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AS Biology A OCR Textbook Summary Notes, Post 2015 Spec
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Summary notes of the official OCR AS Biology A OCR Student Book by Ann Fullick. Made by an A* Biology student.
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OCR A Biology Module 2 (Foundations in Biology) Notes
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Biology ASModule 2 Foundations in Biology
Basic Components of Living Systems
Light Microscopy
• Don’t say microscope images are clear but high resolution.
• Light Microscopes: Uses light underneath sample and glass lenses to see objects magnified. There
is a course and fine focusing knob. Turret where can switch objective lens. Stage where specimen
placed.
• Lenses in Light Microscope: Objective lens magnifies image and then magnified again by eyepiece
lens. Means much higher magnification. To find magnification, multiply eyepiece magnification by
objective lens magnification.
• New Evidence and Theory: Theories proposed, accepted or disproved as new evidence is gained
e.g. as technology advances. Current knowledge may be uncertain and subject to change.
Scientific community should re- test hypothesis.
• Pros of Light Microscope:
- Inexpensive to buy and operate.
- Portable so can be used out in field.
- Can observe living or dead specimens.
- Simple sample preparation which not usually led to distortion.
- Natural colour of sample seen or stains used.
• Cons of Light Microscope:
- Up to x2000 magnification.
- Resolving power is 200nm- can’t see small organelles.
• Four Sample Preparations: For light microscope…
- Dry Mount: Solid specimen viewed whole or sectioned. E.g. muscle tissue or plants.
- Wet Mount: Specimens suspended in droplet of liquid such as water or immersion oil. Cover
slip at angle. Prevents dehydration of tissues. E.g. aquatic samples and living organisms.
- Squash Slides: Wet mount prepared. Lens tissue used to press down cover slip. Damage
avoided to specimen by squashing between two microscope slides. Makes it easier to see cells.
E.g. root tip.
- Smear Slides: Sample smeared to create thin, even coating on slide. E.g. blood.
• Select thin slices or use sharp blade to ensure individual cells visible and maximum light can
penetrate.
• Stains: Images have low contrast as cells don’t absorb light. Cytosol and other structures are
transparent. Stains are dyes which increase contrast as different components within cell bind to
stains to different degree so makes organelles become easier to see. Clearer image can be
obtained.
,• Types of Stains: Crystal violet or methylene blue are positively charged which are attracted to
negatively charged materials in cytoplasm. Nigrosin or Congo red dyes are negatively charged so
are repelled and stay outside the cell. The cell is unstained and stands out against background.
• Differential Staining: Distinguishes two types of organisms or different organelles which would
otherwise be hard.
• Scientific Drawings: Must include title and magnification. Use as much of paper or box given as
possible. Draw smooth, continuous lines, no shading and only outline of structures. Proportions
must be correct. Label lines must not cross, no arrow heads and parallel to top of page AND drawn
with ruler.
Magnification and Calibratio n
• Magnification: How many times larger the image is than the actual size of the object being viewed.
Increasing magnification does not increase detail as resolution needs to be increased.
• Resolution: It is the ability to distinguish individual objects as separate entities.
• Electron Beams: Resolution increased using electron beam as smaller wavelength than light.
Smaller objects can be seen separately without diffraction blurring.
• Calculating Actual Size: Image Size = magnification x actual size. I = AM.
- Keep same units. Measure in mm and then usually convert to smaller unit. Magnification has
no units.
- Image Size- measure scale bar or image with ruler.
• Sometimes will ask to work out actual size but use method below instead if able to work out value
of 1 EPU.
• Eye Piece Graticule: Eyepiece graticule has no units and unchanged with different objective
lenses. Eyepiece graticule is a microscope eyepiece with scale from 1 to 100 and each big division
is 10. Even when says 1 and 4 for the big divisions, it is 10 and 40.
• Micrometre: Stage micrometre is slide with accurate scale etched into it. Usually 10 big divisions
which are 100 µm each. So 1000 µm or 1mm is whole micrometre scale.
• Calibrating Light Microscope Method:
1- Line up eyepiece graticule with micrometre.
2- Count of eyepiece divisions and note number micrometres between points of coincidence
number so doesn’t have to start from zeros.
3- Do calculation to give calibration factor-
One eyepiece division in micrometres = number of micrometres/ number of eyepiece divisions.
4- Can use this value of one eyepiece division in micrometres and multiply by how many eyepiece
divisions specimen measures to get measurement of specimen in micrometres.
Other Microscopes
• Electron Microscope: Microscope with beam of electrons to illuminate the specimen. Two types
of electron microscope- TEM and SEM.
• Pros of Electron Microscope:
- Can have magnifications up to x500, 000.
- High resolution.
• Cons of Electron Microscope:
- Expensive to buy and operate.
- Large.
- Inside is vacuum so electron beams travel in straight lines so only dead specimens.
- Black and white images (can be coloured digitally).
, - Preparation process is complex and distorts material. May produce artefacts which are
structures that have been created during processing of specimen.
• Transmission Electron Microscope: TEM. An electron microscope
where a beam of electrons transmitted through specimen and focused
to produce an image. Has best resolution of 0.5 nm.
• Scanning Electron Microscope: SEM. An electron microscope where
beam of electrons sent across surface of specimen. Reflected electrons
are collected. Resolving power (resolution) is 3- 10 nm. 3D images of
surfaces produced.
• Artefacts: Bubbles trapped under slide in light microscope. In electron
microscope, changes in ultrastructure of cell include loss of continuity
of membrane, distortion in organelles and empty spaces in cytoplasm.
Experience can distinguish artefact.
• Fluorescent Microscope: Light microscope has developed. In
fluorescent microscopes, a higher light intensity illuminates specimen
that has been treated with fluorescent chemical. Fluorescent absorbs
and re-radiates light so light of a longer wavelength emitted and
produces magnified imaged.
• Laser Scanning Confocal Microscopy: A fluorescent microscope. Moves
a single spot of focused light across specimen (point illumination) to produce 2D image. 3D image
produced by creating different images at different focal points.
• Pin-Hole: Emitted light from specimen is filtered through a pin- hole aperture so only light radiated
from very close to the focal plane is detected, so improves resolution.
• Uses:
- Non- invasive so diagnoses eye diseases.
- Can see distribution of molecules so used in developing drugs.
Eukaryotic Cell Structure
• Prokaryotic: Unicellular organisms. No nucleus. No membrane bound organelles.
• Eukaryotic: These cells make up organisms like animals, plants, fungi and protoctista. Contain
nucleus and both membrane bound and non- membrane bound organelles. Both unicellular and
multicellular.
• Cytoplasm: Internal fluid composed of cytosol (water, salts and organic molecules), and
organelles. Reactions take place in cytoplasm.
• Membrane: Selectively permeable and control movement into and out of the cell and
organelles.
• Ultrastructure: It is those features which can be seen using an electron microscope. Everything
below can’t properly be seen with a light microscope.
• DNA: Nucleus contains coded genetic information as DNA. DNA directs the synthesis of all
proteins. So indirectly controls metabolic activities of cell, as many of proteins are enzymes
needed for metabolism. Extra DNA in mitochondria and chloroplast.
• Nuclear Envelope: DNA is contained within a double membrane called nuclear envelope to
protect DNA.
• Nuclear Pores: Nuclear envelope contains nuclear pores for molecules to move into and out, e.g.
mRNA to ribosomes- give examples where can.
,• Chromosomes: DNA supercoiled with proteins histones to form chromatin. Chromatin coils and
condenses to form chromosomes. Chromosome only visible when cells divide.
• Nucleolus: It is an area within the nucleus that produces ribosomes. Dark staining area in
nucleus.
• Mitochondria: Site of the final stages of cellular respiration, where ATP produced. More active
cells, more mitochondria.
- Can make own enzymes in its ribosomes.
- Have a double membrane. Inner membrane is highly folded to form cristae which contains
enzymes used in aerobic respiration.
- Fluid interior is called the matrix.
- Have small amount of DNA called mitochondrial (mtDNA) DNA.
• Vesicles: They transport materials inside the cell.
• Lysosomes: Specialised forms of vesicles. Contain hydrolytic enzymes. Break down waste
materials in cell including pathogens. Also role in apoptosis. Enzymes in lysosomes work best in
acidic environments, so not good in cytoplasm where neutral.
• Cytoskeleton: In eukaryotes. Cytoskeleton has three components…
- Microfilaments: Contractile fibres formed from protein actin. Control cell movement and cell
contraction during cytokinesis.
- Microtubules: Made of globular tubulin proteins. Tubes that give support to shape of cell.
Control organelles movement using ATP and change in length of microtubules. Spindle fibres
made of microtubule.
- Intermediate Fibres: Mechanical strength to cells.
• Centrioles: Not in flowering plants, bacterial and most fungi. Composed of microtubules. Two
associated centrioles form centrosome which assembles the spindle fibres during cell division.
Position flagella and cilia.
• Flagella/ Undulipodium: Enables motility.
• Cilia: Moves materials along tubes.
• 9+2 Arrangement: Both cilium and flagella contains two central microtubules surrounded by
nine pairs of microtubules arranged. Known as 9+2 arrangement. Pairs of parallel microtubules
slide over each other causing it to move back and forth.
• Endoplasmic Reticulum: It is a network of membranes enclosing flattened sacs called cisternae.
Connected to nucleus. Secretory cells that release hormones and enzymes have more of this.
- Smooth Endoplasmic Reticulum: Lipid and carbohydrate production.
- Rough Endoplasmic Reticulum: Ribosomes bound to surface. Protein synthesis and transport.
• Ribosome: Can be in cytoplasm or endoplasmic reticulum. Not membrane- bound. Site of
protein synthesis. Mitochondria and chloroplasts contain ribosomes.
• Golgi apparatus: Formed from cisternae. Modifies proteins and packages proteins into vesicles.
Also produces lysosomes.
• Protein Production: e.g. hormones and enzymes.
- Protein synthesised on ribosomes bound to rough endoplasmic reticulum.
- Pass into endoplasmic reticulum and packaged into vesicles.
- Vesicles transported to Golgi apparatus via cytoskeleton.
- Proteins structurally modified in Golgi apparatus and the proteins stored in vesicles.
- Secretory vesicles transport proteins to plasma cell membrane, releasing contents by
exocytosis.
- If protein made in free ribosomes not attached to RER, then protein stays in cytoplasm.
, Pay attention
to relative
sizes.
Ribsomes
often smallest
organelle.
Ultrastructure of Plant Cells
• Plant Cells: Have all organelles just read. Animal cells don’t have below.
• Cellulose Cell Wall: Cellulose is a carbohydrate. Permeable. Cell wall protects against pathogens.
Fungi cell wall made of chitin.
• Vacuoles: Contain cell sap. Many have permanent vacuoles which maintain turgor so contents
of cell push against cell wall for rigidity. If vacuoles in animal cells they are small and transient
(not permanent).
• Tonoplast: The membrane of the vacuole. Selectively permeable to some small molecules.
• Chloroplast: Responsible for photosynthesis, Like mitochondria, double membrane structure
and contain DNA and ribosomes to make proteins. Fluid interior of chloroplast is stroma. Internal
membranes provide large surface area for proteins needed in photosynthesis.
• Starch produced by photosynthesis is present in starch grains.
• Thylakoids: They are internal network of membranes forming flattened sacs.
• Grana: Several thylakoids stacked together are granum. The grana (pl.) are joined by membrane
called lamellae. The grana contain chlorophyll pigments, where light- dependant reactions occur
during photosynthesis.
Prokaryotic and Eukaryotic
• Extremophiles: Prokaryotic cells among earliest forms of life on Earth when had a very hostile
environment. Became adapted to living in extremes of salinity, pH and temperature.
Extremophiles today found in hydrothermal vents and salt lakes. Usually domain Archaea.
,• DNA: DNA in prokaryotic is not contained within a nucleus and only have one chromosome, which
is supercoiled to make compact. Genes on the chromosome grouped in operons so number of
genes on or off at the same time. Genes in eukaryotic switched on or off individually. Prokaryotic
have extra circular DNA- plasmids.
• Organelles: Prokaryotic have a less complex cytoskeleton. Eukaryotic have membrane bound
organelles and some (named) organelles that prokaryotic doesn’t have.
• Ribosomes: In prokaryotic the ribosomes (70S) are smaller than those in eukaryotic (80S).
• Cell Wall: Prokaryotic cell wall made from peptidoglycan (murein), a polymer.
• Flagella: In prokaryotic, no 9+2 arrangement. Energy to
rotate flagellum is supplied by chemiosmosis and not ATP
in eukaryotic flagella. A basal body attaches it to the cell-
surface membrane.
• Reproduction: Binary fission in prokaryotic cells. Asexual
or sexual in eukaryotic cells.
Biological Molecules
Biological Molecules
• Molecules: Cells and cellular components are composed from atoms. Carbohydrates- carbon,
hydrogen, oxygen- ratio Cx(H2O)x. Lipids- carbon, hydrogen and oxygen. Proteins- carbon,
hydrogen, oxygen, nitrogen and sulphur.
• Organic Molecules: Carbon which can form 4 bonds. Hydrogen can form 1 bond. Oxygen can form
2 bonds. Nitrogen can form 3 bonds. Also phosphorus and sulphur.
• Ions: Ions in solutions are called electrolytes. Inorganic ions may act as cofactors. Need to know
H+, NH4+ ammonium, NO3- nitrate, HCO3- hydrogencarbonate and PO43- phosphate.
• Polymers: Polymers are long molecule made up by linking of multiple monomers.
Water
• Polar Molecules: Covalent bonds share electrons. The atom with the greater share of electrons
will be slightly negative (δ-). Other atom in the bond slightly positive (δ+).
• Water: Oxygen in water has greater share of electrons δ-. Hydrogen in OH bond is δ+.
• Hydroxyl Group: Many organic molecules have OH group so are slightly polar.
• Hydrogen Bonds: The positive and negative regions of individual polar molecule attract each other
and form hydrogen bonds between molecules. They are weak interactions.
• Properties of Water…
- High Specific Heat Capacity: Takes a lot of energy to increase temperature of water- high
specific heat capacity. Helps maintain body temp for enzymes.
- Good Solvent: Water molecules attracted to ions and polar molecules e.g. proteins. Good for
transport of dissolved substances in blood and xylem.
- High Latent Heat of Vaporisation: Lot of thermal energy need to cause water to become water
vapour. So water used efficiently.
, - Cohesion and Adhesion: Cohesion means water molecules will stick together when
transported due to hydrogen bonding. Adhesion occurs between water molecules and other
polar molecules. E.g. water up xylem.
- Less Dense as Solid: Ice less dense than liquid water so ice floats. As water cools, the hydrogen
bonds fix the positions of the molecules slightly further apart than distance in liquid state.
- Remember examples as well.
Carbohydrates
• Saccharides: Carbohydrates are polymers also known as saccharides/ sugars. -ose suffix is a
carbohydrate. Single sugar is monosaccharide.
• Two monosaccharides linked by glycosidic bonds = disaccharide. Two or more monosaccharides
linked = polysaccharide e.g. glycogen, cellulose and starch.
• Glucose: C6H12O6. A hexose monosaccharide has six carbons.
- Product of photosynthesis.
- Glucose used as respiratory substrate, source of energy/ ATP and converted into maltose.
- Polar and soluble molecule as hydrogen bonds form between hydroxyl groups and water
molecule. So soluble in cytosol and easily transported.
- Small molecule so can diffuse across cell membranes.
• Two structural variations of glucose- alpha (α) glucose and beta (β) glucose. Alpha glucose is where
hydrogen on C1 is above the ring.
Must learn these.
• Condensation Reaction of Glucose: When two alpha glucose, two H and an O removed from
glucose to form water- a condensation reaction. Leaves an ‘oxygen bridge’. Forms a covalent bond
called 1, 4 glycosidic bonds between C1 and C4 of two monosaccharides. Forms maltose- a
disaccharide.
• Condensation Reaction: Reaction between two molecules resulting in the formation of a larger
molecule and release of water molecule.
• Sucrose: FGS. Fructose, a hexose monosaccharide, in fruit. Fructose + glucose = disaccharide
sucrose/ cane sugar. Fructose is sweeter than glucose.
• Lactose: GGL. Galactose, a hexose monosaccharide. Galactose + glucose = disaccharide lactose.
Lactose found in milk. Glucose is sweeter than galactose.
• Pentose Monosaccharides: Examples are ribose in RNA nucleotides and deoxyribose in DNA
nucleotides.
• Starch: Many alpha molecules joined by glycosidic bonds form two polysaccharides amylose and
amylopectin, collectively called starch. Glucose made by photosynthesis is stored as starch.
,• Amylose: One of the polysaccharides in starch. Alpha glucose joined only by 1-4 glycosidic bonds.
Angle of bond means chain of glucose forms helix. So more compact and less soluble than glucose.
Not branched.
• Amylopectin: Another type of starch. Made by 1-4 glycosidic bonds and 1-6 glycosidic bonds
(condensation reactions between C1 and C6) between alpha glucose. So has branched structure.
Insoluble so good for storage.
• Glycogen: Branched polysaccharide formed from alpha glucose molecules. Equivalent chemical
energy storage molecule to starch in plants, is glycogen in animal and fungi cells.
- Glycogen more branches than amylopectin so more compact.
- Can be hydrolysed quickly.
- Insoluble so good for storage since large. Does not affect water potential of cell.
• Branching: The branching of amylopectin and glycogen make them compact so good for storage.
Branching means more free ends where glucose can be added or removed so speeds up
condensation and hydrolysation for respiration.
• Hydrolysis Reaction: It is the breakdown of a molecule into two smaller molecules requiring the
addition of a water molecule. Glucose stored as starch and glycogen until needed for respiration.
Reaction catalysed by enzymes. Reverse of condensation.
• Cellulose: A polysaccharide. The C1 and C4 in beta glucose are too far to react like alpha glucose
as the hydroxyl group is above the ring. Alternate beta glucose are turned upside down to join
together. 1,4 glycosidic bonds only. Unable to coil or form branches so straight chain molecule.
• Individual cellulose molecules make hydrogen bonds with each other forming microfibrils, which
form macrofibrils, which form fibres. Fibres are insoluble. Alpha forms no fibres. Cellulose has
staggered ends, giving strength.
Testing For Carbohydrates
• Reducing Sugars: Saccharides that donate electrons resulting in the reduction (gain of electrons)
of another molecule. All monosaccharides and some disaccharides are reducing sugars.
• Benedict’s reagent: An alkaline solution of copper sulphate (II) used in chemical tests for reducing
sugars. A brick- red precipitate indicates a positive result. Green is very low concentration of
reducing sugar. Yellow is low. Orange is medium. Makes test qualitative.
• Method for Test: Place sample in boiling tube. If it is not liquid, grind it up. Add of Benedict’s
reagent. Heat the mixture gently in water bath.
• Benedict’s test: Reducing sugars react with the copper ions in Benedict reagent. Results in
addition of electron to blue Cu2+ ions, reducing them to brick red Cu+ ions. The higher the
concentration of reducing sugars, the more brick-red Cu+ precipitate formed.
• Benedict’s test for Non- Reducing Sugars:. Solution will remain blue.
• Sucrose: Sucrose is non-reducing. But if sucrose is boiled with dilute hydrochloric acid it will give
a positive result with Benedict’s solution. Sucrose has been hydrolysed by the acid to glucose and
fructose which are reducing sugars.
• Reagent Strips: Colour- coded chart, the concentration of the sugar determined.
• Colorimeter: Colorimeter used quantitatively to measure absorbance of light by a solution. The
more concentrated a solution, the more light it will absorb and the less light it will transmit.
Colorimeter needs to be calibrated with distilled water. Can calculate concentration of reducing
sugar present for known range of concentration using calibration curve.
,• Iodine Test: Presence of starch using potassium iodide solution. A colour change from yellow/
brown to purple/ black indicates positive result.
• Imagine you had 50 cm3 of 2 mol/dm3 hydrochloric acid. You could add 50 cm3 of water to it so
that you get 100 cm3 of 1 mol/dm3 hydrochloric acid.
• To get from 100cm3 of 0.8M to 50cm3 of 0.8M, just halve the mixture.
• Volume of water to add = (starting concentration/target concentration -1) × starting volume.
• Making Serial Dilutions:
1- Get to same starting point e.g. get to 300 to get to 3.
2- Use numbers/ fractions but must add up to 10/100. E.g. 75cm3 of 400mM + 25cm3 of water =
100cm3 of 300 mM. Take what you need from previous and add up water to make it up.
3- Make it to x10/ x100 solution by having 10 cm3 of solution and 90 cm3 of water. Resulting
solution would always be divided by 10 but 10cm3/ 100cm3 of it all together.
Lipids
• Lipids: Non- polar molecule. Means lipids not soluble in water as ‘like’
dissolves ‘like’ only. Lipids are macromolecules not a polymer. Carbohydrate
is both.
• Triglycerides:
- One glycerol molecule and three fatty acids make a triglyceride.
- Glycerol is an alcohol. Fatty acids are carboxylic acids.
- Esterification: Both contain hydroxyl group so form ester bonds to make
triglyceride. Leaves ‘oxygen bridge’ between O-C. Example of
condensation reaction.
- Produces three water molecules.
- Hydrolysis: When triglyceride broken down, need three water molecules to reverse reaction.
• Saturated: Fatty acid chains that have no double C=C bond.
• Unsaturated: Fatty acids with double C=C bond. One double C=C bond is monounsaturated. Two
or more C=C bond is polyunsaturated. Double C=C bond causes molecule to kink and therefore
can’t pack as closely together. Makes them liquid at room temperature rather than solid.
• Plants: Plants contain unsaturated triglycerides, healthier than saturated triglycerides.
• Phospholipids: Phospholipids are modified triglycerides.
- One of the fatty acid chains in triglyceride a phosphate group instead.
- Phospholipid Tail: Have a hydrophobic non- polar fatty acid chain. The tails repel water but
mix with fat.
- Phospholipid Head: The inorganic phosphate ions (PO43-) are negatively charged, making them
hydrophilic so soluble in water. Head is not polar.
• Hydrophobic and Hydrophilic: Polar/ charged molecules are hydrophilic. Non- polar molecules
are hydrophobic. Hydrophilic is the physical property of a molecule which is attracted to water.
Hydrophobic is the physical property of a molecule which is repelled by water.
• Sterols: Also known as steroid alcohols, not fat or oil. Another type of lipid. Has hydrophobic
carbon ring with polar/ hydrophilic OH group.
• Cholesterol: It is a sterol.
- Hydrophobic and hydrophilic portions allows cholesterol to bind to phospholipid to prevent
cell membrane being too fluid at high temp.
- Or prevent phospholipids crystallising at low temp.
, - Cholesterol also reduces permeability to polar molecules.
• Roles of Lipids:
- Membrane formation.
- Long term energy storage- since fats are insoluble so do not affect water potential of cell..
Fats contain more energy per molecule.
- Electrical and thermal insulation.
- Source of steroid hormones.
- Source of cholesterol.
• Emulsion Test: Add ethanol + water. Shake. If mixture turns cloudy (white emulsion layer forms
on top), indicates presence of lipid. If solution remains clear, test negative.
Structure of Proteins
• Peptides: Peptides are polymers made of a chain amino acids (the monomers).
• Amino Acid: All amino acids have basic structure- residual group, central carbon, hydrogen, amine
group and carboxyl group (acidic). R- Group- the variable group which leads to different amino
acids. Twenty amino acids in body.
• Dipeptide:
- Amino acids join when the hydroxyl group in carboxyl group of one amino acids reacts with
hydrogen in amine group in other amino acid.
- Peptide bond is formed between two amino acids. The peptide bond is between C - N.
- Dipeptide and water formed- condensation reaction.
• Polypeptide: Three or more amino acids joined together by peptide bonds. Reaction is catalysed
by enzyme peptidyl transferase in ribosomes.
• Proteins: Proteins consist one or more polypeptides arranged as a complex macromolecule.
• R- Group Interactions: Different R-groups of amino acids interact forming different types of bond.
This leads to polypeptides folding into proteins. So particular sequence of amino acids leads to
different shape produced. The shapes of proteins are important for its function.
• Thin Layer Chromatography: TLC used to separate and identify a mixture of amino acids in
solution by comparing to known amino acids. In stationary phase layer of silica gel applied. Amino
acid is spotted on pencil line. Paper submerged in mobile phase solvent. Amino acids move
through gel at different rate depending on their solubility in mobile phase.
• Retention Value: Rf value = distance travelled by pigment or component/ divided by distance
travelled by solvent. Can compare Rf value for known substances to identify. Don’t work out from
solvent front.
• Primary Structure:
- Sequence in which amino acids are joined.
- Directed by DNA.
- Only bonds are peptide bonds.
• Secondary Structure:
- The oxygen, hydrogen and nitrogen of the repeating structure of amino acids form hydrogen
bonds. (R- groups not involved here).
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