Title: Higher Biology
1Higher Biology
- Unit 1
- Cell Biology
- Cell structure in relation to function
2- In a multicellular (many-celled) organism the
cells are organised into tissues. - A tissue is a group of similar cells which work
together to carry out a specific function.
3- Some tissues have only one type of cell (e.g.
muscle). Other tissues have several types of
cells (e.g. phloem contains sieve tubes and
companion cells).
4- The structure of a cell is related to its
function (what the cell does). - In a unicellular (one-celled) organism (e.g.
amoeba, paramecium, euglena or yeast) all the
processes necessary for life are carried out in a
single cell.
5Paramecium
6Euglena
7Root hair
8Leaf epidermis
9Phloem
10Xylem
11Leaf mesophyll
12Parenchyma
13Lining of kidney tubule
14Return
Lining of trachea
15Lining of trachea
16Lining of mouth
17Bone cell
18Fat cell
19Red blood cell
20Muscle Cell
21Nerve cell
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23Cell Ultrastructure
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27Cell Boundries
- Cell wall
- Outer boundary of plant cells
- Made of cellulose fibres in layers
- Strong, slightly elastic
- Absorbs water, providing a pathway for water
movement through plant tissues.
28- Plasma membrane
- Forms the cell membrane and forms or surrounds
all cell organelles.
29- Made of a double layer of phospholipid molecules
with protein molecules embedded. - Called fluid-mosaic model because
- Molecules move around like fluid
- Proteins form a pattern on surface (mosaic)
- Some protein molecules enclose a pore through
which small molecules can pass in/out of the cell.
30Functions of the plasma membrane
- Molecules can enter or leave a cell, across the
membrane, in 5 ways - Diffusion
- Osmosis
- Endocytosis
- Exocytosis
- Active Transport
31Diffusion
- Movement of molecules of (gas or) liquid from an
area of high concentration to an area of low
concentration down a concentration gradient.
32- The concentration gradient is the difference in
concentration between two areas.
33- Molecules cross the plasma membrane in two ways
- Through the phospholipid layer
- Through pores in the protein molecules
-
34Osmosis
- Diffusion of water molecules
- Through a selectively permeable membrane (e.g.
plasma membrane) - (S.P. Membrane is a membrane with pores which
allows small molecules to pass but not large ones)
35- Water moves from a high water concentration to
low water concentration - HWC LWC
36Effects of osmosis on cells
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38- Hypotonic higher water concentration
- Hypertonic lower water concentration
- Isotonic same water concentration
39- Turgid cell swollen with water
- Flaccid cell limp through loss of water
- Plasmolysed in Plant cells, water loss causes
cytoplasm to shrink away from the cell wall.
40Endo- and Exo-cytosis
- Cells sometimes take in, or expel, large
quantities of material by forming a pocket in
the membrane. - This is called endocytosis (taking material into
the cell) or exocytosis (materials leave the
cell).
41- An example of endocytosis is
42Phagocytosis
43- In this form of endocytosis the cell engulfs
solid particles (e.g. amoeba) like eating a
bacterium.
44Active Transport
- Movement of ions across the plasma membrane
against the concentration gradient - i.e. Low concentration ? High concentration
45- Energy is needed.
- Protein molecules transport ions across the
membrane.
46IN
High conc. inside the cell
Low conc. outside the cell
Energy
Low conc. inside the cell
High conc. outside the cell
OUT
47Essay question
- Discuss the role of the plasma membrane under the
following headings - The structure of the plasma membrane (4 marks)
- The role of the plasma membrane in transport (6
marks)
48- Discuss the role of the plasma membrane under the
following headings - The structure of the plasma membrane (4 marks)
- The role of the plasma membrane in transport (6
marks) - Plasma membrane
- Composed of phospholipid bilayer (two layers)
- Contains proteins.
- Some proteins form pores through the membrane.
- Described as a fluid mosaic
- Role of plasma membrane
- Diffusion movement of liquid/gas from area of
high conc. to area of low conc. - Osmosis movement of water from area of HWC to
area of LWC. - Endocytosis description of engulfing a large
molecule. - Phagocytosis is an example of endocytosis (eating
bacteria). - Active transport movement from area of low
conc. to area of high conc. - Active transport requires energy and a carrier
protein. - 1 mark for each bullet point. TOTAL 10 Marks
49Lives in the sea Lives in the sea Lives in fresh water Lives in fresh water Lives in fresh water
Ion Fresh water Sea Water Lobster Mussel Cray-fish Frog Fresh WaterMussel
Na 0.24 478.3 530.9 79 212 109 15.6
K 0.005 10.1 8.7 152 4.1 2.6 0.5
Ca 0.67 10.5 15.8 7.3 15.8 2.1 6.0
Mg 0.04 54.5 7.6 34 1.5 1.3 0.2
Cl 0.23 558.4 558.4 94 199 78 11.7
SO4 0.05 28.8 8.9 8.8 - - -
Concentrations in mM per kg
50- In the example above, the lobster actively
transports sodium inwards (higher concentration
in the body than the sea water), actively
transports magnesium out (lower concentration in
body than sea water), but does not regulate
chloride (concentration equal).
51Higher Biology
- Unit 1
- Cell Biology
- Photosynthesis
52Absorption, reflection and transmission of light
by a leaf
12 of light reflected
Light shining on leaf (100 )
83 of light absorbed but only 4 of this is
used for photosynthesis
5 of light transmitted
53Light absorption by leaf pigments
- Leaves contain several coloured pigments of which
chlorophyll is the most important. - These pigments absorb light energy.
54Which wavelengths of light are used
- White light is made up of several different
wavelengths of light from 400 nm to 700 nm. - Normal spectrum of white light
violet blue green yellow orange red
55- Collect a leaf and cut into small pieces.
- Add some propanone and sand into a mortar and
pestle. - Grind this up, until the propanone turns green.
- Filter the mixture into a test tube.
- Hold the spectroscope up towards the test tube
and look towards the light.
56violet blue green yellow orange red
Spectrum viewed through Chlorophyll
violet blue green yellow orange red
The blue and violet are no longer visible and
only some of the red is still seen. These have
been absorbed by the chlorophyll.
57- The main wavelengths absorbed are violet and
blue, and some red. - These are most important wavelengths for a plant
in photosynthesis.
58Absorbtion and Action Spectra
- A leaf contains several pigments which can be
separated by chromatography. - The main pigments are
- Chlorophyll a (blue-green)
- Chlorophyll b (yellow-green)
- Carotene (yellow)
- Xanthophyll (yellow)
59- An absorption spectrum shows the absorption of
light of each wavelength by each pigment. - An action spectrum shows the rate of
photosynthesis at each light wavelength. - Comparison of absorption and action spectra
reveals a close match this is good evidence for
the importance of leaf pigments in photosynthesis.
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61- The presence of several pigments increases the
range of wavelengths the plant can make use of.
62Separation of photosynthetic pigments by thin
layer chromatography
63Name Rf value
Carotene
Chlorophyll a
Chlorophyll b
Xanthophyll
64Chloroplasts
- The main pigments (chlorophyll ab, carotene and
xanthophyll) are contained in the chloroplasts.
65- Chloroplasts have
- A double plasma membrane
- A liquid stroma
- Stacks of flattened membrane bags called grana
(singular granum) which contain chlorophyll - Connecting tubes between grana called lamellae.
66Chemistry of photosynthesis
- Remember Standard Grade
- Carbon dioxide water light energy ? glucose
oxygen - This takes place in 2 main stages
- Photolysis (needs light)
- Carbon fixation (Calvin cycle)
67Photolysis
- Happens in the GRANA of the chloroplasts.
- Light energy is absorbed by chlorophyll and used
to split water molecules into hydrogen and
oxygen. - Energy is released.
68WATER
Oxygen
Hydrogen
ENERGY
69- These products are treated like this
- OXYGEN released as a by-product.
- HYDROGEN attached to a hydrogen acceptor
molecule (NADP) to form NADPH2 - ENERGY stored as ATP
70- The hydrogen and the ATP play an important part
in the second stage of photosynthesis, called
CARBON FIXATION.
71Quick Quiz
3
5
4
2
6
72Answers
- Carbon dioxide water light energy ? glucose
oxygen - Grana/Granum
- Outer membrane
- Lamellae
- Inner membrane
- Stroma
- Grana
- Water split to hydrogen oxygen, energy released
- Picked up by NADP to form NADPH2/Picked up by
hydrogen acceptor - In ATP
73Carbon Fixation
- Takes place in the STROMA of the chloroplast.
- Molecules of carbon dioxide diffuse into the
chloroplasts where they attach to molecules of
5-carbon Ribulose biphosphate (RuBP)
74- The resulting 6-carbon compound is unstable and
breaks down into two molecules of 3-carbon
glycerate-3-phosphate (GP). - In the next step, GP is reduced to triose
phosphate (3-carbon) by the addition of hydrogen
(from the NADPH2) and energy (from ATP).
75CO2 (1C)
6C unstable
2 x GP (3C)
NADPH2
ATP
RuBP (5C)
NADP
ADP Pi
Triose phosphate (3C)
CALVIN CYCLE
Glucose
Complex carbohydrates other organic molecules
76- Triose phosphate has two possible fates
- Synthesis of glucose (6 carbon) which is then
built up into other carbohydrates (e.g. starch
and cellulose) -
- Plants also use carbohydrates to make other
organic molecules (e.g. proteins, fats and
nucleic acids)
77- 2. Conversion to RuBP so that more carbon dioxide
can be taken up. - The cycle of reactions involved in carbon
fixation is know as the calvin cycle.
78Limiting factors
- A limiting factor is a factor which slows down
the process of photosynthesis if is in short
supply. - Limiting factors are light intensity , carbon
dioxide concentration and temperature.
79B
Rate of photosynthesis
30C
B
20C
B
A
10C
Carbon dioxide concentration
80- At point A Rate of photosynthesis depends on
carbon dioxide concentration, regardless of
temperature. - Carbon dioxide is the limiting factor.
- At point B Further increase in CO2 has no
effect. The rate of photosynthesis is increased
by raising the temperature. - Temperature is the limiting factor
81Limiting factor either Light or Temp
Limiting factor either CO2 or Temp
Rate of photosynthesis
Rate of photosynthesis
Limiting factor Light intensity
Limiting factor CO2 conc.
Light intensity
Carbon dioxide concentration
82Aerobic Respiration
83Energy storage in the cell
- Chemical energy is stored in cells in molecules
of ATP (Adenosine Tri-Phosphate).
84- (Pi Inorganic phosphate)
- In order to release the chemical energy, the bond
attaching the third phosphate is broken (shown in
red).
85ATP formation
- A molecule of ATP forms when a molecule of ADP
(Adenosine Di-Phosphate) joins with an inorganic
phosphate. - The energy required to join the Pi to the ADP
comes from the chemical energy released from the
breakdown of glucose during respiration.
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87- The conversion of ADP to ATP is called
Phosphorylation.
88Summary
89Aerobic respiration S-Grade
90Chemistry of Aerobic respiration
- Aerobic respiration is the complete oxidation of
molecules of glucose to release energy. - Oxidation is the removal of hydrogen with the
release of energy.
91- Aerobic respiration takes place in 3 stages
- Glycolysis
- Krebs Cycle
- Cytochrome system.
92Stage 1 Glycolysis
93- Glucose molecules (6 carbons) are broken down
into 2 molecules of 3-carbon molecule called
Pyruvic acid. - Happen in the cytoplasm.
- No oxygen is required.
94- There is a net gain of 2 ATP molecules.
- Hydrogen is released and temporarily attached to
a co-enzyme carrier molecule called NAD. - NAD 2H NADH2 (reduced co-enzyme)
95Stage 2 The Krebs Cycle
- a.k.a. The Citric Acid cycle OR Tri-carboxylic
acid (TCA) cycle. - This takes place in the mitochondria.
96Mitochondria
- Mitochondria (singular mitochondrion) are
sausage shaped organelles surrounded by a double
plasma membrane. - The centre of the called the Matrix and is filled
with fluid.
97- The inner membrane is folded into cristae which
provide a large surface area for the stalked
particles on which the cytochrome system takes
place.
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100- The pyruvic acid diffuses from the cytoplasm into
the mitochondrion. - In the matrix, the pyruvic acid is converted to a
2-carbon compound called acetyl Co-A, releases
CO2 and hydrogen. The hydrogen is bound to NAD.
101- Acetyl Co-A now enters the Krebs cycle by
combining with a 4-carbon compound to form
6-carbon citric acid. - Citric acid is then broken down in a series of
oxidation reactions to the original 4-carbon
compound and the cycle begins again. - The Hydrogen which is released binds with NAD.
102Stage 3 Cytochrome system
- This takes place on the stalked particles on the
cristae. - Hydrogen is released from the NADH2 and passed
along a chain of hydrogen carriers called the
cytochrome system.
103- As each pair of hydrogen atoms are passed along
the chain enough energy is released to make 3
molecules of ATP. This is called oxidative
phosphorylation. - At the end of the chain the hydrogen combines
with oxygen to form water.
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105Production of ATP
- Complete oxidation of one molecule of glucose
produces 38 molecules of ATP (36 from oxidative
phoshorylation in the cytochrome system and 2
from glycolysis).
106- As the organism respires it uses oxygen (and
produces carbon dioxide which is absorbed by the
sodium hydroxide). This causes the liquid level
to rise and the syringe is used to find the
volume of oxygen consumed.
107Anaerobic respiration
- Aerobic respiration only occurs if oxygen is
available to accept the hydrogen at the end of
the cytochrome system. - If no oxygen is available anaerobic respiration
occurs.
108- During anaerobic respiration Glycolysis occurs as
normal, but there is no Krebs cycle.
109Oxygen available
Krebs cycle
Glucose
Pyruvic Acid
Oxygen not available
ANIMALS
PLANTS
Lactic Acid
Ethanol CO2
110Aerobic respiration Anaerobic respiration
Oxygen required?
Total ATP production (per glucose molecule)
Other products (plants)
Other products (animals)
111- Anaerobic respiration is animals occurs during
heavy exercise. After exercise stops the lactic
acid can be converted back to pyruvic acid by
repaying the oxygen debt by breathing heavily.
It is therefore REVERSIBLE. - Anaerobic respiration is plants is IRREVERSIBLE
as the CO2 diffuses out of the plants.
112Measuring the rate of aerobic respiration
- The rate of aerobic respiration can be measured
using a respirometer.
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114- Parts of this apparatus have the following
purposes - Glass beads They are a control to show how it
would be with something that does not respire. - Water bath keeps the test tubes at a constant
temperature, as the volume of gas would increase
if the temperature increased.
115- Syringe It measures the volume of oxygen used,
by pushing down and returning the dye to the same
level as before. - Sodium hydroxide Absorbs carbon dioxide.
116Synthesis and release of proteins
117Codons
Amino acids
Translation
Single stranded
Ribosomes
Uracil
Peptide bonds
tRNA
C,H,O,N
mRNA
Globular
Transcription
Proteins
Fibrous
Rough ER
synthesis
Genetic code
DNA Polymerase
Replication
Secretion
Golgi body
Double helix
Chromosomes
A,T,C,G
DNA
Base
Nucleotide
A-T C-G
Genes
Sugar
Phosphate
118Structure and variety of proteins
- Proteins are composed of the following elements
- Carbon, Hydrogen, Oxygen, Nitrogen, (often
Sulphur) HONCS - Atoms of these elements form amino acids (20
different ones). - Amino acids link by peptide bonds to form
polypeptides. - Polypeptides link up to form Proteins.
119Role of proteins
TYPE ROLE EXAMPLES
Globular Enzymes
Globular Structural
Globular Hormones
Globular Antibodies
Fibrous Make hair and nails
120Role of genes
- Chromosomes consist of many genes. These carry
out their instructions by producing enzymes.
Enzymes are made of protein. - So, genes produce protein Like this
121Protein Synthesis
- Genes contain a chemical code.
- This code is part of a molecule of DNA
(Deoxyribonucleic acid). - The structure of DNA enables the correct amino
acids to be assembled in the correct sequence to
make a particular protein.
122Structure of DNA
- A DNA molecule is made of 2 chains of
nucleotides. - Each nucleotide contains
- A deoxyribose sugar molecule
- A phosphate molecule
- A base molecule
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124- There are four different bases, and therefore
four different nucleotides
Adenine nucleotide (A)
Guanine nucleotide (G)
Thymine nucleotide (T)
Cytosine nucleotide (C)
125- Nucleotides are linked together by means of
chemical bonds between phosphate and sugar
molecules called sugar-phosphate bonds
126- Two of these nucleotide chains are joined by
means of hydrogen bonds between bases. - ADENINE always bonds with THYMINE
- CYTOSINE always bonds with GUANINE
127- The two, linked, nucleotide chains are twisted
into a coil called a double helix.
128- Each chromosome consists of one double-helix
shaped molecule of DNA containing many thousands
of base pairs. - A gene is a section of DNA molecule whose base
order forms the code to make one protein.
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130Replication of DNA
- Chromosomes must be able to copy themselves so
that cells retain the same genetic information
after cell divisions. - This copying of the DNA in the chromosomes is
called replication.
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132- Replication requires
- A DNA molecule
- unattached nucleotides of 4 types
- enzymes (DNA polymerase)
- energy (in the form of ATP)
133- Replication takes place in these stages
- DNA uncoils
- The hydrogen bonds between bases break (starting
at the end like a zip) - Free nucleotides attach to exposed bases
- Sugar-phosphate back bone reforms
134The Genetic Code
- Proteins are made of a long chain of amino acid
molecules. - A gene contains a code (order of DNA bases) to
ensure that the amino acids are joined in the
correct order to make a specific protein. - The order of the bases is called the genetic
code.
135- This is a triplet code because the sequence of
three bases is needed to code for each amino
acid. - e.g.
- AAG codes for amino acid Phenylalanine
- GAC codes for amino acid Aspartic Acid
- GGA codes for amino acid Glycine.
136- So a DNA strand with base sequence
- Would code for (part of) protein
- (one protein molecule may be hundreds or
thousands of amino acids long)
137RNA (ribonucleic acid)
- Protein synthesis takes place on the ribosomes in
the cytoplasm. - The instructions in the genetic code are carried
from the DNA (in the nucleus) to the ribosomes by
a molecule of messenger RNA (mRNA)
138- RNA differs from DNA in 3 ways
- RNA is single stranded
- RNA contains ribose sugar
- In RNA the base thymine is replaced by Uracil
139- There are two types of RNA
- Messenger RNA (mRNA) which carries the genetic
code from the DNA in the nucleus to a ribosome in
the cytoplasm. - Transfer RNA (tRNA) which carries amino acids to
the ribosomes for assembling into polypeptide
chains.
140Transcription
- The piece of DNA containing the relevant gene
uncoils and the base pairs separate. - Complementary RNA nucleotides then attach to the
exposed DNA bases. - They link together (ribose-phosphate chemical
bonds) to form a messenger RNA (mRNA) molecule.
141G
T
C
A
C
T
A
T
A
G
G
C
G
T
DNA strand
A
A
G
C
C
G
A
T
T
C
G
G
A
T
A
A
C
G
C
T
G
C
C
G
T
T
C
A
C
A
G
T
G
A
T
A
T
C
C
G
One gene
142Ribosomes and rough endoplasmic reticulum
- Ribosomes are
- Found in all cells
- Free in cytoplasm or attached to rough
endoplasmic reticulum - Spherical, with two halves
- Site of translation of mRNA into protein
143Fluid filled cavity between sheets
Ribosomes
Sheets of endoplasmic reticulum
144Assembling the protein translation
- In the cytoplasm are molecules of transfer RNA
(tRNA). - These are composed to one triplet of bases and an
amino acid molecule. - e.g. Alanine Leucine
- Codon triplet of bases on mRNA
- Anti-codon Complementary triplet of bases on tRNA
145Stage 1
Stage 2
Stage 3
146- The mRNA attaches to a ribosome.
- The ribosome moves along the mRNA with successive
codons entering the active site. - Here, a tRNA with the appropriate anti-codon is
attached. - Adjacent amino acids then link up by a peptide
bond to form a polypeptide and eventually a
protein.
147Secretion of proteins
Nucleus
Rough endoplasmic reticulum
Nuclear membrane
Pore
Ribosome
Golgi Apparatus
Vesicle
Cell membrane
148- The golgi apparatus is made up of many flattened
fluid filled sacs. - Vesicles containing newly made protein are
pinched off the rough endoplasmic reticulum. - These move towards the Golgi and use with the
outermost sac.
149- The contents then move down through the golgi
from sac to sac, becoming modified in the
process. - The finished product (e.g. glycoprotein), in a
vesicle, leaves the golgi and moves to the cell
membrane and discharges its contents out of the
cell.
150Cellular Defence Mechanisms
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153Virus Structure
154Reproduction of viruses
- Viruses can only reproduce inside the cells of a
host organism. - They use the hosts nucleotides for replication
and the hosts amino acids to construct protein
coats.
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159Defence against viruses
160First line of defence
- Mechanisms by which our bodies attempt to prevent
entry of harmful microbes.
161Second line of defence
- Mechanisms by which our bodies attempt to kill
harmful microbes which have succeeded in entering.
162Immunity
- Immunity is the ability of an organism to resist
disease. The blood is usually involved. - There are two types
- Non-specific immunity (phagocytosis)
- Specific immunity (antibodies)
1631. Non-specific Immunity
- Provides protection against a wide range of
invading microbes e.g. by phagocytosis carried
out by white blood cells.
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165- Read page 70 of Torrance and make your own notes
on Phagocytosis. - Then
- Prepare a 2-3 min illustrated presentation to
give to the class on the topic, explaining - How invading bacteria are detected
- How invading bacteria are engulfed
- What a lysosome is, what it contains and what it
does - What pus is
166Phagocytosis
- Phagocytosis is the process by which foreign
bodies such as bacteria are engulfed and
destroyed. - Cells capable of phagocytosis are called
phagocytes.
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168- A phagocyte detects chemicals released by the
bacterium and moves up a concentration gradient
towards it. - The phagocyte adheres to the bacterium and
engulfs it into a vacuole formed by an infolding
of the plasma membrane.
169- Lysosomes fuse with the vacuole and release their
enzymes into it. - The bacterium becomes digested and the breakdown
products are absorbed by the phagocyte.
170- During infection hundreds of phagocytes migrate
to the infected area and engulf many bacteria by
phagocytosis. - Dead bacteria and phagocytes often gather at a
site of infection forming pus.
1712. Specific immunity
- A specific invading particle (e.g. A virus) is
attacked by a specific defending chemical.
172- Antigen a complex molecule recognised by our
body as alien (e.g. A virus coat particle). - Antibody a chemical produced a lymphocyte white
blood cell to destroy antigens.
173How antibodies work
- An antibody is a Y-shaped molecule
174- The binding sites on the arms attach to antigen
molecules making them harmless
175- There are many types of lymphocyte, each type
targeting one antigen with specific antibodies.
176Types of specific immunity
- Active immunity
- We produce our own antibodies by
- Suffering from the disease and retaining the
antibodies in the blood (natural) - Receiving a vaccine of treated antigen (e.g.
Empty virus coats) which triggers antibody
formation (artificial).
177- (b) Passive immunity
- We receive ready-made antibodies from
- Mother, across the placenta (natural)
- Another mammal (e.g. A horse) which has made the
antibodies in response to treatment
(artificial).
178Rejection of transplanted tissues
- Make your own notes from Page 73 of Torrance.
179Cellular Defence Mechanisms in Plants
- Plants defend themselves from attack by
- Producing toxic compounds
- Isolating the infected area or infectious
organism
180(a) Production of toxic compounds
- Cyanide
- Made by clover plants by a process called
cyanogenesis. - Cyanide works by blocking the cytochrome system
of e.g. Slugs - It is produced when non-toxic glycoside and an
enzyme are mixed as a result of leaf damage.
181- (ii) Tannins
- Tannins are toxic to micro-organisms
- They defend by preventing pathogens e.g. Fungi
from gaining access to the plant organ under
attack. - The tannins act as enzyme inhibitors.
- Therefore, they interfere with the invading
pathogens metabolism and render it harmless.
182- (iii) Nicotine
- This is toxic chemical produced in the root cells
of tobacco plants and transported to its leaves. - Since it is poisonous it protects leaves against
attack by herbivorous insects. - Nicotine can be extracted from tobacco plants and
used as an insecticide.
183(b) Isolation of the problem
- Insect galls
- When a parasite penetrates the cuticle of a leaf,
the leaf produces a gall in response to a
chemical stimulus. - A gall is an abnormal swelling of plant tissue
resulting from active division of cells at the
site of the injury.
184- The combination of the extra layers of cells and
rich deposits of tannin in a gall provides the
plant with a protective barrier where the
parasite can be isolated.
185- (ii) Resin
- Resin is a sticky substance produced by many
trees. - When a plant becomes wounded by a pathogen the
resin-secreting cells increase in activity,
trapping pathogens.