YEAR 12

BIOLOGY

BIOLOGY NOTES

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INDEX

1.1 CELL STRUCTURE . . . . . . . . . . . . . 8Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . 9

Types of microscopy 9Magnification and Resolution 10Magnification Formula 11Graticule calculations 11Practical light microscopy 12Using a light microscope 13Viewing a sample 13

Eukaryotic cells and organelles . . . . . . . . . . . . . . 14Eukaryotic cell structure 14Structure and function of organelles: 16The cytoskeleton 20

1.2 BIOLOGICAL MOLECULES . . . . . . . . 21Water . . . . . . . . . . . . . . . . . . . . . . . . . . . .22

Liquid properties: 22Structure and Polarity: 23Hydrogen bonding: 24

Biological Molecules and Their Chemical Elements . 26

Carbohydrates . . . . . . . . . . . . . . . . . . . . . . .27Monomers 27Polymers 28

Lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Protein . . . . . . . . . . . . . . . . . . . . . . . . . . .32Amino acid general structure and peptide bonding 32The Levels of Protein Structure 33Globular and Fibrous Proteins 34

Inorganic ions . . . . . . . . . . . . . . . . . . . . . . 36

Biochemical tests . . . . . . . . . . . . . . . . . . . . .37Benedict’s test for reducing and non-reducing sugars 37Determining glucose concentration: 38Tests for other molecules: 39Thin Layer Chromatography 39

Nucleic acids . . . . . . . . . . . . . . . . . . . . . . . . 41Nucleotides, ATP and ADP 41Polynucleotides and DNA 43Functions of DNA 43Base Pairing 44DNA purification 44DNA replication 44The Genetic Code 45Transcription and Translation of Genes 46

1.3 ENZYMES . . . . . . . . . . . . . . . . 48Enzymes — biological catalysts . . . . . . . . . . . . 49

Enzyme structure 50Activation energy 51

Influencing the action of enzymes . . . . . . . . . . . .52Cofactors 52Physical factors 53Investigating rates — Catalase activity 54Enzyme inhibitors 55Enzymes in metabolism 56

1.4 BIOLOGICAL MEMBRANES . . . . . . 57Structure and function . . . . . . . . . . . . . . . . . 58

Role of Membranes 58The Fluid Mosaic Model 59Membrane Permeability 60

The Movement of Molecules Across Membranes . . . . 61Active and passive processes 61

1.5 CELL DIVISION AND DIVERSITY . . . 65The cell cycle . . . . . . . . . . . . . . . . . . . . . . . 66

Mitosis 67Meiosis 69

Diversity of cells . . . . . . . . . . . . . . . . . . . . . .72Bodily organisation 72Specialised cells 73Tissues 75Stem Cells 76

2.1 EXCHANGE SURFACES AND BREATHING . . 78Exchange surfaces . . . . . . . . . . . . . . . . . . . 79

Exchange surfaces 79Features of good exchange surfaces 80Exchange in animals 80

Exchange in mammals . . . . . . . . . . . . . . . . . . 83Mammalian gas exchange 83Structures and tissues 84

2.2 TRANSPORT IN ANIMALS . . . . . . . 87Circulatory systems . . . . . . . . . . . . . . . . . . . 88

Types of circulatory system 88Blood vessels 89

Transport in the blood . . . . . . . . . . . . . . . . . . 90Haemoglobin and oxygen 90Transporting carbon dioxide 91Tissue fluid formation 93Composition of plasma, tissue fluid and lymph 94

The Heart . . . . . . . . . . . . . . . . . . . . . . . . . 95Structure 95Cardiac cycle 96Electrocardiogram (ECG) traces 100

2.3 TRANSPORT IN PLANTS . . . . . . . . 102Transport and transport tissues . . . . . . . . . . . . 103

Transport systems 103Xylem and Phloem 104Translocation 105

The transport of water . . . . . . . . . . . . . . . . . 107Water uptake at the roots 107Water transport in the xylem 109Transpiration from the leaves 111

Adaptations to water availability . . . . . . . . . . . . 113

3.1 COMMUNICABLE DISEASE . . . . . . 115Pathogens . . . . . . . . . . . . . . . . . . . . . . . . 116

Introduction to pathogens 116Examples of pathogens 117Transmission of pathogens to animals 118Transmission in plants 119

Plant defences . . . . . . . . . . . . . . . . . . . . . . 120

Non-specific defences in animals . . . . . . . . . . . . 122Primary defences 122Non-specific secondary defences 124Phagocytosis 125

The Specific Immune Response . . . . . . . . . . . . 126Immune cells and molecules 126Cell signalling and expansion 128Auto-immunity 128Antibody structure 129Antibody function 129Primary and secondary responses 130

Immunity, Vaccination and Medicines . . . . . . . . . 131Types of immunity 131Types of vaccination 131Sources of medicines 132Antibiotic resistance 134

3.2 BIODIVERSITY . . . . . . . . . . . . . 135Measuring Biodiversity . . . . . . . . . . . . . . . . . 136

Levels of Biodiversity 136Sampling in a habitat 137Sampling plants and animals 138Species Diversity 139Simpson’s Index of Biodiversity 139Genetic Diversity 140

The Importance of Biodiversity . . . . . . . . . . . . . 141Factors affecting biodiversity 141Reasons to maintain biodiversity 142

Conservation . . . . . . . . . . . . . . . . . . . . . . . 144In situ conservation 144Ex situ conservation 145National and International Agreements 146

3.3 CLASSIFICATION AND EVOLUTION . 148Classification . . . . . . . . . . . . . . . . . . . . . . . 149

Classification 1495 Kingdom Classification 150Evidence in Classification 151Three-Domain Classification 152Phylogeny 153

Evolution . . . . . . . . . . . . . . . . . . . . . . . . . 154Natural Selection and Evolution 154Darwin and Wallace 155Evidence for Evolution 156Adaptation 157Modern Evolution 158

Variation and Statistical Tests . . . . . . . . . . . . . 159Types of variation 159Quantifying Variation with Statistical Tests 160Student’s t - test: 161

MODULE 1

Foundations in Biology

1.1 Cell Structure

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Microscopy

Specification Points Covered

a) the use of microscopy to observe and investigate different types of cell and cell structure in a range of eukaryotic organisms

b) the preparation and examination of microscope slides for use in light microscopy

c) the use of staining in light microscopy

d) the use and manipulation of the magnification formula magnification = image size/object size

e) the difference between magnification and resolution

f) the representation of cell structure as seen under the light microscope using drawings and annotated diagrams of whole cells or cells in sections of tissue

Types of microscopyThere are four main types of microscope For the exam you need to know their names, their main features, the differences between them and what kind of images they produce

Optical Laser scanning/ confocal

Transmission electron

Scanning electron

Equipment

Images produced

Max magnification X1,500 X1,500 X2,000,000 X200,000

Resolution 200nm 160nm 0 1nm 0 1nm

2.1.1 Cell Structure

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Des

crip

tio

nOptical microscopes shine a light through a sample They were the first microscopes to be invented and today they are used to look at whole cells and tissues

Confocal or Laser Scanning Microscopes use laser beams to analyse a sample point by point These microscopes can look at different depths of a sample making them useful in medical practise

Transmission electron microscopes (TEM) use electromagnets to transmit an electron beam through a sample Denser parts of the specimen absorb more electrons so appear darker

Scanning electron microscopes (SEM) fire a beam of electrons at a specimen This beam knocks electrons off the any surface it hits, and it is these electrons that are detected to produce a 3D scan

Pro

s

• Relatively inexpensive

• Portable and can be used in the field

• Capable of studying whole, living species

• Operable with minimum training

• Images are higher resolution than optical microscopes

• Lasers can scan to different depths in living tissue

• Computer programs can combine multiple images

• TEM has the highest resolution and magnification of any microscope.

• SEM can form complex 3D images of a sample

• Magnifications and resolutions much higher than light microscopes

Co

ns

• Relatively low resolution and magnification

• Specimens often need staining to show specific organelles

• Relatively low resolution and magnification

• Expensive equipment requiring high level training

• Specimens require staining with fluorescent dye

• Large and expensive machinery with high level of training required

• Specimen must be dead

• Staining salts are potentially hazardous

• Large and expensive machinery with high level of training required

• Specimen must be dead

• Specimen has to be mounted in a vacuum

Magnification and Resolution

• Magnification is how much bigger an image appears enlarged by a microscope compared to the original object viewed with the naked eye.

• Resolution is the clarity of an image, so it is determined by the ability of an optical instrument to produce a finely detailed image. Specifically, resolution is defined as the ability of an instrument to distinguish between two points that are close to-gether.

Even at high magnifications some organelles may not be found using an optical microscope because they are too small to be distinguished (eg Ribosomes are 20nm), that is, the resolution of the microscope isn’t great enough to tell them apart from the surroundings

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Magnification Formula

The following formula can help us determine the actual size of the structure we are looking at through the microscope, if we know the magnification and the image size It can also help us determine the magnification if we know the actual object size, and the image size

E g we look through a light microscope and observe squamous epithelial cells Through the microscope, they appear 50mm in diameter The lens piece we are using as a  agnification of x1200 What is the actual diameter of the cell?

Graticule calculationsGraticules are scales placed in a microscope to allow its user to measure the size of a specimen Before a specimen can be measured the eyepiece graticule must be calibrated

Stage graticule (SG): a small scale that is placed on the microscope stage It has a  efined scale, eg it may be 1mm (1000 µm)

Eyepiece graticule (EPG): a small scale placed in the eyepiece that has no defined scale

To calculate the size of an object you need to compare the EPG units (EPU) to the SG units (SU) Don’t forget that the value of each EPU changes at different magnifications!

Example: At x400 magnification the full length of the EPG (ten units) is equal to 2 units on the SG (also ten units in total). How long is each EPU?

Standard SU = 100µm 2 SU = 200µm 10 EPU = 200µm

Therefore, at 400x magnification 1 EPU = 20µm

The practise question given was just an exam-ple Here are the true values of total magnifi-cation and EPU values for most modern micro-scopes used in schools:

Total magnification

Value of one EPU (µm)

X40 25

X100 10

X400 2 5

X1000 1 0

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Practical light microscopyOptical or light microscopes are the most commonly used in labs due to expense and convenience of use For the exam you must be able to describe how to use a light microscope and why we often need to use stains to properly view specimens

To use a light microscope, you must first prepare a slide for viewing:

DRY MOUNT: WET MOUNT:

1. Take a thin slice of your specimen

2. Using tweezers place your slice in the middle of a clean slide

3. Place a cover slip on top of your slice

1. Pipette a small drop of water onto slide

2. Using tweezers place slice and then cover slip on top of water drop, ensuring there are no air bubbles under cover slip

3. Add stain by placing a drop at one edge of the cover slip and a paper towel at the opposite edge to draw stain through.

EXAM TIPRemember 1mm = 1,000µm = 1,000,000 nm — get used to these

conversions because they are important in biology and it will save you precious time in the exams!

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Using a light microscope 1. Select lowest powered objective lens

2. Clip desired slide onto stage

3. Use coarse adjustment knob to raise stage close to objective lens

4. Look down eyepiece and use fine adjustment knob to focus the image

5. Swap to higher power objective lenses for greater magnification taking care not to break slides on the ends of the longer lenses.

Viewing a sampleMany specimens we want to look at are transparent or colourless and this makes viewing them in detail difficult Scientists have come up with a few ways of getting around this:

• Light interference — using the refraction of polarised light beams in a complex se-ries of steps, objects that are normally transparent can be made to appear opaque

• Use of a dark background — a simpler technique to increase the contrast in a specimen by making the surroundings very dark

• Staining — specimens can be washed with different stains to highlight different organelles or tissues (eg Sudan red stains lipids bright red and acetic orcein stains DNA a dark red)

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