AS Biology (9700) Notes

1.
1 The microscope in cell studies
• Magnification is the number of times the image is seen larger compared to the actual size of the object
• Resolution is the ability to distinguish between two separate points. It determines the degree of details
which can be seen by the microscope
• The smaller and closer together the objects that can be distinguished, the higher the resolution
• Magnification vs resolution:
• While higher magnification allows you to see larger details, it doesn't necessarily improve
resolution.
• Improved resolution provides clearer and sharper images, revealing finer details.
• Two types of microscopes:
1. Light Microscope
• Magnification of light microscope: 1500x
• The maximum resolution: 0.2 μm or 200 nm
▪ That means if the distance between two points is smaller than 0.2 μm, the two
points can be seen fused together as one point
2. Electron Microscope
• Used to see structures less than 0.2 μm
• Magnification of electron microscope: 250 000x
• The maximum resolution that can be achieved is 0.5 nm
▪ The limit of the resolution is about one half the wavelength of the radiation used to
view the specimen
□ therefore electron microscopes have a higher resolution because the electron
beam has less wavelength than the visible light
▪ Changing wavelength affects resolution but not magnification
• Very suitable because:
▪ Beam of electrons have short wavelength
▪ They're negatively charged, so easily focused by electromagnets
Light microscope Electron microscope

Light beam is used Electron beam is used
Not affected by magnetic field Affected by magnetic field
Easy to prepare specimen Expert needed to prepare the specimen
Specimen dead or living Specimen dead
Small, portable Large, nonportable
Lower resolution Higher resolution
Colored image Black and white
cheaper Expensive
200 nm 0.5 nm
No stains needed Specimens have to be stained by metal dyes
1 decimeter (dm) = 10 centimeter (cm)

1 centimeter (cm) = 10 millimeter (mm)
1 millimeter (mm) = 1000 micrometers (μm)
1 micrometer (μm) = 1000 nanometer (nm)
1 dm3 = 1000 cm3
1 Cell Structure Page 1

1.1 The microscope in cell studies (cont.)
• Two types of electron microscope
1. TEM: transmission electron microscope
▪ A beam of electrons are passed through the specimen and is dispersed by the
specimen. The transmitted electrons are then captured on a photographic plate.
▪ HIGHER RESOLUTION
▪ 2D images (cannot see surface contours)
2. SEM: Scanning electron microscope
▪ Specimen is coated in a thin layer of metal. The beam of electrons is reflected off
the surface onto a photographic plate. 3D images area formed.
▪ LOWER RESOLUTION
• Eyepiece graticule
○ 100 divisions
○ Placed in the eyepiece lens unit
○ You can look at the sample to determine its diameter in graticule units
• Stage micrometer
○ Each (five lines) division is equal to 0.1 mm
○ It's used to calibrate the eyepiece graticule

1.2 Cells as the basic units of living organisms
• An organelle is a subcellular structure that performs specific functions within a cell
○ Each organelle is separated from the surrounding cytoplasm
• Protoplasm = cytoplasm + organelles
• Main organelles:
1. Nucleus (10 μm)
i. It is the largest organelle and spherical in shape
ii. During cellular division, the nucleus is the first to divide
iii. It makes ribosomes using information from its own DNA
iv. Surrounded by a nuclear envelope which is formed of a double membrane, contains nuclear pores
v. Contains nucleoplasm formed from ions, proteins, and nucleotides (building units of RNA and DNA )
vi. Contains concentrated part called nucleolus which is a dense form of pure DNA and protein
1) Nucleolus is deeply staining
vii. Contains chromosomes which contain chromatin
□ Chromatin: DNA coils around "Histone" proteins then it is condensed inside chromosomes
viii. Function
1) Controls the cell functions (it contains genetic material)
2) Controls cell division (meiosis and mitosis)
3) Surrounded by a nuclear envelope that contains nuclear pores to allow exchange of substances
between nucleus and cytoplasm
4) Contains nucleolus for formation of ribosomes
a) It is a dense form of pure DNA and protein
5) Its nuclear envelope may contains ribosomes for protein synthesis
ix. Its outer membrane joins up to the endoplasmic reticulum
1) If it has ribosomes on the outside it connects to rough ER
2) If it doesn’t have ribosomes it will be attached to smooth ER
2. Endoplasmic reticulum (ER)

i. Formed from membranes that form long sacs called cisternae
ii. Has a role in the formation of the Golgi apparatus
1) Two types:
a) Rough ER: polypeptide (protein synthesis), isolate and transport the synthesized in its
cisternae (found everywhere and covered with ribosomes)
i) The ribosomes are 25 nm in diameter and there are two subunits (large and small)
ii) Build up the proteins
iii) Made of RNA and proteins
 Proteins made by ribosomes on the ER enter and travel through it, and are
modified and then small vesicles break off and join with the Golgi apparatus
b) Smooth ER: synthesis of lipids, steroids (cholesterol), reproductive hormones
i) More commonly found in the gonads (ovaries and testes)
3. Golgi Apparatus (Larger complex in animal cells)

▪ Made of cisternae with vesicles budded off of it (vesicles from ER fuse together)
▪ Constantly receives proteins in vesicles from the ER
▪ Goblet cells contain large numbers of Golgi apparatus
▪ Function:
1) Modifies proteins coming from ER for transport to other parts of the cells or to the cell surface
membrane
2) Used to form lysosome
3) Formation of lipoprotein by adding lipids to proteins
4) Formation of polysaccharides for formation of plant wall
5) It modifies proteins by addition of sugars (glycoproteins) that which take part in formation of cell
membranes and formation of mucus

1.2 Cells as the basic units of living organisms (cont.)
4. Lysosome: (rare in plants because vacuole contains hydrolytic enzymes)
○ Spherical sacs surrounded by a single membrane (0.1-0.5 μm)
▪ Sac contains hydrolytic enzymes (proteases/lysozymes/...)
○ Functions:
▪ Digestion of particles taken by a cell
▪ Autophagy which is the breakdown of unwanted structures or organelles
□ Breakdown of cells/bacteria taken up by WBCs
□ Breakdown of old organelles
□ Enzymes can be released outside the cell (eg. replacement of cartilage with bone during
development or when a cell dies)
5. Mitochondria (1 - 2.5 μm)

○ It has two membranes
▪ Inner membrane is called cristae
□ Contains circular DNA
▪ Interior solution is called matrix
○ Muscles have more mitochondria
○ Release of energy by aerobic respiration, they produce ATP (adenosine triphosphate)
○ ATP is used as the universal energy currency. Releases energy when hydrolyzed
○ Involved in the synthesis of lipids
○ ATP + H2O ⇌ ADP + Phosphate group + energy
○ Mitochondria replicate themselves independently of cell division
○ Adaptation
▪ Contains ribosomes for the synthesis of its proteins
▪ Inner membrane is folded to increase surface area for action of enzymes
▪ Outer membrane contains porin (transport protein) which forms aqueous channels allowing easy access
of small water soluble molecules from the surrounding cytoplasm into the intermembrane space. The
inner membrane is a more selective barrier (because it has smaller gaps between membrane molecules)
and controls what enters the matrix
6. Ribosomes (20-22 nm)

○ Made in the nucleolus
○ Smallest organelle
○ Amino acids are linked together in the ribosomes
○ Made up of rRNA and proteins
▪ last organelle to be sedimented in a centrifuge
□ Size is measured in S units (S = Sedimentation or Svedberg units)
□ The greater the s number the greater the rate of sedimentation
□ These ribosomes are 80S in the cytoplasm
 20-22 nm in cytoplasm of eukaryotic cells, rough ER, sometimes on the nuclear envelope
□ 70S in chloroplasts and mitochondria
 18 nm found in prokaryotic cells, mitochondria, and chloroplast
○ Formed from two subunits, large and small
○ Found on:
1. rough ER
2. nuclear envelope
3. free in cytoplasm
4. in mitochondria and chloroplast
○ Function: Protein synthesis (eg. Enzymes, hormones)

9. Microvilli (50 to 550 nm)

• Micro-villi are extensions of the cell surface membrane that increases the surface area of the cell
membrane
• Useful for absorption in the gut
8. Cilia
• Small hairlike structures on the surface of the cell that moves back and forth for filtration in the
trachea
9. Centrioles (only in animal cells)

• They lie in a region called centrosome that is used as a starting point for growing the spindle for nuclear
division
• Two centrioles found just outside of the nucleus at right angles to each other
• Each centriole is a hollow cylinder formed from a ring of microtubules (9 triplets)
• Made of the protein tubulin that can be assembled by polymerization of subunits in MTOCS (microtubule
organizing centers)
• Plays an important role in cell division
○ The microtubules are long hollow tubes that make up the cytoskeleton of the cell
• Functions:
1. Support the cell
2. move cell components
3. mitotic spindle fiber
4. allowing movement of cilia in a bronchus
10. Chloroplast (only found in plant cells) (3-10 μm)
• Contains photosynthesis pigments

• Inside: Contains thylakoid membranes that stack up to form structures called grana
• Chloroplasts replicate themselves independently of cell division
• Function: site of photosynthesis
• Adaptations:
○ contains ribosomes for synthesis of proteins
○ thylakoid membranes contain photosynthesis pigments
• During photosynthesis ATP is formed due to conversion of light energy into chemical energy
• Both the membranes and the chloroplast can change their orientation within the cell to receive the
maximum amount of light (it is mobile)
Unique structures of a plant cell:
11. Cellulose cell wall

a. Plasmodesmata: strands that connects cytoplasm of neighboring cells for exchange of materials
b. Can be reinforced with lignin
12. Large central vacuole
a. Contain water and solutions of mineral salts, sugars, oxygen and enzymes
b. Maintain cell turgidity (regulate turgor pressure)
c. Contains cell sap
d. Tonoplast is the membrane surrounding the vacuole
• Plant cell VS Animal Cell:

○ Animal cells have a centrosome and lysosomes while plants don't
○ Plant cells have a cellulose cell wall, large central vacuole, and chloroplast while animals do
not.

13. Cell surface membrane (present in ALL living cells) (7 nm)

• Selective barrier between the cell contents and the external environment
• Consists of phospholipid bilayers
• Too thin to be seen under a light microscope
• Fluid mosaic model is used for membrane structure
○ Phospholipid bilayer
○ Fatty acid core
○ Carrier proteins
○ Hydrophilic phosphate head, hydrophobic fatty acid tails
14. Cytoplasm
• Space between cell surface membrane and the nucleus
• Aqueous nature (fluid to jelly like consistency)

• Prokaryotic Cells (Typical Bacterium) (1 - 5 μm):

○ Unicellular organisms with no membrane bound nucleus
○ Circular DNA
○ 70S ribosomes
○ absence of organelles surrounded by double membranes
○ Peptidoglycan cell walls (murein)
▪ protects the cell from bursting due to turgor pressure and maintains cell shape
• Prokaryotic Cell VS Eukaryotic Cells:

○ Eukaryotes are organisms whose cells have a nucleus and membrane bound organelles
○ Eukaryotic cells are large (around 40 μm) and complex
▪ Although, there are unicellular eukaryotes (protistans)
○ Prokaryotes do not have a membrane bound nucleus
○ Eukaryote DNA is double stranded and linear, While prokaryotic DNA is double stranded and circular.
Prokaryotic Cell Eukaryotic Cell

size 1-5 μm Up to 40 μm
DNA Circular, free in cytoplasm, naked Linear, in nucleus and associated with proteins
Ribosomes Smaller 70s Larger 80s
Organelles No ER, few organelles, none with 2 membranes ER present, some organelles surrounded by membranes
Cell wall Peptidoglycan (murein) Sometimes present (plants and fungi)
• All cells, whether prokaryotic or eukaryotic, share these four features:

1. DNA
2. Plasma membrane
3. Cytoplasm
4. Ribosomes
• Viruses:
○ All viruses are non-cellular structures with a nucleic acid core (either DNA or RNA) and a protective protein
coat (capsid)
▪ some viruses have an outer envelope made of phospholipids
○ Always parasitic, they can only reproduce by using their host
• Plant tissues found in roots stems and leaves

1. Epidermis
i. Protective layer that is one cell thick
□ In stems and leaves it might be covered with a waxy cuticle that prevents water loss
□ In leaves it has pores called stomata
□ In roots it may have extensions called root hairs to increase the surface area
2. Parenchyma
i. Many functions:
□ Storage of starch
□ When they are turgid, prevent wilting
□ Allow gas exchange
□ Forms the cortex in roots and stems
□ In stems it forms the central region or pith
□ In leaves it has the palisade mesophyll
3. Endodermis
i. One cell thick surrounding the vascular tissue in stems and roots
4. Pericycle
i. Layers of cells in the endodermis
ii. In roots it grows new roots
iii. In stems made of Sclerenchyma made of lignified cells (support)

Name of Diagram Diagram under One function of organelle
organelle microscope
Nucleus Controls the cell functions
and cell division
Contains the DNA
Rough ER Protein synthesis
Smooth ER Lipid synthesis

Hormone/Cholesterol
synthesis
Golgi Modification of proteins

Apparatus
Lysosome Autophagy (breakdown of

unwanted structures or
organelles)
Mitochondria Production of ATP and the

release of energy by aerobic
respiration
Ribosomes Production of proteins by

- translation
Cell Selective barrier between

Membrane - the cell contents and the
external environment
Centrioles Mitotic Spindle
Chloroplast Site of photosynthesis
Vacuole - - Maintain cell turgidity

(regulate turgor pressure)

2.1 Testing for biological molecules
Molecule Description Result (Color Change)

Starch Add few drops of iodine solution Brown to Blue-black
Reducing Sugars Add benedict's solution and heat to at Blue to Brick red
least 80° or bring to a boil
Non-reducing sugars 1- Negative reducing sugar test Blue to Brick red
2- Boil with HCl (to break glycosidic
bonds (break down to
monosaccharides)) (this is called acid
hydrolysis)
3- Wait for 1 minute
4- Cool, neutralize with sodium hydrogen
carbonate
5- Repeat benedict's test
(if it is a mix of non-reducing and
reducing sugars, do the same
procedure for non-reducing)(the
precipitate will be heavier than the
one obtained)
Proteins Add biuret reagent Blue to lilac
Lipids Emulsion test of lipids: Add ethanol to White emulsion forms
extract, then pour into water in another
test tube
• Colorimeter measures small differences in color more precisely

○ It is an instrument that compares the amount of light getting through a solution with the
amount that can get through a sample of pure solvent
• Iodine is dissolved in potassium iodide because it is not soluble in water
• Biuret reagent
○ Consists of two components
▪ Dilute potassium/sodium hydroxide
▪ Dilute solution of copper (II) sulfate
□ Ready mix has both of them mixed together and potassium tartrate to prevent
any reaction between solutions
• Benedict's Reagent is copper (II) sulfate in an alkaline solution

○ Reducing sugars reduce the soluble CuSO4 to insoluble brick red CuO precipitate
▪ The intensity of the red color is related to the concentration pf the reducing sugar
□ Colors are not fully reliable, so depend on the time (measure the time taken
for first change)
2 Biological molecules Page 9

2.2 Carbohydrates and lipids
• α-glucose and β-glucose are isomers of glucose.

• They can exist in a ring form due to intramolecular reactions.
• α-glucose has the -OH group on carbon 1 below the ring, while β-glucose has it above the ring.
• All organic molecules contain hydrogen and carbon

• Carbon atoms join together to form long chains or ring structures
• Covalent bonds in polymers (one of the strongest bonds)
○ They are skeletons of every organic molecule
▪ In polymerization, covalent bonds form between monomers, holding them together to create
polymers.
▪ CH3 is the building block
• 3 types of macromolecules (large biomolecule) (polymers)
○ All polymers are macromolecules but NOT all macromolecules are polymers
• Made of many repeating similar subunits joined in a chain (monomer)
○ Polysaccharides
○ Proteins (polypeptides)
○ Nucleic acids (polynucleotides)
• Lipids aren't polymers since they lack a monomer unit but they are a macromolecule
○ Monomer: A single, small molecule that can be combined with others to form larger molecules
(polymers).
○ Polymer: A molecule made up of repeating units (monomers).
○ Macromolecule: A large and complex molecule formed by the polymerization of monomers.
• Reducing sugars: all monosaccharides (eg. Glucose, fructose, maltose) and some disaccharides
○ They carry out reduction AND they are oxidized (reducing agent)
• The only common non reducing sugar is sucrose (cannot reduce due to their glycosidic bond config.)
○ It breaks down into fructose and alpha glucose
• Glycosidic bonds are formed by a condensation reaction, where a hydroxyl group (-OH) is removed from
one sugar molecule and a hydrogen atom (H) from another, creating a bond.
○ Two hydroxyl group line up alongside each other. One loses OH and one loses H to form a lost
water
▪ An oxygen bridge forms
• The breakdown of polymers into monomers by the addition of water is called hydrolysis
○ It takes place during the digestion of disaccharides and polysaccharides
• All carbohydrates contain a monosaccharide monomer
○ General formula: Cx(H2O)y

2.2 Carbohydrates and lipids (cont.)
• For storage of sugars:

○ In animals: glycogen (α-1,4 glycosidic linkage with α-1,6 glycosidic branches)
▪ Similar to amylopectin
□ Made of chain of 1,4 linked alpha glucose with 1,6 branches
□ It has more branches than amylopectin
○ In plants: starch
▪ Starch is a mixture of amylose and amylopectin
□ Amylose (α-1,4 glycosidic linkage)
□ Condensation between alpha glucose; forms unbranching chain of 1,4 linked glucose
 The chains curve making the final molecule more compact
□ Amylopectin: (α-1,4 glycosidic linkage with α-1,6 glycosidic branches)

□ many 1,4 linked alpha glucose
□ Chains are shorter and branch out to the side
□ Branches are formed by alpha 1,6 linkage
□ Iodine enters between the amylopectin and amylose to form a blue black starch-iodine complex
▪ They build up into large starch grains
▪ They are found in chloroplasts and in storage organs
• Cellulose (β-1,4 glycosidic linkage)
○ Present in cell wall
○ Strong molecule so it has a structural role
○ Polymer of beta glucose
○ To form the glycosidic bond with OH of C4, one glucose molecule must be upside down (rotated 180 degrees)
• Many cellulose molecules form microfibrils

• Form bundles called macrofibres which form fibres
• Hydrogen bonds makes it strong
• These fibres has very high tensile strength helping the cell to withstand the large pressures developed by osmosis
• They are freely permeable allowing water and solutes
Amylose Cellulose
Alpha glucose Beta glucose
• Same orientation 180 degrees
Individual chains Fibrous molecules chains held together by hydrogen bond
Forms starch grains Cell wall
• Glycogen and amylopectin similarities:

1. Both polymers and both polysaccharides
2. They are made of alpha glucose
3. 1,4 linked alpha glucose and branches are between 1,6 links

2.2 Carbohydrates and lipids (cont.)
Triglycerides
• Lipids aren't polymers since they lack a monomer unit but they are a macromolecule
• Non-polar, hydrophobic molecules
○ Insoluble in water but soluble in organic solvents
• Triglycerides are composed of three fatty acids and a glycerol molecule.
• Fatty acids can be saturated (no double bonds) or unsaturated (with double bonds)(the double bond makes them melt
more easily; more reactive).
• Ester bonds link the fatty acids to the glycerol backbone
• Functions:
○ Energy storage: in the form of fat
▪ When energy is needed, triglycerides can be broken down into fatty acids and glycerol through a process
called lipolysis.
▪ Triglycerides provide a sustained source of energy, ensuring that organisms can function even when food
intake is limited.
□ The C-H bond stores a high amount of energy
 More C-H bonds, more energy
○ Thermal insulation and cushioning: helping to maintain body temperature by reducing heat loss. They act as a
cushion absorbing all mechanical shocks
• They are a major component of cell membranes, forming a phospho-lipid bilayer.
• Structure:
○ Phosphate Head: hydrophilic. It contains a negatively charged phosphate group, which is polar, and a glycerol
molecule. These components make the head of the phospholipid soluble in water.
▪ Instead of having three fatty acids like normal fats, it has 2 fatty acids and it is bonded to a phosphate group
○ Fatty Acid Tails: hydrophobic. Long hydrocarbon chains that are non-polar. Insoluble in water
• This unique amphipathic property is vital for the formation the cell membrane:
○ Aqueous environments: the hydrophilic heads facing outward toward the water (the extracellular or intracellular
environment), and the hydrophobic tails facing inward, away from water.
○ Forms a semi-permeable barrier that separates the cell's interior from the external environment while allowing for
controlled transport of substances in and out of the cell.
Compare and contrast between phospholipids and triglycerides:
1. Both contain glycerol

2. Both contain ester bond between glycerol and 3 fatty acids
3. Both may have saturated/unsaturated fatty acids
4. Triglycerides have three fatty acids whereas phospholipids contain 2 and a phosphate group
5. Both have C,H but only phospholipids contain P
6. Both are insoluble in water
7. Triglycerides are hydrophobic while phospholipids are both hydrophobic and hydrophilic
8. Phospholipids make a bilayer in water while triglycerides cannot

2.3 Proteins
Proteins (polymers of amino acids called polypeptides)
• Amino acids are the building blocks of proteins.

○ There are 20 amino acids
• The sequence, type and number of the amino acids within a protein determines its shape and therefore its function
• Functions:
○ Enzymes
○ Carrier proteins in cell membranes
○ Hormones
○ Immunoproteins (immunoglobulins)
○ Transport proteins (hemoglobin)
• Peptide bonds form between the amino group of one amino acid and the carboxyl group of another during protein
synthesis.
This is a condensation reaction so water is released. The resulting molecule is a dipeptide
• The primary structure refers to the linear sequence of amino acids in its chain
○ Fundamental to a protein's identity and function
○ DNA of a cell dictates the sequence of amino acids and determines its unique properties and function
○ It is specific to each protein
• The secondary structure refers to the local, repetitive folding patterns that occur within segments of the polypeptide
chain.
○ Secondary structures are stabilized by hydrogen bonds between the weak negative carbonyl oxygen and the weak
positive amide hydrogen of the peptide bonds.
○ The two most common types are alpha helices and beta sheets.
▪ Alpha helices are tightly coiled, with hydrogen bonds forming between every fourth peptide bond in the
chain, creating a helical structure.
▪ Beta sheets consist of strands of amino acids running alongside each other, with hydrogen bonds forming
between adjacent strands.
○ Happens because of the hydrogen bonds
▪ They can be broken by high temperatures and pH changes
• The tertiary structure refers to the 3D folding/coiling pattern (arrangement) of a protein due to interactions between R-
groups of side chains.
○ Most common in globular proteins
○ The additional bonds are:
▪ Hydrogen (these are between R groups)
▪ Disulfide (only occurs between cysteine amino acids)
▪ Ionic (occurs between charged R groups)
▪ Weak hydrophobic interactions (between non-polar R groups)
• The quaternary structure is the arrangement of multiple protein subunits (more than one polypeptide chain working
together as one molecule)

2.3 Proteins (cont.)
Peptide Hydrogen bond Disulfide Ionic Hydrophobic
Primary ✓
Secondary ✓ ✓
Tertiary ✓ ✓ ✓ ✓ ✓
Quaternary ✓ ✓ ✓ ✓ ✓
• Globular proteins are spherical (non-polar hydrophobic R groups towards the center and the polar hydrophilic R groups
towards the outside)(this orientation makes them soluble), soluble, and have diverse functions (in metabolic reactions)
because of this solubility (e.g. enzymes, antibodies).
○ Eg: hemoglobin
▪ It consists of four polypeptide chains: two alpha (α) and two beta (β) chains, and a heme group. (binds to 4
oxygen molecules)
▪ Heme groups bind to oxygen, facilitating oxygen transport in the blood.
□ When oxygen binds to hemoglobin in the lungs, it forms oxyhemoglobin, a reversible reaction that
occurs due to the iron atom (Fe) in the heme group.
□ The heme group gives blood its distinctive red color
□ Bright red: with oxyhemoglobin (O 2)
□ Purplish/ dark red: with deoxyhemoglobin (CO 2)
▪ The interactions of the hydrophobic R groups hold the 3D shape and the hydrophilic R groups keep its
solubility.
▪ In sickle cell anemia one polar amino acid of the beta chains is replaced by a non-polar one pointing outwards
□ Makes hemoglobin less soluble
• Fibrous proteins are elongated, insoluble, and have structural roles (e.g., collagen, keratin).
○ Eg: collagen
▪ Collagen is a fibrous protein that provides structural support in connective tissues.
▪ It forms long, strong collagen fibers.
▪ Collagen molecules are composed of three polypeptide chains twisted together (triple helix)
▪ Their triple helix structure provides tensile strength, allowing collagen to resist stretching and maintain tissue
integrity.
▪ Collagen molecules play a crucial role in wound healing and tissue repair, as they form a scaffold for new
tissue growth.
▪ They also help in maintaining tissue structure and elasticity, particularly in skin and blood vessels.
▪ Every third amino acid is glycine
□ Glycine is the simplest
▪ Each molecule of collagen has bonds formed between the R groups of lysine

2.4 Water
• Water is a major component of cells (70%-90%)

• Hydrogen Bonding is a type of intermolecular force that occurs when hydrogen is bonded to a highly
electronegative atom
• It is a weak bond
• Water is a dipolar covalent molecule
• Hydrogen bonds contribute to the many properties water molecules have that make them so important
to living organisms:
• An excellent solvent: due to its ability to form hydrogen bonds with other polar or charged
molecules.
• A relatively high specific heat capacity: This property is crucial for temperature regulation in living
organism
• A relatively high latent heat of vaporization: essential for cooling mechanisms in organisms
• Water is less dense when a solid
• Water has high surface tension and cohesion (the force of attraction between water molecules as
a result of hydrogen bonding)
• It acts as a reagent
• Water is used as a transport medium because it is a great solvent
• In plants:
○ It stores minerals/solutes in the vacuole
○ Transports solutes
○ Metabolic reactions occur in water
○ Dissolves CO2/O2 in photosynthesis/respiration

Alpha and beta glucose

3.1 Mode of action of enzymes
• Enzymes are globular proteins that catalyze reactions inside cells (intracellular (eg. Pepsin)) or secreted to
catalyze reactions outside the cell (extracellular (eg. Digestive enzymes))
• Anabolic reactions are metabolic reactions that build up small molecules to bigger molecules
• Catabolic reactions are metabolic reactions that break down bigger molecules to smaller molecules
• Metabolism is the sum of all catabolic and anabolic reactions in the body
• Enzymes catalyze ALL metabolic reactions
• Importance of enzymes: speed up reactions to maintain life functions
• They catalyze reactions by lowering the activation energy required
• Properties:
• Specific: an enzyme's active site is specific to the substrate
• Increases rate of reaction
• Unchanged at the end of the reaction
• The active site is a specific region on the enzyme surface where the substrate binds during a catalyzed reaction.
• The active site provides a three-dimensional pocket/ groove/depression with a precise shape and chemical
environment that complements the specific shape and properties of the substrate.
• Enzymes exhibit specificity, meaning each enzyme is highly selective for a particular substrate or group of
structurally related substrates.
Lock and Key theory:
• The lock-and-key hypothesis suggests that the active site of an enzyme is a rigid structure, perfectly
complementary to the shape and properties of its specific substrate.
• the shape of the active site of an enzyme is complementary to its substrate
○ An enzyme's active site is specific to the substrate
○ Shows specificity
• The substrate temporarily bonds with some of the amino acids from the enzyme to form the enzyme
substrate complex (ESC)
• Substrate: the molecule(s) before they are made to react
• Product: the molecule(s) that are made in a reaction
Induced Fit hypothesis:
• The induced-fit hypothesis proposes that the active site of an enzyme is flexible and undergoes conformational
changes upon substrate binding.
• A substrate binds to an active site and both change shape slightly, creating an ideal fit (to form an ESC)
• Enzyme is not an exact fit
• It is still specific
• In enzyme-catalyzed reactions with color changes, the colorimeter can be used to quantify the progress of the
reaction by measuring the absorbance or transmittance of light through the reaction mixture
• Advantages: quantitative results
3 Enzymes Page 18
3.2 Factors that affect enzyme action
• Factors that affect enzyme action

1. Temperature:
▪ Increasing temperature initially increases the rate of reaction due to higher kinetic energy
▪ However, excessively high temperatures can denature enzymes.
□ Denatured: hydrogen bonds break so it loses its secondary and tertiary structure
□ Does not start at the origin because the rate can't be zero
2. pH:
▪ Enzymes have optimal pH ranges; enzyme can be denatured (because the ionic bonds are
disturbed)
□ The denaturation is reversible (when it is not an extreme change)
▪ Buffer solutions help maintain a constant pH, stabilizing enzyme activity.
3. Enzyme concentration:
▪ When there is enough substrate, the enzyme concentration is directly proportional to the
rate.
4. Substrate concentration:
▪ With the same amount of enzyme, the substrate concentration is indirectly proportional to
the rate
5. Inhibitor concentration:
▪ Inhibitors can decrease the rate of reaction.
• Activation energy is the minimum amount of energy required to initiate a reaction
• Enzymes lower the activation energy by finding an alternate pathway

• Course of enzyme controlled reaction
○ In the beginning the rate of the reaction depends on:
▪ The number of enzyme molecules
▪ The speed at which the enzymes convert substrate into product
○ In the end
▪ Rate is 0
▪ Flattens off because all substrate has broken down
3 Enzymes Page 19
3.2 Factors that affect enzyme action
• Turnover rate is the number of substrate molecules converted into product per second
• The maximum possible rate of the enzyme (Vmax) is reached when all enzyme active sites are saturated
• Km: Michaelis–Menten constant, the substrate concentration at which the reaction rate is half of Vmax.
○ As Km decreases, enzyme affinity for its substrate increases, and vice versa.
▪ Enzyme affinity is the strength of binding between enzyme and substrate
• Enzyme inhibitors are molecules that can bind to an enzyme and alter its activity.
○ Inhibitors can decrease the rate of reaction.
• Reversible inhibitors can bind to and dissociate from the enzyme, allowing the enzyme to recover its activity.
• There are two types of inhibitors:
○ Competitive Inhibitor
▪ Molecule that binds to the active site
▪ They compete with the substrate for the active site
▪ Competitive inhibition is reversible. If the concentration of the substrate is increased, it can outcompete
the inhibitor, and the enzyme activity will be restored.
□ Vmax (Maximum Velocity): Unchanged – once the substrate outcompetes the inhibitor, the reaction
can proceed at its maximum rate.
□ Km (Michaelis–Menten Constant): Increases – more substrate is required to reach half of the
maximum velocity.
○ Non-competitive Inhibitor
▪ Binds to another part of the enzyme, so it blocks its function
□ Vmax: Decreases – the inhibitor directly affects the catalytic activity of the enzyme.
□ Km: Unchanged – the affinity of the enzyme for the substrate remains the same.
• Immobilized enzymes are enzymes that have been fixed to a surface or trapped inside beads
○ How?:
▪ Trapped in gel
▪ Trapped in microcapsule
▪ Alginate beads
• They are immobilized because (advantages):
○ Reusability: Immobilized enzymes can be reused for multiple cycles, which is particularly useful in industrial
processes.
○ Enhanced Stability: Immobilization often enhances the stability of enzymes, making them more resistant to
changes in temperature, pH, or other environmental factors.
○ Easy Separation: The immobilized enzyme can be easily separated from the reaction mixture (enzyme free
products (no contamination with enzyme))(no need for purification)
○ Reduced Cost
○ Reaction can be faster and have higher yield
○ Longer Shelf Life
• Disadvantages:
○ Diffusion Limitations: The immobilized enzyme may experience diffusion limitations, as substrates and products
must diffuse through the alginate matrix to reach the active sites.
○ Changes in Microenvironment: The immobilization process may alter the microenvironment around the enzyme,
affecting its activity.
• Process of immobilization in alginate beads:
○ Enzyme is mixed with a solution of sodium alginate
○ Dripped drop by drop through a syringe into a solution of calcium chloride
○ Sodium ions are displaced by the calcium ions- forms strong hard beads
○ Left to harden, then rinsed
• Immobilization often makes enzymes more useful because the hydrogen bonds are less easily broken
3 Enzymes Page 20
3 Enzymes Page 21
4.1 Fluid mosaic membranes 7 nm
• Membranes are primarily composed of a lipid bilayer (phospholipids)
○ Hydrophilic phosphate head and hydrophobic fatty acid tails
▪ Aqueous environments: the hydrophilic heads facing outward toward the water (the extracellular or intracellular
environment), and the hydrophobic tails facing inward, away from water.
▪ Forms a semi-permeable barrier that separates the cell's interior from the external environment while allowing for controlled
transport of substances in and out of the cell.
○ When mixed with water phospholipids form:
▪ Ball like structures called micelles
▪ Sheet like called bilayers
• The fluid mosaic model states that both the phospholipids and the proteins can move by diffusion
○ Called mosaic because there is a scattering of different proteins, lipids, and molecules throughout the surface
• There are two types of proteins in cell membranes:
○ Integral proteins:
▪ embedded within the phospholipid bilayer
▪ They have hydrophobic regions that interact with the lipid tails and hydrophilic "head" that extends into the aqueous
environment and form hydrogen bonds with the water.
▪ Globular protein
○ Peripheral proteins:
▪ Associated with the membrane but are not embedded within it. They may interact with the hydrophilic regions of integral
proteins or the polar heads of phospholipids.
• Cholesterol molecules are interspersed among phospholipids
○ Strengthens the membranes by getting in between the phospholipid molecules and reduces fluidity
○ Maintains/regulates the membrane's fluidity and stability by preventing the fatty acid chains of phospholipids from packing t oo
closely together.
○ Decreases fluidity as temperature increases
○ Animal cells contain MUCH more cholesterol than plants or fungi
• Glycolipids: lipids with attached carbohydrate chains. Found on the extracellular surface
• Glycoproteins: Proteins with attached carbohydrate chains. Found on the extracellular surface
• Roles
1. Phospholipids:
i. form the basic structural framework
ii. The amphipathic nature of phospholipids allows the membrane to be flexible and dynamic
2. Cholesterol:
i. modulates membrane fluidity.
ii. Enhances the stability of the membrane under different environmental conditions
3. Glycolipids and glycoproteins:
i. Act as cell surface antigens involved in cell recognition and immune response
ii. Cell Adhesion: Play a role in cell adhesion, allowing cells to adhere to each other
iii. Receptor Function: Some glycoproteins serve as receptors for signaling molecules, contributing to cell signaling.
iv. The carbohydrate chain act as receptor molecules
v. Form H-bonds with water
vi. Enzyme
4. Integral Proteins:
i. Transport: Act as channels or carriers for the transport of ions, molecules, and nutrients across the membrane.
ii. Enzymatic Activity: Serve as enzymes, catalyzing specific reactions at the membrane surface.
iii. Cell Signaling: Function as receptors for signaling molecules, initiating intracellular signaling cascades.
Structural Support: Contribute to the structural integrity of the membrane.
5. Peripheral Proteins:
i. Cell Signaling: Participate in cell signaling by interacting with integral proteins or other cellular components.
ii. Support: Provide structural support to the membrane.
Cell signaling process:
1. Secretion of Ligands:
○ Specific chemicals (ligands) are secreted by cells.
▪ These ligands may include hormones, neurotransmitters, or other signaling molecules.
2. Transport of Ligands:
○ Ligands are transported through the extracellular fluid to reach target cells.
▪ Transport mechanisms include diffusion, facilitated diffusion, and active transport.
3. Binding to Cell Surface Receptors:
○ Ligands bind to specific cell surface receptors on the membrane of target cells.
▪ Receptors are often proteins with binding sites that match the ligands.
4. Specific Responses:
○ Binding triggers intracellular signaling cascades, leading to specific cellular responses.
▪ Responses may include changes in gene expression, alterations in cell metabolism, or other cellular activities.
4 Cell membranes and transport Page 22

4.2 Movement into and out of cells
• Simple diffusion is the movement of molecules from an area of high concentration to low concentration
○ It is a passive process (no energy is required)
○ Occurs down the concentration gradient
• Facilitated diffusion is the movement of water soluble/ polar molecules with the help of transport proteins
○ It is a passive process (no energy is required)
○ Types of proteins:
▪ Channel proteins:
□ Integral membrane proteins that form pores in the cell membrane
□ Channels are often selective, allowing only certain types of ions or molecules to pass through based on
size and charge.
▪ Carrier proteins:
□ Integral membrane proteins with a specific binding site for the molecule they transport.
□ Undergo a structural change when they bind to the molecule
□ Carrier proteins exhibit specificity for particular molecules and may transport them against their
concentration gradient.
□ Rate of transport can reach a maximum when all available binding sites are occupied
• Osmosis is the net movement of water across a partially permeable membrane from an area of high water potential to
lower (down a water potential gradient)
○ Critical for maintaining turgor pressure in plants
Hypertonic solution: Conc. of salts

outside cell > conc. inside cell
Isotonic solution: Conc. of salts
○ outside cell = conc. inside cell
Hypotonic solution: Conc. of salts
outside cell < conc. inside cell
• Active transport is the movement of molecules against a concentration gradient by using energy
○ Utilizes integral membrane proteins
○ Uses energy to make the carrier protein change its shape
○ Used in:
▪ Reabsorption of glucose in the kidneys
▪ Absorption of products of digestion from the gut
▪ In plants, used to load sugar from the photosynthesizing cells to the phloem
• Endocytosis is the uptake of large particles by forming vesicles. Requires energy from ATP
○ Phagocytosis: takes in solids
○ Pinocytosis: takes in liquids
• Exocytosis is the release of substances from a cell by vesicle fusion with the cell membrane. Requires energy from ATP
• Surface Area to Volume Ratio: It is a relation that describes the proportion between the surface area of an object and its
volume.
○ A higher surface area to volume ratio facilitates faster diffusion.
▪ Smaller cells or structures have a larger surface area relative to their volume, allowing for more efficient
diffusion of substances.
• The surface area to volume ratio affects how quickly water molecules can move into and out of cells.
○ Cells with a higher SA/V ratio can maintain osmotic balance more effectively.
• A higher ratio can provide more surface area for the placement of transport proteins, enhancing the capacity for active
transport processes.
4 Cell membranes and transport Page 23

5.1 Replication and division of nuclei and cells
• A chromosome is a long strand of DNA wound around proteins.
○ It is made up of 2 genetically identical sister chromatids connected by a centromere
□ The centromere is the site of attachment to spindle fibres
▪ Each chromatid is made up of a long strand of DNA wound around histone proteins
□ The tightly coiled combination of DNA is called a chromatid
 Histone proteins are positively charged, globular proteins that are basic in nature
◊ That is because they can interact easily with DNA, which is acidic.
• Each chromatid has telomeres at both ends.

▪ Its function is to protect the ends of chromosomes from deterioration and loss of genes during
DNA replication
□ Prevents the loss of genes
□ Permit continued replication
□ Protects the ends of chromosomes from being degraded
• Mitosis is the nuclear division that results in 2 daughter cells that are genetically identical
○ The produced cells are genetically identical to each other and to the parent cell
• Role of Mitosis:
1. Growth of multicellular organisms (ensures that the new cells are genetically identical to parent cell)
i. Unicellular zygotes grow into multicellular
2. repair of tissues by cell replacement
3. replacement of damaged or dead cells
4. asexual reproduction
• Stem cells are unspecialized cells that divide by mitosis to result in daughter cells that can become specialized
○ They contribute to tissue repair and replacement through mitosis
○ Found in embryonic cells
○ In adults: bone marrow, skin, gut, heart, and brain
• Uncontrolled cell division can cause cancerous tumors to form
○ This occurs because of a mutation (change) in genes
General Past Paper notes:
• ATP provides energy for:

○ The movement of centrioles to poles
○ Spindle formation and organization of the microtubule
○ Movement of chromosomes to the spindle equator (metaphase plate)
○ Separation of sister chromatids during anaphase
○ Condensation of chromatin
• Role of centrioles in mitosis:
○ Organize microtubules
○ The centrioles direct the assembly of spindle fibers, which extend from the centrosomes toward the
chromosomes during prophase
• Describe the behavior of the nuclear envelope during mitosis:
○ Breaks down into vesicles at prophase
○ Re-forms after anaphase (at telophase)
5 The mitotic cell cycle Page 24

5.1 Replication and division of nuclei and cells &
5.2 Chromosome behavior in mitosis
The cell cycle
The cell cycle has 3 phases (the movement from one phase to another is triggered by chemical signals
called cyclins):
1. Interphase (Three phases):
○ G1 (gap one):
▪ A signal is received telling the cell to divide
▪ Cell grows in size (synthesizing new proteins, RNA, centrosomes, and organelles)
○ S (synthesis):
▪ DNA in the nucleus replicates
▪ Each chromosome produces an identical copy, resulting in the formation of sister
chromatids connected by a centromere.
○ G2 (gap two):
▪ Cell continues to grow
▪ New DNA is checked for errors and is repaired
□ G2 acts as a checkpoint before the cell enters mitosis, ensuring that DNA
replication is complete and accurate.
▪ Produces high amount of the protein tubulin which is needed to make microtubules
for the mitotic spindle
2. Mitosis (M phase) (nuclear division) (cell growth stops during M phase) (four stages):
○ Prophase:
▪ Chromosomes condense (now visible when stained)
▪ Centrosomes move toward opposite poles and spindle fibres begin to emerge
▪ Nuclear envelope breaks down into vesicles
○ Metaphase:
▪ Centrosomes reach opposite poles
▪ Chromosomes line up at the equator of the spindle (metaphase plate)
▪ Spindle fibres reach the chromosomes and attach to the centromeres
▪ Each sister chromatid is attached to a spindle fiber originating from opposite poles
○ Anaphase:
▪ The sister chromatids separate at the centromere
▪ Spindle fibers shorten
▪ The separated sister chromatids are pulled to opposite poled by the spindle fibers
○ Telophase:
▪ Chromosomes arrive at opposite poles and begin to decondense
▪ Nuclear envelopes begin to reform around each group of chromosomes
▪ Spindle fibres break down
▪ Nucleolus reforms
3. Cytokinesis (cell division):
○ Once the nucleus divides into two genetically identical nuclei, the whole cell divides
▪ Creating two genetically identical daughter cells
○ In animal cells: constriction of cytoplasm between the two nuclei
○ In plant cells: a new cell wall is formed
Outline what happens in a cell in preparation for cytokinesis. [2]

• increase in cytoplasm / increase in number of (named) organelle(s), during interphase ;
• (re)formation of nuclear envelope ;
• nuclear envelope, forms around each group of chromosomes ;
• (movement of) organelles to be shared between two daughter cells ;
• spindle, disassembles / breaks down / degrades / disappears / AW ;
• cleavage furrow forms ;
• A cytoplasm / cell membrane, pinches in / constricts / in folds

5.2 Chromosome behavior in mitosis

6.1 Structure of nucleic acids and replication of DNA
• DNA and RNA are polymers of nucleotides
○ They are polynucleotides
▪ Nucleotides are molecules consisting of a nitrogen containing base, a pentose sugar (ribose in RNA and
deoxyribose in DNA), and a phosphate group
□ The phosphate group is attached to the 5' carbon on the pentose sugar
▪ Polynucleotide is a chain of nucleotides joined together by phosphodiester bonds
▪ Phosphate group gives nucleic acids their acidic nature
• ATP (Adenosine triphosphate) is a phosphorylated nucleotide that serves as a primary energy carrier in cells
○ A nucleotide molecule that has one or more phosphate groups attached to it.
▪ AMP = 1 phosphate group
▪ ADP= 2 phosphate groups
▪ ATP = 3 phosphate groups
• There are two types of bases:
○ Purines: double ring structure
▪ Adenine (A) and Guanine (G)
○ Pyrimidines: single ring structure
▪ Cytosine (C), Thymine (T, in DNA), and Uracil (U, in RNA)
○ A purine always pairs with a pyrimidine.
▪ This means that the distance between 2 strands is always 3 rings
• DNA is made up of 2 polynucleotide chains
○ Each chain is a right handed helix
▪ A complete turn is 2 circles and a half - 10 base pairs
○ 2 chains make a double helix
○ Chains are antiparallel (opposite direction)
▪ Alternating complementary base pairing between the 5′ to 3′ strand and the 3′ to 5′ strand
□ 3′ and 5′ refer to the number of carbon atoms in a deoxyribose sugar molecule that a phosphate group
binds to.
□ These specific base pairing rules ensure accuracy in the replication and transmission of genetic
information.
○ Adenine pairs with Thymine (A-T), and Guanine pairs with Cytosine (G-C) through hydrogen bonds.
▪ The hydrogen bonds hold the 2 strands together in a double helix shape. Give stability to the DNA molecule so
the sequence will not spontaneously change. Can be broken for transcription. Contributes to the 3D structure
of DNA.
▪ A links with T by two hydrogen bonds; G links with C by three hydrogen bonds.
Semi-conservative Replication of DNA
• DNA replication occurs during the S phase of the cell cycle (interphase)
• "Semi-conservative" because the new DNA molecules have one parent stand and one new daughter strand & each strand
of DNA acts as a template for the synthesis of a complementary strand
• DNA unwinds and the hydrogen bonds between the complementary nitrogenous bases are broken (helicase enzyme)
• Both strands of DNA are used as a template (this results in 2 daughter DNA strands)
• The enzyme DNA polymerase is used for the copying process
○ A molecule of the enzyme attaches to each strand, It adds 1 nucleotide at a time
○ DNA polymerase synthesizes the leading strand continuously
▪ Leading strand is the 3' to 5' direction
○ DNA polymerase adds nucleotides complementary to the template strand in the 5' to 3' direction.
○ DNA polymerase synthesizes the lagging strand discontinuously.
○ DNA polymerase adds nucleotides in the 5' to 3' direction, creating Okazaki fragments.
○ due to the antiparallel nature of DNA and the requirement for synthesis in the 5' to 3' direction by DNA polymerase,
the lagging strand is synthesized in short, separated segments known as Okazaki fragments.
• DNA ligase joins the Okazaki fragments (nucleotides by phosphodiester bonds) on the lagging strand
○ Before this - they are only holding on to the parent strand with hydrogen bonds between complementary bases
• Sugar phosphate backbone
6 Nucleic acids and protein synthesis Page 27

6.2 Protein synthesis
• A gene is a sequence of nucleotides that forms part of DNA
○ A gene codes for a polypeptide
○ Each set of three bases codes for one amino acid (triplet)
The universal genetic code:

1. The genetic code is written in the form of triplets of nucleotides called codons.
i. Each codon consists of three consecutive nucleotides in a DNA or mRNA sequence.
2. Each codon codes for a specific amino acid, and some codons serve as start or stop signals.
i. There are 64 possible codons, with 61 coding for amino acids and 3 acting as stop codons.
3. Start Codon (AUG (Met.)): serves as the initiation codon, codes for the amino acid methionine (Met).
4. Stop Codons (UAA, UAG, UGA): signal the termination of translation.
i. prompt the release of the polypeptide chain from the ribosome.
5. The genetic code is degenerate, meaning that multiple codons can code for the same amino acid.
6. The genetic code is nearly universal among all living organisms. The same codons code for the same amino acids in diverse
species, from bacteria to humans.
Transcription
• RNA polymerase attaches to the beginning of the gene to be copied.

• It starts to unwind the DNA of the gene and another enzyme breaks the hydrogen bonds between the two strands
• This creates two single-stranded sections of DNA with the normal double helical structure either side of the unzipped section
• Only one of the exposed strands is copied.
• This is called the template strand or transcribed strand.
• The other strand is called the non-transcribed strand.
• A complementary RNA copy of the template strand is made
• The bases A, G, T and C in DNA are copied in the RNA as U, C, A
and G respectively.
• Free activated RNA nucleotides line up with their complementary base
and forms H-bonds.
• RNA polymerase catalyzes the synthesis of phosphodiester bonds to form
• sugar-phosphate backbone.
• Hydrogen bonds between the DNA and mRNA strand are then broken
• DNA is reformed
• RNA strand then leaves the nucleus through the nuclear pores
• RNA is made from nucleotides found free in solution in the nucleus
Post Transcriptional RNA Modification (RNA processing) (in eukaryotic cells):
• The original RNA molecule (before modification) is called the primary script
• Eukaryotic genes are made of introns are exons
• Exons: coding sequence
• Introns: non-coding sequence which is not translated
• Both introns and exons are transcribed but only exons will be translated into amino acids by RNA splicing.
• RNA splicing: removal of introns from primary transcript
• Exons are joined together to form continuous strand called mature mRNA.
Translation
The process by which a sequence of bases in mRNA is converted into a sequence of amino acids in polypeptides in the
ribosome.
• mRNA moves towards the ribosomes. Enters the space between the large and small subunit.
• tRNA contains an anticodon that is complementary to the base pairing in the codons of the mRNA. Attached to the end of the
tRNA molecule is the corresponding amino acid. (two tRNA molecules can fit inside the ribosome at once)
• The amino acids carried by the 2 tRNA are side by side and form a peptide bond
• Catalyzed by peptidyl transferase

6.2 Protein synthesis (cont.)
• A gene mutation is a change in the sequence of base pairs in a DNA molecule (could result in an altered polypeptide). May be
because of errors during DNA replication or because of damage done to DNA (eg. Radiation, carcinogens).
Types of gene mutations:
• Substitution: a base is replaced by a different base

• Sickle cell anemia: base substitution in the gene coding for beta-globin
○ Different mRNA codon results in a change in the 6th amino acid (CTT replaced by CAT (Val instead of Glu))
○ Alters the primary structure
○ Glutamic acid is polar whereas valine is non-polar
○ Changed secondary, tertiary and quaternary structure
• Insertion/Addition: an extra base is added
• Deletion: a base is lost and not replaced
• Both insertion and deletion cause frame-shift mutations (incorrect reading of the sequence of triplets in the genetic code
due to a shift in the reading frame)
○ The rest of the code is altered
○ All triplets from the mutation onwards are affected

Xylem looks thicker under microscope because
of the lignified cell walls.
7.1 Structure of transport tissues Parenchyma fibers come in colored part (stains
easily)
• The vascular system in plants is a complex network of tissues that facilitates the transport of water, nutrients, and other substances
throughout the plant body.
• This system is crucial for the growth, development, and survival of plants. They need it to meet their metabolic demands.
• It runs through the leaves, stem, and roots (organs involved).
• The vascular system consists of two main types of vascular tissues: xylem and phloem.
Xylem: transports water and mineral ions from the roots to the rest of the plant.
• Dead cells (to not impede the transpiration stream of water) that form long, narrow, and hollow tubes/Narrow diameter (increased
capillary action).
• Wide lumen for greater water volume transported.
• Lignified cell walls for strength (to withstand the hydrostatic pressure) and support and waterproof (impermeable to water).
• Cellulose cell wall allows adhesion of water molecules because it is hydrophilic.
• Pits in the walls that allow lateral movement of water (allows continual flow in case of air bubbles forming in the vessels).
Components:
• Xylem Vessel Elements: Elongated, dead cells with lignified walls, forming vessels for efficient water transport.
• Tracheids: Elongated cells with tapered ends and lignified walls, contributing to water transport.
Function: Xylem primarily transports water and minerals from the roots to the rest of the plant. The water movement is unidirectional,
driven by transpiration and cohesion-tension. Transpiration
Phloem: Living cells that transport dissolved organic substances (mainly sucrose) from the source to the sink. It can also carry substances
from storage organs to other parts of the plant.
Components:
• Sieve Tube Elements: Living cells with perforated end walls (sieve plates) that allow for the continuous flow of organic nutrients,
mainly sugars. (assisting in nutrient loading and support)
• Companion Cells: Living cells associated with sieve tube elements, providing metabolic support.
□ Contains transport proteins in membrane to move substances into and out the sieve tube elements.
□ Large number of mitochondria to provide ATP for active transport of substances into or out of the companion cells.
□ Contain plasmodesmata which allows substances to move from the companion cells into the sieve tube elements.
Function: Phloem transports organic nutrients, such as sugars produced in photosynthesis, from the leaves (source) to various parts of the
plant, including roots and developing tissues (sink). Contain no nucleus, vacuole or ribosomes to maximize the space for the translocation
of substances. Thin cytoplasm to reduce friction. Active translocation.
Organization:
Stems:
In stems, vascular bundles are arranged in a cylindrical pattern. Xylem is typically found on the interior side of the bundle, while
phloem is on the exterior side. To help support the plant.
Roots:
The central part of the root contains xylem at the center and phloem between the xylem vessel . This helps the roots withstand the
pulling strains they are subjected to as the plant transports water upwards and grows
Leaves:
Vascular bundles in leaves are scattered, with xylem usually closer to the upper epidermis and phloem closer to the lower
epidermis.
Parenchyma: used as a packing tissue between specialized structures.

i. Many functions:
□ Storage of starch
□ When they are turgid, prevent wilting
□ Allow gas exchange
□ Forms the cortex in roots and stems
□ In stems it forms the central region or pith
□ In leaves it has the palisade mesophyll
Sclerenchyma (fibres and sclereids): strength and support. Lignified cell wall and dead cells
7 Transport in plants Page 30

Sclerenchyma (fibres and sclereids): strength and support. Lignified cell wall and dead cells
Adaptations of Phloem

7.2 Transport mechanisms
• Some mineral ions and organic compounds within plants are transported dissolved in water.
○ The dissolved mineral ions are transported in the xylem tissue and the dissolved organic compounds are transported
in the phloem tissue
• Water moves from the soil solution to the cytoplasm of root hair cells by osmosis
○ It is a passive process
• There are two pathways that water (and the dissolved solutes) can take to move across the cortex:
▪ Apoplastic: the movement of water through the non-living spaces outside cell membranes.
□ The water moves by diffusion (no partially permeable membrane)
 Movement occurs more rapidly than in symplastic
○ When the water reaches the endodermis the presence of a thick, waterproof, waxy band of suberin within the cell
wall blocks the apoplast pathway
▪ This band is called the Casparian strip and forms an impassable barrier for the water
○ When the water and dissolved minerals reach the Casparian strip they must take the symplast pathway.
▪ Symplastic: the movement of water through the living spaces crossing cell membranes
□ involves the cytoplasm and plasmodesmata, and vacuole of the cells
• Transpiration refers to the loss of water vapor via the stomata by diffusion
○ Transpiration involves the evaporation of water from mesophyll cell walls, followed by the diffusion of water vapor
to the atmosphere. This process plays a vital role in nutrient absorption and temperature regulation.
• The movement of water through a plant's xylem occurs due to the evaporation of water vapor from the leaves and the
cohesive and adhesive properties exhibited by water molecules
○ Hydrogen bonds form between water molecules which results in cohesion between water molecules and adhesion
between the cellulose in the cell walls and the water molecules
• The evaporation of water into the air spaces in the leaves creates tension in the xylem tissue which is transmitted all the
way down the plant because of the cohesive nature of water molecules.
• The cohesive force results in a continuous column of water with high tensile strength (it is unlikely to break) and the
adhesive force stops the water column from pulling away from the walls of the xylem vessels
Xerophytic adaptations of leaves:
1. Fleshy succulent leaves

a. Water storage
2. Leaves curled or rolled when flaccid
a. Reduce transpiration by reducing surface area
3. Leaf surface covered in hairs (trichomes)
a. Traps moist air
4. Sunken stomata
a. Minimize water loss by trapping the moist air close to the area of water
loss
5. Thick waxy cuticle on leaves
a. Water loss reduced
Water moves from the soil solution to the cytoplasm of root hair cells by osmosis
Water moves from the xylem in the root to the leaf by transpiration pull/cohesion-tension
Water moves from mesophyll cell walls to intercellular air spaces by evaporation
Water vapor moves from intercellular air spaces to the atmosphere outside the leaf by diffusion

7.2 Transport mechanisms (cont.)
• Assimilates, such as sucrose and amino acids, move from sources (sites of production) to sinks (sites of utilization) in
phloem sieve tubes.
○ Requires the input of metabolic energy by the form of ATP
• The loading and unloading of the sucrose from the source to the phloem, and from the phloem to the sink is an active
process
○ Sucrose loading into the phloem involves an active transport process facilitated by companion cells.
Translocation of phloem sap:
1. Sucrose is loaded into the companion cell (either by facilitated diffusion or active transport)
2. H⁺ pumps actively pump H⁺ ions from the companion cell into the cell wall.
a. This creates a proton gradient and a lower pH in the cell wall.
b. The low pH in the cell wall facilitates the symport of protons and sucrose.
3. Sucrose molecules are co-transported with protons from the companion cell into the sieve tube elements through a
cotransport protein
4. The active transport of sucrose and protons into the sieve tubes increases the concentration of solutes, particularly
sucrose, in the phloem sap.
a. This results in an increase in osmotic pressure within the sieve tubes.
b. The increased osmotic pressure in the sieve tubes creates a hydrostatic pressure gradient.
5. Water flows into the phloem
6. Hydrostatic pressure builds up
7. Sucrose is unloaded into the sink
a. There is low hydrostatic pressure
8. Water moves back into the xylem by osmosis
The established pressure gradient drives the mass flow of phloem sap from source to sink.

8.1 The circulatory system
• The mammalian circulatory system is a closed double circulation, comprising the heart, blood, and blood vessels, including arteries,
arterioles, capillaries, venules, and veins.
○ Closed double circulation: pulmonary circulation and systemic circulation. The term "closed" emphasizes that blood is contained
within vessels and does not escape into the tissue fluid. blood travels through the heart twice for every one complete circuit.
• Pulmonary Circulation:
○ Pulmonary Artery: Carries deoxygenated blood from the heart to the lungs.
○ Pulmonary Vein: Returns oxygenated blood from the lungs to the heart.
• Systemic Circulation:
○ Aorta: Main artery that carries oxygenated blood from the heart to the body.
○ Vena Cava: Returns deoxygenated blood from the body to the heart.
Artery
Vein
• Arteries have relatively thick walls which allow them to withstand the high pressure of blood as it surges through with each ventricular
contraction of the heart (to prevent rupturing/bursting)
○ Thicker tunica media
○ More elastic tissues and smooth muscle tissue to maintain blood flow
• The lumen of the arteries is relatively narrow; this ensures that blood remains at relatively high pressure
○ Capillaries have a diameter of between 5-10 μm Blood flowing through the capillaries is brought close to the cells of the body to
allow efficient exchange of materials (particularly the diffusion of oxygen) Capillaries have pores in their walls
○ The endothelial wall of the capillaries is only one-cell thick, which ensures that substances can diffuse easily
• The middle layer of the veins is relatively thin in comparison and contains only a small amount of smooth muscle and elastic fiber
○ This is because the blood flowing through veins is under very low pressures
• Blood is composed of red blood cells, monocytes, neutrophils and lymphocytes
• Adaptations of the Red Blood Cells

○ Biconcave shape to increase surface area: volume ration
○ No nucleus, no mitochondria, no endoplasmic reticulum to have more room for haemoglobin
○ Flexible to pass through narrow capillaries (special cytoskeleton)
• Water is the main component of blood and tissue fluid
○ An excellent solvent: due to its ability to form hydrogen bonds with other polar or charged molecules.
○ A relatively high specific heat capacity: This property is crucial for temperature regulation in living organism
• Tissue fluid is the exchange medium between blood and cells
○ It is formed by filtration at the arterial end of capillaries due to hydrostatic pressure. Oxygen and nutrients pass from the blood to
cells via this fluid, while waste products move from cells to the venous end of the capillary.
○ The fluid is then reabsorbed back into circulation at the venous end
○ It contains far fewer protein molecules than blood plasma, because these are too large to escape easily through the capillary
endothelium
○ It also contains a high percentage of water. The high heat capacity of the water in tissue fluid helps the whole body to maintain a
relatively constant temperature.
8 Transport in mammals Page 34

8.2 Transport of oxygen and carbon dioxide
• Haemoglobin is a globular protein that facilitates oxygen and carbon dioxide transport in the blood
• CO2 combines with -NH2 terminal of Hb to form carbaminohaemoglobin. (10% carried this way)
• Most CO2 combines with water (catalyzed by carbonic anhydrase) to form carbonic acid which then dissociates into H+ and
HCO3- ions.
○ The chloride shift is the movement of chloride ions into red blood cells that occurs when hydrogen carbonate ions
are formed
○ To prevent an electrical imbalance, negatively charged chloride ions are transported into the red blood cells via the
same transport protein
• In the lungs: the pO2 is high and the pCO2 low.

• CO2 in plasma diffuses from the blood into the alveoli and oxygen diffuses into the blood from the alveoli.
• Carbaminohaemoglobin dissociates to form CO2 and Hb
• Hb then picks up O2, and HHb (haemoglobinic acid) dissociates to form H+ and Hb.
• The H+ ions combine with HCO3- to form carbonic acid, which dissociates to form CO2 and water (catalyzed by carbonic
anhydrase). CO2 diffuses into alveoli.
• The presence of a high pCO2 causes Hb to release oxygen.
○ This is called the Bohr Effect.
• High pCO2 are found in actively respiring tissues which need oxygen.
• This causes Hb to release oxygen even more readily than it would otherwise.
• The oxygen dissociation curve shows the rate at which oxygen associates, and also
dissociates, with haemoglobin at different partial pressures of oxygen (pO2)
• When the curve is read from left to right, it provides information about the rate at which
haemoglobin binds to oxygen at different partial pressures of oxygen
○ At low pO2, in the bottom left corner of the graph, oxygen binds slowly to
haemoglobin; this means that haemoglobin cannot pick up oxygen and become
saturated as blood passes through the body's oxygen-depleted tissues
▪ Haemoglobin has a low affinity for oxygen at low pO2, so saturation
percentage is low
○ At medium pO2, in the central region of the graph, oxygen binds more easily to
haemoglobin and saturation increases quickly; at this point on the graph a small
increase in pO2 causes a large increase in haemoglobin saturation
○ At high pO2, in the top right corner of the graph, oxygen binds easily to haemoglobin;
this means that haemoglobin can pick up oxygen and become saturated as blood
passes through the lungs
▪ Haemoglobin has a high affinity for oxygen at high pO2, so saturation
percentage is high
• When read from right to left, the curve provides information about the rate at which
haemoglobin dissociates with oxygen at different partial pressures of oxygen
• In the lungs, where pO2 is high, there is very little dissociation of oxygen from
haemoglobin
• At medium pO2, oxygen dissociates readily from haemoglobin, as shown by the steep
region of the curve; this region corresponds with the partial pressures of oxygen present in
the respiring tissues of the body, so ready release of oxygen is important for cellular
respiration
○ At this point on the graph a small decrease in pO2 causes a large decrease in
percentage saturation of haemoglobin, leading to easy release of plenty of oxygen
to the cells
• At low pO2 dissociation slows again; there are few oxygen molecules left on the binding
sites, and the release of the final oxygen molecule becomes more difficult, in a similar way
to the slow binding of the first oxygen molecule

8.2 Transport of oxygen and carbon dioxide (cont.)

8.3 The heart
• Atria have thinner walls compared to ventricles.
○ Since atria pump blood to the adjacent ventricles, less
force is needed, resulting in thinner walls.
• Atria receive blood from veins and pump it into the
ventricles.
• Ventricles have thicker and more muscular walls.
• Ventricles pump blood to either the lungs (right ventricle) or
the entire body (left ventricle).
○ Thicker walls are necessary to generate the force
required to push blood through the circulatory system.
(high pressure)
• The left ventricle has a thicker muscular wall.
○ It pumps oxygenated blood to the entire body through
the systemic circulation.
○ The left ventricle needs more force to pump blood
throughout the body's extensive network.
• The right ventricle has a thinner muscular wall.
○ It pumps deoxygenated blood to the lungs through the
pulmonary circulation.
The cardiac cycle is divided into 2 stages, systole and diastole: ○ The right ventricle has a shorter distance to pump
• Systole:
blood (to the nearby lungs), requiring less force/ less
○ Atrial Systole, Ventricular Diastole: resistance
▪ muscles in both atria contract.
▪ Blood flows from atria into ventricles.
▪ The bicuspid and tricuspid valves open while the semilunar valves are closed.
▪ Atrial volume decreases, atrial pressure increases
□ The pressure in the atria rises above that in the ventricles, forcing the atrioventricular (AV) valves (bicuspid/tricuspid
valves) open
○ Ventricular Systole, Atrial Diastole:
▪ muscles in both ventricles contract.
▪ Blood flows from ventricles out of the heart
▪ The semilunar valves open and the bicuspid and tricuspid valves are closed.
▪ Ventricular volume decreases, ventricular pressure increases
□ The pressure in the ventricles rises above that in the atria, forcing the atrioventricular (AV) valves (bicuspid/tricuspid
valves) to close- preventing blood backflow
• Cardiac Diastole:
○ The ventricles and atria are both relaxed
○ The pressure in the ventricles drops below that in the aorta and pulmonary artery, forcing the semilunar valves to close
○ The atria continue to fill with blood from the veins
○ The pressure in the atria rises above that in the ventricles, forcing the atrioventricular (AV) valves (bicuspid/tricuspid valves) open
○ The cycle then begins again with atrial systole
There is a specialized patch of muscles in the wall of the right atrium known as the Sino-Atrial node.
Cells at the SAN set the rhythm for all of the cardiac muscle cells to beat as they send out electrical impulses to the rest of the atria.
This causes atrial contraction.
The electrical impulses do not pass down to the ventricles. Instead, a second node (Atrio-ventricular node (AVN)) picks up the electrical impulses from
the atria.
The atria contract before the ventricles, giving the ventricles time to fill up with blood- because of the delay of electrical impulses between the SAN
and AVM
The impulse swiftly moves down to the septum of the heart, along fibres called Purkyne tissue.
Once the impulse arrive at the base of the ventricles, it moves outwards and upwards through ventricular walls.
This causes the ventricle to contract.
Stages in the cardiac cycle

1. Wave of excitation spreads from the sinoatrial node.
2. Atrial walls contract.
3. Impulse is delayed by a fraction of a second.
4. Wave of excitation enters the atrioventricular node.
5. Wave of excitation passes down the Purkyne tissue.
6. Ventricles contract.

6. Ventricles contract.

Past Paper

9.1 The gas exchange system
• The gas exchange system consists of:
1. Lungs: Main organs for gas exchange, containing bronchi, bronchioles, and alveoli.
2. Trachea: Windpipe that connects the larynx to the bronchi, providing a pathway for air.
3. Bronchi: Two main branches of the trachea, leading to the lungs.
4. Bronchioles: Smaller air passages within the lungs branching off from bronchi.
5. Alveoli: Tiny air sacs where gas exchange (oxygen and carbon dioxide) occurs. The walls
contain elastic fibres which allows them to stretch and recoil when breathing (stretch to
prevent bursting/rupture)
6. Capillary Network: Network of tiny blood vessels surrounding the alveoli for efficient
gas exchange. Trachea
Component Location in Gas Exchange System Function

Cartilage Trachea (as C-shaped rings and 1. Structural support and maintenance of
surrounds smooth muscle) airway shape.
Bronchi (as irregular plates) 2. Keeps airways open and provides support. Bronchiole
(prevents collapse)
3. Rings allow widening during inhalation
Ciliated Trachea 1. Moves mucus and trapped particles out of
Epithelium Bronchi airways
Bronchioles
Goblet Cells Trachea 1. Produces mucus to trap and remove Bronchus
Bronchi foreign particles.
Bronchioles 2. Secrete mucus for airway lubrication and
protection.
3. Contains cilia to sweep mucus away.
Squamous Alveoli 1. Facilitates efficient gas exchange Ciliated epithelium
Epithelium
Smooth Muscle Bronchi 1. Regulates airway diameter
Bronchioles 2. Contraction and relaxion.
Trachea 3. Changes diameter of lumen of
trachea/bronchus.
4. Control of air flow in the bronchioles
Alveoli
Capillaries Surrounds Alveoli 1. Facilitates exchange of gases with
bloodstream Plan Diagrams
• Ciliated epithelial cells, goblet cells, and mucous glands maintain the health of the gas exchange
system by performing their functions (producing, secreting, and moving mucus)
• Cartilage, Smooth Muscle, Elastic Fibers, Squamous Epithelium provide structural support, regulate
airway diameter, and allow for flexibility during breathing.
• Mucus (made of mucin droplets which are glycoproteins) produced by goblet cells will capture dust, Bronchus
pollen grains, fungal spores, pathogens (made in the mucous gland cells and goblet cells)
• The exchange of oxygen and carbon dioxide occurs between the alveoli and the capillaries in the
lungs
• Oxygen and carbon dioxide are exchanged in a process of simple diffusion;(passive movement from
high to low concentration)
• Alveoli adaptations:
1. alveoli have thin wall that is one cell thick Trachea
2. short diffusion distance between alveolar space and capillary
3. elastic tissue: stretch and recoil for ventilation / inhalation and exhalation
4. many alveoli provide a large surface area for diffusion
5. Surfactant (oxygen dissolves in surfactant fluid), prevents alveolar collapse
9 Gas exchange Page 42

9.1 The gas exchange system (cont.)
• Describe the differences between:
Elastic Walls of Alveoli

10.1 Infectious diseases
• Infectious diseases are caused by microorganisms known as pathogens and can be transmitted from one person to another.
Disease Pathogen Type of Mode of transmission Site of action Symptoms

pathogen of pathogen
Cholera Vibrio cholerae Bacterium Contaminated water and food Wall of small Diarrhea
(water-borne and food-borne) intestine Dehydration
(contaminated with human faeces)
Malaria Four species of Protoctists Bites from infected female Liver Fever
Plasmodium: Anopheles mosquitoes (it is a Red blood cells Shivering
Plasmodium vector) Brain Headaches
falciparum (most Anemia
severe form)
Plasmodium
malariae
Plasmodium ovale
Plasmodium vivax
Tuberculosis Mycobacterium Bacteria Airborne, through respiratory Infects the Coughing
(TB) tuberculosis droplets lungs, lymph Fever
Mycobacterium nodes, bones, Weight loss
bovis intestines
HIV/AIDS Human Virus Unprotected sexual activity T-helper Flu-like symptoms
Immunodeficiency Sharing needles lymphocytes and then
Virus (HIV) Mother-to-child during childbirth or Macrophages opportunistic
breastfeeding Brain cells infections
• Factors in Prevention:
○ Biological Factors:
▪ Adequate sewage treatment infrastructure
▪ Malaria: Use of insecticides and biological controls
▪ Tuberculosis: BCG Vaccine
▪ HIV/AIDS: Safe blood donations, drug treatments
○ Social Factors:
▪ Provision of clean, piped water with chlorination
▪ Vaccination programs
▪ Public health education
○ Economic Factors:
▪ Monitoring programs by WHO
▪ Public health programs, access to treatments
▪ Testing and preventive measures
• Factors in Control:
○ Biological Factors:
▪ Ready access to treatments (oral rehydration therapy, antibiotics)
▪ Improved diagnosis (dipstick tests)
○ Social Factors:
▪ Public health education
○ Economic Factors:
▪ Access to healthcare, testing, and preventive measures
10 Infectious diseases Page 47

Penicillin inhibits the strengthening of the cell wall
10.2 Antibiotics
• Antibiotics are drugs that kill or stop the growth of bacteria (prokaryotes) but do not harm the cells of the infected organism
• Antibiotics work by interfering with the growth or metabolism of the target bacterium.
○ Inhibit the synthesis of bacterial cell walls
○ Inhibit the activity of proteins in the cell surface membrane
○ Inhibit enzyme action
○ Inhibit DNA synthesis
○ Inhibit protein synthesis
• Antibiotics do not affect viruses because they lack the distinctive cell structures targeted by antibiotics.
○ they do not have cells (or cell walls) and therefore cannot be targeted in any of the ways that an antibiotic targets a
bacterial cell
• Penicillin is not effective against all bacteria (eg. tuberculosis) because the bacteria may have:
○ Thick cell walls which reduce permeability
○ Enzymes which breakdown penicillin
How penicillin affects bacteria:

• Bacterial cell walls are made of peptidoglycans. (molecules containing peptides and sugars held by cross links that form
between them)
• Penicillin prevents the synthesis of the cross-links between the peptidoglycan polymers in the cell walls of bacteria by
inhibiting the enzymes that build these cross-links
○ penicillin is only active against bacteria while they are growing.
• Bacteria live in watery environments so when they are weakened, the cell walls cannot withstand the turgor pressure
exerted on them by the cell contents and the cells burst
• Antibiotic resistance is caused by a mutation in the bacteria

○ When the population is treated with this antibiotic, the resistant bacteria do not die
• The mutated bacteria can reproduce and pass on the genes for antibiotic resistance
• Over time, the whole population of bacteria becomes antibiotic-resistant because the antibiotic-resistant bacteria are best
suited to their environment
○ This is an example of evolution by natural selection
• Some bacteria are resistant to penicillin as they have acquired genes that code for the production of the enzyme β-lactamase
• Consequences of antibiotic resistance:

○ Reduced Treatment Efficacy:
▪ Antibiotic resistance diminishes the effectiveness of antibiotics in treating bacterial infections.
○ Prolonged Illness and Increased Mortality:
▪ Infections caused by resistant bacteria may persist for longer durations.
○ Limited Treatment Options:
▪ Available treatment options become limited.
○ Increased Healthcare Costs:
▪ Treating antibiotic-resistant infections often requires more expensive medications and healthcare resources.
• Reducing the impact of antibiotic resistance:

○ using antibiotics only when appropriate and necessary; not prescribing them for viral infections
○ reducing the number of countries in which antibiotics are sold without a doctor’s prescription
○ avoiding the use of so-called wide-spectrum antibiotics and using instead an antibiotic specific to the infection (known
as narrow spectrum)
○ making sure that patients complete their course of medication, which is essential in the treatment of TB
○ making sure that patients do not keep unused antibiotics for self-medication in the future or give them to someone
else

11.1 The immune system
• Phagocytes are white blood cells that are produced continuously in the bone marrow
○ They're stored in the bone marrow before being distributed around the body in the blood
• They're responsible for removing dead cells and invasive microorganisms
• They carry out what is known as a non-specific immune response
• There are two main types of phagocyte:
○ Neutrophils (form 60% of the WBCs)
▪ During an infection, neutrophils are released in large numbers from their stores, but they are short-lived cells (after
killing and digesting the pathogens, they die)
▪ Remain in the blood
▪ "Patrol" the body tissues
▪ They have receptor proteins on their surfaces that recognize antibody molecule and attach to them
▪ Play a crucial role in the early stages of the immune response by actively seeking out, engulfing, and destroying
pathogens to prevent infection and promote tissue repair.
○ Macrophages
▪ long-lived cells and play a crucial role in initiating immune responses. (larger than neutrophils)
▪ Remain in the organs (lungs, liver, spleen, kidney, and lymph nodes)
▪ Travel in the blood as monocytes
▪ Do not destroy pathogens completely
▪ Cuts up the pathogens up so that they can display the antigens on their surface
▪ The displayed antigens can be recognized by lymphocytes
▪ Response is non-specific
Neutrophils Mode of Action:

1. Chemicals released by pathogen and infected body cells (histamine) attract the neutrophils (this response is called
chemotaxis)
2. The antibodies trigger to stimulate neutrophils to attack the pathogens
3. Attach to the antibody molecule
4. The cell surface membrane extends out around the pathogen and engulfs it (endocytosis)
□ Traps it within a phagocytic vacuole
5. Neutrophil secretes digestive enzymes (released from lysosomes which fuse with the phagocytic vacuole)
6. Enzymes destroy the pathogen (after killing, the neutrophils die and form pus).
Macrophages Mode of Action:

1. Detects/Recognizes (foreign) antigens
□ Has receptors for foreign antigen
2. Engulfs / envelops pathogen
3. Forms vacuole / phagosome
□ Lysosomes contain digestive enzymes, such as lysozyme and proteases, which degrade the internalized pathogen.
4. Antigen presentation (Cuts up the pathogens up so that they can display the antigens on their surface)
Antigens, Self & Non-Self

• Antigens are cell markers that allow cell to cell recognition (distinctive macromolecules)
• Self-antigens are those present on the body's cells, recognized as "self" by the immune system
○ Do not stimulate an immune response
• Non-Self antigens are (foreign) protein / glycoprotein, that stimulates, an immune response / production of antibodies / activation of
lymphocytes
○ from foreign invaders, such as bacteria or viruses.
Stages of phagocytosis:
Neutrophils Monocytes
11 Immunity Page 50
11.1 The immune system (cont.)
• Lymphocytes have receptors complementary to an antigen
○ Highly specific
• Lymphocytes are formed in the bone marrow
○ B-lymphocytes mature in the bone marrow
○ T-lymphocytes mature in the thymus
• In Maturation size increases and receptor proteins form on cell surface
• Difference between B and T Lymphocytes:
○ Area of maturation
○ Immune response is different
Mode of Action of B- Lymphocytes (Humoral Response or Antibody mediated response)
1. Clonal Selection (receptors complementary to the antigen)

2. Clonal expansion (cell undergoes mitosis)
3. Differentiation
a. Plasma B cells - produce antibodies
i. Antibodies are glycoproteins so plasma B cells have more Golgi body and rough endoplasmic reticulum
ii. Survive for a few days
iii. Cannot undergo mitosis
b. Memory B-cells - Produce a faster immune response if the same pathogen enters the body
i. Remain in body system for life
Mode of Action of T- Lymphocytes (Humoral Response or Antibody mediated response)
1. Clonal Selection (receptors complementary to the antigen)

2. Clonal expansion (cell undergoes mitosis)
3. Differentiation
a. Helper T-cells - Form the antibodies
i. Antibodies are glycoproteins so plasma B cells have more Golgi body and rough endoplasmic reticulum
ii. Survive for a few days
□ Forms memory T helper - Produce a faster immune response
□ Activated T helper: releases cytokines which is a cell signaling molecule
 It stimulates the appropriate B lymphocytes/ T killer to undergo immune response and produce
antibodies and increases the rate of phagocytosis by macrophages)
b. Killer T-cells - Destroy infected body cells (or cancer cells)

i. Forms activated T killer that release chemicals into the infected cells
ii. Memory T killer that produce a faster immune response
Secondary immune response
1. Memory cells will react faster to the antigens

2. Forms more memory B lymphocytes and plasma cells
3. Releases more antibodies
4. Faster immune response
• Secondary immune response is much faster because of the memory B-cells.
Primary - slow & little antibodies released

Secondary - faster & lots of antibodies released
11 Immunity Page 51
11.2 Antibodies and vaccination
• Antibodies, or immunoglobulins, are globular glycoproteins
○ Y-shaped proteins produced by plasma cells. (Quaternary structure)
▪ two ‘heavy’ (long) polypeptide chains bonded by disulfide bonds to two ‘light’ (short) polypeptide chains
• Their structure allows them to bind specifically to antigens, neutralizing pathogens and marking them for destruction by other immune
cells.
• The constant region determines the mechanism used to destroy the antigens
• The primary structure (the amino acid sequence) in the variable region is different for each antibody
○ variable region is where the antibody attaches to the antigen to form an antigen-antibody complex
• At the end of the variable region is a site called the antigen-binding site
○ Change greatly giving the antibody its specificity
• The ‘hinge’ region (where the disulfide bonds join the heavy chains) gives flexibility to the antibody molecule
• What do antibodies actually do?
 Bind to viruses and prevent them from infecting our cells
 Bind to flagella on bacteria and slow them down
 Neutralize toxins produced by pathogens
 Clump (agglutinate) pathogens
 Increases the rate of phagocytosis
Active Immunity
• Active Immunity results from the body's own immune response to an antigen
• It triggers the production of antibodies and memory cells.
• Provides long-lasting protection against future infections.
• Example:
○ Natural (Occurs through natural exposure to pathogens in the environment): immunity acquired after recovering from an
infection
○ Artificial (through deliberate intervention): immunity acquired after vaccination.
Passive Immunity
• Passive Immunity results from the transfer of pre-formed antibodies from another individual or source.
• Provides immediate, but temporary, protection against specific pathogens.
• Does not involve the recipient's immune system in generating an immune response.
• Examples:
○ Natural (Occurs through natural exposure to pathogens in the environment): maternal antibodies transferred to a fetus or
newborn through the placenta or breast milk
○ Artificial (through deliberate intervention): The administration of immune serum or monoclonal antibodies.
Vaccination Programs to Control Infectious Diseases:
• Vaccines contain antigens that mimic the pathogens responsible for infectious diseases.
• When administered, vaccines stimulate the immune system to produce an immune response, including the production of antibodies
and memory cells.
• Vaccination programs aim to immunize a large portion of the population, creating herd immunity.
• Herd immunity reduces the transmission of infectious diseases within communities by limiting the number of susceptible individuals.
• By decreasing the prevalence of diseases, vaccination programs help prevent outbreaks, reduce morbidity and mortality rates, and
contribute to public health efforts to control and eliminate infectious diseases.
11 Immunity Page 52
11.2 Antibodies and vaccination (cont.)
Steps of Monoclonal Antibodies (Mabs) production:
1. Antigens are injected into a mouse (or any small mammal)
2. Clonal selection and clonal expansion of B-lymphocytes
3. Plasma cells are produced and extracted from mouse
4. Plasma cells fuse with cancer cells to form hybridoma cells (because plasma cells are short lived, and cancer cells can divide
continuously therefore producing large quantities of a wanted antibody.)
i. Cell membrane fusion by electric fusion
5. Put into "wells" where each well contains 1 cell only
6. The correct hybridoma is identified and cultured
Uses of Monoclonal Antibodies in Diagnosis
• To detect blood clots in the body

○ By producing Mabs that are complementary to fibrin and attach a radioactive material to the Mabs
• Pregnancy tests
• Diagnosing HIV
• Detecting cancer cells
Uses of Monoclonal Antibodies in Treatment
• Traditional cancer therapy (targeted chemotherapy)

○ Produce Mabs that are complementary to the cancer cells (because they have a lot of cell surface receptors) and signal to the
immune system
○ OR Mabs that are attached with drugs
• Treat Infectious diseases
○ Example: rabies
(iii) Outline the use of monoclonal antibodies in the treatment of disease.
11 Immunity Page 53
Past Paper
11 Immunity Page 54
Lab Page 55
2.1 Testing for biological molecules
Molecule Description Result (Color Change)

Starch Add few drops of iodine solution Brown to Blue-black
Reducing Sugars Add equal or more volume of benedict's Blue to Brick red
solution and heat to at least 80°C or
bring to a boil
Non-reducing sugars 1- Negative reducing sugar test Blue to Brick red
2- Boil with HCl (to break glycosidic
bonds (break down to
monosaccharides)) (this is called acid
hydrolysis)
3- Wait for 1 minute
4- Cool, neutralize with sodium hydrogen
carbonate or sodium hydroxide (any
base)(add until no more fizzing)
5- Repeat benedict's test
(if it is a mix of non-reducing and
reducing sugars, do the same
procedure for non-reducing)(the
precipitate will be heavier than the
one obtained)
Proteins Add biuret reagent Blue to lilac
Lipids Emulsion test of lipids: Add ethanol to White layer of emulsion forms
extract, then pour into water in another
test tube. Then shake
• Colorimeter measures small differences in color more precisely
○ It is an instrument that compares the amount of light getting through a solution with the
amount that can get through a sample of pure solvent
Colorimeter is only used when comparing the colors NOT when looking for a color change
• Iodine is given in potassium iodide form because it is not soluble in water
• Biuret reagent
□ Ready mix has both of them mixed together and potassium tartrate to prevent
any reaction between solutions

▪ The intensity of the red color is related to the concentration of the reducing sugar
□ Colors are not fully reliable, so depend on the time (measure the time taken
for first change)
Lab Page 56
Lab Page 57
Lab Page 58
Most common table headers:
Percentage concentration of Time taken for the first appearance Color Color
protein/reducing sugar U (%) of a color change (s) observation symbol
When writing units, put them in brackets or put a / before
When taking time ALWAYS put it as whole seconds (round up) (NEVER as a decimal)
Lab Page 59
Lab Page 60
Serial Dilution Notes
Lab Page 61
Lab Page 62
▪ The intensity of the red color is related to the concentration pf the reducing sugar
□ Colors are not fully reliable, so depend on the time
• Biuret reagent
□ Ready mix has both of them mixed together and potassium tartrate to prevent any
reaction between solutions
Lab Page 63
Food Tests - Precautions
Describe how you would modify this procedure to give a more accurate estimate of U.
Colorimeter is only used when comparing the

colors NOT when looking for a color change
(v) Identify one significant source of error in the investigation described in step 1 to step 12.
Identifying color (color is subjective, so it is hard to judge)
Use a white tile and standardize the range of colors (pick a color from an already specified list of colors),
or use a colorimeter
(vi) State two significant sources of error when carrying out step 7. (all the test tubes put in the hot
water bath at the same time)
Difficult to judge endpoint OR difficult to judge the time of the first color change
Starting all the test tubes all at the same time is difficult to judge because:
You have to subtract to get the time change for 1 test tube
Harder to accurately reach endpoints
OR
Repeat three times, compare, and take average
Your result for U may be anomalous. State how you could confirm that your result for U is correct.
Repeat three times, compare, and take average
Theory question at the end of question is (most probably) ALWAYS:
water potential
transport in plants
kinetic energy and factors affecting enzymes
Lab Page 64
Whenever talking about enzymes (in part B) ALWAYS mention enzyme substrate complex and active site.
Lab Page 65
Enzymes - Precautions
Suggest and explain how increasing the temperature by 10°C above room temperature would affect the results
you obtained in (b)(iii).
Immobilized Enzymes
Using syringes to drop by drop:
Lab Page 66
Lab Page 67
Potato Osmosis Experiment
Sources of error: difficulty of measuring and cutting pieces of potato to correct dimensions
Lab Page 68
Use pH values on
either side of the
optimum pH
according to
results
Lab Page 69
Microscopes - Make a comparison
Lab Page 70

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1.

1 The microscope in cell studies

Light microscope Electron microscope

1 decimeter (dm) = 10 centimeter (cm)

1 Cell Structure Page 1

1 Cell Structure Page 2

2. Endoplasmic reticulum (ER)

3. Golgi Apparatus (Larger complex in animal cells)

1 Cell Structure Page 3

5. Mitochondria (1 - 2.5 μm)

6. Ribosomes (20-22 nm)

1 Cell Structure Page 4

9. Microvilli (50 to 550 nm)

9. Centrioles (only in animal cells)

10. Chloroplast (only found in plant cells) (3-10 μm)

• Contains photosynthesis pigments

Unique structures of a plant cell:

11. Cellulose cell wall

• Plant cell VS Animal Cell:

1 Cell Structure Page 5

13. Cell surface membrane (present in ALL living cells) (7 nm)

1 Cell Structure Page 6

• Prokaryotic Cells (Typical Bacterium) (1 - 5 μm):

• Prokaryotic Cell VS Eukaryotic Cells:

Prokaryotic Cell Eukaryotic Cell

• All cells, whether prokaryotic or eukaryotic, share these four features:

• Plant tissues found in roots stems and leaves

1 Cell Structure Page 7

Smooth ER Lipid synthesis

Golgi Modification of proteins

Lysosome Autophagy (breakdown of

Mitochondria Production of ATP and the

Ribosomes Production of proteins by

Cell Selective barrier between

Centrioles Mitotic Spindle

Chloroplast Site of photosynthesis

Vacuole - - Maintain cell turgidity

1 Cell Structure Page 8

Molecule Description Result (Color Change)

• Colorimeter measures small differences in color more precisely

• Iodine is dissolved in potassium iodide because it is not soluble in water

• Benedict's Reagent is copper (II) sulfate in an alkaline solution

2 Biological molecules Page 9

• α-glucose and β-glucose are isomers of glucose.

• All organic molecules contain hydrogen and carbon

2 Biological molecules Page 10

• For storage of sugars:

□ Amylopectin: (α-1,4 glycosidic linkage with α-1,6 glycosidic branches)

• Many cellulose molecules form microfibrils

• Glycogen and amylopectin similarities:

2 Biological molecules Page 11

Compare and contrast between phospholipids and triglycerides:

1. Both contain glycerol

2 Biological molecules Page 12

• Amino acids are the building blocks of proteins.

This is a condensation reaction so water is released. The resulting molecule is a dipeptide

2 Biological molecules Page 13

2 Biological molecules Page 14

• Water is a major component of cells (70%-90%)

2 Biological molecules Page 15

2 Biological molecules Page 16

Lock and Key theory:

Induced Fit hypothesis: