1
CAPE BIOLOGY
UNIT ONE MANUAL
(by Sperwin Zinger)
MODULE ONE – CELL AND MOLECULAR BIOLOGY
THIS MODULE CONTAINS FOUR TOPICS:
1.
2.
3.
4.
ASPECTS OF BIOCHEMISTRY
CELL STRUCTURE
MEMBRANE STRUCTURE AND FUNCTION
ENZYMES
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TOPIC 1: ASPECTS OF BIOCHEMISTRY
1.1: Discuss how the structure and properties of water relate to the role that water plays as a medium of
life.
Your body is comprised of numerous elements,
which make also combine to form molecules.
These include macronutrients such as
carbohydrates (such as starch and glucose,
required for release of ATP), proteins (which are
used for growth and repair of cells and also to
form hormones) and fats (used for as an energy
store).
However, the molecule that comprises the
majority of the human body (more than 70% of a
cell‟s mass) is WATER.
Why are water molecules attracted to each other?
First, observe the molecular structure of water. Water consists of two hydrogen atoms COVALENTLY
bonded to one oxygen atom. This means that electrons are shared between them.
On the diagram, you will observe the symbol δ
(delta), and a symbol for +ve or –ve charge. In
this case, the OXYGEN has the negative charge
and the HYDROGEN atoms have the positive
charge.
Water itself is electrically balanced or
NEUTRAL. However, there is uneven
distribution of these charges in the structure.
This is called a DIPOLE. This allows weak
electrical attraction between the water
molecules, which results in COHESION and the
ability to undego MASS FLOW. They also
result in HYDROGEN BONDS, which are
essential for many biological molecules.
Property of Water
What Allows This
Temp. regulation
Its high specific heat capacity and ability to evaporate easily.
„Universal‟ solvent
Its tiny charges attract other molecules or ions to form bonds.
Allows mass flow
Its H-bonds produce cohesion and surface tension. Suitable for excretion.
Assists buffers
Its neutral pH allows H ions or OH ions to be absorbed by proteins.
Reactivity
Used in hydrolysis reactions during digestion and in photosynthesis.
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1.2/3: Explain the relationship between the structure and function of glucose and sucrose.
What exactly are CARBOHYDRATES?
Carbohydrates are organic molecules that comprise a ratio of carbon, hydrogen and oxygen. They are
comprised of at least one sugar unit. However, they can be linked together to form increasingly complex
molecules.
Type of carbohydrate
Number of units
Examples
MONOSACCHARIDE One
Glucose, fructose, ribose, galactose, glyceraldehyde
DISACCHARIDE
Two
Maltose, sucrose, lactose
POLYSACCHARIDE
More than two
Starch, glycogen, cellulose, chitin
MONOSACCHARIDES are the simplest
carbohydrate and cannot be further hydrolysed.
They are written with the general formula
(CH2O)n. The „n‟ depends on the type of sugar.
For example, a hexose sugar (e.g. glucose) has a
value of „6‟, so glucose is written as C6H12O6.
A pentose such as ribose has a value of „5‟ and
is written as C5H10O5. However, modifications
occur, such as deoxyribose having one less
oxygen atom, so deoxyribose is written as
C5H10O4
As previously mentioned, glucose is a HEXOSE, which means it has a six-membered ring consisting of
five carbons and one oxygen. Observe the straight-chain and ring structures of glucose below.
NOTE:
Betaglucose’s
ring
structure
is similar
but H and
OH are
swapped
on C-1.
It can be observed that the 6th carbon atom in the ring structure does not exist as part of the ring structure.
As a result of this, glucose tends to alternate between its ring and its chain form. This is why there are two
different types of glucose (alpha and beta).
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How are DISACCHARIDES formed then?
As previously mentioned, a DISACCHARIDE forms when two monosaccharide molecules are bonded.
When this linkage occurs, it is known as a GLYCOSIDIC bond. These types of bonds are very strong.
One common example of a disaccharide is SUCROSE, which we commonly know as the sugar that is
sweet (such as in sugar cane).
So, what two monosaccharides combine to form sucrose? That would be an ALPHA GLUCOSE and a
BETA FRUCTOSE. What is notable about sucrose is that when it undergoes enzyme breakdown, sucrose
yields two glucose molecules. However, one of those molecules has been reformed from fructose.
Here are their ring structures:
Carbon-1 of the alpha glucose will now bond with the Carbon-2 of beta-fructose. This is thus called a 1-2
glycosidic bond. A CONDENSATION reaction removes a water molecule in the process.
Now observe the structure of SUCROSE:
Sucrose is used for
transport instead of
glucose because it is
much more complex,
more energy-efficient
and not as reactive as
glucose.
What is the difference between a REDUCING and NON-REDUCING sugar?
In O‟ levels you would‟ve learned that Benedict‟s solution can be used to test for reducing sugar.
However, the addition of HYDROCHLORIC ACID and then SODIUM HYDROXIDE was needed for
non-reducing sugars.
This is because disaccharides such as sucrose have a glycosidic bond that prevents Benedict‟s reageant
from reacting with it. The HCl is needed to break that glycosidic bond and the NaOH is needed to
neutralize the HCl.
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1.4: Discuss how the molecular structure of starch, glycogen and cellulose relate to their functions in
living organisms.
NOW WHAT ABOUT POLYSACCHARIDES?
A polysaccharide can contain thousands of sugar molecules and can be quite large and complex. As a
result, they are insoluble. Not all of them are arranged in long chains, however. Some of them form
compact spirals. Polysaccharide nutrients such as starch must be hydrolysed before they can be absorbed
through the small intestine and into the bloodstream.
We‟ll be looking at three main polysaccharides:
Polysaccharide
Function
Miscellaneous short notes
STARCH
Energy reserve in plants
after photosynthesis.
A mixture of two polymers, AMYLOSE and
AMYLOPECTIN. Stored in PLASTIDS, which form grains.
Never found in animal cells. Digested by AMYLASE.
GLYCOGEN
Energy reserve in
animals.
Easier to break down into glucose. Usually found in the
LIVER and in MUSCLES.
CELLULOSE
Found in cell walls.
Used for structural
support.
Always has a straight structure. Very strong due to thousands
of hydrogen bonds. Large bundles of them are called
FIBRES. Difficult for animals to digest.
Now let’s be more specific about these molecules:

Amylose forms a spiral from many α-glucose molecules. It is
held together by H-bonds that form between –OH groups
attached to C-1 of each unit.

Glycogen is also made of many α-glucose molecules and are
linked through α 1-4 glycosidic bonds with α 1-6 branches.
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
Cellulose is also made up of thousands of β- glucose molecules. Cellulose molecules form a straight
structure instead of a spiral or branches. As said, their bonds are extremely strong due to the multitude of
hydrogen linkages. The type of bonds in cellulose are β 1-4 glycosidic bonds between the glucose
molecules. This is what it makes it INSOLUBLE and sturdy to provide structural support in cell walls.
The ring structure combines many different glucoses. However, each alternating glucose molecule is
INVERTED. Observe the structure below. Notice how each successive one is ‘flipped’.
The table below will provide a summary of all of this complex information.
Feature
Amylose
Glycogen
Cellulose
Sugar unit
α-glucose
α-glucose
β-glucose
Overall shape
Linear and spiral
Linear, spiral, branches
Only linear
Solubility in water
Insoluble or very low
Insoluble or very low
Insoluble
Glycosidic bond type
α 1-4
α 1-4 and α 1-6
β 1-4
H-bonds
Within
Within
Within and between
Location
Starch grains, plastids
Animal liver cells
Cell walls
REMINDERS ABOUT BREAKING AND FORMING BONDS

Breaking a covalent bond is called a HYDROLYSIS REACTION, while formation of the bond is
called a CONDENSATION REACTION.

Hydrolysis reactions use a water molecule during the breakdown of polymers into monomers.
Condensation reactions release a molecule during the formation of a bond. If that molecule is
water, this is known as a DEHYDRATION reaction.

Examples of dehydration reactions include the formation of SUCROSE (from glucose & fructose)
and the formation of a DIPEPTIDE molecule from two amino acids.

Hydrogen bonds form between water molecules. HYDROXYL groups (-OH) form hydrogen
bonds because hydrogen is slightly +ve and oxygen is slightly –ve. Dipole or polar molecules are
hydrophilic while non-polar molecules (without dipoles) are hydrophobic.
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1.5: Describe the molecular structure of a triglyceride and its role as a source of energy.
WHAT ARE LIPIDS AND TRIGLYCERIDES?
Lipids have a similar chemical structure to carbohydrates. The main difference is that they contain a
much higher proportion of HYDROGEN. They also tend to be insoluble in water. The main lipids that
you would have previously learned of are fats and oils, which are used as energy reserves in the body and
also used to provide insulation for organs.
Fats are broken down by the enzyme LIPASE
(secreted by the pancreas). This results in the
formation of FATTY ACIDS AND
GLYCEROL. These fatty acids can be classified
as either saturated or unsaturated (more on
this later).
A TRIGLYCERIDE is comprised of three fatty
acids attached to a glycerol molecule. They are
insoluble in water and are HYDROPHOBIC,
meaning that they are not attracted to water. The
fatty acids contain a –COOH, which is called a
CARBOXYL group. These carboxyl groups
react with the –OH groups of glycerol. This
forms a very strong covalent bond called an
ESTER BOND.
Thus, think of the glycerol as the „backbone‟ of the triglyceride structure. Observe the detailed structure
of a glycerol molecule and a triglyceride below:
You should also get familiar with how it is represented in simpler diagrams:
In triglycerides,
all the C atoms
are bonded to H,
which makes it a
yield more energy
upon breakdown
than carbs.
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SO WHICH FATS ARE „BAD‟?
Triglycerides are an energy reserve and are stored in tissues in humans called ADIPOSE tissue.
Accumulation of excess adipose tissue will eventually lead to OBESITY. Studies of fat are constantly
yielding new information and show that fats act almost like endocrine organs, affecting hormonal
secretion and metabolism.
The cells shown are called ADIPOCYTES.
„White fat‟ cells have a much higher
concentration of triglycerides than „brown fat‟
cells.
Brown fat cells tend to have a high concentration
of mitochondria, which regularly „burn‟ off the
energy reserves.
As previously stated, fatty acids are typically classified into two types: saturated and unsaturated. What
is the main difference between these two?

A SATURATED fat molecule has its
last carbon atom bonded to three
hydrogens. Thus, it has been „saturated‟
with hydrogen.
This is usually referred to as the „bad‟
fat, as it forms a dense structure that can
contribute to the build-up of LDL (lowdensity lipoprotein) cholesterol, leading
to coronary heart disease.

An UNSATURATED fat molecule has
at least one carbon atom double-bonded
to another, reducing the amount of
hydrogen that is holds.
Observe below to see that it causes a
slight bend in the linear structure.
Imagine that this bend prevents the fat
from packing too tightly and
contributing to arterial plaque build-up.
EXTRA NOTE: Another type of „bad‟ fat is called TRANS fat. Trans fats are formed when oils are
artificially made semi-solid during artificial hydrogenation. Hydrogenation involves the insertion of gases
through oils to solidify them. This affects the bonding linkages. Examples of such foods that have contained
trans fats in the past are margarine and shortening, and certain fast foods. They have since been banned.
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1.6: Describe the structure of phospholipids and their role in membrane structure and function.
WHAT IS A PHOSPHOLIPID?
Observe the diagram shown. It shows a
phospholipid bilayer (which forms the plasma
membrane). Imagine a triglyceride where one of
its fatty acids has been replaced by a
PHOSPHATE group.
On the diagram, you‟ll notice that the phosphate
„heads‟ are HYDROPHILIC while the „fatty
acid‟ tails are HYDROPHOBIC. If you recall,
hydrophobic means they are not attracted to
water molecules. Hydrophilic means they are
attracted. So in water, they form this „bilayer‟
structure. Without this structure, cells would not
be able to keep their organelles together.
NOTE: The reason the „head‟ is attracted is because it has a
negative charge. This is attracted to the positive charge of the
H atoms on the water molecule. The „head‟ is water-soluble.
1.7: Describe the generalised structure of an amino acid, & the formation & breakage of a peptide bond.
WHAT ARE PROTEINS AND AMINO ACIDS?
You will recall from O‟ Level Biology that proteins are mainly used for cellular growth and repair in the
body. They also form a entire roster of other molecules in the body, including enzymes and hormones. An
amino acid is a single unit and many of these combine to form a protein, just like with monosaccharides
and polysaccharides.
1.
2.
3.
4.
Observe the structure. There is a central carbon
atom connected to FOUR other groups. These
include:
An AMINO group (-NH2)
A CARBOXYL group (-COOH)
A HYDROGEN (H) atom.
Another group or chain of amino acids,
which is represented as „R‟.
Amino acids can bond with each other during
condensation reactions. The linkages formed are
very strong covalent bonds called PEPTIDE
BONDS.
When this occurs, a H atom joins with an –OH
to form a water molecule.
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WHAT IS A POLYPEPTIDE?
Protein synthesis occurs in the RIBOSOMES of
the cells. As previously said, condensation
reactions occur when amino acids are bonded,
which produce water molecules.
The chains can be non-linear in shape. For
example, HAEMOGLOBIN (found in the red
blood cells) has four polypeptides connected in a
coiled structure.
When many of these amino acids are linked by
peptide bonds, the chain itself is called a
POLYPEPTIDE. These polypeptide chains
eventually come together to form structures of
protein.
When polypeptide chains are broken, a water
molecule is consumed during a hydrolysis
reaction. An example of this would be when
PEPSIN digests proteins in the stomach.
Observe the linkage between two amino acids to form a dipeptide molecule:
It can be seen that the
PEPTIDE BOND forms
between the C and N after
the dehydration reaction.
WHAT ARE SOME EXAMPLES OF AMINO ACIDS?
There are 20 amino acids. They may be hydrophilic or hydrophobic. Only the ones with side chains („R‟
groups) that contain ring structures are hydrophobic. Here are a few examples of amino acids.
-
Serine – Used in the synthesis of components in the brain cell membranes and neurones.
Leucine – Involved in increasing lean muscle mass.
Valine – High levels are associated with insulin resistance and diabetes.
Tryptophan – Converts to serotonin, which affects mood and sleep
Aspartic acid – Contributes to the formation of urea.
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1.8: Explain the meaning of terms: primary, secondary, tertiary and quaternary structures of proteins.
HOW ARE PROTEINS ARRANGED?
Recall that proteins are comprised of amino acid units which form polypeptide chains. The way in which
these are sequenced can occur in multiple levels of increasing complexity in proteins, resulting in what
are known as the primary, secondary, tertiary and quaternary structures.
Structure
Primary
Diagram
Notes
- A sequence of a chain of amino acids.
- Determined by a gene.
- The sequence of amino acids on the chain
determines the type of protein.
Secondary
- Occurs when the amino acid sequences are
linked by weak hydrogen bonds.
- The bond occurs between an O in the –CO
group and the H of the –NH2 group.
- Can be α helix or β pleated sheet.
Tertiary
- Occurs when multiple secondary structures
fold together.
- Four types of bonds involved: Hydrogen,
Disulphide, Ionic and Hydrophobic Interaction.
- May have separate PROSTHETIC groups
attached to it such as haem in HAEMOGLOBIN
- Also forms the structures of ENZYMES.
Quaternary
- The highest level of complexity for proteins.
- The example depicted is haemoglobin, which
consists of numerous secondary and tertiary
structures, as well as FOUR HAEM groups.
- The role of haemoglobin is to transport oxygen.
When the oxygen binds to a haem group, uptake
is made easier by the other three.*
- Haemoglobin is a GLOBULAR protein, as
opposed to COLLAGEN which is a FIBROUS
protein.
* Haemoglobin’s structure will change any time an O2 molecule is bound to the haem group.
The results in what is called a conformational change and protein ‘folds’, allowing quicker
binding of each successive O2 molecule. This is referred to as positive cooperativity.
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HOW ARE PROTEINS BONDED?
There are four main types of bonds that help form the linkages that hold protein molecules in shape.
Name of Bond
Strength of
Bond
Can be broken by…
How It Occurs
Hydrogen
Weak.
High temperatures and
changes in pH.
Slightly negative and positive
molecules become attracted (e.g.
H and O)
Ionic
Strong.
Changes in pH.
Forms between R groups that
have full positive and negative
charges.
Disulphide
Strong and
covalent.
Reducing agents.
Forms between the R groups of
cysteine, an amino acid.
Hydrophobic
Interaction
Very weak.
Not considered a bond. But
can denature in high heat.
Forms between R groups which
contain only C and H atoms.
1.9: Outline the molecular structure of collagen, as an example of a fibrous protein;
WHAT IS COLLAGEN? HOW IS IT DIFFERENT FROM GLOBULAR PROTEINS?
Collagen is a protein found in our bodies that is mainly used for STRUCTURAL SUPPORT. It can be
found in areas such as cartilage, bones and tendons. Due to its structural role, its insolubility in water and
its repeating sequences, it is referred to as a FIBROUS protein. This contrasts with GLOBULAR proteins,
such as haemoglobin, antibodies and enzymes, which partake in chemical reactions, are often soluble in
water and the primary structures usually have specific shapes instead of repeated sequences.
As can be seen in the molecular structure, it
consists of THREE polypeptide chains. These
form three helical strands, which intertwine and
are held together by HYDROGEN bonds.
These collagen molecules form cross-links and
form FIBRILS, which form bundles known as
FIBRES.
The following are some roles of globular and fibrous proteins:
- Enzymes (globular) – Lowers activation energy to catalyze certain chemical reactions.
- Keratin (fibrous) – Forms protective layers and filaments, such as in hair and nails.
- Insulin (globular) – Converts glucose to glycogen for storage in the cell.
- Elastin (fibrous) – Allows elasticity to organs such as the lungs and bladder.
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1.10: Carry out tests for reducing and nonreducing sugars, starch, lipids and proteins.
TEST FOR REDUCING AND NON-REDUCING SUGARS
Examples of reducing sugars include
GLUCOSE, MALTOSE and FRUCTOSE, while
an example of a non-reducing sugar is
SUCROSE. The solution needed to test for both
of these is called BENEDICT‟S SOLUTION, a
blue liquid that contains copper (II) sulphate.
Upon heating, Cu2+ is reduced to Cu+ and forms
copper (I) oxide in the presence of reducing
sugar, which forms a BRICK RED precipitate.
Trace amounts of sugars results in a GREEN
colour.
FOR NON-REDUCING SUGARS: Recall that sucrose has a GLYCOSIDIC bond. To break this bond,
heat the solution with dilute HCl and then neutralize with SODIUM HYDROXIDE. This will yield
GLUCOSE and FRUCTOSE from the sucrose.
TEST FOR STARCH
TEST FOR PROTEINS
Starch is a polysaccharide that is comprised of
amylose and amylopectin. The test for starch
presence involves the addition of IODINE
SOLUTION IN POTASSIUM IODIDE (KI/I2).
The iodine is able to bind to the helical structure
of amylose and produce the BLUE-BLACK
colour.
Proteins have linkages called PEPTIDE bonds
(between the C and N of adjacent amino acids).
BIURET reagent is used to test for proteins,
which contains copper (II) sulphate and
potassium hydroxide.
EMULSION TEST FOR LIPIDS
Recall that lipids are hydrophobic and are thus
INSOLUBLE in water. To test for the presence
of lipids, ETHANOL is first poured into the
sample. The lipid molecules will dissolve in the
ethanol. WATER is then added.
The hydrophobic lipid molecules begin to
disassociate from the solution and form an
opaque milky white layer of droplets that float to
the top called an EMULSION.
When BIURET reagent is added, the copper ions
produce a PURPLE colour.
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TOPIC 2: CELL STRUCTURE
2.1 and 2.2: Make drawings of typical animal and plant cells as seen under the light microscope and
describe and interpret drawings and electron micrographs of cells;
DIFFERENCES BETWEEN LIGHT AND ELECTRON MICROSCOPES
Characteristic
Light Microscope
Electron Microscope
Max. Magnification
x 1400
x 300,000
Type of lens used
Glass
Electromagnets
Type of radiation used
Visible light
Electron beams
Colour
Image will appear in colour.
Image will be in black and white.
Preparation of specimen
Living cells and tissues are used. Nonliving tissues may be used if they are
mounted on a slide in a transparent liquid.
Only non-living and dehydrated
cells are used. They are cut very
thinly and placed in a vacuum.
Staining of specimen
Cells absorb many different coloured
stains.
Cells and organelles absorb
heavy metals.
Viewing of specimen
By eye or projection on a screen.
Electrons fall onto a fluorescent
screen.
Main advantages
- Much more affordable than electron
microscopes.
- Much higher resolution
- Much higher magnification
- Slides can last for a very long time.
- Little risk of distortion while viewing.
Main disadvantages
- Much lower resolution
- Expensive, requires expertise
- Much lower magnification
- Specimen deteriorates during
viewing (unlike slides)
- High risk of distortion
Two types of electron microscopes:
1. SEM (Scanning Electron Microscope)
2. TEM (Transmission Electron Microscope)
SEM usually observes the surface of an specimen
while TEM is used to observe a very thinly cut
section of specimen, supported on grids.
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PHOTOMICROGRAPH AND ULTRASTRUCTURE OF CELLS
Recall that light microscopes have a much lower resolution and magnification than electron microscopes.
Photomicrographs therefore are unable to clearly show all of the organelles present in the structures of the
animal and plant cells. When an electron microscope is used to view the structure, the visible image is
called an ULTRASTRUCTURE.
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2.4. Compare the structure of typical animal and plant cells;
TABLE SHOWING DIFFERENCES BETWEEN ANIMAL AND PLANT CELLS
Organelle or Structure
Animal Cells
Plant Cells
Chloroplasts
Chloroplasts and any plastids are absent.
Present in photosynthetic cells.
Cell wall and
plasmodesmata
Cell wall and plasmodesmata are absent.
Present in cells, usually containing
cellulose, pectin or lignin.
Vacuole
Small, temporary vacuoles.
Large, permanent vacuoles
surrounded by tonoplast.
Centrioles
Usually present.
Centrioles are absent.
Waste removal
Digestion by lysosomes.
Vacuoles move to plasma membrane
Sugar storage
Stored in glycogen granules.
Starch grains (in amyloplasts)
Cilia and flagella
Present in some (e.g. sperm, respiratory
epithelium)
Mostly absent.
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2.3. Outline the functions of membrane systems and organelles.
Organelle or
Structure
Nucleus
Diagrams
Notes
- The nucleus contains long
molecules of DNA called
CHROMOSOMES, which is made
up of threads called CHROMATIN.
- The nucleus is surrounded by a
pair of membranes known as
NUCLEAR ENVELOPE.
- The nuclear envelope has tiny
openings called NUCLEAR
PORES, which allow movement of
ATP and RNA.
- The NUCLEOLUS contains
ribosomal RNA or rRNA, which
helps with PROTEIN SYNTHESIS.
- Two types of cells that don‟t have
nuclei are RED BLOOD CELLS
and PHLOEM SIEVE TUBES.
Mitochondrion
- Mitochondria are the site of
AEROBIC RESPIRATION in both
plant and animal cells.
- This mostly occurs in the tiny
folds of the inner membrane called
the CRISTAE.
- Several chemical reactions also
occur in the MATRIX.
Chloroplast
- Chloroplasts are sites of
PHOTOSYNTHESIS.
- It has a double membrane, like
mitochondria.
- Sacs called THYLAKOIDS
contain chlorophyll necessary for
the light-dependent reactions, while
light-independent reactions occur in
the STROMA.
- Stacks of thylakoids are GRANA.
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Cell wall and
plasmodesmata
- Cell walls are comprised of very
strong cellulose fibres. These give it
structural support.
- The cell wall can withstand strong
forces and internal pressures, so a
cell will not burst if too much water
is taken in.
- Plasmodesmata are tiny pores or
passages that lead from one cell to
another.
- The middle lamella lies between
both cells. Pectin holds the cells
together at this point.
Plasma
membrane
(cell surface
membrane)
We previously learned of a
PHOSPHOLIPID BILAYER,
shown in the diagram. All plasma
membranes have this structure.
They are sometimes lain with
protein structures and channels that
allow transport processes such as
diffusion and active transport to
occur.
Endoplasmic
reticulum
- The rough ER (RER) has
ribosomes attached to it, while the
smooth ER (SER) doesn‟t.
- Ribosomes and the RER are the
sites of PROTEIN SYNTHESIS.
- Ribosomes form inside enclosed
spaces in the membrane called
CISTERNAE.
- SER occupies various roles, such
as breaking down toxins or
producing lipids.
Lysosomes
- Lysosomes contain digestive
enzymes that are mainly used to
break down large molecules into
soluble substances that would get
absorbed by the cytoplasm.
- They may also break down
denatured organelles.
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Centrioles
- Centrioles are only found in
animal cells. They produce
filaments known as
MICROTUBULES, which then
form a SPINDLE.
- This helps pull chromosomes to
the polar ends of the cell during cell
division.
- These are only found in animal
cells.
Golgi body
and vesicles
- The Golgi body receives vesicles
containing proteins from the ER.
- It „processes‟ these proteins by
modifying them (such as by adding
sugar) and packages these proteins
and transports them through other
vesicles.
- The vesicles transport materials to
the plasma membrane and then
outside the cell. This is called
EXOCYTOSIS.
- They also produce lysosomes.
- They are not a fixed shape.
You also have to be able to look at electron
micrographs and label the organelles on the
ultrastructure. The arrangement of these will
vary in specialized cells. Look at this mouse‟s
hepatocyte (liver cell). It is very dense with
membranes from the ER and has many secretory
vesicles and lysosomes.
The reason for this being that the liver must
form a highly active transport network for
proteins, lipids and sugars. They must also break
down many toxins, such as alcohol.
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2.5. Describe the structure of a prokaryotic cell. Compare their structure with eukaryotic cells.
WHAT IS A PROKARYOTIC CELL?
Prokaryotes (which means “before the nucleus”)
are organisms that have DNA but in a circular or
freely dispersed form not present in a nucleus.
They form their own kingdom and includes
organisms such as BACTERIA and ARCHAEA.
Eukaryotes (which means “true nucleus”) have a
nucleus and so also have a nuclear envelope and
nucleolus. They also have membrane-bound
organelles such as MITOCHONDRIA and
CHLOROPLASTS. They belong to more
complex organisms such as animals, plants and
protists. So far, we‟ve mainly been looking at
eukaryotic cells.
WHAT ARE THE DIFFERENCES BETWEEN PROKARYOTIC AND EUKARYOTIC CELLS?
Feature
Prokaryotic Cell
Eukaryotic Cell
Genetic material
No nucleus but contains
plasmids (circular DNA) and a
nucleoid region of
protoplasmic DNA.
Has a nucleus and all internal
structures. DNA in long strands,
connected to histones.
Protein synthesis
Small, 70S ribosomes
Larger, 80S ribosomes
Membrane-bound
organelles
Mitochondria, chloroplasts,
Golgi body and ER are all
absent.
These same structures are
usually present. Chloroplasts
only in plants.
Cell wall
Made of peptidoglycan (e.g.
bacteria).
Made of cellulose (in plants)
Flagella
Present in many cells (e.g. E.
coli bacteria).
Present in a few, such as sperm
cells or some protists.
Photosynthetic
structures
Contains infolds in the plasma
membrane for chlorophyll
attachment.
Contains chloroplasts, which
contain chlorophyll.
Size
Usually between 5-10 µm.
As large as 100 µm.
The “S” refers to
Svedberg unit,
which is a measure
of how fast a
particle settles in a
solution.
Though prokaryotes
do not have
chromosomes,
scientists still refer
to bacterial DNA as
chromosomes.
22
2.6. Outline the basis of the endosymbiosis development of eukaryotic cells.
WHAT IS THE ORIGIN OF LIFE (ENDOSYMBIONT THEORY)?
As previously noted, the word “prokaryote” means “before the nucleus” and are thus this type of
organism is ancient (approximately 3.5 billion years). It was also previously noted that prokaryotes do not
have membrane-bound organelles such as MITOCHONDRIA and CHLOROPLASTS. It was believed a
very long time ago that three main types of cells existed:
1. A prokaryote/eukaryote with a very large globular structure.
2. A prokaryote that could absorb solar energy to produce sugars.
3. A prokaryote that could use oxygen to produce energy.
It is now thought that the latter two organisms were absorbed by the first, thus giving rise to a new type of
cell that would be able to carry out the processes of PHOTOSYNTHESIS and RESPIRATION. They
were called ENDOSYMBIONTS, which eventually gave rise to other types of organelles and specialized
cells, which led to the rise of many different organisms as time passed.
WHAT IS THE EVIDENCE FOR THIS?
1. Mitochondria and chloroplasts have their
own DNA, which exists in a circular form
like plasmids.
2. Mitochondria and chloroplasts have their
own RIBOSOMES and so are able to
synthesize their own proteins. The
ribosomes are also similar size to
prokaryotes.
3. Mitochondria and chloroplasts both have
a PAIR OF MEMBRANES (inner and outer
membranes) that form an envelope. The
inner membrane has a prokaryotic structure
while the other has a eukaryotic structure.
4. Mitochondria and chloroplasts are similar
in SIZE to many prokaryotes.
A modern example of
endosymbionts are the
NITROGEN-FIXING
BACTERIA (RHIZOBIUM)
that are found in
leguminous plants. They
perform their functions as
if they are organelles.
5. Mitochondria and chloroplasts divide by
BINARY FISSION, while eukaryotic cells
divide by MITOSIS.
23
2.7: Explain the concepts of tissue and organ using as an example the dicotyledonous root and stem.
WHAT ARE TISSUES AND ORGANS?
Cells are known as the basic functional and
biological units of all living organisms, whether
they are unicellular or multicellular. Many cells
can be SPECIALIZED to perform specific
functions, such as red blood cells containing
haemoglobin to carry oxygen, sperm cells
having a flagellum or muscle cells being able to
contract.
When multiple cells form groups the carry out
the same function, they are known as TISSUES.
An example of this would be multiple cells
called neurones forming a tissue called a nerve.
Blood is also an example of a tissue, since it
contains many cells, such as red blood cells,
lymphocytes and phagocytes. These tissues are
then grouped together to form ORGANS and
then ORGAN SYSTEMS. Examples of organs
include the heart, liver, eye, leaf and root.
Observe the structures through a transverse cross-section of a buttercup (Ramunculus) root shown below.
Name of Structure
Function or Notes
Epidermis
Has root hairs to provide large surface area for water absorption.
Cortex/Parenchyma Move water to the centre of the root either through cell walls or cells.
Air spaces
Contains oxygen for aerobic respiration. Pathway for rapid diffusion.
Endodermis
Waterproof layer to limit capillary action, due to presence of Casparian strips.
Vascular bundle
Contains xylem for transporting water (across lignified walls) and phloem for
translocation of sucrose (through phloem sieve elements).
24
NOTE: The diagram to the left
represents a PLAN
DRAWING. These are
drawings depicting the general
structure and main parts of a
specimen without illustrating
the complexity of cell
arrangement.
When making a plan drawing,
you should never draw the
individual cells, only the larger
structures.
The diagrams above and below depict a transverse section from a stem tissue taken from a Dahlia
specimen. Look at the above plan diagram and label the microscopic image similarly.
Name of Structure
Function or Notes
Cambium
A layer of dividing cells responsible for secondary growth of stems.
Sclerenchyma
A very thick, hard layer of tissue used for support. Usually dead cells.
Collenchyma
Layer of elongated cells with thick cell walls used for support. Usually alive.
Pith
Usually comprised of parenchyma, for transport and storage of nutrients.
25
TOPIC 3: MEMBRANE STRUCTURE AND FUNCTION
3.1: Explain the fluid mosaic model of membrane structure.
WHAT IS THE FLUID MOSAIC MODEL?
The phosphilipid bilayer forms the basis of the
plasma membrane around the cell, separating the
inner cytoplasm from the extracellular content. It
is made up of phospholipids, which have
HYDROPHILIC (attracted to water) phosphate
heads and HYDROPHOBIC (repelled by water)
fatty acid tails.
This creates a double layer with larger proteins
and other structures known as the fluid mosaic
model. The model can be thought as a “sea of
phospholipids with protein icebergs”.
Membranes are important for transfer of
materials, acting as sites for receptors and
enzymes. They also allow passage of electrical
signals, such as in the axons of neurones.
If the outer surface of the
membrane is covered
with glycoproteins or
glycolipids, this is called a
GLYCOCALYX.
Structure
Function or Notes
Channel and Carrier
Proteins
Function as transporters for passage of hydrophilic substances or ATP.
Glycoproteins and
Glycolipids
Can act as receptor sites to allow binding of certain molecules such as
HORMONES or NEUROTRANSMITTERS.
Cholesterol
Maintains FLUIDITY of membrane throughout extremes in temperature.
Extrinsic Proteins
Do not penetrate the bilayer. May have glycoproteins attached to them.
Intrinsic Proteins
Fixed into structure.. Have hydrophilic and hydrophic regions. The
hydrophobic regions are usually attracted to the lipid tails by
HYDROPHOBIC INTERACTIONS. May also act as ENZYMES.
26
3.2: Explain the processes of diffusion, facilitated diffusion, osmosis, active transport, endocytosis and
exocytosis.
WHAT IS DIFFUSION AND FACILITATED DIFFUSION?
The plasma membrane allows movement of
molecules into and out of the cells. This can
happen in a number of ways. This process can
occur without the use of ATP (called PASSIVE
transport) or with the use of ATP (called
ACTIVE transport).
These two types of transport usually rely on the
creation of a difference in concentrations on
both sides (or a concentration gradient).
Movement of molecules can also occur via
VESICLES either from the inside to the exterior
of the cell (EXOCYTOSIS) or from the exterior
into the cell (ENDOCYTOSIS).
Diffusion and Facilitated Diffusion are both examples of passive transport, which means that they do not
require the use of ATP.
Using the example with the KMnO4 crystals,
diffusion occurs because the water molecules
have an „internal energy‟ causing them to be in
constant random motion.
We can thus define diffusion as: THE NET
MOVEMENT OF MOLECULES OR IONS
FROM REGIONS OF HIGHER TO LOWER
CONCENTRATION.
They bombard the crystals, causing them to
break apart and move outward. This movement
will naturally shift the crystals down a
concentration gradient.
Multiple factors affect rate of diffusion, such as
The size of the particles as well as their charge.
Heat may also increase rate of diffusion.
FACILITATED DIFFUSION
DIFFUSION is
is very
very much
much similar to
FACILITATED
simple to
diffusion.
similar
diffusion.
However, the
the main
main difference
difference is
is that
that SIMPLE
However,
DIFFUSION
allows
molecules
to
enter the
the cell
cell by
DIFFUSION allows molecules to enter
moving
through
thethe
phospholipid
bilayer
(imagine like
by
moving
through
phospholipid
bilayer
water draining
through
a layer
of sand).
(imagine
like water
draining
through
a layer of
sand). Facilitated diffusion requires the use of
Facilitated
diffusion
requires
the use of
specific
specific
pathways
called
CHANNEL
PROTEINS,
pathways
CHANNEL
PROTEINS,
which
formcalled
hydrophilic
passages.
Imagine which
these form
hydrophilic
passages.
Imagine
these
channels
like open
channels like gates that will only allow entry for
gates that
will onlyorallow
specific
molecules
ions.entry for specific molecules
or ions. CARRIER PROTEINS are involved too.
27
SO HOW DO THE RATES OF DIFFUSION DIFFER FOR THE TWO?
Observe the graph shown. You will see that both
types of diffusion yield different rates, with the
rate of simple diffusion mostly being
DIRECTLY PROPORTIONAL to the
concentration of substance. Facilitated diffusion,
however, has a rate of increase that decreases
over time until it reaches a peak, where the rate
is capped. Why is this?
Since facilitated diffusion requires the use of
protein channels (think of them as „tunnels‟), the
limiting factor is the number of carriers
themselves. Increasing the concentration of the
substance would eventually create a „bottleneck
effect‟ on these „tunnels‟, greatly reducing the
rate of transfer.
These carriers may open and close in response to
factors such as mechanical changes, attachment
of a signalling molecule (a LIGAND) or in
response to a potential difference (VOLTAGE).
WHAT IS ACTIVE TRANSPORT?
There are TWO main differences between both types of diffusion and active transport.
1. Unlike the other two, active transport requires the use of ATP.
2. Active transport moves molecules from up or AGAINST a concentration gradient (from a region
of LOW concentration to a region of HIGH concentration).
Active transport is carried out by CARRIER PROTEINS in
the plasma membrane, which are supplied with ATP to carry
out the process. It does this by altering the shape of the
proteins. These carriers can by SYMPORT or ANTIPORT as
shown.
An example of this occurring is when maintaining the balance
K+ ions and Na+ ions in a cell. The K+ ions are pumped into
the cell by the carrier protein as it changes shape, and Na+
ions are pumped out.
Sometimes other incidental molecules can move through the
carrier protein when it is open. This happens with glucose in
the ileum when Na+ is being taken in by the villi. This is called
INDIRECT active transport.
28
WHAT IS EXOCYTOSIS AND ENDOCYTOSIS?
These two methods of transport are used for
BULK movement of materials across the
membrane. These require ATP to occur, though
do not require a concentration gradient. The
basic difference between the two being:

EXOCYTOSIS moves substances out,
releasing them from the cell.

ENDOCYTOSIS moves substances in,
absorbing them.
In exocytosis, a VESICLE is used as the
transport sac for the material. The vesicle will
move to the plasma membrane, combine with it
and release the contents. This process allows the
secretion of substances such as enzymes and
antibodies.
Sometimes cells can absorb masses of fluid into the
cell by forming a vacuole called a PINOSOME
Around it. This type of endocytosis is called
PINOCYTOSIS.
In endocytosis, the substance usually enters the
cell through the plasma membrane. Sometimes
the cell changes shape to accommodate the
material (such as during PHAGOCYTOSIS in
macrophages). The area becomes enclosed,
forms a vesicle and is absorbed by the
cytoplasm.
TO SUM UP, WHAT ARE SOME APPLICATIONS OF EACH PROCESS SO FAR?
Simple Diffusion
Facilitated Diffusion
Active Transport
Exocytosis
Endocytosis
Removal of carbon
dioxide from the
body.
Movement of glucose
through plasma
membrane in ileum.
Movement of ions
from soil into plant
roots.
Removing toxins
from the cell‟s
interior.
Capturing pathogens that
may endanger the
organism.
Movement of oxygen
molecules through
plasma membrane.
Movement of ions
through the plasma
membrane.
Creation of
sodium-potassium
pump.
Delivery of
proteins from
Golgi body.
Transport of cholesterol
into cells. Absorption of
nutrients in ileum.
Removal of alcohol
from kidney
nephrons.
Movement of oxygen
into the red blood
cells.
Transmission of
neurotransmitters
in synapses.
Delivery of
neurotransmitters
to other cells.
Bulk transport of water
into the cell.
29
WHAT IS OSMOSIS AND
ψ?
Water molecules are small enough to pass through the tiny spaces in the phosopholipid bilayer, but only
at low rates (due to the hydrophobic fatty acid tails) It thus can be said to be PARTIALLY
PERMEABLE. There are also specialized channels called AQUAPORINS that allow the movement of
water molecules from a higher to lower water potential. Why not say „concentration‟?
Water potential is depicted as the Greek symbol
„psi‟ (ψ). Think of water potential as “the
tendency of water to leave the solution” or the
pressure that will push water molecules across,
so the higher the value is more likely the water
molecules will move across the membrane.


HYPOTONIC solutions have very low
conc. of solute and so have a high ψ.
HYPERTONIC solutions have high
conc. of solute and have a low ψ.
You will see water potential usually being represented as a negative (-) number. In fact, the water
potential of pure water at atmospheric pressure (with absolutely no solute in it) has a water potential of
ZERO. The more solute there is, the more negative Ψ becomes, since the solute molecules will attract the
water molecules and restrict their freedom to move.
HOW DOES OSMOSIS AFFECT CELLS?
Recall that about 60% of your body is water. A
great amount of that is found in the cells as
components of protoplasm and cytoplasm.
Moisture is also used to line membranes, such as
in the alveoli, and water is a main component of
blood plasma. It is an absolute necessity to
regulate the water-salt balance in the human
body to prevent the cells from either shrivelling
(CRENATION) or bursting (LYSIS).
Since plant cells have a CELL WALL, it does not
undergo lysis. As water enters the cell, it expands and
exerts a force called a PRESSURE POTENTIAL.
If the plant cell loses water, it causes retraction of
PLASMA MEMBRANE from the cell wall, which keeps
its shape. The external solutions begins filling the gaps
created (as the cell wall is freely permeable). The cell
dies if all parts disconnect.
30
3.3: Investigate the effects on plant cells of immersion into solutions of different water potentials.
HOW TO DETERMINE THE WATER POTENTIAL OF A PLANT TISSUE
You may recall performing an experiment in O‟
Level Biology involving submerging potato
cylinders in solutions of varying sucrose
concentrations. You would‟ve then compared
the final lengths/masses to the initial
lengths/masses of the cylinders to determine
whether or not water flowed into the cell or
flowed out.
If a cylinder happens to have no change in
length and mass, then it could be assumed that
there was no difference in water potential inside
and outside of the cell (ψsolution = ψpotato). The
basis of this experiment is to perform trials with
multiple sucrose solutions and graph the %
change. When there is 0% change, that would be
equal to the water potential of the plant tissue.
Let‟s do this sample question below to plot the graph and determine the water potential of the tissue:
Molarity of sucrose sol’n (mol dm-3)
0.0
0.1
0.2
0.3
0.4
0.5
% change in mass
24
15
11
2
-4
-8
From the graph, the water potential of the tissue will be found at a molarity of 0.35 mol dm-3.
31
HOW TO DETERMINE SOLUTE POTENTIAL OF A PLANT TISSUE
Solute potential (or ψs) can be defined as the
amount by which a dissolved solute lowers the
water potential. Simply put, the higher the solute
potential, the lower the water potential. It is
represented as a negative number and the higher
the solute potential, the more negative that
number is (e.g. 0.50 mol dm-3 of sucrose has a
ψs = -1450 while 1.00 mol dm-3 of sucrose has a
ψs = -3500).
If there is too much solute in the cell, water will
leave and the cell loses turgor and is said to have
undergone PLASMOLYSIS. There is a point
where the cell loses enough internal water
pressure that it stops pressing against the cell
wall. As a result, the cell wall stops pushing
back. The pressure potential now becomes zero.
This is the moment just before plasmolysis
occurs, when the plasma membrane will begin to
retract. This point is called INCIPIENT
plasmolysis.
This experiment seeks to determine that point. You can think of it as the point where the water potential
inside is equal to the solute potential inside (ψinside = ψs inside), that will cause water to start to flow out. To
observe this, the tissue will be observed under a microscope under varying sucrose concentrations.
The higher the sucrose concentration, the more cells will become plasmolysed. However, this will not
happen immediately. There will be a sucrose concentration that will act as a sudden „tipping point‟. The
aim to determine that point. Observe the sample readings below and plot the graph:
Salt conc. / 0.0
g dm-3
%
0
plasmolysis
0.5
1.3
1.6
1.8
2.1
2.3
2.5
2.7
3.5
4.0
5.0
6.0
0
0
15
30
60
80
96
100
100
100
100
100
From the graph, the
point of incipient
plasmolysis is usually
determined by the 50%
plasmolysis point.
Therefore, the solute
potential of the plant
tissue will be found at a
molarity of 2.0 g dm-3.
32
TOPIC 4: ENZYMES
4.1 and 2: Explain that enzymes are globular proteins that catalyse metabolic reactions. Also explain the
mode of action of enzymes in terms of an active site, enzyme and/or substrate complex, lowering of
activation energy and enzyme specificity.
WHAT IS AN ENZYME AND WHAT IS A METABOLIC REACTION?
Enzymes are globular proteins. They tend to be involved in metabolic reactions because their TERTIARY
structures (which are folded 3D structures of α helices and β sheets) are quite unique. As a result,
enzymes tend to be involved in specific reactions instead of structural roles, like fibrous proteins (e.g.
collagen).
Enzymes act as BIOLOGICAL CATALYSTS, which means that they speed up a chemical reaction.
Without them, many processes in the body would occur too slowly. Before continuing, let us define three
important terms when it comes to chemical reactions in the body.
Term
Definition
Example
Metabolism
All the chemical reactions that occur in the
body.
Respiration occurring in the
mitochondria of a cell.
Anabolism
The combination of small molecules to
produce larger, more complex molecules.
Ribosomes synthesizing proteins from
amino acids.
Catabolism
The breakdown of larger molecules to
produce smaller, simpler molecules.
The breakdown of triglycerides into
fatty acids and glycerol.
The table below shows examples of a few enzymes you will learn in A‟ Level Biology.
Term
Function or Note
Amylase
Breaks down starch into maltose. Secreted by salivary glands and the pancreas.
Maltase
Breaks down maltose into glucose.
Pepsin / Trypsin
Breaks down proteins into polypeptides and into amino acids.
ATPase
Involved in the synthesis of ATP during aerobic respiration. Found in mitochondria.
Catalase
Breaks down toxic hydrogen peroxide in the body (2H2O2  2H2 + O2)
DNA ligase
Joins two pieces of DNA molecules together, such as during genetic engineering.
Acetylcholinesterase Breaks down acetylcholine (a neurotransmitter) to cease transmission of impulses.
33
WHAT ARE THE LOCK-AND-KEY AND INDUCED FIT MECHANISMS?
As mentioned before, enzymes are globular proteins with 3D tertiary structures. They can either be
intracellular (inside the cell) or extracellular (outside of the cell, such as pepsin).
Enzymes bind with SUBSTRATE molecules to form an ENZYME-SUBSTRATE COMPLEX and finally
convert them into PRODUCTS. For a breakdown of starch, for example, starch would be the substrate,
amylase is the enzyme and maltase is the product. The enzyme is left unaltered at the end.
The substrates are always in motion due to their kinetic energy, so think of them as rapidly colliding with
the enzymes until they bind. The active site has R groups that interact with the substrate.
The substrate temporarily binds with the
enzyme‟s ACTIVE SITE, which is a specific
shape on the enzyme‟s surface. This is often
referred to as a LOCK AND KEY mechanism if
it is a perfect fit. However, some enzymes alter
their shape slightly to accommodate holding the
substrate in place.
This is known as INDUCED FIT. Think of how
a glove may stretch slightly to accommodate a
hand. The diagram below shows this.
The maximum number of
substrate molecules that can be
converted to product per
minute is known as the
enzyme‟s
TURNOVER NUMBER.
HOW DO ENZYMES SPEED UP A REACTION?
Sometimes energy is required to initiate a reaction,
such as adding heat to Benedict‟s solution when
testing for reducing sugar. This energy is known
as ACTIVATION ENERGY.
Enzymes LOWER the amount of activation energy
required to initiate the reaction, which means that
the substrate will be converted into product at a
much faster rate.
However, if too much heat energy is applied, the
enzyme can be permanently altered and would not
work. It would experience DENATURATION.
34
4.3: Explain the effects of pH, temperature, enzyme concentration and substrate concentration on enzyme
action.
THE USUAL RATE OF ENZYME REACTION
The graph shows the usual course of an enzyme reaction. With the enzyme, you will see that the initial
rate is very high. However, as a little time passes, it plateaus. Why is this? First, keep in mind there are
usually more substrate molecules than enzyme molecules.
At A, the substrates are rapidly binding with the
available enzymes so the rate of conversion of
substrate to product is at its PEAK here.
At B, all of the enzymes are currently „occupied‟
and as such, the rate of product formation
DECREASES as the substrates now must „wait‟
for an enzyme active site to become free.
At A, the graph might actually look like a straight line
close to t = 0. Measuring slope at this region gives
INITIAL RATE OF REACTION.
At C, there are very few substrate molecules left.
Very little product remains to be formed now, so
the rate is very low (almost a plateau) until all of
it has been converted.
The graph also shows that without the enzyme, the SAME AMOUNT of substrate would be converted
into product, but it would take a much longer time. This would also happen in a more LINEAR manner.
WHAT HAPPENS IF YOU INCREASE THE AMOUNT OF SUBSTRATE?
This is given that ENZYME
CONCENTRATION remains a constant, of
course.
On the graph, you will notice that nothing has
really changed in terms of how rate of reaction
occurs when the amount of substrate has been
increased. It still begins rapidly, slows down and
eventually plateaus.
As before, more substrates with the same
amount of enzymes means that the enzymes
become quickly „occupied‟. Other substrates
would be rapidly colliding with the enzymes but
would be unable to bind and must „wait‟ until
one‟s active site is free. The section marked Vm
indicates that the enzyme is working at its
maximum possible rate, at full capacity.
Think of it as many people lining up to go into a
building. They will eventually get in, but it will
take a while.
35
WHAT HAPPENS IF YOU INCREASE THE AMOUNT OF ENZYME?
In an experiment, imagine if the amount of
starch substrate is in equal amounts in each trial.
However, what is being varied now is the
amount of enzymes available. With the same
amount of substrate but more enzymes, the
reaction will INCREASE. The INITIAL rate of
reaction will increase PROPORTIONATELY.
Recall that starch is broken down into maltose
by the enzyme amylase.
Think of it as people queueing up at a bank.
However, more tellers have now opened up their
stations and now more lines can form. As a
result, the transactions will occur at a much
faster rate. In this analogy, the „people‟ are
STARCH. The „tellers‟ are AMYLASE. The
„transactions‟ refer to the conversion of starch to
MALTOSE.
HOW DOES TEMPERATURE AFFECT ENZYME ACTIVITY?
Recall that substrates have KINETIC energy in
their molecules that allow them to rapidly move,
collide and eventually bind with enzymes.
If this energy is too low, they will move much
more slowly and with much less momentum, so
it is less likely for them to bind. As such, the rate
of reaction INCREASES as TEMPERATURE
increases. Reaction rate is actually said to
DOUBLE every 10oC increase. This is called
the Q10 TEMPERATURE COEFFICIENT.
This continues until about 40oC, where the rate of
reaction peaks (called the OPTIMUM
temperature). If the temperature increases past this
point, the enzyme vibrates too energetically and
the tertiary protein structure of the enzyme begins
to break down.
This is because high temperatures BREAK THE
HYDROGEN BONDS that hold the structure
together. The structure deforms and the substrate
CAN NO LONGER FIT in the active site. This is
called DENATURATION.
SAMPLE
GRAPH:
36
QUESTIONS:
1. Where do you think
those prokaryotes live?
2. What are the optimum
temperatures for both
proteases? Mark on the
graph.
3. Name TWO mammalian
proteases found in the
human body. State their
function and location.
37
HOW DOES PH AFFECT ENZYME ACTIVITY?
Think of pH as the suppression of HYDROGEN
IONS in a solution. So we can say that the lower
the pH, the higher the number of hydrogen ions.
The issue with having many hydrogen ions is
that they tend to react with other groups, such as
the R groups of protein molecules and disrupt
the tertiary structure of enzymes. Differences in
pH can break IONIC bonds, change the shape of
the enzyme‟s active site and cause it to
DENATURE.
The graph shows the effect of pH on two
proteases, pepsin and trypsin. Both perform the
same function (hydrolysing proteins into amino
acids) but are found in different parts of the
body. As a result, they both have different
optimum pH‟s. Pepsin works best in an ACIDIC
pH while trypsin works best in an ALKALINE
pH.
4.4: Explain the effects of competitive and non-competitive inhibitors on enzyme activity.
WHAT ARE ENZYME INHIBITORS? HOW DO INSECTICIDES WORK?
An INHIBITOR is a substance that will decrease
the rate of an enzyme reaction, or stop it
altogether. It might do this by preventing the
substrate from binding to the active site.
Sometimes, inhibitors have very similar shapes
to the substrates and may bind to the enzyme
instead of the substrate, „occupying‟ the space.
This is called COMPETITIVE INHIBITION.
Many times, this is a REVERSIBLE process and
does no damage to the enzyme or the active site
and it functions normally afterwards. Sometimes
it can permanently alter the enzyme‟s shape,
thus preventing any substrate molecule from
attaching to it.
Sometimes an enzyme may have another
attachment site aside from the active site
called an ALLOSTERIC site.
It is possible for foreign substrates to bind
there and disrupt the shape of the enzyme
(recall the “induced fit” model).
This is called NON-COMPETITIVE
INHIBITION and can be either reversible
or irreversible. Increasing the amount of
substrate has no effect, whatsoever, as the
enzyme itself has changed.
38
From the graph, it can be seen that with
COMPETITIVE inhibition, INCREASING the
amount of substrate will raise the initial rate of
reaction. This is because the enzyme is still
functioning but the substrate is temporarily
blocked from the active site from time to time.
This is not so with NON-COMPETITIVE
inhibition. Because the enzyme has been altered
(reversibly or irreversibly), increasing the
substrate concentration does NOT increase the
rate of reaction. It makes no difference if the
enzyme itself cannot function properly.
The table below shows some examples of competitive and non-competitive inhibitors:
Name of Inhibitor
Competitive or
Non-Competitive
Notes
Malathion
(organophosphate)
Non-Competitive
Disrupts acetylcholinesterase, neurotransmitters and muscular
activity. Common in insecticides.
Digitalis
Non-Competitive
Binds with ATPases to treat heart rhythm problems.
Alpha-Amanitin
Non-Competitive
Prevents production of DNA and proteins. Fatal.
Antabuse
Competitive
Inhibits alcohol dehydrogenase. Prevents conversion of ethanol
to the harmless acetyl coenzyme A. Induces hangovers.
Penicillin
Competitive
Permanently binds to bacterial enzyme, preventing the
formation of their cell walls. Antibiotic.
Malonate
Competitive
Blocks the enzyme „succinic dehydrogenase‟ from converting
succinate to fumarate, necessary for cellular respiration.
To sum up the differences between the two:

Competitive inhibition is usually REVERSIBLE. Non-competitive inhibition has a higher
tendency to be IRREVERSIBLE as there is a higher chance of permanent distortion of enzyme.

Competitive inhibitors prevent substrate from binding to ACTIVE site. No significant change in
active site shape occurs but substrate is blocked. Non-competitive inhibitors bind to
ALLOSTERIC site and significantly changes active site shape while inhibitor is binded.

INCREASING SUBSTRATE concentration can reverse the effects of competitive inhibition. It is
futile for non-competitive inhibition.
END OF MODULE ONE 
39
MODULE TWO – GENETICS AND VARIATION
THIS MODULE CONTAINS FIVE TOPICS:
1.
2.
3.
4.
5.
STRUCTURE AND ROLES OF NUCLEIC ACIDS
CELL DIVISION AND VARIATION
PATTERNS OF INHERITANCE
ASPECTS OF GENETIC ENGINEERING
NATURAL SELECTION
40
TOPIC 1: STRUCTURE AND ROLES OF NUCLEIC ACIDS
1.1: Illustrate the structure of RNA and DNA using simple labelled diagrams.
WHAT IS DNA? HOW IS IT STRUCTURED?
It is important to recall that DNA stands for
DEOXYRIBONUCLEIC ACID and RNA
stands for RIBONUCLEIC ACID. This is
because DNA lacks an OXYGEN that RNA has.
They are mainly found in the NUCLEUS of the
cells and their tasks are to produce a genetic
code to express certain traits, such as eye colour,
blood type and whether or not a disease is
present, such as haemophilia.
The DNA has the shape of a DOUBLE HELIX.
Each chain of this helix is made of
NUCLEOTIDES, which each have organic
BASES that are connected by HYDROGEN
bonds.
There are FOUR DNA bases, named ADENINE,
CYTOSINE, THYMINE and GUANINE.
Respectively, these are represented as the letters
A, C, T and G.
We can see from the diagram that a single nucleotide
comprises the following:
1. A phosphate group
2. A pentose sugar, deoxyribose or ribose
3. A nitrogenous base (A, C, T, G)


A and G have two rings and are called PURINES.
C and T have one ring and are called PYRIMIDINES.
From the diagram, you will notice numbers
marked 3‟ and 5‟. This relates to how the
PHOSPHATES are connected.
5‟ means it is connected to the 5th carbon
(just off the deoxyribose ring).
3‟ means it is connected to the 3rd carbon.
When the phosphate links with the sugar, it
forms a PHOSPHODIESTER bond. This is
a CONDENSATION reaction.
You‟ll also notice that the two antiparallel strands are connected at the
BASES. These form COMPLEMENTARY BASE PAIRS and are linked
by HYDROGEN bonds. Observe in the diagram that a purine can only
bond with a pyrimidine, thus:


A can only pair with T (think „apple under a tree‟).
C can only pair with G (think „car in the garage‟).
Both chains actually run in opposite
directions (notice the inverted sugars). They
are thus said to be ANTIPARALLEL.
41
Base
Type
Pairs With
A
Purine
T
G
Purine
C
C
Pyrimidine G
T
Pyrimidine A
NOTE: There is an
exception to this, but it
occurs in RNA.
Thymine is not found in
RNA and is replaced by
another base called
URACIL (U).
So A binds with U in
RNA.
1.2: Explain the importance of hydrogen bonds and base pairing in DNA replication
HOW DOES DNA REPLICATION OCCUR?
You may recall that when cell division occurs, this is called MITOSIS. Mitosis allows one parent cell to
divide into two identical (clone) daughter cells. When mitosis occurs, the DNA replicates. What this
means is that it produces TWO copies. Where does this other copy come from?
What exactly is happening here? Let‟s make sense of this.
1. An enzyme known as DNA HELICASE
„unzips‟ the DNA into two strands by
breaking the HYDROGEN bonds
between the bases. There is now a
„leading‟ and „lagging‟ strand.
Since there is one old strand (the original) and one
new strand (the one built by DNA polymerase), this
is given a name: SEMICONSERVATIVE
REPLICATION.
2. Another enzyme known as DNA
POLYMERASE slides along the strands
and pairs free nucleotides with the ones
attached to the original strands (for e.g.
a free-floating C in the nucleus will bind
to the G on the original strand).
3. HYDROGEN bonds form, linking the
two, and there are now two DNA
molecules!
42
HOW WAS SEMICONSERVATIVE REPLICATION PROVEN?
The concept was proven by two scientists named Meselson and Stahl. They submerged E. coli bacteria
in ammonium chloride with the nitrogen isotope being „dense‟ (N-15). This meant that this isotope was
all the bacteria should‟ve had N-15 in its DNA. The cells were then transferred to a medium containing
the isotope N-14, which is „less dense‟.
The bacteria were harvested and the DNA collected and dissolved in caesium chloride (CsCl). This was
then put in a centrifuge and a concentration gradient was established. Observe the diagram below. After 1
generation, it showed a band of DNA of intermediate density.
This meant that it contained a strand of
both the N-14 DNA and N-15 DNA.
This proved that DNA was built by
separating parent strands and adding
new nucleotides to form complementary
strands on the new templates.
DIFFERENCES BETWEEN DNA AND RNA
Feature
DNA (deoxyribonucleic acid)
RNA (ribonucleic acid)
Bases
A, C, G, T
A, C, G, U
Number of strands
Two
One
Location
Nucleus
Nucleus and cytoplasm
Pentose sugar
Deoxyribose
Ribose
Role
Storage of genetic code.
Copying and transfer of code from DNA to
ribosomes to synthesize proteins.
WHAT ARE RIBOSOMES?
Ribosomes synthesize proteins. They are found in both
eukaryotes and prokaryotes. They are found held onto the
ROUGH ER. They contain ribosomal RNA or rRNA and
some protein. Think of ribosomes as having two parts, a
large and small sub-unit.
The large sub-unit helps hold substances like mRNA in
place while the smaller sub-unit is more flexible. rRNA
can catalyze the formation of PEPTIDE bonds between
amino acids when synthesizing proteins.
43
1.3: Explain the relationship between the sequence of nucleotides and the amino acid sequence in a
polypeptide.
HOW DOES THE GENETIC CODE WORK?
We understand now that DNA is a double helical
structure of NUCLEOTIDES along a SUGARPHOSPHATE backbone with HYDROGEN
bonds and wrapped around HISTONES. It is
code used by the cell to make PROTEINS,
which we learnt have many different functions
in the body. These instructions are taken to
RIBOSOMES, which synthesize these proteins.
A GENE is the length of DNA that codes for a
single polypeptide. A tiny alteration in the
sequence of the DNA can cause a large change
in the protein synthesized. If this occurs
randomly (usually due to a „copying error‟), it is
called a MUTATION.
As shown in the image below, there are a number of processes that take place for the DNA to be coded
into an amino acid, which will comprise the protein. The two main ones are:
1. TRANSCRIPTION – The DNA code is
copied onto a molecule called
MESSENGER RNA (mRNA). This is
done three bases at a time, called a base
TRIPLET or a CODON. Remember that
RNA does not have thymine (T) so
adenine (A) on the coding strands is
transcripted as URACIL (U) on the
mRNA.
2. TRANSLATION – The 3-letter codon
serves as instructions for the formation
of an amino acid molecule by the
RIBOSOME. Sometimes an amino acid
may form from multiple codons, e.g.
CCA, CCC and CCG all form glycine.
These are DEGENERATE codons.
The bases are said to be NONOVERLAPPING, which means that they
are only used once per translation. It is
also read from the 5‟ to 3‟ direction.
A START codon (TAC) initiates the
translation, while a STOP codon
terminates it (ATT, ATC or ACT).
There are up to 64 amino acids which
can be coded for with the triplets.
44
1.4: Describe the roles of DNA and RNA in protein synthesis.
WHAT EXACTLY HAPPENS DURING TRANSCRIPTION AND TRANSLATION?
Firstly, let‟s form an overview of the THREE different types of RNA:
Type of RNA
Role
rRNA
Comprises ribosomes. Helps form peptide bonds between amino acids.
mRNA
DNA code is copied onto this molecule. Helps build polypeptide with tRNA.
tRNA
Helps transfer an amino acid molecule towards mRNA and build polypeptides.
Transcription onto mRNA molecule
During TRANSCRIPTION, mRNA is produced
from the complementary base sequence of a
DNA strand, one gene at a time. The enzyme
DNA HELICASE breaks the hydrogen bonds
between the bases, thus unwinding the structure
into two strands.
An enzyme called RNA POLYMERASE allows
free nucleotides to bind to the DNA strand and
ensures correct pairing. More and more
nucleotides keep linking, thus ELONGATING
the mRNA molecule. The mRNA exits the
nucleus and goes to a RIBOSOME for the next
step.
Structure of a tRNA nucleotide
During TRANSLATION, the bases from the mRNA
line up to make a polypeptide. Recall that the codons
are in triplets and that each triplet is linked to the
production of an amino acid.
TRANSFER RNA (or tRNA) in the cytoplasm makes
this happen. What tRNA does is bind an AMINO ACID
at a point of attachment at the top of its structure.
It attaches to the mRNA‟s bases by pairing them with a
complementary ANTICODON, e.g. AAA on the pairs
with a tRNA with an anticodon of UUU.
Enzymes in the cytoplasm called tRNA transferases
help with loading these amino acids onto the tRNA
molecules.
When the STOP CODON is read, the process terminates
for that particular mRNA molecule.
45
The INITIATION of the translation process occurs when
the anticodon to the mRNA START codon is paired. The
mRNA start codon is AUG so the anticodon would be
UAC. All of this occurs through a slit in the ribosome.
Remember that the start codon will have an amino acid
attached to its top. The amino acid disconnects from the
tRNA to make the first molecule of the polypeptide.
Picture it like a people throwing coins in a fountain,
except there are various types of coins. The people are
the tRNA and the coins are the amino acids.
The tRNA is now empty and moves away. The mRNA
moves through the ribosome and other tRNA molecules
now attach, allowing more and more amino acids to be
linked via PEPTIDE bonds. This continues until the
STOP codon on the mRNA is reached (termination).
1.5 & 6: Explain the relationship between the structure of DNA, protein structure and the phenotype of an
organism; and describe the relationship between DNA, chromatin and chromosomes.
WHAT IS PHENOTYPE?
- CHROMATIN can be thought of
DNA in its unravelled structure for the
purpose of packaging in the nucleus.
- A CHROMOSOME, however, is
highly condensed, meant for the
separation of genetic material.
Chromosomes usually come in pairs.
Humans have 22 pairs of
HOMOLOGOUS chromosomes and 2
sex chromosomes (X or Y).
Chromatin comes in two forms:
HETEROCHROMATIN and EUCHROMATIN.
Heterochromatin is denser, more tightly coiled
and darker in colour. This is found in DNA not
being used for transcription.
Euchromatin is lighter-coloured and less tightlycoiled, as it is prepared for transcription.
The PHENOTYPE of an organism refers to the
expression of a set of genes (e.g. black fur, blue
eyes, having a widow‟s peak).
Recall that DNA determines the sequencing of
the amino acids that produce the polypeptides
and proteins for these genes. Therefore, DNA
highly influences phenotype.
It should be noted that phenotype can be
influenced by the ENVIRONMENT. For
example, genes can code for expressions of light
complexions. However, exposure to sunlight can
stimulate MELANIN production in the basal
epidermis, giving that person a darker
complexion.
46
TOPIC 2: CELL DIVISION AND VARIATION
2.1 & 2.2: Describe, with the aid of diagrams, the processes involved in mitotic cell division (including
interphase); AND observe freshly prepared root tip squash to show the stages of mitosis;
WHAT ARE THE DIFFERENT STAGES OF MITOSIS?
Stage
INTERPHASE
Diagrams
Notes
- Not considered an actual stage of
mitosis. The nucleolus is still intact
here. Cell activities are normal.
- DNA is being replicated at this
stage in the SEMICONSERVATIVE
replication manner to avoid errors.
- The majority of the cell division
process (about 95%) is interphase.
PROPHASE
- The DNA needs to be more tightly
packed to allow for easier separation.
At the start of prophase, chromatin
begins condensing into
CHROMOSOMES.
- Nuclear membrane begins
breakdown. Mitotic SPINDLES made
from microtubules form. They
originate from the CENTRIOLES.
METAPHASE
- The NUCLEAR MEMBRANE has
broken down, allowing the
chromosomes to move.
- The SPINDLE fibres pull along the
centromeres of the chromosomes.
- The chromosomes align at the
EQUATOR of the cell. The
centrioles are on the polar ends of the
cell.
ANAPHASE
- The CENTROMERES split.
- The MICROTUBULES pull
towards the poles of the cell.
- The sister chromatids move towards
the opposite ends of the cell and
assemble at each end.
47
TELOPHASE
- The chromatids are now at the
poles, which then become
chromosomes.
- The spindle fibres BREAK DOWN.
- The NUCLEAR MEMBRANE and
nucleolus reform.
- The chromosomes unwind and
become CHROMATIN once again.
- During CYTOKINESIS, the
CYTOPLASM divides and two
identical daughter cells are formed
from the one parent cell.
The figure to the left represents
an electron micrograph of a
sample of Allium tissue.
Observe the internal cell
arrangements and complete the
blanks with the words
„interphase‟, „prophase‟,
„metaphase‟, „anaphase‟ and
„telophase‟.
On the lower specimen, draw
label lines for five cells for each
of the aforementioned phases.
It should be reiterated that
PLANT CELLS do not have
centriole organelles.
Instead, their nuclear envelopes
perform the similar functions as
the cell cleaves along the middle
to divide.
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2.4: Discuss the role and importance of mitosis in growth, repair and asexual reproduction.
WHAT IS MITOSIS INVOLVED IN?
Role
Explanation
Asexual
reproduction
When one parent cell splits into two identical daughter cells, this leads to asexual
reproduction in many organisms, both unicellular (such as AMOEBA) and
multicellular (such as in BRYOPHYLLUM meristems or in HYDRA). This is
because there is only ONE parent.
Growth
Since mitosis results in cloned daughter cells, growth can normally occur in areas
such as the MERISTEMS of plants or of the ZYGOTE of animals, which will keep
dividing to eventually form the embryo.
Tissue repair
Mitosis is used to regenerate any cells or tissue that has been lost due to damage or
age. The cells will divide and form new cloned daughter cells.
Immunity
When exposed to pathogens, the body will ensure that there are adequate
LYMPHOCYTES to produce sufficient antibodies to destroy the foreign invaders.
When one is ill, there is always an excess production of white blood cells.
2.5: Explain what is meant by homologous pairs of chromosomes, and the terms haploid and diploid.
The top figure shows the human KARYOTYPE,
which is a micrograph of the visual appearance of
the chromosomes in the nucleus.
There are 23 pairs of chromosomes, with pair
number 23 being the SEX chromosomes (X or Y).
All other 22 pairs are considered HOMOLOGOUS,
which means they carry the same genes on the
same positions or LOCI.
Due to MEIOSIS, gametes each have half of the
chromosomes. This is represented as „n‟ and is
called a HAPLOID cell.
Other body cells, called SOMATIC cells, have the
full number of chromosomes (2n). These are called
DIPLOID cells. A typical human would thus have
a diploid number of 46.
It should be worth noting that individuals with
DOWN‟S SYNDROME have an extra
chromosome on pair 21 (called TRISOMY 21).
They would have a diploid number of 47.
49
2.6 & 7: Describe with the aid of diagrams, the processes involved in meiotic cell division, and describe
how meiosis contributes to heritable variation.
WHAT IS MEIOSIS? HOW IS IT DIFFERENT FROM MITOSIS?
Meiosis is type of cell division, in ways similar
to mitosis, but with many key differences,
especially concerning the daughter cells that are
formed from the parent cell. Meiosis occurs in
any organisms that undergo SEXUAL
reproduction and must produce sex cells or
GAMETES.
When two gametes fuse during
FERTILIZATION, they form a ZYGOTE and
be the first cell of a new organism. This cell then
repeatedly divides by MITOSIS as the organism
undergoes growth and further development.
Meiosis is mainly different due to the fact that it
produces daughter cells with GENETIC
VARIATION, meaning each is different from
the parent and from each other. This is due to
DNA CROSSING OVER.
Chromosomes arrange themselves in pairs called
BIVALENTS and cross at CHIASMATA.
Meiotic daughter cells also only have HAPLOID
numbers, meaning they have half the number of
chromosomes.
Table showing differences between mitosis and meiosis:
Feature
Mitosis
Meiosis
Daughter cell DNA
Genetically identical (clones).
No crossing over or chiasmata.
Undergo genetic variation due to crossing
over, independent assortment and random
segregation.
Number of divisions
One
Two
No. of daughter cells
Four
Two
Daughter cell
chromosome number
Diploid (2n)
Haploid (n)
Behaviour of homologous Act independently of each
chromosomes
other.
Pair up to become bivalents.
The diagram shows a CHIASMA
forming between a bivalent. Here,
the chromatids break and rejoin and
„exchange‟ alleles.
Chiasmata can form at numerous
points in the chromatids, at various
gene locations or loci.
This happens during meiosis at the
stage called PROPHASE I.
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HOW ELSE DOES MEIOSIS CONTRIBUTE TO GENETIC VARIATION?
There are THREE main mechanisms involved in sexual reproduction that contribute to genetic variation.
Two of these occur during meiosis and the third occurs during fertilization.
Mechanism
Explanation
INDEPENDENT
ASSORTMENT
Chromosomes pair up into bivalents and align at the equator of the cell. One from
this pair come from the mother and the other from the father. These pairs are each
sorted into the daughter cells independently and can result in a massive number of
combinations.
CROSSING
OVER
Previously mentioned, crossing over in the bivalents occur in fusion and breakage
points in the bivalent chromatids called chiasmata.
RANDOM
Remember that gametes have a haploid number of chromosomes, which are all
FERTILIZATION independently assorted and crossed over. Each gamete is genetically unique. During
sexual reproduction, the gametes that fuse are up to chance.
WHAT ARE THE ADVANTAGES OF HERITABLE GENETIC VARIATION?
Reason
Explanation
Limiting spread of
disease
Genetic variation ensures that each member of a species has varying levels of
immunity against communicable diseases. If all the organisms were genetically
uniform, diseases would spread very quickly through populations.
A popular example involves the fungal Panama disease against Gros Michel
banana cultivars.
Ensuring a species can
adapt to environmental
changes
Genetic variation ensures that individuals are diverse enough to be able to
survive in different climates, temperatures and differences in abiotic factors.
With climate change on the rise, vegetatively propagated plants that cannot
adapt to high fluctuations in temperature may die.
Preventing
If organisms are diverse, so would their needs for survival such as diet and
overcompetition
habitat. Due to this, these species would not have to fight for limited resources.
between members of the
The basic example of this are the finches on the Galapagos Islands, studied by
species.
Charles Darwin to form his theory of evolution.
51
WHAT ARE THE STAGES OF MEIOSIS?
It is important to note that meiosis occurs in TWO main stages that are simply named MEIOSIS I and
MEIOSIS II. Meiosis I involves independent assortment and crossing over, while the stages in Meiosis II
is almost identical to mitosis.
MOST NOTABLE EVENTS:

PROPHASE I – Homologous chromosomes arrange into bivalents. Chiasmata form.

ANAPHASE I – The number of chromosomes are halved as the bivalents are pulled to the
opposite poles. From here on and throughout Meiosis II, the daughter cells are HAPLOID.

ANAPHASE II – The sister chromatids are pulled apart again.

CYTOKINESIS II – The four daughter cells are formed. This is the end of meiosis.
NOTE: What may seem confusing at first are the terms „chromosome‟ and „chromatid‟. When
chromosomes are in their duplicated state, they are „2 sister chromatids‟ but still „1 chromosome‟. So when
DNA is replicated, there are 92 chromatids but still only 46 chromosomes. It is easier to determine the
chromosome number not by counting the chromatid strands but each unit as a whole.
52
2.8-2.11: Describe gene and chromosome mutations; sickle cell anaemia; mutations & genetic variation.
WHAT IS GENETIC STABILITY? WHAT IS A MUTATION?
If a cell dies, the body must replace that cell. The only way to replace the cells is to first copy the
information that the cell contained. There is a complex system of proteins and enzymes that unravel the
DNA double helix so that the DNA can be copied.
If a single cell dies it can be replaced through
MITOSIS. This system works well with single
cell and simple organisms. More complex
organisms use meiosis to produce gametes (egg
or sperm cells) for sexual reproduction. Meiosis
also begins with DNA replication. The genetic
stability of a multicellular organism is reliant on
an accurate DNA replication system.
Sometimes, a MUTATION may occur. This
occurs when there is a RANDOM and
unpredictable error in this copying system. This
can occur in numerous ways, such as a base
being deleted, substituted or an extra base being
added. Sometimes MUTAGENS, such as
carcinogens of high-frequency radiation, can
increase the likelihood of mutations by
damaging the DNA.
Note that mutations can be categorised into two main groups: GENE and CHROMOSOME. There are
also numerous ways in which gene mutations can occur:
Type of Gene Mutation
Explanation
Example
SUBSTITUTION (or
POINT MUTATION)
Replaces one base with another. Sometimes this does not
result in any change (as many triplets code for the same
protein), so it is often called a SILENT mutation.
Examples include SICKLE CELL ANAEMIA and PKU.
DELETION
The loss of a base pair. Changes how the entire DNA
sequence is read. Also called a FRAME SHIFT
mutation, due all the bases being „shifted‟.
INSERTION
The addition of a new base pair. Also is called a
FRAME SHIFT mutation. An example of this is
CYSTIC FIBROSIS.
SICKLE CELL ANAEMIA is caused by the
SUBSTITUTION in the gene that codes for the
polypeptide chains in haemoglobin. This single base
pair change translates into a fully different protein
called VALINE, affecting the curvature of the cells.
These cells are unable to transport OXYGEN.
Moreso, the cells now have the ability to bond with
each other, causing them to aggregate and cause
painful blockages.
53
WHAT ARE CHROMOSOME MUTATIONS?
While gene mutations are changes in the
nucleotide sequences in the DNA (such as by
insertion, substitution or deletion), chromosome
mutations are changes in the cell‟s chromosome
NUMBER or chromosome STRUCTURE.
When the cell divides during the first phases of
MEIOSIS, there is a random chance of the
chromosomes being pulled apart unevenly
between the daughter cells. When this happens,
it is called NON-DISJUNCTION.
The diagram to the left shows
several ways in which
chromosome mutations may
occur.
Examples of chromosome
mutations include Down‟s
Syndrome, Klinefelter‟s
syndrome (XXY
chromosomes) and Turner
syndrome. (only one X
chromosome in women).
DOWN‟S SYNDROME is caused by a type of
chromosome mutation called ANEUPLOIDY,
which means there is either one less or one extra
chromosome.
A person with Down‟s syndrome has 47
chromosomes. This is because Chromosome 21
puts two copies into one EGG and no copies in
another. The one with no copies will die. The one
with two copies will fuse with the third from the
sperm cell, causing 3 copies, TRISOMY 21.
HOW IS MUTATION RELATED TO GENETIC VARIATION?
Recall that all members of the same species are able to interbreed and produce FERTILE offspring. Every
species has some genetic variation, due to only half of the chromosomes being passed down from each
parent after being independently assorted and crossed over. Note that ENVIRONMENTAL variation
(such as sunlight exposure affecting skin complexion) is not passed down through genes.
A MUTATION is a random change in the DNA, sometimes involving a trait not present in the parent
organism. As a result of this, new PROTEINS may be translated from the new nucleotide sequences,
resulting in new PHENOTYPES. This can have a great impact on NATURAL SELECTION, if these new
phenotypes give the organism an advantage over others in its environment.
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TOPIC 3: PATTERNS OF INHERITANCE
3.1 & 2: Explain the terms: gene, allele, dominant, recessive, codominant, homozygous and heterozygous.
Use genetic diagrams to solve problems involving monohybrid and dihybrid crosses.
FIRST, A VERY HANDY GLOSSARY OF INHERITANCE TERMS
Term
Definition
Gene
A nucleotide sequence which determines the formation of a protein.
A length of DNA that codes for a particular trait by formation of a protein.
Allele
A different form of a gene, found on the same locus of the chromosome.
„Wild type‟ alleles refer to those found naturally in populations.
Dominant
Describes an allele that will express its trait even if a different allele is present.
Recessive
Describes an allele that will only express its trait if a dominant allele is absent.
Codominance
Describes alleles that produce a combined effect when expressed together.
Genotype
A gene combination that will express a trait. (e.g. FF, Ff and ff are all genotypes)
Phenotype
The observable characteristics expressed by that trait. (e.g. round or wrinkled seeds).
Ultimately determined by genes, which are sequences of DNA that lead to the
formation of proteins. Changing a gene can thus change expression and phenotype.
Homozygous
A genotype where both alleles are the same. (e.g. FF or ff)
Heterozygous
A genotype where both alleles are different. (e.g. Ff)
Autosomes
Refers to chromosomes that are not sex chromosomes (the first 22 pairs).
Sex-linked
Traits inherited by genes on loci on the X or Y chromosomes (e.g. haemophilia).
Dihybrid inheritance
The inheritance of two genes at the same time (e.g. AABB, AaBb, aaBB, AAbb, etc.)
Epistasis
The event where the genotype for one gene affects the expression of another gene.
Chi-square (χ2) test
A statistical test that determines whether or not observed ratios are significally different
from expected ratios.
Null hypothesis
A statement in a chi-square test that says that there is no significant difference between
what is observed and expected.
55
MONOHYBRID INHERITANCE AND MULTIPLE ALLELES
When a single gene is inherited at a time, this is called monohybrid inheritance. Most of the Punnett
squares you‟ve done previously has been related to this type of inheritance. Many traits, such as blood
type and eye colour, and inheritance of mutant alleles that cause diseases come as a result of this.
Let‟s use CYSTIC FIBROSIS (CF) as an
example. This is an inheritable disease that
causes the body to produce large amounts of
thick mucus in the lungs and pancreas.
This mucus becomes a breeding ground for
bacteria, which leads to other infections. CF is
caused by a „faulty‟ allele, which would usually
produce a channel protein called CFTR, which
allows flow of CHLORIDE ions in and out of a
cell.

The faulty allele ensures that the protein is not
produced and chloride ions build up, resulting in
the mucus build-up. CF is inherited in an
AUTOSOMAL RECESSIVE manner, meaning
that the disease only occurs if both RECESSIVE
alleles are present in the genotype (ff). The
presence of a dominant allele (F) prevents the
expression of the faulty recessive allele.
Let‟s observe how two parents who are carriers for CF can produce a child with CF.
The setup to the left is called a
PUNNETT square. Keep in mind what
these represent are probabilities.
It does not mean that the parents have
four children and one has CF. It means
that for every child that they have, there
is a 1 in 4 (25%) chance of having CF.
Also note that the expected phenotypic
ratio is written below. In some problems,
this can deviate from what is actually
observed. This is usually done by
performing a χ2 TEST.
This shows inheritance of the ABO
blood group. There are three alleles,
which code for either antigen A, B or O.
It is notable that A and B are both
CODOMINANT, which means they will
be expressed together as a new
phenotype if both are present (AB type).
O is recessive to A and B.
Let‟s see how two parents who are not
blood type O can produce a child with
blood type O.
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WHAT ARE SEX-LINKED TRAITS?
Sex-linked (not to be confused with sexually
transmitted) traits occur when the alleles are
placed in either the X or Y chromosomes. Note
that these two chromosomes are not
HOMOLOGOUS, which means that they would
not have the same number of gene loci.
The Y chromosome is small compared to the X
and has less available positions for alleles, so
some alleles will be present in the X but not the
Y.
It is notable that men cannot pass on an allele
from their sole X-chromosome to their sons as
their sons would always inherit their Y
chromosome and the X from the mother.
One popular example of a sex-linked disease is HAEMOPHILIA, which occurs due to inheritance of a
faulty allele that is placed on the X chromosome but which locus is absent on the Y chromosome.
Therefore, if a boy only has one faulty allele, he will have haemophilia. A girl would need two faulty
alleles. As a result, it is more likely for boys to inherit haemophilia.
Using XH as the normal blood clotting allele and Xh as the haemophilia allele, complete the Punnett
square below. (Remember the Y chromosome does not have a locus for the allele, so it‟s left blank.)
Haemophilia restricts the
production of Factor VIII,
a protein necessary for
blood clotting. As a result,
a haemophiliac may
experience haemorrhaging
in certain parts of the
body.
WHAT IS DIHYBRID INHERITANCE?
Genotype
Phenotype
The concept of dihybrid inheritance is mostly similar
to monohybrid inheritance, with the standout
difference being that it occurs when TWO alleles are
inherited at the same time.
RRYY
Round, yellow peas
RRYy
Round, yellow peas
RRyy
Round, green peas
RrYY
Round, yellow peas
These two alleles could be on two separate
chromosomes but often act together. One pair of
alleles may also influence the expression of another
pair. When this occurs, it is called EPISTASIS.
RrYy
Round, yellow peas
Rryy
Round, green peas
rrYY
Wrinkled, yellow peas
Let‟s look at traits of peas, where round (R) is
dominant to wrinkled (r) and yellow (Y) is dominant to
green (y).
rrYy
Wrinkled, yellow peas
rryy
Wrinkled, green peas
57
WHAT IS EPISTASIS?
As previously said, sometimes during dihybrid
inheritance, the expression of a pair of alleles
can have influence over the expression of others.
Sometimes a trait will not manifest because of
the expression of another trait, or if a pair codes
for the absence of a certain enzyme. A very
common example occurs with coat colour in
animals. Coat colour depends on the presence of
pigments.
However, if a pair of alleles determines the
organism does not have a pigment (an
ALBINO), then the other allele combinations
would not matter. If the first pair of alleles
determines the animal is an albino, then no other
coat colour is even possible.
This is known as EPISTASIS. It should be noted
that epistasis can be either dominant or
recessive.
Let‟s look at this example below. Picture a species of mouse that can have either a brown (b) or black (B)
alleles for coat colour. Black is dominant to brown. However, another pair of alleles code for the presence
of melanin to produce the coat. „C‟ represents melanin production and „c‟ represents no melanin.
From the dihybrid test cross, ANY mice that
have a combination of „cc‟ will be albino and
have white fur colour, despite the second pair.
The phenotypic ratio would thus be:
6 black coats: 6 brown coats: 4 white coats
Now imagine if „C‟ represented no melanin
production. What would be the ratio then?
2 black coats: 2 brown coats: 12 white coats
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3.3: Analyse the results of a genetic cross by applying the
Chi-square test.
WHAT IS THE χ2 (CHI-SQUARE) TEST?
The χ2 test is a statistical test that is often used to compare OBSERVED results with EXPECTED results
to determine if there are any significant differences between them. This is done to see if there are any
external variables affecting the results, such as environmental factors, mutations or human intervention.
To do any statistical test, a NULL HYPOTHESIS is first set up. A null hypothesis would read as:
H0: The observed results are not significantly different from the expected results.
If this is not so, then the ALTERNATIVE HYPOTHESIS must be accepted, which would read as:
H1: The observed results and expected results have a significant difference between them.
Let‟s try an example:
Let‟s observe the Punnett square to the left. „R‟ represents round peas,
which is dominant to „r‟, which is wrinkled peas. If you cross-breed two
heterozygous pea plants, the ratio obtained is 3 ROUND : 1 WRINKLED.
Now here was what was actually observed: 5474 plants with round peas
and 1850 plants with wrinkled peas. The total was thus 7324. We now
have to determine what was expected to happen. To do this, we just
multiply the total by the percentages:
Round = 75% x 7324 = 5493
Wrinkled = 25% x 7324 = 1831
(O – E)
Expected (E)
(O – E)2
(O – E)2 / E
Phenotype
Observed (O)
Round
5474
5493
-19
361
0.066
Wrinkled
1850
1831
19
361
0.197
Sum (χ2 value) = 0.263
Degrees
of
freedom
Probability
0.9
0.5
0.1
1
0.02
0.46
2.71
2
0.21
1.39
3
0.58
4
1.61
0.05
0.01
0.001
3.84
6.64
10.83
4.60
5.99
9.21
13.82
2.37
6.25
7.82
11.34 16.27
3.36
7.78
9.49
13.28 18.46
You‟ll see that our probability lies between 0.5 and 0.9 (much
higher than 0.05). So we can fail to reject the null hypothesis.
The next step is to determine the number of
degrees of freedom, which is simply (No. of
phenotypes – 1). In this case, there were only two
phenotypes observed, so the degrees of freedom in
this case is 1.
Now, determine the „p value‟ on the table
provided. The „p value‟ is used to determine if
there are any significant differences between
observed and expected values.
Typically a „p value‟ of > 0.05 or 5% means that
there is no statistical significant difference between
the two and we fail to reject the null hypothesis.
59
Let‟s try two more questions:
QUESTION ONE: “During dihybrid inheritance, two pea plants of genotypes RrYy were crossed. This
should have yielded a 9:3:3:1 ratio. The offspring were counted and the numbers were recorded.”
The degrees of freedom would be 3. Use the table on the previous page to determine whether to accept the
null hypothesis or alternative hypothesis.
(O – E)
(O – E)2
(O – E)2 / E
Phenotype
Observed (O)
Expected (E)
Round, yellow
365
390.94
- 25.94
672.88
1.72
Round, green
125
130.31
- 5.31
28.20
0.22
Wrinkled, yellow
140
130.31
9.69
93.90
0.72
Wrinkled, green
65
43.44
21.56
464.83
10.70
Sum (χ2 value) = 13.36
In this case, the ALTERNATIVE hypothesis would be accepted, meaning that there IS a significant
difference between the observed and expected results. We have rejected the null hypothesis.
QUESTION TWO: “During dihybrid inheritance, brown coat and black coat mice were mated and their
offspring observed. They experienced recessive epistasis, meaning some offspring had white coats. Their
expected ratio was 3 brown : 3 black : 2 white.”
Use the table on the previous page to determine the „p‟ value.
(O – E)
(O – E)2
(O – E)2 / E
Phenotype
Observed (O)
Expected (E)
Brown coat
64
67.50
- 3.50
12.25
0.18
Black coat
66
67.50
- 1.50
2.25
0.03
White coat
50
45.00
5.00
25.00
0.56
Sum (χ2 value) = 0.77
In this case, the NULL hypothesis would be accepted, meaning that there ISN‟T a significant difference
between the observed and expected results.
NOTE: Even though we have been saying „accept‟ null hypothesis, the actual terminology is to „fail to
reject‟ the null hypothesis. The difference in the language is minor but therein still lies a difference.
60
TOPIC 4: ASPECTS OF GENETIC ENGINEERING
4.1 & 4.2: Outline the principles of restriction enzyme use in removing sections of the genome, and
explain the steps involved in recombinant DNA technology.
WHAT EXACTLY IS GENETIC ENGINEERING?
Genetic engineering (GE) can be defined as THE ALTERING OF THE DNA in an organism, usually by
extracting and inserting the DNA from a member of one species to another species. This altered DNA is
called RECOMBINANT DNA and the organism which genome now contains it is called a GMO, which
is short for GENETICALLY MODIFIED ORGANISM.
It is often compared to ARTIFICIAL SELECTION (or selective breeding), but they remain two entirely
separate processes. Whereas both involve the passing of traits from one organism to another, GE is a
more specific and expensive process, using enzymes to cut, transfer and attach DNA, one gene at a time.
It can also change the DNA of the organism without having it inherit the traits from its parents. This
means it can be used to treat certain diseases, such as SICKLE CELL ANAEMIA.
So what happens?
NOTE: Think of restriction
enzymes as molecular
“SCISSORS” and think of DNA
ligase as molecular “GLUE”.

First, lengths of DNA are cut from the human DNA. This is done using a RESTRICTION
enzyme. These are made by bacteria to fight off bacteriophage viruses.

Similarly, the restriction enzyme makes cuts on a bacteria PLASMID (a circular length of DNA).
Imagine that this leaves a gap in that DNA. This is also called a VECTOR.

Another enzyme named DNA LIGASE is used to join both sets of DNA to make a segment of
RECOMBINANT DNA.

The recombinant DNA is inserted into the bacteria, which now becomes a GMO. The
recombinant bacterial cells are now cloned. This can be done using a process called PCR.

This process is just a general overview. There are many variations and processes involved.
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NOW LET‟S GET MORE SPECIFIC... How is the gene isolated?
INSULIN is a hormone (a protein) that is produced by the BETA cells of the human PANCREAS. It is
necessary for the conversion of GLUCOSE TO GLYCOGEN. GE is used in the modern day to produce
large amounts of insulin from transgenic E. coli. The first step is to extract the human DNA code for
insulin production.
This is done using an enzyme called REVERSE
TRANSCRIPTASE. This enzyme takes the
mRNA extracted from the pancreatic beta cells
and uses it as a template to produce a single
complementary strand of DNA.
DNA POLYMERASE is now used to attach free
nucleotides to form the other strand. The insulin
gene has now been isolated.
NOTE: CRISPR-Cas9 is a modern example of
genetic technology that has allowed genome editing
by adding or altering sections of the DNA sequence.
It is one of the most precise methods right now.
How exactly is the DNA inserted into the plasmid?
A PLASMID is commonly used as a vector to
transport genetic material from one organism to
another. Recall that plasmids refer to DNA
packaged in a circular form and are usually
found in bacterial cells. Another thing to note is
that plasmids often contain some genes that
make them resistant to ANTIBIOTICS.
When bacteria are attacked by viruses, they
produce RESTRICTION ENZYMES. These can
be used to cut particular base sequences of
DNA. A popular example of a restriction
enzyme is EcoRI, which cuts a GAATTC
sequence (as well as cDNA sequence).
Observe that the cuts are asymmetrical and so
leave points that jut out. These are known as
STICKY ENDS and can easily form hydrogen
bonds with complementary base pairs and form
new DNA. This is also done to the insulin DNA.
The bacterial plasmids and the insulin DNA are
then mixed until they pair with each other to
form RECOMBINANT DNA. An enzyme called
DNA LIGASE is then used to „tie‟ everything
together, linking the sugar-phosphate backbones
of the DNA molecule.
62
Now how do we get the recombinant plasmids into the bacteria?
The recombinant plasmids are mixed in a
solution containing the bacterial culture.
However, most of the bacteria do not get the
plasmids into their cells. Only about 1% actually
take the plasmid into them.
IMPORTANT: There‟s also a gene on the E.
coli plasmid that gives it resistance to another
antibiotic called AMPICILLIN.
So how do we know which ones are of that 1%?
It so happens that when the plasmid was altered
before fitting it with the insulin gene, another
gene was inactivated. This gene provided
ANTIBIOTIC RESISTANCE for an antibiotic
named TETRACYCLINE.
A few samples of the bacterial colonies are now placed in an
agar plate containing the ampicillin antibiotic and also in
tetracycline antibiotic. Those without the plasmid would die
after exposure to either antibiotic.
The recombinant plasmids would not survive in tetracycline
as their tetracycline-resistance gene has been inactivated.
The ones that survive ampicillin but die in tetracycline are
singled out and those colonies are then isolated and regarded
as the ones that contain the INSULIN gene.
The culture containing the recombinant bacteria are now
placed in a FERMENTER, as shown to the left. There, the
culture is stirred with nutrients to encourage the bacteria to
multiply. The TEMPERATURE is maintained using the
water-cooling jacket.
Let‟s recap some of the important factors needed:
The insulin is then extracted and collected.
Compound
Role
RESTRICTION
ENZYMES
Used as “molecular scissors” to cut pieces of DNA. Leaves sticky ends to
attach complementary pieces of DNA.
REVERSE
TRANSCRIPTASE
Synthesizes DNA molecules from mRNA template.
DNA LIGASE
Used as “molecular glue” to connect lengths of DNA and form bonds.
DNA POLYMERASE
Used in DNA replication, to produce a complementary strand of DNA from a
single DNA molecule.
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4.3: Discuss the successes and challenges of gene therapy in modern medicine.
WHAT IS GENE THERAPY USED FOR?
Gene therapy is the process of TREATING OR PREVENTING DISEASE BY ALTERING THE GENES
IN A PERSON‟S CELLS.
There are numerous success stories and challenges associated with gene therapy:
SCID: The first human to receive gene therapy was an infant girl with SCID (severe combined immunedeficiency), which is caused by a faulty gene that prevented the production of an enzyme. Due to this, the
girl was unable to fight off PATHOGENS. The correct allele was inserted into the girl‟s white blood cells
using a RETROVIRUS vector and re-inserted into her body. She was then able to resist pathogens and
lead a normal life.
CYSTIC FIBROSIS (CF): Patients with CF
tend to produce thick MUCUS in multiple parts
of the body. This mucus can become breeding
grounds for bacteria and thus, many organs may
be prone to infections. It may even cause men to
be sterile due to blocking ducts in the male
reproductive system.
CF is caused by a defective recessive allele that
is responsible for a carrier protein called CFTR.
The protein is not placed on the plasma
membrane. Researchers first placed the correct
allele in a LIPOSOME, which could diffuse
through the phospholipid bilayer. It worked only
temporarily. Researchers then tried VIRUS
vectors to transport the gene but patients began
to suffer side-effects from infection. The studies
are ongoing.
With the advent of technologies such as CRISPR-Cas9, studies are currently being done on treating
diseases such as: SICKLE CELL ANAEMIA, HAEMOPHILIA, AIDS and LYMPHOMA.
64
4.4: Discuss the implications of the use of GMO’s on humans and the environment.
Type of implication
Environmental
Ethical and Social
Medical
Details

The release of a GMO species would have the possibility of causing an
ECOLOGICAL IMBALANCE. The main concern is that crops can spread
their genes to wild plants through pollination.

Crops, such as maize, are also engineered to produce their own PESTICIDES.
However, due to NATURAL SELECTION, insects may become resistant to
the pesticides. The insecticides may also inadvertently harm insects that are not
considered pests.

The production of GOLDEN RICE in developing countries has been a success.
Golden rice is engineered from transferring genes from daffodils, which allow
the rice to produce BETA-CAROTENE for VITAMIN A.

There is a strong argument that, because the process is often irreversible, GE is
viewed as PLAYING GOD.

The possibility of CLONING humans raises many social issues, as well as
producing DESIGNER BABIES for cosmetic desirable traits.

The use of GE to produce BIOLOGICAL WEAPONRY is another concern in
terms of warfare between nations and for use of terrorist groups. GMO‟s can
be produced quite quickly, further increasing levels of potential devastation.

It is possible for ALLERGENS can be transferred from one food crop to
another through genetic engineering. Another concern is that pregnant women
eating GMO products may endanger their offspring by harming normal fetal
development and altering gene expression.

GMO‟s may lead to diseases not yet known. As defective genes are replaced
with functional genes, it is expected that there will be a reduction in genetic
DIVERSITY, making the population more susceptible to infections.
GERMLINE VS. SOMATIC
There are also concerns of using GERMLINE
gene therapy, which will allow the GAMETES
to transfer the recombinant DNA and thus, pass
it on to offspring. This can alter the entire gene
pool.
Gene therapy, so far, such as for CF has been
SOMATIC gene therapy, only targeted at
altering certain body cells but not the germline
cells (gametes).
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TOPIC 5: NATURAL SELECTION
5.1 – 5.3: Explain how environmental factors act as forces of natural selection; how natural selection
may be an agent of change or constancy; and how it is a mechanism of evolution.
WHAT IS THE THEORY OF NATURAL SELECTION?
Recall that whenever species reproduce SEXUALLY, the offspring receives half of each parent‟s
chromosomes after being independently assorted and crossed over, resulting in unique nucleotide
sequences. Due to this, each member is said to have GENETIC variation. This combines with
environmental factors such as climate, geography, temperature and water availability. As a result, some
members of the same species may exhibit slightly different physical characteristics from others, such as
size, colour and even susceptibility to disease.
During a trip to the Galapagos Islands in the
Pacific, a biologist named CHARLES DARWIN
observed the animals living there, including a
group of finches.
He realized that they had no NATURAL
PREDATORS and thus were able to reproduce
quickly. They were also physically separated from
each other, living on different islands or habitats.
Because of this, they avoided COMPETITION
with each other.
Finally, he observed that their beak size or
thickness was linked to their diets. Thick-beaked
birds tended to feed on SEEDS and FRUITS while
thin-beaked birds fed on INSECTS and WORMS.
Darwin hypothesized that the birds must have had a common
ancestor.
Genetic variation allowed the common ancestor birds to have
slightly different beak sizes, which played a major role in them
being able to survive. Birds of similar beak sizes would have
grouped together according to these ecological NICHES and
thus, mated.
When mating, they passed down their physical traits to their
offspring. Eventually, the offspring from the different groups
would have been so varied from each other that they were unable
to mate, resulting in new distinct species (SPECIATION).
66
Darwin‟s observations and deductions:
Only the organisms BEST ADAPTED are the
ones more likely to survive and pass on these
advantageous traits to their offspring. The
species eventually becomes better and better
adapted to overcome these selective pressures.
Darwin made several observations and
deductions when coming up with the theory of
natural selection. The theory of natural selection
posits that certain environmental challenges (or
SELECTIVE PRESSURES) may arise. These
selective pressures could be a change in
temperature, the rise of a pathogen or the
introduction of a new predator, for example.
E.g. if members of a species develop immunity
to a certain infectious, deadly disease, these are
the ones that will survive and reproduce.
Observation
Deduction
Members of a species VARY between each other.
Some of these variations are INHERITED.
If traits can be inherited then the organisms will pass them
on to their offspring.
All organisms produce EXCESS offspring.
There is a STRUGGLE FOR EXISTENCE, or
competition for survival among members of each species.
Population numbers remain fairly CONSTANT
over long periods of time.
Members that are BEST ADAPTED to their environment
are the ones most likely to survive, reproduce and pass on
their ADVANTAGEOUS traits.
REGIONAL CASES OF NATURAL SELECTION
Observation
Deduction
TRINIDADIAN GUPPIES
Trinidadian guppies are models of natural selection. They have
developed various mechanisms that help them evade predators.
They can produce excess PIGMENT in their eyes, making them
black, to throw off predators‟ aim.
Depending on their predators, they will grow to different SIZES
upon sexual maturity. For e.g. guppies with cichlid predators
grow to smaller sizes since cichlids tend to hunt larger fish.
CARIBBEAN ANOLE LIZARDS
Anole lizards have been observed to branch into many different
colours and sizes, called ECOMORPHS. This is totally
dependent on their habitat and diets, just like with Darwin‟s
finches.
It was observed that a single type of anole lizard in each island
branched into the same ecomorphs on the different islands,
providing evidence that evolution can be predicted and repeated.
This, along with the guppies, have also shown evolution
occurring on a much shorter timespan.
67
THE CASE OF THE PEPPERED MOTH (Biston Betularia)
Biston betularia is a nocturnal moth, common in
Continental Europe. „White‟ variants of the moth were
more prevalent when it was first observed. In the 1800‟s,
a rare „black‟ variant was also observed.
It was deduced that the „white‟ variant was more
prevalent because of its ability to CAMOUFLAGE
against the pale LICHEN of tree trunks. „Black‟ variants
were more easily spotted by predators.
Can you spot the black and white variants?
Later in the century, the „black‟ variants became much
more common after the tree trunks darkened due to soot
deposits. This was called INDUSTRIAL MELANISM.
The white moths were now at a disadvantage and more
easily spotted by predators.
THE CASE OF ANTIBIOTIC RESISTANCE
Antibiotics are chemicals that are ingested to kill bacteria. They are usually produced by other living
organisms. A prime example is PENICILLIN, which is produced by the Penicillium fungus. Penicillin
prevents the formation of CELL WALLS in bacteria cells. However, some MUTANT bacteria have
produced an enzyme which inactivates penicillin and thus, have become RESISTANT to it.
As a result, any bacteria that isn‟t resistant to penicillin will die, leaving the mutant population to
REPRODUCE and rapidly increase. This is highly dangerous, especially to patients who are already very
ill. The antibiotics in this case would be an example of a SELECTIVE PRESSURE. There exists a type of
bacteria called MRSA (methicillin-resistant Staphylococcus aureus) which are resistant to numerous
antibiotics and usually infect patients with compromised immune systems.
There is also the case of INSECTICIDE resistance, where many pests have grown resistant to them. This
is usually an argument for BIOLOGICAL CONTROLS being used instead of insectides.
68
WHAT ARE THE DIFFERENT TYPES OF SELECTION?
Observation
Deduction
In directional selection, one variant that has an
EXTREME FORM of the trait is selected over the
average and other extreme.
The black OR white variants of B. betularia are
selected due to their abilities to camouflage and
selective pressures in their environments.
Another example would be the GIRAFFE, which
selected for long necks instead of short or
average-length necks to feed from high trees.
In stabilizing selection, only the variant of
AVERAGE FORM is selected. Those considered
„extreme‟ for the trait are selected against.
In this case, ROBINS that lay eggs in fours are the
ones with the highest chance of survival. Too few
means less would survive and too many would
lead to OVERCOMPETITION..
Another example of this would be the Siberian
husky, which must have enough muscle to move
quickly but light enough to stay on top of snow.
In disruptive selection, both extremes of the trait
are selected over the one with average form.
In this case, male CHINOOK SALMON compete
to fertilize the females‟ eggs. Large fish will be
competitive fighters while smaller fish can
fertilize the eggs while evading fights. The
average-sized salmon is at the disadvantage here.
Another example is the HIMAYALAN RABBIT,
where both black and white rabbits can
camouflage easily against rocks, but grey ones
cannot.
69
5.4 & 5.5: Discuss the biological species concept and explain the process of speciation.
WHAT EXACTLY IS A SPECIES?
At O‟ Level, you would have learnt that two members of the same species:
-
Have very similar PHYSIOLOGICAL and GENETIC characteristics
Are able to INTERBREED and produce FERTILE offspring
This is known as the BIOLOGICAL SPECIES
CONCEPT and has been used to classify
organisms into different taxa quite successfully,
with each species being given their own
binomial name, e.g. Canis lupus, Ursus arctos,
Leo panthera and Homo sapiens.
There exists one major limitation with rigidly
sticking with this concept, however: It only
applies to organisms that reproduce
SEXUALLY. It also cannot be used to classify
organisms that are EXTINCT. By definition, it
also includes inbreeding, which reduces vigour.
This is where an alternate method exists called the PHYLOGENETIC SPECIES CONCEPT. In this
method, organisms are classified according to certain defining traits or MORPHOLOGY. This is used to
trace a „genetic history‟ of the organism, tracing back to its common ancestors.
One major limitation with this method, however, is dealing with species that demonstrate
POLYMORPHISM, or having many different forms that can be mistaken for different species. Both
white and dark variants of the peppered moth, for example, could easily be mistaken as two separate
species just by looking at them.
Feature
Biological Species Concept
Phylogenetic Species Concept
Inclusion of species Limited to species that reproduce
SEXUALLY.
Includes all species.
Organizational
Integrity
Rigorous and organized. Clear-cut
definitions of each species.
Error-prone method. Classifications based on
morphology and common inherited traits.
Extinct species
Cannot be used to classify extinct
species and fossils.
Can be used to classify extinct species and
fossils.
70
WHAT IS SPECIATION?
Speciation, put simply, is the formation of a new
species or when two or more species branch out
from a common ancestor. This usually occurs
due to a mechanism known as ISOLATION,
which sets up different kinds of barriers that
prevent members of a species from interacting.
These barriers can be geographical, behavioural
or even based on times of sexual maturity.
When isolation occurs, various groups of the
same species may be subjected to different
SELECTIVE PRESSURES and would have to
ADAPT to varying circumstances. After a while,
no GENE FLOW will occur between the
splintered populations and each population will
evolve into a new species.
Type of Barrier
Description
Example
GEOGRAPHICAL
Occurs when two species are
PHYSICALLY SEPARATED by a
large mass, such as an ocean or
mountain.
Darwin‟s finches were separated from each
other by living on different islands in the
Galapagos. Gene flow was not possible.
Leads to ALLOPATRIC speciation.
ECOLOGICAL
Occurs when two species live in the
same area but RARELY OR NEVER
MEET.
Red-legged frogs and American bullfrogs
live in the same ecosystem. However, redlegged frogs dwell in streams while bullfrogs
breed in ponds.
BEHAVIOURAL
Occurs when two species have
different COURTSHIP behaviours.
Eastern and western meadowlark birds have
different mating calls. Different species of
fireflies have different lighting signals.
MECHANICAL
Occurs when the two species are
incompatible, either in terms of size,
genitalia or GAMETES.
It is unlikely for white sage and black sage to
form hybrids in the wild as they are
pollinated by two different types of bees.
TEMPORAL
Occurs when two species live in the
same place but experience different
TIMES of sexual maturity.
Some cicadas tend to have 13-year cycles
while others have 17-year cycles. It is rare
that these sync up for them to mate.
71
ALLOPATRIC SPECIATION
Recall GEOGRAPHICAL isolation, where species will form splinter groups due to a separation by a land
mass, such as a mountain. The presence of this mountain means that the groups will not meet and thus,
will not mate. On either side of the mountain, there may be different selective pressures, such as different
coloured trees, terrain, predators, rainfall. Each member must now adapt to these pressures. This
geographical barrier will thus cause new species to arise.
This is called ALLOPATRIC SPECIATION. Examples include:
-
DARWIN‟S FINCHES being physically separated by the water masses between islands.
The PORKFISH and PANAMIC PORKFISH being separated by the isthmus of Panama.
The KAIBAB, a subspecies of the ABERT squirrel live on opposite ends of the Grand Canyon.
SYMPATRIC SPECIATION
Whereas allopatric speciation deals with speciation arising in two geographically separated areas,
SYMPATRIC SPECIATION occurs when there is no geographical separation. If organisms living in
the same habitat, for example, can somehow overcome their temporal, ecological or behavioural barriers,
they may undergo sympatric speciation.
Examples include:
A species of fruit fly in North America named R. pomonella
usually fed and laid their eggs on hawthorn berries. However,
after apples were introduced in the 1800‟s, some began laying
eggs in apples. These populations are becoming increasingly
distinct from each other and will one day undergo speciation.
Sometimes some wild wheat plants can randomly
double their chromosome number. These are
called POLYPLOIDS. These polyploids are
usually sterile but some can thrive and fertilize
each other.
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MODULE THREE – REPRODUCTIVE BIOLOGY
THIS MODULE CONTAINS TWO TOPICS:
1. REPRODUCTION IN PLANTS
2. REPRODUCTION IN ANIMALS
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TOPIC 1: REPRODUCTION IN PLANTS
1.1 & 2: Describe the structure of the anther and the formation of pollen grains; and the structure of the
ovule and formation of the embryo sac
REPRODUCTION IN FLOWERING PLANTS
Flowering plants are also called
ANGIOSPERMS. They contain reproductive
organs, which produce sex cells called
GAMETES, similar to animals. These gametes,
both male and female, are HAPLOID in nature,
meaning they contain half the number of
chromosomes.
Male gametes are formed within the POLLEN
grains, found in the ANTHERS, while female
gametes are found within EMBRYO SACS,
found inside of the OVULE.
Unlike sperm cells in animals, pollen
grains are not MOTILE and thus
require an external agent to transport
them. When these grains are deposited
on the STIGMA of a flower, this is
called POLLINATION. When the
male and female gamete fuse, this is
called FERTILIZATION, though this
requires a sequence of steps to occur.
The petals of a colour serve to attract
birds and insect, which may assist as
agents of pollination. The entire whorl
of petals is called the COROLLA.
The sepals serve to protect the flower
in the bud phase. The entire whorl of
sepals is known as the CALYX.
Reproductive Parts
Comprises of
Notes
STAMEN
(androecium)
Anther
Contain male gametes within pollen grains.
Filament
Supports the anther.
Stigma
Capturing pollen grains during pollination.
Style
Supports the stigma.
Ovary
Contains female gametes, found in embryo sacs in
ovules.
PISTIL
(gynoecium)
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THE MALE PARTS OF THE FLOWER
As previously stated, the male gametes are formed inside pollen grains. These pollen grains are formed
from MICROSPORANGIAL cells found within four pollen SACS in the ANTHER of the flower.
Observe the micrograph and table below for the placement and roles of the various structures within the
anther:
Key Structure
Function
Fibrous Layer
Thickened cellulose walls. Eventually separates to release pollen grains.
Tapetum
Inner layer of pollen sac that provides nutrition to developing grains.
Stomium
The point at which dehiscence occurs, to release the pollen grains.
Pollen mother cell
Diploid. Divide by meiosis to produce four haploid gamete nuclei.
Formation of pollen grains occur when a POLLEN MOTHER CELL undergoes MEIOSIS to form a
TETRAD of haploid cells called MICROSPORES. These then undergo MITOSIS to form two types of
nuclei within each, eventually maturing to form the protective walls of the pollen grain.
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The pollen grains contain two walls, an outer water proof
EXINE (containing a polymer called sporopollenin) and inner
INTINE (usually containing enzymes), and two haploid nuclei,
called the TUBE nucleus and GENERATIVE nucleus.
The generative nucleus would undergo MITOSIS to form TWO
MALE GAMETE NUCLEI. The tube nucleus will eventually
form the POLLEN TUBE, which would be used to deliver those
gametes to the female structure.
THE FEMALE PARTS OF THE FLOWER
The female gametes are formed inside embryo sacs. These are located within the ovules and are formed
from MEGASPORANGIAL cells. Observe the diagram and table below for the placement and roles of
the various structures within the ovule:
Structure
Role / Description
Funicle
Stalk-like connection point between ovule to ovary.
Integuments Develop into seed coat or testa.
Micropyle
Allows passage of pollen tube during fertilization.
Antipodal
cells
Nourishes the embryo sac and endosperm. Located at
chalaza, opposite to synergids.
Synergids
Directs pollen tube growth to egg cell.
Polar nuclei
Becomes the endosperm nucleus after fertilization.
FORMATION OF FEMALE GAMETE
The diploid MEGASPORE MOTHER CELL in the
ovule undergoes MEIOSIS to produce a TETRAD of
haploid megaspores. However, only one remains
functional. The others degenerate.
The functional megaspore continuously undergoes
MITOSIS and eventually forms the EMBRYO SAC
of eight haploid nuclei.
Six nuclei migrate to the poles of the
embryo sac to form the antipodals and
the synergids, one of them functioning
as the EGG there. Two polar nuclei
remain, which will fuse with a sperm
cell to form the ENDOSPERM nucleus.
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1.3 & 1.6: Explain the sequence of events from pollination to fertilization; and the significance of double
fertilization in the embryo sac.
HOW DOES POLLINATION OCCUR?
Pollination is the transfer of pollen from the anther to the
stigma. Flowers that exhibit AUTOGAMY are SELFPOLLINATED (within the same flower, or between two
flowers of the same plant) and flowers that exhibit
ALLOGAMY are CROSS-POLLINATED (between two
flowers of different plants).
CLEISTOGAMOUS flowers are non-opening and
promote self-fertilization, e.g. peas and pansies.
It was previously noted that pollen grains require agents
to move. Typically, flowers that have brightly coloured
petals, and pollen or nectar rich in nutrients, will attract
INSECTS. Some even produce sex hormones called
PHEROMONES, such as orchids.
Those that have relatively dull and small petals and no scent, but have long filaments that extend out of
the flower will likely be pollinated by WIND. These types produce vast amounts of light pollen grains
and have feathery stigmas for them to attach.
WHAT HAPPENS TO THE POLLEN GRAIN AFTERWARDS?
Recall that in the pollen grains in the anther, there were TWO nuclei. One was the GENERATIVE
nucleus and the other was the TUBE nucleus. The generative nucleus divides by mitosis into two haploid
male GAMETES, while the TUBE nucleus allows the growth of a structure called a POLLEN TUBE.
So what is happening here? If the pollen grain
is compatible with the stigma, it will begin to
germinate. The pollen tube uses SUCROSE
and develops as digestive enzymes are
secreted. This is called CHEMOTAXIS. This
allows the tube to grow in a downward fashion
along the STYLE and towards the ovule.
The two male gametes will follow the path of
the pollen tube as it enters the MICROPYLE
and to the synergids, where the EGG is located.
One gamete fuses with the egg, forming the
ZYGOTE. The other fuses with the primary
nucleus to form the ENDOSPERM
NUCLEUS. What is notable is the endosperm
nucleus now has three sets of chromosomes
(3n) and is now considered TRIPLOID.
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That might have been a lot to take in! So let‟s recap the various parts involved:
Structure
Chromosome No.
Notes
Generative nucleus
n
Divides by mitosis to form two male gametes (n)
Tube nucleus
n
Enables and regulates growth of pollen tube to carry gametes.
Primary nucleus
2n
Formed in embryo sac after two haploid nuclei fuse. In centre.
Egg cell
n
Found among synergids in embryo sac. The female gamete.
Zygote
2n
Formed after first male gamete fuses with egg.
Endosperm nucleus
3n
Formed after second male gamete fuses with primary nucleus.
1.4 & 1.5: Explain how cross-fertilization is promoted; and genetic consequences of sexual reproduction
ENSURING THAT CROSS-FERTILIZATION OCCURS
There are numerous reasons why some flowers or florists will want to allow self-pollination and selffertilization to occur (also called INBREEDING), as desirable traits can be predictably passed down
along generations and the flowers can be produced in very large numbers at a rapid rate. This happens
very easily with HERMAPHRODITIC plants, which mean they have both male and female parts.
However, it is highly advantageous to a plant species if
different members fertilize each other (called
OUTBREEDING).
-
It ensures DIVERSITY of the species, having a
variety of alleles among members.
This increases the chances of the plant having
RESISTANCE to factors such as pathogens and
allows EVOLUTION to occur.
As a result, plants have developed certain outbreeding mechanisms to help
them prevent the negative effects of self-fertilization and ensure diversity of
the species.
In the top diagram, the plant has a genotype ascribed S1S2. The pollen grains
containing either the S1 or S2 allele are incompatible with the stigma and will
not germinate on this flower. This is called SELF-INCOMPATIBILITY.
In the one to the left, notice that there are two different types of flowers (pin
and thrum). Primroses are like this. It is difficult for pin flowers to selfpollinate due to the stigmas being higher than the anthers.
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Outbreeding Mechanism
How it Works
Examples
Dioecious plants (Dioecy)
Male and female flowers of the same species are found
on separate plants, making self-pollination difficult.
Dioecious: Chenet, pawpaw, marijuana
In monoecious plants, male and female flowers are
located on the same plants.
Monoecious: Pumpkin,
maize, castor oil
Either stamens mature before the stigmas (protandry) or
stigmas are receptive to pollen before release (protogyny)
Protandry – Fireweed
Self-incompatibility
The pollen with the same genetic code as the stigma of
the same flower will not germinate if contact is made.
Tobacco, cabbage
Heterostyly
The various forms of the flowers‟ reproductive organs
make it difficult for self-pollination to occur due to
stigma and anther position. See previous page.
Primrose, red cordia
Protandry and protogyny
Protogyny – Soursop,
avocado
1.7: Discuss the development of the seed and the fruit from the embryo sac and its contents.
EMBRYONIC DEVELOPMENT IN SEED
From the diagram, the following steps can be observed:
1. The zygote begins dividing by mitosis. A smaller TERMINAL cell is formed, with the initial zygotic
cell being called the BASAL cell. Surrounding the zygote is the ENDOSPERM, which nourishes it
and allows development to occur.
2. As mitosis continues, the terminal cells
keep dividing until they form a „belt‟ called a
SUSPENSOR. At the end, the first terminal
cell keeps dividing in a globular manner to
form the EMBRYO.
\
3. Embryonic shoots and roots, and
cotyledons begin to develop and grow from
meristematic tissue. As these structures grow
and nutrients are continuously absorbed, the
endosperm tissue is depleted.
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After fertilization occurs, the embryo sac and the ovule begin to undergo numerous changes as the ovary
becomes a fruit and the ovules become seeds. The table below will list some of those changes:
Part of Flower
Post-Fertilization Structure
Egg cell
Becomes a ZYGOTE (2n) and then undergoes mitosis to become an EMBRYO.
When this occurs, multiple structures develop such as a root (RADICLE), embryo
shoot (PLUMULE) and first leaves (COTYLEDONS).
Ovule
Becomes a SEED, still attached to the parent plant.
Integuments
Becomes the seed coat or TESTA as it becomes thickened and waterproof with
lignin and cellulose.
Petals
Wither and fall off, along with the sepals. Exceptions include dandelions.
Endosperm nucleus
Becomes the ENDOSPERM after mitosis, which nourishes the embryo during
germination, usually high in proteins and starches.
Ovary and ovary wall
The ovary becomes the FRUIT and the wall becomes the PERICARP, the „flesh‟
of the fruit. The pericarp usually has some role to play in seed dispersal.
1.8: Discuss the advantages and disadvantages of asexual reproduction.
WHAT IS ASEXUAL REPRODUCTION?
Asexual reproduction is defined as the
production of new offspring by ONE parent
through the process of MITOSIS. The offspring
are genetically identical to their parents or
CLONES.
It is important to distinguish asexual
reproduction from self-pollination, as the latter
involves the production and fusion of gametes
from male and female parts and is thus
considered SEXUAL reproduction.
Aspect
Self-pollination
Asexual reproduction
Type of cell division
Meiosis
Mitosis
Crossing over
Present, but limited
None. Offspring are clones.
Seed production
Present
Absent
Method of reproduction
Fertilization or fusion of
gametes
Vegetative structures such as rhizomes
and tubers; processes such as budding
and fragmentation.
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WHAT ARE THE ADVANTAGES AND DISADVANTAGES OF ASEXUAL REPRODUCTION?
Advantages
Disadvantages
Offspring remain well-adapted to a non-changing
Due to lack of genetic variation, pathogens and
environment as all traits are inherited from parent
diseases may be able to spread very quickly through
organism.
populations.
Rapid growth of population can occur since only
Overcompetition may occur, either among offspring or
one parent is needed and no gestation period. New
between parent and offspring, especially in plants due
habitats can be colonized quickly.
to being in close proximity.
Offspring may be able to utilize parent as a nutrient
Very low genetic diversity can lead to lack of
source during the early stages of life.
evolutionary changes in species.
MECHANISMS OF ASEXUAL REPRODUCTION IN PLANTS
Mechanism
Explanation
Budding
The Bryophyllum plant shown
produces numerous adventitious
leaves, which can grow into new
plants when they fall off.
Fragmentation
The plant splits into fragments,
which can each develop into a
mature clone, identical to the
parent.
In ginger, a rhizome, meristematic
buds can grow into new ginger
plants when pieces are broken off.
Spore production and
binary fission
The fungus Penicillium develop
aerial hyphae. Mitosis occurs to
produce “conidiospores” at the tips
(called conidiophores). The spores
germinate and differentiate to form
new fungi. Red algae is another
example of this reproduction type.
Illustration
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METHODS OF VEGETATIVE PROPAGATION
Vegetative propagation is the process of producing plant offspring on a large scale, taking advantage of
the facets of asexual reproduction. This is usually done for commercial purposes and can be done with the
use of cuttings and tissue culture.
Cuttings
Cuttings are usually done for crops such as sugar
cane. Stems are broken off and lain horizontally
on soil. After a period of time, buds grow into
new stems and adventitious roots grow from the
leaf scars. It happens quickly as no
POLLINATING AGENT is needed, so the crop
is quite profitable.
For other plants (African violets, for example),
the cutting is made on the stem and is plced in a
medium containing a growth hormone such as
AUXIN, which stimulates root growth. The
plant can then be transferred to soil.
Tissue culture
Tissue culture is more frequently used in large scale production and can be done in a laboratory at any
location. Plant tissue is differentiated from animal tissue in that they are able to produce other cell types
(similar to stem cells). Because plant tissue can do this, they are said to exhibit TOTIPOTENCY.
A meristematic clump of cells called an EXPLANT is removed from the parent and placed in a STERILE
nutrient solution (usually high in sucrose, Vitamin B, nitrates and mineral ions) containing AUXIN and
CYTOKININ, hormones that stimulate cell growth and division. Sterility is key to prevent infection by
pathogens and fungi. The explants then undergo mitosis to form larger clumps called CALLUSES. When
the plant is at a certain point of development, they are transplanted into sterile soil.
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TOPIC 2: REPRODUCTION IN ANIMALS
2.1&2: Describe the structure & function of the male & female reproductive systems; and gametogenesis
STAGES OF HUMAN REPRODUCTION
Stage
Description
Gametogenesis
The production of male (spermatogenesis) and female (oogenesis) gametes.
Ovulation
The release of a secondary oocyte (not ovum) from the ovary.
Copulation / Coitus
The act of intercourse, where male gametes are delivered to the female gametes.
Fertilization
The fusion of the nuclei of the male and female gametes.
Implantation
The action of the early embryo sinking into the endometrium.
Gestation
The period between conception and birth, where foetal development occurs.
Parturition
The final stages of pregnancy, involving labour and childbirth.
THE MALE REPRODUCTIVE SYSTEM
The urogenital system of the male is
depicted here, which combines the urinary
and reproductive systems. The production of
sperm begins in the TESTES, where diploid
cells form haploid cells by MEIOSIS.
Within the testes are SEMINIFEROUS
TUBULES, where spermatogenesis occurs
within the walls, from the epithelium.
A hormone, TESTOSTERONE, is secreted
by the LEYDIG cells in the testes to
stimulate sperm production.
The prostate gland, seminal vesicles and Cowper‟s glands are all involved with SEMEN production. The
scrotum is kept external to the body as sperm production is optimum at a slightly COOLER temperature.
Remember that semen and sperm are two different things. The semen is simply the nourishing and transport
medium for the spermatozoa. A man has the ability to ejaculate semen which contains no spermatozoa, in which
he is said to be infertile.
The male urethra is notable as being much longer than the female urethra, making urinary tract infections less
likely for men. The female urethra is separate from the female reproductive tract.
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SPERMATOGENESIS (Formation of Sperm Cells)
Recall that for gametes to be produced, diploid cells must divide by meiosis to produce haploid cells. So
where does this occur?
Our focus will be on the diagram to the right, within the the lumens of the seminiferous tubules within the
lobules of the testes. These are usually convoluted structures, where spermatogenesis take place. Special
large cells called SERTOLI cells help “nurse” or nourish the cells and regulate the process.
Spermatogenesis begins at a layer of cells called SPERMATOGONIA placed along the outer wall (called
the germinal epithelium). These divide by mitosis and grow into larger structures called PRIMARY
SPERMATOCYTES.
The diploid primary spermatocytes divide by MEIOSIS to now to first become haploid SECONDARY
SPERMATOCYTES and then into SPERMATIDS. Spermatids will then grow a tail-like structure as they
specialize to become SPERMATOZOA, the male gametes.
The micrograph to the right is of a TS of a
seminiferous tubule. State which parts the
numbers represent.
1 – Spermatozoa
2 – Spermatid
3 – Primary spermatocyte
4 – Spermatogonia
5 – Sertoli cell
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THE FEMALE REPRODUCTIVE SYSTEM
There are a few idiosyncrasies when it comes to the production of female gametes (oogenesis). You may
have learnt at O‟ Level that the egg cells (or ova) are released from the ovaries during ovulation. This is
not entirely true as the actual structure that is released is a precursor to the ovum, called a SECONDARY
OOCYTE.
When ovulation occurs, the oocyte is pushed
along the Fallopian tubes by cilia. If
fertilization occurs, then the zygote will be
implanted on the ENDOMETRIUM, where
it will grow structures to exchange materials
with the mother during pregnancy, or
GESTATION.
During PARTURITION or childbirth,
contractions occur along the
MYOMETRIUM, which help push the
foetus through the cervix and the vagina.
OOGENESIS
In order to understand what is happening during oogenesis, we should look at a cross-section of the ovary.
There are notable similarities and differences when compared to spermatogenesis. For example, haploid
cells are produced during meiosis and the process begins along germinal epithelial cells in the ovaries.
However, this begins when the girl is an embryo instead of at puberty, like a boy.
A layer of cells called OOGONIA begin to divide by
meiosis to form a large number of PRIMARY
OOCYTES. Remember this happens before birth.
The process suddenly stops at PROPHASE I and only
continues at puberty, where two haploid cells are
produced. One is a POLAR BODY, which degenerates.
The second, much larger, is a SECONDARY OOCYTE.
Meiosis continues but stops again at METAPHASE II.
The process resumes after the secondary oocyte is
released during ovulation and fertilized. It will finish the
meiotic division to form the OVUM and another polar
body, which degenerates as well.
Therefore, strangely enough, the ovum actually forms in
the Fallopian tube AFTER fertilization.
Structures called FOLLICLES are formed within the
ovary, which gradually mature. When ovulation occurs,
the follicle ruptures leaving behind a CORPUS
LUTEUM, which secretes PROGESTERONE, allowing
the endometrium to thicken.
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2.3: Discuss how the structure of the ovum and the sperm facilitate their functional roles in fertilization.
First, let‟s recap some facts and comparisons about spermatogenesis and oogenesis.
Aspect
Spermatogenesis
Oogenesis
Occurs where?
Seminiferous tubules in testes
Mostly in ovaries
Forms what?
4 spermatozoa.
1 secondary oocyte and 2-3 much smaller polar
bodies.
Timeline
Starts at puberty and continues into old
Starts when female is a foetus, then stops.
age. Uninterrupted until death.
Resumes at puberty and an egg is released
monthly. Terminates at menopause.
Production rate
About 200 million sperm daily, fully
Releases one secondary oocyte every menstrual
matured.
cycle.
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GAMETE STRUCTURE
The role of spermatozoa is to transport the male genetic
material to the female gamete. The two gametes will
eventually fuse to become the zygote. It is notable that the
only part that enters the female gamete‟s cytoplasm is the
NUCLEUS.
The head contains an ACROSOME, loaded with hydrolytic
ENZYMES which is used to digest a path into the female
gamete during fertilization.
The neck of the sperm cell has CENTRIOLES that help
form the FLAGELLUM, which is comprised of several
MICROTUBULES (the central strand called the
AXONEME), which allow the sperm to be motile and to
swim to the female gamete. Sperm cells are only about 3µm
wide but more than 50µm long.
This uses ATP, which is supplied by the MITOCHONDRIA
in the middle piece of the sperm. It is notable that sperm
have NO FOOD RESERVES.
The secondary oocyte is significantly larger than the
spermatozoa, being about 100µm in diameter. This serves to
make them non-motile and allows slow passage through the
oviduct after ovulation.
Their NUCLEUS contains half of the maternal DNA, while the
POLAR BODY, still attached, contains the other half. The
polar body will degenerate after fertilization, however, and
itself cannot be fertilized.
The cytoplasm of the oocyte has a food source in the form of
LIPIDS to allow survival before implantation. Mitochondria are
also present to facilitate development of gamete.
The plasma membrane of the egg cell is also different as it is
folded into MICROVILLI, which may help with adhesion to
incoming sperm. It contains a ZONA PELLUCIDA, consisting
of glycoproteins, and a CORONA RADIATA, consisting of
granulosa (follicle) cells which the sperm must penetrate.
In the ovarian follicle, surrouding the oocyte, is an fluid-filled
ANTRUM, which provides nourishment. Directly outside of
the zona granulosa are THECA cells, which stimulate synthesis
of oestrogen.
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Some key comparisons between the two gametes:
Aspect
Spermatozoa
Secondary oocyte
Size
Head is about 3µm wide and tail is 50µm
About 100µm in diameter. Much larger.
long. Much smaller.
Motion
Motile, due to flagellum.
Non-motile.
Nucleus
Haploid. Can contain either X or Y sex
Haploid. Only contains X chromosomes.
chromosomes.
Food source
Very limited.
Considerably more. Has lipids in cytoplasm.
Membranes
Plasma membrane around head with
Has multiple layers: a plasma membrane with
glycoproteins that support union with
microvilli, glycoprotein-rich zona pellucida and
oocyte.
corona radiata.
Already completed meiosis II upon
Only completes meiosis II after fertilization to become
release.
ovum.
Meiotic stage
2.4: Discuss the basic process of fertilization.
FERTILIZATION
The basic definition of fertilization is the fusion of the nuclei of both male and female gametes.
Fertilization takes place in the OVIDUCT. Sperm are ejaculated during coitus, caused by the stimulation
of nerves along the vasa deferentia and muscular contractions push sperm out of the urethra. The sperm
use semen as a medium, a fluid containing CALCIUM ions, CITRATE and FRUCTOSE.
Over time, uterine enzymes HYDROLYSE the plasma
membranes of the sperm cells, as well as removing cholesterol.
This puts the sperm into a state of CAPACITATION, allowing
them to swim faster and prepares the ACROSOME for eventual
penetration of the oocyte.
Upon contact with the oocyte, the ZONA PELLUCIDA
stimulates the release of enzymes from the acrosome. As soon as
this occurs, lysosomes in the oocyte change its protein structure
so that it becomes an impermeable FERTILIZATION
MEMBRANE. This is called the CORTICAL REACTION.
MEIOSIS finally completes and the polar body helps discard the
other set of chromatids. The male and female gamete nuclei fuse
to form a diploid zygote.
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2.5, 2.8 & 2.9: Discuss the process of implantation; the structure & functions of the placenta and amnion.
IMPLANTATION
When the zygote forms, it continuously divides by MITOSIS to form a ball of cells known as a
BLASTOCYST. The blastocyst moves along the Fallopian tube due to contractions along its muscular
wall and with help from cilia. It will finally reach the uterus, where it will attach itself to the lining of the
uterus wall, or ENDOMETRIUM. It is now said to have been implanted.
Specialized cells lining the surface of the blastocyst called
TROPHOBLASTS allow this to occur. They secrete
enzymes to digest a „nook‟ into the endometrium, similar to
what the pollen tube or acrosome do, but the blastocyst does
not burrow far under.
The trophoblast cells undergo mitosis and specialize to form
CHORIONIC VILLI, which project into the endometrium,
and blood-filled INTERVILLOUS SPACES. At this point,
the structure contains tissues from both the mother and the
blastocyst. It is now called the PLACENTA.
As the embryo develops into a FOETUS, other extraembryonic membranes form and fuse to the chorion, such as
the AMNION, YOLK SAC and ALLANTOIS.
Placental function
Notes
Gas exchange
Villi in the CHORION help
oxygen flow from the
maternal blood to the foetal
blood at the
INTERVILLOUS SPACES.
Nutrient and
antibody intake
CHORION facilitates
diffusion of glucose and
amino acids. Active transport
of ions. Nutrients stored in
YOLK SAC.
Waste transfer
Allantois helps remove
excreta from kidneys.
Blood pressure
regulation
Reduces maternal blood
pressure to avoid
jeopardizing foetus.
NOTE: It is notable that the umbilical veins
are oxygenated and umbilical arteries are
deoxygenated.
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AMNION AND PROTECTION
The amnion is a fluid-filled membrane that encloses the
embryo and acts as a SHOCK ABSORBER, meaning that it
protects it from physical damage.
It also helps with regulation of the foetus‟ TEMPERATURE,
due to water‟s high specific heat capacity. Similar to the
placenta, it plays roles, though to a smaller extent, in nutrient
intake and waste transfer. Since the foetus can swim in the
fluid, it allows skeletal development to occur.
Amniotic fluid can also be located inside the foetus, allowing
movement of nutrients along the alimentary canal. It should be
noted that the placenta also plays a role as a partially permeable
barrier, preventing intermingling of foetal and maternal blood
and even offering some protection against MATERNAL HIV.
2.6: Discuss the importance of hormones in gametogenesis and the menstrual cycle.
Before we discuss the intricate systems that these hormones belong to, let‟s summarize them:
Hormone
Source
Role
GnRH
Hypothalamus
Stimulates release of LH and FSH.
FSH
Pituitary
Stimulates growth of eggs; regulates sperm production.
LH
Pituitary
Stimulates ovulation; release of gonadal hormones (e.g. oestrogen)
Oestrogen
Gonads
Stimulates LH production; secondary sex characteristics
Progesterone
Gonads
Maintains lining of uterus for implantation; produced by corpus luteum
Testosterone
Gonads
Stimulates sperm production; secondary sex characteristics
Inhibin
Testes
Inhibits the release of GnRH, thus also inhibiting release of FSH and LH.
hCG
Blastocyst
Stimulates continuous progesterone production; recognition of pregnancy
Prolactin
Pituitary
Lactation (production of breast milk)
hPL
Placenta
Lipolysis to provide nutrients for foetus. May result in gestational diabetes
DMPA and Progestin
Synthetic
Prevents ovulation or thickens cervical mucus. Used for birth control.
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HORMONAL CONTROL OF GAMETOGENESIS
Spermatogenesis
Gonadotropin-releasing hormone (or GnRH) stimulates
production of two other hormones, LH and FSH. LH
binds to receptors on the LEYDIG cells in the TESTES
to secrete TESTOSTERONE and begin
spermatogenesis. FSH binds to the SERTOLI cells,
making them more receptive to testosterone.
There is a NEGATIVE FEEDBACK system involved
to regulate testosterone concentration in the blood.
Sertoli cells also release another hormone known as
INHIBIN that inhibits release of FSH.
Oogenesis
This means that less FSH and LH are produced as a
result, thus preventing testosterone levels from rising
too high.
The steps involved in oogenesis are, in some ways,
similar to spermatogenesis. GnRH is still involved,
stimulating the release of LH and FSH. As LH and
FSH levels rise, a layer of cells surrounding an ovarian
follicle known as a THECA secretes OESTROGEN.
Oestrogen acts similar to inhibin in its capacity as a
negative feedback mechanism, in that it inhibits release
of GnRH, LH and FSH.
However, it also plays a role in
POSITIVE FEEDBACK, as very
high levels cause a surge in LH. This
allows the mature Graafian follicle to
rupture and release the
SECONDARY OOCYTE into the
oviduct. This is OVULATION.
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HORMONAL CONTROL OF MENSTRUATION
NOTE ON PREGNANCY
: Keep in mind that a large
amount of progesterone is
being secreted by the corpus
luteum. When the corpus
luteum decays, the levels
severely drop, resulting in
menses.
If a woman becomes pregnant,
the progesterone levels
REMAIN HIGH. This is due to
another hormone called
HUMAN CHORIONIC
GONADOTROPIN (or hCG)
being released from the
blastocyst.
hCG ensures that menses does
not take place while the embryo
is being implanted. It is notable
as the hormone tested for in a
PREGNANCY TEST.
Observe the diagram above, as it correlates hormonal activity to the development of the follicle and
changes in the uterus during the menstrual cycle. Here, we will break it down the timeline:

Day 6 – 14 – FOLLICULAR PHASE – The presence of FSH and LH triggers the release of
OESTROGEN from the ovarian THECA. As oestrogen levels rise, this causes a positive feedback
effect and a surge in LH. Oestrogen levels plummet as GnRH is inhibited.

Day 14 – This surge in LH triggers OVULATION, causing the follicle to rupture and secondary
oocyte to release. The ruptured follicle becomes a CORPUS LUTEUM.

Day 14 – 28 – LUTEAL PHASE – The corpus luteum secretes PROGESTERONE to keep the
uterus lining thick for implantation. If pregnancy does not occur, the corpus luteum decays into a
scar called a CORPUS ALBICANS. Oestrogen and progesterone levels decrease.

Day 0 – 6 – MENSES then occurs as the uterus lining sheds. The drop in the gonadal hormones
causes a slight increase in FSH and LH, restarting the cycle.
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2.7: Discuss how knowledge of human reproductive anatomy and physiology has been applied to the
development of contraceptive methods;.
WHAT IS BIRTH CONTROL?
Birth control, you would have learnt, involves methods of preventing pregnancy from occurring. We can
class birth control into two categories:


CONTRACEPTION - which prevents fertilization of the egg.
ANTI-IMPLANTATION - where fertilization occurs but the blastocyst cannot be implanted on
the endometrium.
Contraceptive Method
How it works
Extra notes
Barriers (e.g. condoms,
femidoms and diaphragms)
They create an impermeable physical
barrier that prevents sperm cells from
entering the vagina or uterus. As a
result, no contact can be made with
the egg.
Most popular method, though some
say they reduce pleasure. Also
prevents transmission of STI‟s. More
effective when used with a
SPERMICIDAL CREAM.
Progestin implants
A rod-shaped device is implanted in
the uterus. It releases synthetic
progestin into the blood, which
inhibits ovulation.
Does not protect against STI‟s.
Works similarly to birth control pills.
Depo-Provera (DMPA)
A synthetic hormone that is injected
into the body every 3 months. Acts
similar to the implants.
Also used to treat menopausal
symptoms.
Oral contraceptives (birth
control pills)
Usually contain synthentic oestrogen
and progesterone to mimic pregnancy
and suppressing ovulation.
The “mini-pill” thickens cervical
mucus, preventing the sperm from
entering.
Sterilization
The vasa deferentia of the men are cut Is 100% effective, so patients must
and tied, preventing sperm from
be certain they want no more
entering the urethra. Or the oviducts
children.
are cut and tied (tubal ligation).
Filshie clips
A device that is clipped across each
oviduct during tubal ligation.
Reversal of ligation more likely to be
successful when this is implemented.
But there are infectious risks if the
clip opens or migrates.
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Anti-Implantation Method
How it works
Extra notes
Emergency contraception or
the “morning after” pill
Various types exist. The mechanism
of action usually involves delaying
ovulation or causing changes in the
endometrium that limit implantation.
Despite its name, many of them can
be taken from 3 – 5 days after and
certainly just in the morning.
However, success increases when it
is taken closer to period of coitus.
Intra-uterine devices (or
IUD‟s)
A T-shaped device made of copper
and plastic that is inserted into the
uterus by a physician. It stimulates
immune responses in the uterus to
attack the sperm or embryo.
Copper is toxic to the sperm as well,
so it can be seen as a contraceptive
method as well.
There are usually ethical debates about birth control. The table below summarizes some of the arguments
that are pro and con:
For
Against
It is an effective way to reducing population
Anti-implantation methods can be seen as a „legalized‟
growth, especially in overcrowded countries that
method of abortion, for those who are pro-life.
lack resources.
Can be seen as a way to reduce the need for clinical
May be seen as a stimulus for pre-marital sex and
abortions and unwanted pregnancies, which could
promiscuity, especially in teenagers and young adults, due
lead to child neglect and depriving young parents of
to the easy availability of condoms.
future opportunities.
Allows either partner to maintain control of their
Some methods may have physiological risks such as birth
bodies if the other wishes not to use birth control,
control pills, or may cause infection if not done correctly,
especially during pre-marital sex.
such as Filshie clips.
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2.10: Discuss the possible effects of maternal behaviour on foetal development.
PRE-NATAL CARE
Pre-natal or post-conceptual care refers to the behaviours or routines that a mother should adopt to
reduce the incidence of ill health or hindrance to development of the foetus. Before pregnancy, however,
the mother should ensure that she has the RUBELLA vaccine, as rubella can be fatal for the foetus. The
table below will summarize the main points of pre-natal care:
Category
Crucial Components/Concerns
Notes
Diet and Nutrition
Folic acid (cereals, dairy, cabbage,
Helps develop the neural tube of
kale, spinach, bananas)
foetus. Without it, the foetus can
suffer from SPINA BIFIDA.
Lipids (dairy, oily fish)
Formation of nerve cells and cell
membranes. Energy source.
Iron (beans, meat, eggs)
Formation of haemoglobin.
Calcium, phosphorous (dairy, bony
Formation of bones.
fish)
Avoiding alcohol
Avoiding foods that are precooked or
May contain Listeria bacteria, which
unpasteurized milk
infect foetus.
Reduced growth and development
Undeveloped limbs, reduced muscle
tone, heart defects
Rhesus factor
Cleft palate
A split in the mouth‟s roof.
Foetal alcohol syndrome (FAS)
Lifelong mental impairment.
If the mother is Rh-negative then she
Without the anti-Rh antibodies, the
should be injected with anti-Rh
mother‟s own antibodies will attack
antibodies if she has a Rh-positive
the Rh-positive foetus.
foetus.
Smoking, one of the worst offenders of foetal malformation, will be discussed in the next page.
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THE EFFECT OF SMOKING ON PREGNANCY
Keep in mind that whatever the mother takes into her bloodstream will transfer to the foetal bloodstream
via the chorion and umbilical cord connected to the placenta. Tobacco cigarettes contain a massive
number of chemicals that have detrimental effects to the human body. So we‟ll look at the impact of three
of the main components: nicotine, carbon monoxide and tar.
Component
Nicotine
Effect on Human Body
-
Is a STIMULANT and so increases BLOOD PRESSURE.
Causes the foetus‟ blood vessels to CONSTRICT, thus reducing the
flow of OXYGEN to the tissues.
Baby can be born with an ADDICTION and experience harmful
WITHDRAWAL symptoms shortly after birth.
Carbon monoxide (CO)
-
Binds to HAEMOGLOBIN to form CARBOXYHAEMOGLOBIN.
Limits the binding of OXYGEN in mother‟s bloodstream, so less is
transferred to foetus, hindering development.
Tar
-
Lines the alveolar membrane, limiting GASEOUS EXCHANGE of
oxygen and carbon dioxide in the mother‟s lungs, so less oxygen is
transferred to foetus.
Destroys CILIA and mucus membranes, so increases prevalence of
respiratory infections in mother.
-
PRE-NATAL MONITORING PROGRAMS
In pregnancy, it is recommended that a healthcare provider check the health of the foetus. This is done by
checking the baby‟s heart rate and other functions. The details may vary, but typical electronic fetal
monitoring may go like this:

EXTERNAL - The provider puts a device called an ULTRASOUND PROBE on the
mother‟s belly. This device sends the foetal heartbeat to a recorder. The foetal heart rate is
displayed on a screen.

INTERNAL – This is usually done if the amnion has already ruptured and labour has begun. The
provider puts a small wire called a SCALP ELECTRODE through the cervix and attaches to the
baby‟s scalp. The electrode is attached to a wire. The wire sends information about the foetal
heartbeat to a computer.
END OF UNIT ONE 