The smaller the distance molecules have to travel the faster transport will occur
 This is why blood capillaries and alveoli have walls which are only one cell thick,
ensure the rate of diffusion across them is as fast as possible

Temperature

 The higher the temperature, the faster molecules move as they have more energy
 This results in more collisions against the cell membrane and therefore a faster rate
of movement across them

Concentration Gradient

 The greater the difference in concentration either side of the membrane, the faster
movement across it will occur
 This is because on the side with the higher concentration, more random collisions
against the membrane will occur

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3.1.3 Water
 Water is important for all living organisms as many substances are able to
dissolve in it (it is a solvent)
 This makes it incredibly useful and essential for all life on Earth
 Water is important as a solvent in the following situations within organisms:
o Dissolved substances can be easily transported around organisms - eg
xylem and phloem of plants and dissolved food molecules in the blood
o Digested food molecules are in the alimentary canal but need to be moved
to cells all over the body - without water as a solvent this would not be able
to happen
o Toxic substances such as urea and substances in excess of requirements
such as salts can dissolve in water which makes them easy to remove from
the body in urine
o Water is also an important part of the cytoplasm and plays a role in
ensuring metabolic reactions can happen as necessary in cells

Water as a solvent

3.1.4 Osmosis
 All cells are surrounded by a cell membrane which is partially permeable
 Water can move in and out of cells by osmosis
 Osmosis is the diffusion of water molecules from a dilute solution (high
concentration of water) to a more concentrated solution (low concentration of
water) across a partially permeable membrane
 In doing this, water is moving down its concentration gradient

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 The cell membrane is partially permeable which means it allows small
molecules (like water) through but not larger molecules (like solute molecules)

3.1.5 Osmosis Experiments


Osmosis Experiments
Immersing plant cells in solutions of different concentrations

 The most common osmosis practical involves cutting cylinders of root


vegetables such as potato or radish and placing them into distilled
water and sucrose solutions of increasing concentration
 The cylinders are weighed before placing into the solutions
 They are left in the solutions for 20 - 30 minutes and then removed, dried to remove
excess liquid and reweighed

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Potatoes are usually used in osmosis experiments to show how the concentration of
a solution affects the movement of water, but radishes can be used too

 If the plant tissue gains mass:


o Water must have moved into the plant tissue from the solution surrounding it
by osmosis
o The solution surrounding the tissue is more dilute than the plant tissue (which
is more concentrated)
 If plant tissue loses mass:
o Water must have moved out of the plant tissue into the solution surrounding it
by osmosis
o The solution surrounding the tissue is more concentrated than the plant tissue
(which is more dilute)
 If there is no overall change in mass:

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o There has been no net movement of water as the concentration in both the
plant tissue and the solution surrounding it must be equal
o Remember that water will still be moving into and out of the plant tissue, but
there wouldn’t be any net movement in this case

Investigating osmosis using dialysis tubing

 Dialysis tubing (sometimes referred to as visking tubing) is a non-living partially


permeable membrane made from cellulose
 Pores in this membrane are small enough to prevent the passage of large
molecules (such sucrose) but allow smaller molecules (such as glucose and
water) to pass through by diffusion and osmosis
 This can be demonstrated by:
o Filling a section of dialysis tubing with concentrated sucrose solution
o Suspending the tubing in a boiling tube of water for a set period of time
o Noting whether the water level outside the tubing decreases as water moves
into the tubing via osmosis
 Water moves from a region of higher water potential (dilute solution) to
a region of lower water potential (concentrated solution), through a
partially permeable membrane

An example setup of a dialysis tubing experiment.

3.1.6 Osmosis in Animals & Plants


Osmosis in Plant Tissues

 When water moves into a plant cell, the vacuole gets bigger, pushing the cell
membrane against the cell wall
 Water entering the cell by osmosis makes the cell rigid and firm
 This is important for plants as the effect of all the cells in a plant being firm is
to provide support and strength for the plant - making the plant stand upright with
its leaves held out to catch sunlight

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 The pressure created by the cell wall stops too much water entering and prevents
the cell from bursting
 If plants do not receive enough water the cells cannot remain rigid and firm (turgid)
and the plant wilts

Osmosis: Extended

 Osmosis is the net movement of water molecules from a region of higher water
potential (dilute solution) to a region of lower water potential (concentrated
solution), through a partially permeable membrane
 It can get a little confusing to talk about the 'concentration of water' when we also
talk about solutions being ‘concentrated’ (having a lot of solute in them), so instead
we can say that a dilute solution has a high water potential (the right-hand side of
the diagram below) and a concentrated solution has a low water potential (the
left-hand side of the diagram below):

How osmosis works

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Osmosis in Animals & Plants: Extended
Plant cells in solutions of different concentrations

 When plant cells are placed in a solution that has a higher water potential (dilute
solution) than inside the cells (e.g. distilled water) then water moves into the plant
cells via osmosis
 These water molecules push the cell membrane against the cell wall, increasing
the turgor pressure in the cells which makes them turgid

 When plant cells are placed in a concentrated solution (with a lower water potential
than inside the cells) water molecules will move out of the plant cells by osmosis,
making them flaccid
o If plant cells become flaccid it can negatively affect the plant's ability to
support itself

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 If looked at underneath the microscope, the plant cells might be plasmolysed,
meaning the cell membrane has pulled away from the cell wall

Animal cells in solutions of different concentrations

 Animal cells also lose and gain water as a result of osmosis


 As animal cells do not have a supporting cell wall, the results on the cell are more
severe
 If an animal cell is placed into a strong sugar solution (with a lower water potential
than the cell), it will lose water by osmosis and become crenated (shrivelled up)
 If an animal cell is placed into distilled water (with a higher water potential than the
cell), it will gain water by osmosis and, as it has no cell wall to create turgor
pressure, will continue to do so until the cell membrane is stretched too far and it
bursts

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Effect of osmosis on animal cells

3.1.7 Active Transport


Active Transport

 Active transport is the movement of particles through a cell membrane from a region
of lower concentration to a region of higher concentration using energy from
respiration

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The process of active transport

3.1.8 Proteins & Active Transport


Importance of Active Transport: Extended

 Energy is needed because particles are being moved against a concentration


gradient, in the opposite direction from which they would naturally move (by
diffusion)
 Active transport is vital process for the movement of molecules or ions across
membranes
 Including:

o uptake of glucose by epithelial cells in the villi of the small intestine and by
kidney tubules in the nephron
o uptake of ions from soil water by root hair cells in plants

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Protein Carriers: Extended

 Active transport works by using carrier proteins embedded in the cell membrane to
pick up specific molecules and take them through the cell membrane against their
concentration gradient:

1.
1. Substance combines with carrier protein molecule in the cell membrane
2. Carrier transports substances across membrane using energy from
respiration to give them the kinetic energy needed to change shape and
move the substance through the cell membrane
3. Substance released into cell

Carrier proteins in active transport.

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4. Biological Molecules
4.1.1 Chemicals & Life
Chemical Elements

 Most of the molecules in living organisms fall into three categories: carbohydrates,
proteins and lipids
 These all contain carbon and so are described as organic molecules

Chemical Elements Table

Large Molecules are Made from Smaller Molecules


Carbohydrates

 Long chains of simple sugars


 Glucose is a simple sugar ( a monosaccharide)
 When 2 glucose molecules join together maltose is formed (a disaccharide)
 When lots of glucose molecules join together starch, glycogen or cellulose can
form (a polysaccharide)

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Glycogen, cellulose and starch are all made from glucose molecules

Fats

 Most fats (lipids) in the body are made up of triglycerides


 Their basic unit is 1 glycerol molecule chemically bonded to 3 fatty acid chains
 The fatty acids vary in size and structure
 Lipids are divided into fats (solids at room temperature) and oils (liquids at room
temperature)

Structure of a triglyceride

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Proteins

 Long chains of amino acids


 There are about 20 different amino acids
 They all contain the same basic structure but the ‘R’ group is different for each
one
 When amino acids are joined together a protein is formed
 The amino acids can be arranged in any order, resulting in hundreds of thousands of
different proteins
 Even a small difference in the order of the amino acids results in a different protein
being formed

General amino acid structure

Amino acids join together to form proteins

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4.1.2 Food Tests
Food Tests
Test for glucose (a reducing sugar)

 Add Benedict's solution into sample solution in test tube


 Heat at 60 - 70 °c in water bath for 5 minutes
 Take test tube out of water bath and observe the colour
 A positive test will show a colour change from blue to orange or brick red

The
Benedict's test for glucose

Test for starch using iodine

 We can use iodine to test for the presence or absence of starch in a food sample.

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The iodine test for starch

 Add drops of iodine solution to the food sample


 A positive test will show a colour change from orange-brown to blue-black

Testing a potato to prove the presence of starch

Test for protein

 Add drops of Biuret solution to the food sample


 A positive test will show a colour change from blue to violet / purple

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The Biuret test for protein

Test for lipids

 Food sample is mixed with 2cm3 of ethanol and shaken


 The ethanol is added to an equal volume of cold water
 A positive test will show a cloudy emulsion forming

The ethanol test for lipids

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Test for vitamin C

 Add 1cm3 of DCPIP solution to a test tube


 Add a small amount of food sample (as a solution)
 A positive test will show the blue colour of the dye disappearing

The DCPIP test for vitamin C

4.1.3 DNA Structure: Extended


Structure of a DNA Molecule: Extended

 DNA, or deoxyribonucleic acid, is the molecule that contains the instructions for
growth and development of all organisms
 It consists of two strands of DNA wound around each other in what is called
a double helix

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DNA, chromosomes and the nucleus

 The individual units of DNA are called nucleotides

A nucleotide

 All nucleotides contain the same phosphate and deoxyribose sugar, but differ from
each other in the base attached
 There are four different bases, Adenine (A), Cytosine (C), Thymine (T) and
Guanine (G)
 The bases on each strand pair up with each other, holding the two strands of DNA in
the double helix
 The bases always pair up in the same way:
o Adenine always pairs with Thymine (A-T)
o Cytosine always pairs with Guanine (C-G)

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DNA base pairs

 The phosphate and sugar section of the nucleotides form the ‘backbone’ of the DNA
strand (like the sides of a ladder) and the base pairs of each strand connect to form
the rungs of the ladder

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The DNA helix is made from two strands of DNA held together by hydrogen bonds

 It is this sequence of bases that holds the code for the formation of proteins

5. Enzymes
What Are Enzymes?

 Enzymes are:
o Catalysts that speed up the rate of a chemical reaction without being
changed or used up in the reaction
o Proteins
o Biological catalysts (biological because they are made in living cells,
catalysts because they speed up the rate of chemical reactions without being
changed)
o Necessary to all living organisms as they maintain reaction speeds of all
metabolic reactions (all the reactions that keep an organism alive) at a rate
that can sustain life
 For example, if we did not produce digestive enzymes, it would take
around 2 - 3 weeks to digest one meal; with enzymes, it takes around
4 hours

How Do Enzymes Work?

Enzyme substrate specificity

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 Enzymes are specific to one particular substrate (molecule/s that get broken down
or joined together in the reaction) as the enzyme is a complementary shape to the
substrate
 The product is made from the substrate(s) and is released

Enzyme specificity: lock and key model of enzyme activity

5.1.2 Enzyme Investigations


Investigating the Effect of Temperature on Amylase

 Starch solution is heated to a set temperature


 Iodine is added to wells of a spotting tile
 Amylase is added to the starch solution and mixed well
 Every minute, droplets of solution are added to a new well of iodine solution
 This is continued until the iodine stops turning blue-black (this means there is no
more starch left in the solution as the amylase has broken it all down)
 Time taken for the reaction to be completed is recorded
 Experiment is repeated at different temperatures
 The quicker the reaction is completed, the faster the enzyme is working

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Investigating the Effect of pH on Amylase

 Place single drops of iodine solution in rows on the tile


 Label a test tube with the pH to be tested
 Use the syringe to place 2cm3 of amylase in the test tube
 Add 1cm3 of buffer solution to the test tube using a syringe
 Use another test tube to add 2cm3 of starch solution to the amylase and buffer
solution, start the stopwatch whilst mixing using a pipette
 After 10 seconds, use a pipette to place one drop of mixture on the first drop of
iodine, which should turn blue-black
 Wait another 10 seconds and place another drop of mixture on the second drop of
iodine
 Repeat every 10 seconds until iodine solution remains orange-brown
 Repeat experiment at different pH values - the less time the iodine solution takes to
remain orange-brown, the quicker all the starch has been digested and so the better
the enzyme works at that pH

Investigating the effect of pH on enzyme activity

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5.1.3 Enzyme Action & Specificity: Extended
Enzyme Action & Specificity: Extended

 Enzymes are specific to one particular substrate(s) as the active site of the
enzyme, where the substrate attaches, is a complementary shape to the substrate
 This is because the enzyme is a protein and has a specific 3-D shape
 This is known as the lock and key hypothesis
 When the substrate moves into the enzyme’s active site they become known as
the enzyme-substrate complex
 After the reaction has occurred, the products leave the enzyme’s active site as they
no longer fit it and it is free to take up another substrate

How enzymes work

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1. Enzymes and substrates randomly move about in solution

2. When an enzyme and its complementary substrate randomly collide - with the substrate
fitting into the active site of the enzyme - an enzyme-substrate complex forms, and the
reaction occurs.

3. A product (or products) forms from the substrate(s) which are then released from the
active site. The enzyme is unchanged and will go on to catalyse further reactions.

5.1.4 Enzymes & Temperature: Extended


Enzymes & Temperature: Extended

 Enzymes are proteins and have a specific shape, held in place by bonds
 This is extremely important around the active site area as the specific shape is what
ensures the substrate will fit into the active site and enable the reaction to
proceed
 Enzymes work fastest at their ‘optimum temperature’ – in the human body, the
optimum temperature is 37⁰C
 Heating to high temperatures (beyond the optimum) will break the bonds that hold
the enzyme together and it will lose its shape -this is known as denaturation
 Substrates cannot fit into denatured enzymes as the shape of their active site has
been lost
 Denaturation is irreversible - once enzymes are denatured they cannot regain their
proper shape and activity will stop

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Effect of temperature on enzyme activity

 Increasing the temperature from 0⁰C to the optimum increases the activity of
enzymes as the more energy the molecules have the faster they move and the
number of collisions with the substrate molecules increases, leading to a faster
rate of reaction
 This means that low temperatures do not denature enzymes, they just make them
work more slowly

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Graph showing the effect of temperature on the rate of enzyme activity

5.1.5 Enzymes & pH: Extended


Enzymes & pH: Extended

 The optimum pH for most enzymes is 7 but some that are produced in acidic
conditions, such as the stomach, have a lower optimum pH (pH 2) and some that are
produced in alkaline conditions, such as the duodenum, have a higher optimum pH
(pH 8 or 9)
 If the pH is too high or too low, the bonds that hold the amino acid chain together to
make up the protein can be destroyed
 This will change the shape of the active site, so the substrate can no longer fit into it,
reducing the rate of activity
 Moving too far away from the optimum pH will cause the enzyme to denature and
activity will stop

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Effect of pH on enzyme activity

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Graph showing the effect of pH on rate of activity for an enzyme from the duodenum

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6. Plant Nutrition
6.1.1 Photosynthesis
 Green plants make the carbohydrate glucose from the raw materials carbon
dioxide and water
 At the same time oxygen is made and released as a waste product
 The reaction requires energy which is obtained by the pigment chlorophyll trapping
light from the Sun
 So photosynthesis can be defined as the process by which plants manufacture
carbohydrates from raw materials using energy from light
 It can be summed up in the following equation:

Photosynthesis Word Equation

How plants get the materials they need

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6.1.2 Chlorophyll
 Chlorophyll is a green pigment that is found in chloroplasts within plant cells
o It is this pigment which gives plants their characteristic green colour
 Chlorophyll transfers energy from light into energy in chemicals, for the synthesis of
carbohydrates
o It is essential for photosynthesis to occur

6.1.3 Use & Storage of Carbohydrates

How are the products of photosynthesis used?

 The carbohydrates produced by plants during photosynthesis can be used in the


following ways:
o Converted into starch molecules which act as an effective energy store
o Converted into cellulose to build cell walls
o Glucose can be used in respiration to provide energy
o Converted to sucrose for transport in the phloem
o As nectar to attract insects for pollination
 Plants can also convert the carbohydrates made into lipids for an energy source in
seeds and into amino acids (used to make proteins) when combined with nitrogen
and other mineral ions absorbed by roots

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The fate of glucose

6.1.4 Minerals in Plants


 Photosynthesis produces carbohydrates, but plants contain many other types of
biological molecule; such as proteins, lipids and nucleic acid (DNA)
 As plants do not eat, they need to make these substances themselves

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 Carbohydrates contain the elements carbon, hydrogen and oxygen but proteins, for
example, contain nitrogen as well (and certain amino acids contain other elements
too)
 Other chemicals in plants contain different elements as well, for example chlorophyll
contains magnesium and nitrogen
 This means that without a source of these elements, plants cannot photosynthesise
or grow properly
 Plants obtain these elements in the form of mineral ions actively absorbed from
the soil by root hair cells
 ‘Mineral’ is a term used to describe any naturally occurring inorganic substance

Mineral deficiencies in plants

Mineral Deficiencies Table

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6.1.5 Investigating the Need for Chlorophyll, Light & Carbon Dioxide
Investigating the Need for Chlorophyll

 Although plants make glucose in photosynthesis, leaves cannot be tested for its
presence as the glucose is quickly used, converted into other substances and
transported or stored as starch.
 Starch is stored in chloroplasts where photosynthesis occurs so testing a leaf for
starch is a reliable indicator of which parts of the leaf are photosynthesising.
 Leaves can be tested for starch using the following procedure:
o A leaf is dropped in boiling water to kill the cells and break down the cell
membranes
o The leaf is left for 5-10 minutes in hot ethanol in a boiling tube. This removes
the chlorophyll so colour changes from iodine can be seen more clearly
o The leaf is dipped in boiling water to soften it
o The leaf is spread out on a white tile and covered with iodine solution
o In a green leaf, the entire leaf will turn blue-black as photosynthesis is
occuring in all areas of the leaf
o This method can also be used to test whether chlorophyll is needed for
photosynthesis by using a variegated leaf (one that is partially green and
partially white)
o The white areas of the leaf contain no chlorophyll and when the leaf is
tested only the areas that contain chlorophyll stain blue-black
o The areas that had no chlorophyll remain orange-brown as no
photosynthesis is occurring here and so no starch is stored

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Testing a variegated leaf for starch

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 Care must be taken when carrying out this practical as ethanol is extremely
flammable, so at that stage of the experiment the Bunsen burner should be turned
off.
 The safest way to heat the ethanol is in an electric water bath rather than using a
beaker over a Bunsen burner with an open flame

Investigating the Need for Light

 The same procedure as above can be used to investigate if light is needed for
photosynthesis
 Before starting the experiment the plant needs to be destarched by placing in a dark
cupboard for 24 hours
 This ensures that any starch already present in the leaves will be used up and
will not affect the results of the experiment
 Following destarching, a leaf of the plant can be partially covered with aluminium
foil and the plant placed in sunlight for a day
 The leaf can then be removed and tested for starch using iodine
 The area of the leaf that was covered with aluminium foil will remain orange-
brown as it did not receive any sunlight and could not photosynthesise, while the
area exposed to sunlight will turn blue-black
 This proves that light is necessary for photosynthesis and the production of starch

Investigating the Need for Carbon Dioxide

 Destarch two plants by placing in the dark for a prolonged period of time
 Place one plant in a bell jar which contains a beaker of sodium hydroxide (which
will absorb carbon dioxide from the surrounding air)
 Place the other plant in a bell har which contains a beaker of water (control
experiment), which will not absorb carbon dioxide from the surrounding air
 Place both plants in bright light for several hours
 Test both plants for starch using iodine
 The leaf from the plant placed near sodium hydroxide will remain orange-brown as
it could not photosynthesise due to lack of carbon dioxide
 The leaf from the plant placed near water should turn blue-black as it had all
necessary requirements for photosynthesis

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An example setup for an experiment to test whether carbon dioxide is necessary for
photosynthesis in plants.

6.1.6 Investigating the Rate of Photosynthesis


Investigating the Rate of Photosynthesis

 The plants usually used are Elodea or Camboba - types of pondweed


 As photosynthesis occurs, oxygen gas produced is released
 As the plant is in water, the oxygen released can be seen as bubbles leaving the cut
end of the pondweed
 The number of bubbles produced over a minute can be counted to record the rate
 The more bubbles produced per minute, the faster the rate of photosynthesis
 A more accurate version of this experiment is to collect the oxygen released in a test
tube inverted over the top of the pondweed over a longer period of time and then
measure the volume of oxygen collected
 This practical can be used in the following ways:

Investigating the effect of changing light intensity

 This can be done by moving a lamp different distances away from the beaker
containing the pondweed

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Investigating the effect of changing light intensity on the rate of photosynthesis

Investigating the effect of changing temperature

 This can be done by changing the temperature of the water in the beaker

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nvestigating the effect of changing temperature on the rate of photosynthesis

Investigating the effect of changing carbon dioxide concentration

 This can be done by dissolving different amounts of sodium hydrogen carbonate in


the water in the beaker

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Investigating the effect of changing carbon dioxide concentration on the rate of
photosynthesis

 Care must be taken when investigating a condition to keep all other variables
constant in order to ensure a fair test
 For example, when investigating changing light intensity, a glass tank should be
placed in between the lamp and the beaker to absorb heat from the lamp and so
avoid changing the temperature of the water as well as the light intensity

6.1.7 Investigating Gas Exchange

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Investigating Gas Exchange

 Plants are respiring all the time and so plant cells are taking in oxygen and
releasing carbon dioxide as a result of aerobic respiration
 Plants also photosynthesise during daylight hours, for which they need to take in
carbon dioxide and release the oxygen made in photosynthesis
 At night, plants do not photosynthesise but they continue to respire, meaning
they take in oxygen and give out carbon dioxide

Photosynthesis and respiration in plants

 During the day, especially when the sun is bright, plants are photosynthesising at
a faster rate than they are respiring, so there is a net intake of carbon dioxide
and a net output of oxygen
 We can investigate the effect of light on the net gas exchange in an aquatic plant
using a pH indicator such as hydrogencarbonate indicator
 This is possible because carbon dioxide is an acidic gas when dissolved in water

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 Hydrogencarbonate indicator shows the carbon dioxide concentration in solution
 The table below shows the colour that the indicator turns at different levels of
carbon dioxide concentration

 Several leaves from the same plant are placed in stoppered boiling tubes containing
some hydrogencarbonate indicator
 The effect of light can then be investigated over a period of a few hours
 Results from a typical experiment are shown in the table below:

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6.1.8 Photosynthesis Chemical Equation: Extended

 The balanced chemical equation for photosynthesis is:

Balanced chemical equation for photosynthesis

 The light energy is converted into chemical energy in the bonds holding the atoms
in the glucose molecules together

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6.1.9 Limiting Factors: Extended
Limiting Factors: Extended

 If a plant is given unlimited sunlight, carbon dioxide and water and is at a warm
temperature, the limit on the rate (speed) at which it can photosynthesise is its own
ability to absorb these materials and make them react
 However, most often plants do not have unlimited supplies of their raw materials so
their rate of photosynthesis is limited by whatever factor is the lowest at that time
 So a limiting factor can be defined as something present in the environment in
such short supply that it restricts life processes
 There are three main factors which limit the rate of photosynthesis:
o Temperature
o Light intensity
o Carbon dioxide concentration

 Although water is necessary for photosynthesis, it is not considered a limiting


factor as the amount needed is relatively small compared to the amount of water
transpired from a plant so there is hardly ever a situation where there is not enough
water for photosynthesis

Temperature

 As temperature increases the rate of photosynthesis increases as the reaction


is controlled by enzymes
 However, as the reaction is controlled by enzymes, this trend only continues up to a
certain temperature beyond which the enzymes begin to denature and the rate of
reaction decreases

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The effect of temperature on the rate of photosynthesis

Light intensity

 The more light a plant receives, the faster the rate of photosynthesis
 This trend will continue until some other factor required for photosynthesis prevents
the rate from increasing further because it is now in short supply

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The effect of light intensity on the rate of photosynthesis

 At low light intensities, increasing the intensity will initially increase the rate of
photosynthesis. At a certain point, increasing the light intensity stops increasing the
rate. The rate becomes constant regardless of how much light intensity increases as
something else is limiting the rate
 The factors which could be limiting the rate when the line on the graph is horizontal
include temperature not being high enough or not enough carbon dioxide.

Carbon dioxide concentration

 Carbon dioxide is one of the raw materials required for photosynthesis


 This means the more carbon dioxide that is present, the faster the reaction can
occur
 This trend will continue until some other factor required for photosynthesis prevents
the rate from increasing further because it is now in short supply

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The effect of carbon dioxide concentration on the rate of photosynthesis

 The factors which could be limiting the rate when the line on the graph is horizontal
include temperature not being high enough or not enough light

6.1.10 Leaf Structure

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Leaf Structure & Adaptations for Photosynthesis

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Diagram showing the cross-section of a leaf

How photosynthesising cells obtain carbon dioxide

 Pathway of carbon dioxide from the atmosphere to chloroplasts by diffusion:

atmosphere → air spaces around spongy mesophyll tissue → leaf mesophyll cells →
chloroplast

Leaf Structure Table

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Adaptations of Leaf Structure for Photosynthesis Table

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6.1.11 Identifying Leaf Structures in a Dicotyledonous Plant

Identifying Leaf Structures in a Dicotyledonous Plant

 You will be expected to identify the following structures in the leaf of a


dicotyledonous plant:
o Chloroplasts
o Cuticle
o Guard cells
o Stomata
o Upper and lower epidermis
o Palisade mesophyll
o Spongy mesophyll
o Air spaces
o Vascular bundles (xylem and phloem)

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Dia
gram showing the cross-section of a leaf

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An electron micrograph of a leaf.

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7. Human Nutrition
7.1.1 Diet & Deficiencies

Balanced Diet

 A balanced diet consists of all of the food groups in the correct proportions
 The necessary food groups are:
o Carbohydrates
o Proteins
o Lipids
o Vitamins
o Minerals
o Dietary Fibre
o Water

Food Groups Table

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Vitamin and Mineral Requirements Table

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Varying Dietary Needs of Individuals Table

Scurvy & Rickets


Scurvy

 Scurvy is the name for a severe vitamin C deficiency


o It is caused by a lack of vitamin C in the diet for over 3 months
 Its symptoms include:
o Anemia
o Exhaustion
o Spontaneous bleeding
o Pain in the limbs
o Swelling
o Gum ulcerations
o Tooth loss
 It is a condition that was commonly seen in sailors between the 15th to 18th
centuries
o Long sea voyages made it very hard to access a ready supply of fresh
produce
 Scurvy can be treated with oral or intravenous vitamin C supplements

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Rickets

 Rickets is a condition in children characterised by poor bone development


 Symtpoms include:
o Bone pain
o Lack of bone growth
o Soft, weak bones (sometimes causing deformities)
 Rickets is caused by a severe lack of vitamin D
o Vitamin D is required for the absorption of calcium into the body
 Calcium is a key component of bones and teeth
 Vitamin D mostly comes from exposure to sunlight but it can also be found in some
foods (fish, eggs and butter)
 The treatment for rickets is to increase consumption of foods containing calcium
and vitamin D
o Alternatively vitamin D supplements can be prescribed

7.1.2 Digestive System

Identifying Organs of the Digestive System

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Organs of the Digestive System: Function
Stages of food breakdown

 Food taken into the body goes through 5 different stages during its passage through
the alimentary canal (the gut):

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o Ingestion - the taking of substances, e.g. food and drink, into the body
through the mouth
o Mechanical digestion - the breakdown of food into smaller pieces without
chemical change to the food molecules
o Chemical digestion - the breakdown of large, insoluble molecules into small,
soluble molecules
o Absorption - the movement of small food molecules and ions through the
wall of the intestine into the blood
o Assimilation - the movement of digested food molecules into the cells of the
body where they are used, becoming part of the cells
o Egestion - the passing out of food that has not been digested or absorbed,
as faeces, through the anus

Functions of the Digestive Organs Table

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7.1.3 Physical Digestion

Physical Digestion

 Physical digestion (sometimes referred to as mechanical digestion) is the breakdown


of food into smaller pieces without chemical change to the food molecules
 The processes that take place during physical digestion help to increase the
surface area of food for the action of enzymes during chemical digestion
 It is mainly carried out by the chewing action of the teeth, the churning action of
the stomach and the emulsification of fats by bile in the duodenum

7.1.4 Teeth & Digestion

Types of Human Teeth

 Mechanical digestion is the breakdown of food into smaller pieces without


chemical change to the food molecules
 It is mainly carried out by the chewing action of the teeth, the churning action of
the stomach and the emulsification of fats by bile in the duodenum
 Teeth are held firmly in the bone of the jaw
o They are used for chewing to increase the surface area of the food so that
it can be exposed to saliva and other digestive juices and broken
down more quickly
 The differing shapes and sizes of teeth enable them to perform slightly different
functions:
o Incisors - chisel-shaped for biting and cutting
o Canines - pointed for tearing, holding and biting
o Premolars and molars - larger, flat surfaces with ridges at the edges for
chewing and grinding up food

Types of teeth

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Structure of a
typical tooth

7.1.5 The Stomach

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19.1.1 Transfer of Energy
Transfer of Energy
Transfer of Energy

 The Sun is the principal source of energy input to biological systems

 Energy flows through living organisms


o Including light energy from the Sun and chemical energy in organisms
o Energy is eventually transferred to the environment eg. as heat

19.1.2 Food Chains & Food Webs

Food Chains & Food Webs

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 A food chain shows the transfer of energy from one organism to the next, starting
with a producer
 The source of all energy in a food chain is light energy from the Sun
 The arrows in a food chain show the transfer of energy from one trophic level to the
next
 Energy is transferred from one organism to another by ingestion (eating)
 In the food chain above:

Food Webs

 A food web is a network of interconnected food chains


 Food webs are more realistic ways of showing connections between organisms
within an ecosystem as animals rarely exist on just one type of food source

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A food web shows the interdependence of organisms

 Food webs give us a lot more information about the transfer of energy in an
ecosystem
 They also show interdependence - how the change in one population can affect
others within the food web
 For example, in the food web above, if the population of earthworms decreased:
o The population of grass plants would increase as there are now fewer
species feeding off them
o The populations of frogs and mice would decrease significantly as
earthworms are their only food source
o The population of sparrows would decrease slightly as they eat
earthworms but also have another food source to rely on (caterpillars)
 Most of the changes in populations of animals and plants happen as a result
of human impact - either by overharvesting of food species or by
the introduction of foreign species to a habitat
 Due to interdependence, these can have long-lasting knock-on effects to
organisms throughout a food chain or web

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19.1.3 Pyramids of Number & Biomass
Pyramids of Number

 A pyramid of numbers shows how many organisms we are talking about at each
level of a food chain.
 The width of the box indicates the number of organisms at that trophic level
 For example, consider the following food chain:

A food chain shows the transfer of energy

 Ask yourself the following questions:


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o Is it likely that there would be more voles in an area than grass plants?
o How many voles might one barn owl need to eat per day? If it’s more than
one, is it likely that there are more barn owls in an area than voles?
 So, a pyramid of numbers for this food chain would look like this:

A pyramid of numbers

 Despite the name (and the example above), a pyramid of numbers doesn’t always
have to be pyramid-shaped, for example:

Pyramids of numbers are not always pyramid-shaped

 This is because the size of the organism is also important - one large organism,
like the oak tree in the pyramid above, contains enough energy to support many
smaller organisms (the insects)

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Rules to remember when drawing a pyramid of numbers:

 You cannot change the trophic level of the organisms - they must stay in the
same order as in the food chain with producers on the bottom, followed by primary
consumers, then secondary consumers, then tertiary consumers
 Generally, the larger an individual organism is, the less of them there are

Pyramids of Biomass

 A pyramid of biomass shows how much mass the creatures at each level would
have without including all the water that is in the organisms (their ‘dry mass’)
 Pyramids of biomass are ALWAYS pyramid-shaped, regardless of what the
pyramid of numbers for that food chain looks like
 This is because the mass of organisms has to decrease as you go up a food
chain – if we take our first food chain as an example, it’s impossible to have 10kg of
grass feeding 50kg of voles feeding 100kg of barn owls

A pyramid of biomass

 Pyramids of biomass provide a much better idea of the quantity of the plant or
animal material at each level of a food chain and therefore are a better way of
representing interdependence within the food chain

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19.1.4 Pyramids of Energy: Extended
Pyramids of Energy: Extended

 In order for the energy to be passed on, it has to be consumed (eaten)


 However not all of the energy grass plants receive goes into making new
cells that can be eaten
 The same goes for the energy the vole gets from the grass, and the energy the barn
owl gets from the vole
 Only the energy that is made into new cells remains with the organism to be
passed on
 Even then, some of this energy does not get consumed - for example few
organisms eat an entire organism, including roots of plants or bones of animals -
but energy is still stored in these parts and so it does not get passed on
 The majority of the energy an organism receives gets ‘lost’ (or ‘used’) through:
o making waste products eg (urine) that get removed from the organism
o as movement
o as heat (in mammals and birds that maintain a constant body temperature)
o as undigested waste (faeces) that is removed from the body and provides
food for decomposers
 This inefficient loss of energy at each trophic level explains why food chains are
rarely more than 5 organisms long
 In the example above, something that preyed regularly on the barn owl would only
get 0.1J of energy from each barn owl it ate
 In order to survive, it would have to:
o eat a huge number of them every day to get the amount of energy it needed
to survive (are there that many barn owls close together?)
o not expend much energy itself hunting them (is this likely?)

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Energy is lost at each trophic level for several reasons

typical pyramid of energy would look like this:

Energy Transfer in a Human Food Chain

 Humans are omnivores, obtaining energy from both plants and animals, and this
gives us a choice of what we eat

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 These choices, however, have an impact on what we grow and how we use
ecosystems
 Think of the following food chains both involving humans:

wheat → cow → human

wheat → human

 Given what we know about energy transfer in food chains, it is clear that if
humans eat the wheat there is much more energy available to them than if they eat
the cows that eat the wheat
 This is because energy is lost from the cows, so there is less available to pass on
to humans
 Therefore, it is more energy efficient within a crop food chain for humans to be
the herbivores rather than the carnivores
 In reality, we often feed animals on plants that we cannot eat (eg grass) or that are
too widely distributed for us to collect (eg algae in the ocean which form the food of
fish we eat)

19.1.5 Nutrient Cycles


The Carbon Cycle

 Nutrients such as carbon and nitrogen are not endless resources


 There is a finite amount of each element on the planet and as such, they need to
be recycled in order to allow new organisms to be made and grow
 Carbon is taken out of the atmosphere in the form of carbon dioxide by plants to be
used for photosynthesis
 It is passed on to animals (and microorganisms) by feeding
 It is returned to the atmosphere in the form of carbon dioxide by plants, animals
and microorganisms as a result of respiration
 If animals and plants die in conditions where decomposing microorganisms are not
present the carbon in their bodies can be converted, over millions of years and
significant pressure, into fossil fuels

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 When fossil fuels are burned (the process is known as combustion), the carbon
combines with oxygen and carbon dioxide is released into the atmosphere
 Increased use of fossil fuels is contributing to an increase in the carbon dioxide
content of the atmosphere
 In addition, mass deforestation is reducing the amount of producers available to
take carbon dioxide out of the atmosphere by photosynthesis
 This problem is exacerbated by the fact that in many areas of the world,
deforestation is taking place for land rather than for the trees themselves, and as
such they are burnt down, releasing yet more carbon dioxide into the
atmosphere

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The Carbon Cycle

The Nitrogen Cycle: Extended

 Nitrogen as an element is required to make proteins


 Neither plants nor animals can absorb it from the air as N2 gas is very stable and
the bonds holding the nitrogen atoms together would need massive amounts of
energy to break (the two nitrogen atoms in a nitrogen molecule are held together by
a triple covalent bond)
 However, there are two ways it can be taken out of the air and converted into
something easier to absorb:
o Nitrogen fixing bacteria found ‘free living’ in soil and also in the root nodules
of certain plants (peas, beans, clover – we call them leguminous plants) take
N2 gas and change it into nitrates in the soil
o Lightning can ‘fix’ N2 gas, splitting the bond between the two atoms and
turning them into nitrous oxides like N2O and NO2 that dissolve in rainwater
and ‘leach’ into the soil
 Plants absorb the nitrates they find in the soil and use the nitrogen in them to make
proteins
 Animals eat the plants (or other animals) and get the nitrogen they need from the
proteins in the plant or animal
 Waste (urine and faeces) from animals sends nitrogen back into the soil as
ammonium compounds (the urea in urine contains nitrogen)
 When the animals and plants die, they decay and all the proteins inside them are
broken down into ammonium compounds and put back into the soil by decomposers
 The plants can’t absorb ammonium compounds though, so a second type of soil
bacteria, nitrifying bacteria, convert the ammonium compounds to nitrites and then
to nitrates, which can then be absorbed by plants – and so the cycle goes on
 Finally, there is a third, unhelpful type of (anaerobic) bacteria called denitrifying
bacteria found in poorly aerated soil (ie not much oxygen)
 These bacteria take the nitrates out of the soil and convert them back into N2 gas

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 Farmers can help reduce the amount of these unhelpful bacteria by ploughing and
turning over soil

The Nitrogen Cycle

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19.1.6 Populations
Definition of Population

 A population is defined as a group of organisms of one species, living in the


same area at the same time

Other important definitions

 A community is defined as all of the populations of different species in an


ecosystem
 An ecosystem is defined as a unit containing the community of organisms and
their environment, interacting together (eg a decomposing log, a lake)

Population Growth

 All living organisms compete with each other for food, water and living space
 Those which are the best adapted to their environments generally increase their
populations at the expense of those less well adapted
 Population growth in most organisms is controlled by the following three factors:
o Food supply
o Predation
o Disease

The Population Growth Curve: Extended

 If the growth of microorganisms in a fermenter is measured over time, the


population growth looks like the graph below

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A typical growth curve for a population in an enclosed environment

 The shape of this curve ( a little like an ‘S’), gives it its name - a sigmoid growth
curve
 The curve has four distinct phases:
o Lag phase - organisms are adapting to the environment before they are
able to reproduce; in addition, at this stage there are very few organisms and
so reproduction is not producing larger numbers of offspring
o Log phase (aka exponential phase) - food supply is abundant, birth rate
is rapid and death rate is low; growth is exponential and only limited by
the number of new individuals that can be produced
o Stationary phase - population levels out due to a factor in the
environment, such as a nutrient, becoming limited as it is not being
replenished; birth rate and death rate are equal and will remain so until either
the nutrient is replenished or becomes severely limited
o Death phase - population decreases as death rate is now greater than birth
rate; this is usually because food supply is short or metabolic wastes
produced by the population have built up to toxic levels
 Organisms in a natural environment are unlikely to show population growth like a
sigmoid growth curve because they are affected by many other factors, including:
o changing temperature or light
o predators
o disease
o immigration (individuals moving into the area)
o emigration (individuals moving out of the area)

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20. Biotechnology & Genetic Engineering
20.1.1 Microorganisms & Biotech

Use of Bacteria

 Microorganisms can be used by humans to produce foods and other useful


substances
 The most common type of microorganisms used in biotechnology are bacteria
 They are useful because they are capable of producing complex molecules (eg
certain bacteria added to milk produce enzymes that turn the milk into yoghurt)
 They are also useful because they reproduce rapidly, meaning the amount of
chemicals they can produce can also rapidly increase

Biofuels

 Yeast is a single celled fungus that uses sugar as its food source
 When it respires, ethanol and carbon dioxide are produced (and energy is released)

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The alcohol produced by fermentation of glucose can be used as biofuel

 The ethanol produced in this reaction is increasingly being used as a biofuel (a fuel
made from living organisms rather than a fossil fuel like oil, coal or gas)
 In countries such as Brazil, biofuel is partly replacing petrol as the fuel for cars and
other vehicles
 Plant material is used as the substrate for producing ethanol (as a source of
glucose) - it is chopped up into small pieces and mixed with yeast which respires
anaerobically and produces ethanol
 The liquid is separated from the remaining solids and any water is removed, leaving
a concentrated solution of ethanol
 Sometimes the waste parts of crop plants, such as the stalks or outer leaves, are
used, but in other places, crops are grown specifically to be harvested for making
ethanol
 In some places, this is causing concern that there is less land available for local
people to grow food crops needed for survival

Bread Making

 Yeast will respire anaerobically if it has access to plenty of sugar, even if oxygen is
available
 This is taken advantage of in bread making, where the yeast is mixed with flour and
water and respires anaerobically, producing carbon dioxide:

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The carbon dioxide produced by fermentation (anaerobic respiration) of glucose is
what makes bread dough rise

 The carbon dioxide produced by the yeast during respiration is caught in the dough,
causing the bread to rise

20.1.2 Fruit Juice


Fruit Juice Production

 Fruit juice is produced by squeezing the fruits to remove the juice


 Chopping the fruit up before squeezing helps to release a lot more juice, but this
does not break open all the cells so a lot of juice is lost
 By adding an enzyme called pectinase to the chopped up fruit, more juice is
released
 Pectinase works by breaking down a chemical called pectin that is found inside
plant cell walls
 Once pectin is broken down, the cell walls break more easily and more juice can
be squeezed out of the fruit
 Adding pectinase to fruits also helps to produce a clearer juice as larger
polysaccharides like pectin can make the juice seem cloudy - once they are broken
down into smaller molecules, the juice becomes clearer

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Biological Washing Powders

 Many stains on clothes are organic molecules – oil from skin, protein from blood,
fat and protein from food
 Detergents that only contain soap can remove some of these stains when mixed with
hot water, but it can take a lot of time and effort and very high temperatures to
remove the stains entirely
 Biological washing powders contain enzymes similar to the digestive enzymes
produced in the alimentary canal that help to break down large food molecules
 Using biological washing powders has several advantages, including:
o Quickly breaking down large, insoluble molecules such as fats and
proteins into smaller, soluble ones that will dissolve in washing water
o They are effective at lower temperatures, meaning less energy (and
money) has to be used in order to wash clothes to get them clean as
washing water does not need to be heated to higher temperatures
o They can be used to clean delicate fabrics that would not be suitable for
washing at high temperatures

Lactose-Free Milk

 Lactose is the sugar found in milk


 Human babies are born with the ability to produce lactase, the enzyme that breaks
down lactose
 In certain areas of the world, many people lose the ability to produce lactase as
they get older
 This means that they can become lactose intolerant and react badly to the lactose
in milk and products made from milk (cheese, yoghurt etc)
 Symptoms of lactose intolerance include nausea, flatulence and diarrhoea as their
digestive system is upset by the lactose
 Milk can be made lactose free by adding the enzyme lactase to it and leaving it to
stand for a while to allow the enzyme to break down the lactose

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Lactose-free milk is a product made from adding the enzyme lactase to dairy milk to
break down the sugars in it

Penicillin Production

 Penicillin was the first antibiotic discovered in 1928 by Alexander Fleming


 He noticed that some bacteria he had left in a Petri dish had been killed by the
naturally occurring Penicillium mould
 The penicillium mould produces a chemical to prevent it being infected by certain
types of bacteria

Penicillin produced by the fungus Penicillium inhibits bacterial growth

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 The chemical was isolated and named penicillin
 Since the discovery of penicillin, methods have been developed to produce it on a
large scale, using an industrial fermenter

A diagram of an industrial fermenter used to produce large quantities of


microorganisms

 Fermenters are containers used to grow (‘culture’) microorganisms like bacteria


and fungi in large amounts
 These can then be used for many biotechnological processes like
producing genetically modified bacteria and the penicillium mould that
produces penicillin
 The advantage of using a fermenter is that conditions can be carefully
controlled to produce large quantities of exactly the right type of microorganism

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20.2.1 Genetic Engineering
Genetic Engineering Examples

 Genetic engineering is changing the genetic material of an organism by


removing, changing or inserting individual genes from another organism
 The organism receiving the genetic material is said to be ‘genetically modified’, or
is described as a ‘transgenic organism’
 The DNA of the organism that now contains DNA from another organism as well is
known as ‘recombinant DNA’
 There are many examples of genetically modified organisms, including:

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 The gene for human insulin has been inserted into bacteria which then produce
human insulin which can be collected and purified for medical use for diabetics
 Crop plants, such as wheat and maize, have been genetically modified to contain a
gene from a bacterium that produces a poison that kills insects, making
them resistant to insect pests such as caterpillars
 Crop plants have also been genetically modified to make them resistant to certain
herbicides (chemicals that kill plants), meaning that when the herbicide is sprayed
on the crop it only kills weeds and does not affect the crop plant
 Some crops have been genetically modified to produce additional vitamins,
eg ‘golden rice’ contains genes from another plant and a bacterium which make the
rice grains produce a chemical that is turned into vitamin A in the human body,
which could help prevent deficiency diseases in certain areas of the world

Advantages & Disadvantages of GM Crops

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Process of Genetic Engineering

 The gene that is to be inserted is located in the original organism (for example, this
could be the gene for human insulin)
 Restriction enzymes are used to isolate the required gene, leaving it with ‘sticky
ends’ (a short section of unpaired bases)
 A bacterial plasmid is cut by the same restriction enzyme leaving it with
corresponding sticky ends (plasmids are circles of DNA found inside bacterial
cells)

Restriction enzymes cut DNA strands at specific sequences to form ‘sticky ends’

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 The plasmid and the isolated gene are joined together by DNA ligase enzyme
 If two pieces of DNA have matching sticky ends (because they have been cut by
the same restriction enzyme), DNA ligase will link them to form a single, unbroken
molecule of DNA

DNA ligase is used to join two separate pieces of DNA together

 The genetically engineered plasmid is inserted into a bacterial cell


 When the bacteria reproduce the plasmids are copied as well and so a
recombinant plasmid can quickly be spread as the bacteria multiply and they will
then all express the gene and make the human protein
 The genetically engineered bacteria can be placed in a fermenter to reproduce
quickly in controlled conditions and make large quantities of the human protein
 Bacteria are extremely useful for genetic engineering purposes because:
o They contain the same genetic code as the organisms we are taking the
genes from, meaning they can easily ‘read’ it and produce the same
proteins
o There are no ethical concerns over their manipulation and growth (unlike
if animals were used, as they can feel pain and distress)

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o The presence of plasmids in bacteria, separate from the main bacterial
chromosome, makes them easy to remove and manipulate to insert genes
into them and then place back inside the bacterial cells

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21. Human Influences on Ecosystems
Improving Food Production

 Modern technology has increased food supply substantially in the following ways:
o Agricultural machinery has replaced humans and improved efficiency due
to the ability to farm much larger areas of land
o Chemical fertilisers improve yields - fertilisers increase the amount of
nutrients in the soil for plants, meaning that they can grow larger and produce
more fruit
o Insecticides and herbicides - these chemicals kill off unwanted insects and
weed species, meaning that there is less damage done to plants and fruit
lost to insects (insecticides), as well as reducing competition from other
plant species (herbicides)
o Selective breeding - animals and crop plants which produce a large yield are
selectively bred to produce breeds that reliably produce high yields

Modern agricultural processes allows for cultivation of much larger areas of land for
crop plants

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Monocultures

 Monoculture farming means that on a given area of agricultural land only one type
of crop is grown (eg trees for palm oil grown in Indonesian rainforest)
 This large scale growth of a single variety of plant does not happen naturally in
ecosystems, where there are usually many different species of plants growing
which, in turn, support many species of animals (high biodiversity)
 In monocultures, biodiversity is much lower
 Another issue with monocultures is the increase in pest populations – if a
particular pest feeds on a crop, farming it in large areas repeatedly means there is
an ample supply of food for the pest, causing the population to increase
 Often farmers will spray insecticides onto crops in order to control the pests. This
leads to:
o harmless insects being killed as well
o pollution by pesticides (which are often persistent chemicals which
accumulate in food chains)
o in many instances where they are used repeatedly for specific pests, the
pests may eventually become resistant to them, reducing their effectiveness

Palm oil production has increased rapidly over the last 30 years

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21.1.2 Livestock Farming
Intensive Livestock Farming

 In developed countries, large numbers of livestock are often kept in an area that
would not normally be able to support more than a very small number
 They are often fed high energy foods, regularly given medication such
as antibiotics as a preventative measure against disease and kept in artificially
warm temperatures and small spaces that do not allow for much movement
 Ecological issues with intensive farming include:
o reduction in biodiversity in areas where large amounts of land are used to
graze cattle (as only grass is grown so in effect it becomes a monoculture)
o overgrazing can lead to soil erosion
o large numbers of cattle produce large amounts of methane, a greenhouse
gas

Global Food Supply

 When people do not receive enough food, famine occurs


 This can be caused by a variety of factors, including natural disasters, such as
drought and flooding, increasing population, poverty, and unequal food
distribution
 As the global human population increases, food production must also be increased
to support the increasing population
 This is a problem as more land is required to grow crops and animals, meaning
that deforestation is happening at an increasing rate, and there is also an
increasing amount of greenhouse gases emitted from animal production
 Greenhouse gases cause global warming, which is a worldwide issue that leads to
increased natural disasters, such as tropical storms and drought, as well as rising
sea levels, which floods homes and decreases the amount of habitable land

21.2.1 Habitat Destruction

Reasons for Habitat Destruction

 The increasing human population of the planet is causing destruction of many


habitats from rainforest to woodland to marine
 Many habitats are destroyed by humans to make space for other economic activities,
or by pollution from these activities, and this reduces the biodiversity of these areas
 This interrupts food chains and webs, meaning that more species may die because
their prey is gone
 The main reasons for habitat destruction include:

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Deforestation

 Deforestation is the clearing of trees (usually on a large scale)


 If trees are replaced by replanting it can be a sustainable practise
 Generally the trees are being cleared for the land to be used in a different way (for
building, grazing for cattle, planting of monocultures such as palm oil plantations etc)
and therefore it is not sustainable
 As the amount of the Earth’s surface covered by trees decreases, it causes
increasingly negative effects on the environment and is a particularly severe
example of habitat destruction
 Undesirable effects of deforestation include:
o Extinction of species
o Loss of soil
o Flooding
o Increase of carbon dioxide in the atmosphere

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Consequences of Deforestation

21.3.1 Causes & Effects of Pollution


Causes & Effects of Pollution

 Human activities have led to the pollution of land, water and air
 Pollution comes from a variety of sources, including industry and manufacturing
processes, waste and discarded rubbish, chemicals from farming practices, nuclear
fall-out, and untreated sewage

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21.4.1 Types of Pollution
Plastic Pollution

 Plastics have a large negative impact on both land and water habitats due to their
non-biodegradability
 In marine habitats:
o Animals often try to eat plastic or become caught in it, leading to injuries
and death
o As the plastic breaks down it can release toxins that affect marine organisms
o Once it has broken down into very small particles, it is commonly ingested
by animals and enters the food chain
 On land:
o Plastic is generally disposed of by burying in landfills
o As it breaks down, it releases toxins into the surrounding soil and as such
the land is no good for growing crops or grazing animals and can only be
used for building on several decades after burial

Female Hormones

 Female contraceptive hormones are excreted from the body in urine and
then make their way into the water supply, as they are not filtered out by sewage
treatment plants
 If they reach male aquatic organisms, such as fish and frogs, which are very
sensitive to the hormones, it causes feminisation
 This is where male organisms begin to produce eggs and lose the ability to
reproduce
 Consequently, a smaller amount of offspring is produced which can harm the
species survival and also disrupts food chains for animals that usually feed off
these organisms
 In addition, these hormones can reduce the sperm count in human males, which
causes fertility problems

Eutrophication

 Runoff of fertiliser from farmland enters the water and causes increased growth of
algae and water plants
 The resulting ‘algal bloom’ blocks sunlight so water plants on the bottom start to
die, as does the algae when competition for nutrients becomes too intense
 As water plants and algae die in greater numbers, decomposing bacteria increase
in number and use up the dissolved oxygen whilst respiring aerobically
 As a result there is less oxygen dissolved in water, so aquatic organisms such as
fish and insects may be unable to survive

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Sequence of events causing eutrophication in lakes and rivers

Acid Rain

 Combustion of fossil fuels that contain sulfur impurities creates sulfur dioxide
 This is released into the atmosphere where it combines with oxygen to form sulfur
trioxide
 Sulfur trioxide dissolves in water droplets in clouds and forms acid rain

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21.4.2 Climate Change
Climate Change

 A greenhouse gas is a gas that absorbs infrared radiation from the Sun so it
remains trapped in the Earth’s atmosphere
 This is important to ensure Earth is warm enough for life, however if levels of these
gases in the atmosphere increase it leads to an increase in the greenhouse effect
which causes the Earth’s average temperature to rise
 There are many greenhouse gases, the most important are:
o Water vapour
o Carbon dioxide
o Methane
o Nitrous oxides
o CFCs
 The greenhouse effect works in the following way:
o The Sun emits rays that enters the Earth’s atmosphere
o The heat bounces back from the Earth’s surface
o Some heat is reflected back out into space
o Some heat is absorbed by greenhouse gases and is trapped within the
Earth’s atmosphere - this is normal
o However, as the levels of greenhouse gases in the atmosphere rise due to
human activities the Earth’s average temperature rises beyond
normal (an enhanced greenhouse effect), causing global
warming or climate change

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How the greenhouse effect works

Consequences of global warming due to an enhanced greenhouse effect

 Ocean temperatures increase which causes melting of polar ice caps / rising sea
levels / flooding / coral bleaching

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 Increasing temperatures can cause extreme weather like super storms, flooding,
droughts
 These extreme weather events can lead to changes in or loss of habitats
 This means that there will be a decrease in biodiversity as food chains are
disrupted and extinction rates increase
 There could also be increases in migration of species to new places,
increased spread of pests and disease

21.5.1 Sustainability
Sustainable Resources

 We use many resources from the Earth; some, such as food, water and wood,
are sustainable resources
 A sustainable resource is one which is produced as rapidly as it is removed from
the environment so that it does not run out
 Some resources, such as fossil fuels (coal, oil and natural gas), are non-
renewable because what we use cannot be replaced
 These resources, once used, cannot be produced anymore and so they need to
be conserved by reducing the amount we use and finding other, sustainable
resources to replace them
 Fossil fuels are being used as an energy source in increasing amounts
 In addition, they are the raw materials for many other products we make - eg almost
all plastics that are made start with oil as a raw material
 Some products, especially those made from paper, plastic, glass or metal, can
be reused and recycled - this reduces waste in the environment and reduces the
amounts of raw materials and energy needed to make new products
 Some resources, such as forests and fish stocks, can be maintained - enabling us
to harvest them sustainably so that they will not run out in the future

Sustainable Development

 Sustainable development is defined as development providing for the needs of


an increasing human population without harming the environment

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 When developing the way in which we use resources to manage them sustainably,
we have to balance conflicting demands - eg:
o the need for local people to be able to utilise the resources they have in their
immediate environment with the needs of large companies to make money
from resources such as forests and fish
o the need for balancing the needs of humans for resources with the needs
of the animals and plants that live in the areas the resources are taken from
(preventing loss of habitat and extinction)
o the need to balance what current populations need with what future
populations might need - for example if we harvest all the fish we need to
feed people now, this might lead to overfishing which would deplete stocks for
future generations
 For development to occur sustainably, people need to cooperate at local, national
and international levels in the planning and management of resources

Sustaining Forests

 Forests are needed to produce paper products and provide wood for timber
 Much of the world’s paper is now produced from forests which replant similar trees
when mature trees are cut, ensuring that there will be adequate supply in the future
 Tropical hardwoods such as teak and mahogany take many years to regrow but are
highly desirable for furniture
 Using these types of wood has now been made more sustainable due to
the introduction of several schemes designed to monitor logging
companies and track the wood produced (eg the Forestry Stewardship Council)
 Education helps to ensure logging companies are aware of sustainable practices
and consumers are aware of the importance of buying products made from
sustainable sources

More efforts are being made to manage forests sustainably so consumers know they
are not causing damage to forests

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Sustaining Fish Stocks

 Managing fish stocks sustainably includes:


o Controlling the number of fish caught each year (quotas)
o Controlling the size of fish caught (to ensure there are enough fish of a
suitable age for breeding remaining)
o Controlling the time of year that certain fish can be caught (to prevent large
scale depletion of stocks when fish come together in large numbers in certain
areas to breed)
o Restocking (breeding and keeping offspring until they are large enough to
survive in their natural habitat then releasing)
o Educating fishermen as to local and international laws and consumers so
they are aware of types of fish which are not produced sustainably and can
avoid them when buying fish

21.5.2 Sewage
Sewage Treatment

 As human population grows, the need for fresh water increases


 A significant amount of water we consume is used to flush away human
waste (sewage) into pipes
 The pipes carry the sewage and water to treatment plants where the organic
waste is removed and the water cleaned so it can be returned to natural water
sources without causing eutrophication
 Crude sewage flows through a screen in which large materials like paper and
sticks are trapped so they can be removed and burned
 The sewage is passed slowly through channels where grit and other heavy
particles picked up along the way settle to the bottom - the grit is later washed
and returned to the land
 The channels lead into sedimentation tanks where the solid material settles on
the bottom as sludge and the liquid part, called effluent, remains on top
 The sludge is removed by pumping it into tanks where anaerobic
bacteria decompose it - often the bacteria produce methane which can be collected
and used as an energy source for the plant
 The effluent (liquid) is treated with aerobic bacteria to remove any organic waste
in it, before being treated with chlorine to kill the bacteria
 At this point it is clean enough to return to natural water systems or be passed on
to a second treatment plant where it is processed further to make it pure enough to
reuse as drinking water

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Water containing sewage goes through several stages of treatment before being
returned to natural water systems

21.5.3 Endangered Species


Endangered Species: Basics

 An endangered species is at risk of becoming extinct


 There are several reasons why a species can become endangered - the population
of the species may fall below a critical level due to
o hunting
o climate change
o pollution
o loss of habitat
o introduction of non-native species that outcompete native species
 Endangered species can be helped by conservation measures such as:
o education programmes
o captive breeding programmes
o monitoring and legal protection of the species and of their habitats
o seed banks as a conservation measure for plants - seeds of endangered
plant species are carefully stored so that new plants may be grown in the
future

Endangered Species

 A species may be at risk of becoming extinct if there is not enough genetic


variation in the population as random changes in the environment may quickly
cause extinction because the remaining organisms are all very similar and may
not have the adaptations to survive such changes

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 There are moral, cultural and scientific reasons for conservation programmes,
including:
o reducing extinction rates of both plant and animal species
o keeping damage to food chains and food webs to a minimum and protecting
vulnerable ecosystems (eg the rainforests)
o protecting our future food supply and maintaining nutrient cycles and
possible sources of future medical drugs and fuels

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