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Microscopes

Magnification: number of times larger the image appears compared to actual actual size of object
Resolution: clarity of image ability to distinguish between two objects that are very close
together
...
1nm

Scanning electron microscope
secondary electrons to bounce off specimen surface and focus on to a screen
produces a 3D image
B/w but computer adds false colour
Vacuum & coated with a fine film of metal
magnification of x100 000 & resolution 50nm
Expensive, requires training, sample dead, large

Acetic orcein- binds to DNA- stains chromosome dark red
Eosin- stain cytoplasm
Sudan red- stains lipids
Potassium iodide solution- stains cellulose plant walls yellow & starch granules blue/black
Prepared specimen- dehydrated, embedded in wax- prevent distortion when sliced, thin slices in
chemical to preserve
Transverse- cut cross way & Longitudinal - lengthways

Why stain? to make specimen visible provide contrast and see details- organelles like nucleus

Eye piece graticule- measuring device- placed in eyepiece of microscope- acts as ruler to view object
Stage graticule- Precise measuring device- small scale placed on microscope stage- calibrates value
of eye piece graticule divisions at different magnifications

Value of eye piece division= Number of divisions of eyepiece / Total mag (Eye piece x objective lens)

2
...
1 Biological Molecules

Condensation reaction: two molecules are joined together with the removal of water
Hydrolysis reaction: molecule is split into two smaller molecules with the addition of water

Hydrogen bond: a weak interaction- a slightly –ve charged atom bonded to a slightly +ve charged
hydrogen atom
- Many hydrogen bonds- helps stabilise structure of biological molecules

2 monomers- dimer 2+ monomers- polymer

Molecule
Monomer
polymer
Carbohydrate (C,H,O)
Monosaccharides- glucose
Polysaccharides- starch
Proteins (C,H,O,N,S)
Amino acids
Polypeptides and proteins
Nucleic acids (C,H,O,N,P)
Nucleotides
DNA and RNA

Properties of water

1
...
Density
- Lower density as ice from 4°c to freezing point
- water molecules align themselves in a structure- less dense than water
- allows aquatic animals- stable environment
- water insulated against cold, reduced heat loss

3
...
Cohesion and surface tension
- Cohesion- hydrogen bonding between molecules pulls them together
- Surface tension- surface of water contracts- pulled inwards- surface ability to resist force
applied to it
- Xylem tissue- columns of water- pulled up from roots
- Insects walk on water like pond-skaters

5
...
High latent heat of vaporisation
- amounts of heat energy required to convert substance from liquid-gas
- allows us to cool- sweat
- mesophyll cells- evaporate



Carbohydrates 1: sugars
• Carbon, hydrogen, oxygen
• Source of energy (glucose), store of energy (starch + glycogen)
• structural units (cellulose + chitin)

Monosaccharides
- source of energy
- high C-H bonds
- sugars- sweet
- soluble in water- polar solvent
- straight/ring

Disaccharides- 2 monosaccharides join
together- condensation- glycosidic
bond
...
Maltose = α glucose + α glucose
2
...
Sucrose = α glucose + fructose
Maltose, lactose à reducing sugars
Sucrose à non-reducing sugar

Ribose- component of RNA
Deoxyribose- component of DNA


Carbs 2: polysaccharides as energy stores

Polysaccharides- polymers of monosaccharides
Starch- homopolysaccharides- same monosaccharides (heteropolysaccharides- different)

Glucose – source of energy, reactant in respiration
...

• Polysaccharides are less soluble than monosaccharides

1
...
Amylopectin(plant)

3
...


- hydrogen and hydroxyl groups on carbon 1 are inverted in β glucose
- every other β glucose molecule in chain is rotated by 180°
- 1-4 glycosidic bonds prevent spiralling

Hydrogen bonding within the chain stops spiralling, hydrogen bonding between chains strengthens
and stabilises the molecules
...

Condensation reaction occurs between –COOH of fatty acid and –OH of glycerol, forming ester bond












Carbon double bond- provides kink in structure- make fatty acids- more fluid


Functions of triglycerides:
• Energy source- Hydrolyse ester bonds – glycerol + fatty acids can be broken down into
carbon dioxide + water
...


1
...
Membrane selectively permeable- small & non-polar molecules can move through tails in
bilayer- oxygen and carbon dioxide
...
Membrane- controls what enters + leaves, allowing cell to function to properly

Cholesterol: steroid alcohol – four carbon-based rings
...

















Proteins 1: Amino acids

Amino acid: monomers for all proteins- all proteins have same basic structure

Properties of protein:
• Structural component – muscles made of protein
• Adopt specific shapes and- important as enzymes, antibodies + hormones
• Act as carriers + pores for active transport across the membrane and facilitated diffusion

Structure of amino acid- C,H,O,N (SOME S)

Glycine- R group = H
Alanine- R group = CH3
Cysteine- R group = CH3S

Amino group (-NH2) and carboxyl group (-COOH) at ends

- Amino acids- peptide bonds
- protease enzymes in the intestine break peptide bonds during digestion
...
g
...
Hydrogen Bonds: weak bonds- between δ +ve charged hydrogen in some R groups & δ –ve
charged atoms-R groups- polypeptide chain
...
Ionic Bonds: attractions between –ve charged R groups and +ve charged R groups
3
...

4
...


-

Hydrophilic parts- edge of the polypeptide- close to water
interactions cause twisting of the amino acid chain, changing the shape of the
protein
...

-
Properties + functions of fibrous proteins

1
...
Elastin: cross-linking + coiling makes structure strong + extensible like skin- stretch & lungsinflate
3
...


Properties + functions of globular proteins

1
...


2
...
Pepsin: enzyme- digests protein in stomach- single polypeptide chain

Computer modelling: predicts shape of a protein molecule from its primary structure
- Scans amino acid against database of possible match sequence
- useful for investigating the different levels of structure in a protein molecule
...
3 Nucleic Acids

Nucleotides- biological molecules- pentose sugar & nitrogenous base &
phosphate group-
- forms the monomers of DNA and RNA
- elements C, H,O,N and P
- Phosphorylated nucleotides- Adenosine triphosphate ATP &
adenosine diphosphate ADP

- ADP and ATP: phosphorylated nucleotides- has more than one phosphate group
- ADP- base adenine, sugar ribose and two phosphate groups
- ATP- base adenine, sugar ribose and three phosphate groups
Making and using ATP
Plant + animal cells release energy from glucose in respiration
...
ATP is synthesised from
ADP and inorganic phosphate
...
Energy is stored in the phosphate bond
...


DNA copies itself before cell division- each new cell has the full amount of DNA
...
DNA unwinds- double helix is untwisted- catalysed by enzyme gyrase

2
...
Each original strand acts as a template for a new strand- free phosphorylated nucleotides
join- exposed bases on each original strand, through complementary base pairing

4
...

Hydrogen bonds form between bases
...
Each DNA
molecule contains one new + one original strand
...



How DNA codes for polypeptide:

RNA- single polynucleotide strand- uracil instead of thymine- pairs with adenine

used to make proteins:
• nucleotides with a ribose sugar
• Uracil instead of thymine- pyrimidine
• Single-stranded polynucleotide chain- shorter than DNA
• 3 types- messenger, transfer and ribosomal RNA
Gene: a length of DNA codes for a polypeptide/ length of RNA involved in regulating gene expression

• Each amino acid is coded for by a sequence of 3 bases (triplet) in a gene
• Different sequences of bases code- different amino acids- genetic code
• Sequence of bases in a section of DNA- template- to make proteins-protein synthesis
Codon: a DNA triplet-3 bases- specific to an aa

The nature of the genetic code:
• Universal- in almost all organisms- same triplet of DNA codes- same aa
• Degenerate- different codons specify same aa- reducing the effect of mutations
• Non-overlapping- it is read from a fixed point in groups of three bases- Any bases added or
deleted will causes a frame shift

Protein synthesis
• DNA- found in the nucleus but ribosomes (make proteins) found in cytoplasm
• DNA too large to move out of the nucleus
• section is copied into mRNA- transcription
• mRNA leaves nucleus – joins ribosome in cytoplasm- synthesis a protein- translation
...
A gene unwinds & unzips- hydrogen bonds break between complementary nucleotides-one
strand is used as a template to make an mRNA copy
2
...
Enzyme- Forms temporary hydrogen bonds between RNA nucleotide & complementary
unpaired DNA bases
4
...
RNA polymerase moves along DNA, separating strands + assembling mRNA strand
...

6
...
stops making mRNA and detaches from DNA
8
...


Translation (2nd stage of protein synthesis)- ribosomes- involves aa into polypeptide chainsequence of codons carried by the mRNA

1
...
A tRNA molecule, with an anticodon that’s complementary to the start codon on the
mRNA, attaches itself to the mRNA through complementary base pairing
...

3
...
tRNA molecule moves away, leaving aa behind
...
This process produces a chain of linked aa until there is a stop codon on the mRNA
molecule
5
...
mRNA breaks down- recycled into new length of mRNA
























2
...
Don’t directly
participate in the reaction in the reaction- not used up/changed
• Coenzymes- organic not protein- participate in the reaction + are changed by it- But only
temporarily bind
...

• Substrate has to be right shape + make active site change- having a good fit
• Active site moulds around substrate molecule
• Subtle changes of shape of side chains of amino acid
• Enzyme product complex – different shape to substrate- detaches

Low activation energy
• Enzymes reduce activation energy required- reactions take place at lower temperatures
• Increases the rate of reaction/ metabolic reactions

Effect of temperature on enzyme activity

• temp increases- more heat- more KE- the molecules move faster
• substrate molecules more likely to collide- enzymes active site
• energy of collisions increases- each collision more likely to result in successful collision-
increase formation of ES complex

Optimum temperature- the rate of reaction is at its maximum

• If temp gets too high- reaction stops
• rise in temp make enzyme molecules vibrate more
• vibration breaks some of the 4 bonds that hold the enzyme in shape- tertiary
• Active site changes shape- enzyme + substrate no longer fit together
• Enzyme is denatured

The temperature coefficient (Q10): shows how much the rate of reaction changes when the
temperature is raised by 10°c
...

If optimum pH is restored, then bonds can re-form + active site’s shape is restored
...



Buffer: resists changes in pH

Effect of substrate/enzyme concentration- rate on enzyme-catalysed reaction

• more enzyme molecule- increased chance of a successful collision
• a HIGH enzyme concentration INCREASES the rate of reaction
• if amount of substrate is limited- increasing enzyme concentration- no further effect

• More substrate molecules, increases chances of successful collisions
• more enzyme-substrate complexes will be formed
• until ‘saturation’- enzyme concentration becomes limiting factor

• Substrate concentration decreases with time during a reaction
• rate of reaction will decrease over time
• initial rate of reaction the highest rate of reaction
...
Measure how fast the product of the reaction appears and use this to compare the rate of
reaction under different conditions
...
You can measure how fast the substrate is broken down and use this to compare the rate of
reaction under different conditions
...
Blocks the active site- prevents enzyme substrate complex
• Inhibition- depends on relative concentration of substrate & inhibitor
• Reduces free enzymes- bind to substrate molecules
• More inhibitors- more collision- effect of inhibitor greater- enzyme inhibitor complex
• Increasing substrate conc- dilutes effect of inhibitor- enough substrate- active site unlikely
to collide with enzyme
• Some can bind reversibly and irreversibly- inactivator

Non-competitive inhibitors- bind to the enzyme away from the active site- allosteric site- active site
to change shape- substrate molecules- no longer complementary to substrate
• They distort the tertiary structure and shape
• Changes the active shape- ES complex- doesn’t form
• Maximum rate of reaction is reduced
• Increasing substrate conc- no effect on rate of reaction
• Some can bind reversibly and irreversibly

Control of metabolic sequences:

- Enzyme catalyzed reactions regulated- end product inhibition- after reaction completion-
product tightly bound to active site- inhibition- negative feedback


-

Non-competitive inhibition- last enzyme catalyzed product- attaches to 1st enzyme in the
sequence- reversible- when conc of this product decrease- the product detaches from
enzyme- metabolic pathway can run again















Drugs
Toxins- inhibit/inactivate enzymes

Cyanide

- Inhibits aerobic respiration & catalase
- KCN- hydrolyzed- hydrogen cyanide
- CN negative ions- irreversibly binds to enzyme
- mitochondria- final stage of respiration

Snake venom

- inhibits AChE
- breaks down neuro transmitter- at synapse by ‘ACh’
- Ach- stays attached to receptor- muscle membrane- muscles kept contracted
- Paralysis- muscles for breathing- paralyzed- suffocation

Aspirin

- Salicylic acid inhibits enzymes- forms prostaglandins
- Cell signaling molecule- tissue- infected/damaged
- Reduces risk of blood clot- vessels
- Some take low does- reduce stroke risk

ATPase inhibitor

- Treat heart failure & atrial arrhythmia
- Inhibits sodium potassium pump- heart muscles
- More Ca ions- increase muscle contraction- strengthens heartbeat






The structure of cell membrane
cell surface plasma membranes:
• Control substances that enter + leave
• Partially permeable
• Substances can move across the membrane by diffusion, osmosis or active transport
• Allow recognition by other cells + cell communication

Membrane structure:

Fluid mosaic model: theory of cell membrane structure- proteins embedded in a sea od
phospholipid
• Phospholipid bilayer made of 2 phospholipid molecules- moving constantly
• Hydrophilic head in contact with watery exterior or interior- cytoplasm
• Hydrophilic tail regions in center of membrane- away from water- barrier to watersoluble substances/polar molecules
• Fat soluble substance like vitamins pass through
• Protein molecules are scattered through the bilayer – constantly moving

Proteins with chain of carb attached- glycoprotein
Lipid with chain carb attached- glycolipids

Glycoproteins + glycolipids
• Stabilise membranes by forming hydrogen bonds with surrounding water molecules
...

• Channel proteins: allow small, charged particles through
• Carrier proteins: transport larger molecules + charged particles across the protein
through facilitated diffusion + active transport
• Act as receptors for molecules in cell signaling
...

The higher the permeability of the membrane, the more pigment leaks out
...


Cell membrane and signalling

Cell signalling:
• cells need to communicate with each other to control processes inside the body +
respond to changes in the environment- cell signalling, which uses messenger
molecules
...


Membrane Receptors
• Proteins in the cell membrane act as receptors for messenger molecules
• Receptor proteins are called ‘membrane-bound receptors’
• Have specific shapes- complementary to messenger molecules
• Cell that responds to particular messenger molecule = target cell

Hormones as messenger molecules
Glucagon- hormone released when lack of glucose in blood, binds to receptors on liver cells,
causing liver cells to break down stores of glycogen to glucose
...

Partially permeable
• RNA leaves nucleus via nuclear membrane
• DNA too large to pas through
Membranes within organelles
• Thylakoid membranes in chloroplasts- keep components need for light dependent
reactions of photosynthesis together
Site of chemical reactions- some membranes folded to increase S
...
+ make reactions more
efficient
• Mitochondrion contains enzymes needed for respiration
• Large S
...
- increase no
...

Diffusion

Diffusion: - net movement of molecules from an area of high concentration to an area of low
concentration, down a water potential gradient,

• CO2 and O2- pass though cell membrane via simple diffusion
• Fat-soluble molecules- steroid hormone- larger- dissolve in bilayer-diffuse


Water- insoluble in lipid bilayer- specific water channel proteins- aquaporin

• Net movement of particles
• Area of é conc
...
grad)
to ê
• Passive- no energy

Factors affecting the rate of diffusion:
1
...
grad - é
= faster
2
...
S
...
Temp – warmer = faster because of increased kinetic energy
5
...


• Large molecules + charged particles too slow to diffuse
• channel/carrier proteins used
• Diffuses down a conc
...


Active processes

Active transport: movement of substances from an area of low to high concentration of
substance, against concentration gradient, across cell membrane- using ATP and protein
carriers

Carrier protein:
- Specific regions/sites- combine reversibly with solute molecule/ions
- ATP- allows carrier protein shape change its confirmation to carry ion from one side
to other

Endocytosis: bulk transport of molecule into the cell, too large to pass through a cell
membrane via channel or carrier protein
- some molecules are too large- proteins, lipids + some carbs
- ATP is need to provide energy for:
- a cell can surround a substance with a section- its plasma membrane + pinch off to
form a vesicle
- moves using motor proteins- along cytoskeleton threads into cell interior

Exocytosis: bulk transport of molecule out of the cell, too large to pass through a cell
membrane via channel or carrier protein

- some substances produced by a cell need to be released

-

E
...
digestive enzymes, hormones + lipids
...

• Microscopes can be used to view the different stages of the cycle
...
Ensures cell is
ready to enter the S phase and begin DNA synthesis
...
(Mitosis)
•

Cell growth stops

•

Nuclear division: PMAT (Mitosis)

•

Cytokinesis: cytoplasmic division after nuclear division - 2 new genetically identical daughter
cells

Checkpoints: G1/S, G2/M, G1
•

To prevent uncontrolled division- tumours (cancer)

•

Detect and repair damage to DNA (Example: UV light damage)

•

Controls cell cycle, so its not reversed and DNA is replicated once in each cell cycle
Mitosis (PMAT)

Type of nuclear division that maintains the chromosome number; each new daughter cell contains
same genetic information as parent cell
...

The significance of mitosis in life cycles:
• growth, tissue repair and asexual reproduction in plants (strawberry’s), animals (female
sharks) and fungi (yeast)
...
A
new cell wall forms between the two membranes of the cell plate
...

The significance of meiosis in life cycles:

• production of haploid cells and genetic variation by producing haploid gametes to form a
diploid zygote, where it combines 2 unrelated individuals of the same species
...
Cells have been in interphase prior meiosis
...

First stage is meiosis 1, then inter interphase, before meiosis 2
...

• Centromere do not divide, each chromosome consists of two chromatids
• Crossed over areas are separate from each other, thus swapped areas of chromosome
...

• Some genes switched off, and others expressed more so:
• Proportion of organelles change
• Shape of cell changes
• Contents of cell changes

Erythrocytes(RBC):
• high SA/V ratio-biconcave shape, O2 diffuses across membrane easily
• flexible, well developed cytoskeleton to change shape- twist and turn though narrow
capillaries
• lack in organelles like nucleus, mitochondria, R/SER- more space for hemoglobin

Neutrophils(WBC):
• Twice size of erythrocytes
• Multilobed nucleus
• Attracted to and travel toward infection sites
• Ingest bacteria and some fungi by phagocytosis

Sperm cells:
• Lots of mitochondria- ATP energy for undulipodium (tail) to move towards the ovum
• Small, long and thing-move easily
• Sperms head has digestive enzymes to enter ovum
• Contain haploid male gamete


Epithelial cells:
• Lining tissue- flattened in shape
• Many have cilia

Guard cells:
• Within the lower epidermis
• Using ATP- active transports potassium ions from surrounding epidermal cells into guard’s
cells
• Lowers water potential-water is drawn into the guard cells from neighboring epidermal cellsosmosis
• Guard cells swell- tip of cellulose wall is flexible/ more rigid where it’s thicker
• Tips swell and stomata opens- air enters the spaces within the layer of cells beneath palisade
layer
• Gaseous exchange-CO2 diffuses into palisade cells-photosynthesis- maintains steep
concentration gradient
• Oxygen produced diffuses out of palisade cells out of stomata; water vapor exits
(transpiration)

Paliside cells:
• Within leaves- adapted for photosynthesis
• Long and packed together, with little space for air to circulate; CO2 diffuse into cells from
this space
• Large vacuole- chloroplast are near to edge of cell- reduces CO2 diffusion distance
• Many chloroplast- a lot of photosynthesis
• Cytoskeleton threads and motor proteins- move chloroplasts to upper surface at low light
intensity (vice versa)

Root hair cells:
• Hair-like projection increases SA for water and mineral ions (nitrates) absorption
• Mineral ions actively transported- decreases water potential in roots- increases
osmosis
• Special carrier proteins in membrane to actively transport mineral ions in
• Produces ATP for active transport

Animal tissues

Tissue: group of cells that work together to perform a specific function/ set of functions

4 main tissue types:
• Epithelial (lining tissue)- skin, gut, airways, vessels, walls of organs-specialized for
absorption, filtration, secretion, protection
• Connective tissue – holds structures together and provide support-bone and cartilage
• Muscle tissue- made of cells specialized to contract and cause movement
• Nervous tissue- made of cells specialized to conduct electrical impulses

Plant tissues

Organ: collection of tissues working together to perform a function

Vascular tissue: to do with transport

Xylem: tissue that carries water and mineral ions from roots to all parts of plants
Phloem: sieve tubes that carries products of photosynthesis, in solution within plants (roots
and flowers)

Meristematic tissue: contains stem cells (root and shoot tips)
• Meristem: area of unspecialized cells within plants that divide into other cell types
• Cambium cells: differentiate into xylem-lignin (woody substance) deposits in cell wall-
strengthens and waterproofs them- also kills cells
• Ends of cells break down- xylem forms continuous columns with wide lumens to carry water
and mineral ions
• Cambium cells: differentiate into phloem sieve tubes- lose most or organelles- sieve plates
develop between them
• companion cells retain organelles and have metabolic functions to produce ATP for active
loading of sugars




Stem cells

Stem cell: unspecialized cell able to express all of its genes and divide by mitosis
• Undifferentiated cells- can become any cell
• Pluripotent-form different type of cells
• Can express all their genes
Source:
• Embryonic stem cells-in an early embryo formed- zygote begins to divide
• Umbilical-cord
• Found in developed tissue like brain, muscle, bone-act like a repair system
• Induced pluripotent stem cells (IPS cells)- reprogramming differentiated cells to switch on
certain key genes- to become undifferentiated

Potential uses in research and medicines
Bone marrow transplant: - stem cells from bone marrow-treat blood diseases, immune system
diseases; Used to restore patients blood system after treatment for specific cancers

Drug research: -new drugs can be tested on tissues made by stem cells rather than animal tissue

Development biology: study of how cells develop to make particular cells- learn cell type function
and what goes wrong when they are diseased
...
3
...
3
...
no cross-walls
2
...
Lignin thickening prevents the walls- collapsing

Phloem

• Tissue- transport assimilates (sucrose and amino acids) around the plant
• Phloem consists of sieve tubes- consisting of sieve tube elements & companion cells
Sieve tube elements

• Elongated sieve tube elements- lined up end to end to form sieve tubes – no nucleus &
little cytoplasm- space for mass flow of sap (sucrose dissolved in water) to occur
• At ends of the sieve tube elements- perforated cross-walls- sieve plates
• Perforations in sieve plate - movement of sap from one element to another
• Sieve tubes- thin walls
Companion cells

• Companion cells- in between sieve tubes- small cells- each with a large nucleus & dense
cytoplasm
• Numerous amount of mitochondria to produce ATP- active processes
• Companion cells carry out- metabollic processes needed to load assimilates actively into
the sieve tubes













3
...
3 Movement of water through plants
Pathways taken by water
→ Cellulose cell walls- fully permeable to water
→ Water molecules- move freely between cellulose molecules/ gaps between the cells
→ Water- pass across the cell wall- through partially permeable plasma membrane- cell
cytoplasm/vacuole
→ many plant cells- joined by special cytoplasmic bridges- cell junctions cytoplasm of one cell
is connected to another via a gap in cell walls
...

The apoplast pathway
•
•
•


water passes- spaces in the cell walls & between the cells- does not pass- plasma
membranes into the cells
water moves- mass flow rather than osmosis
dissolved mineral ions & salts- carried with the water
...

- cytoplasm- mineral ions & sugars (solutes)- reduce the water potential
...
3
...
Water enters the leaf by the xylem & moves by osmosis- cells of the spongy mesophyll
2
...

3
...

This movement:
• Transports useful mineral ions up the plant
• Maintains cell turgidity
• Supplies water- growth, cell elongation & photosynthesis
• Supplies water that, as it evaporates can keep the plant cool- hot day
Environmental factor
Light intensity
Temperature

Relative humidity
Air movement (wind)
Water availability


Environmental factors that affect the transpiration rate:
Explanation
Higher light intensity increases transpiration rate as stomata- open for gaseous exchange
Higher temperature- increase transpiration rate in 3 ways:
1
...
Increase in rate of diffusion through the stomata as water particles have more kinetic
energy
3
...

- used to estimate transpiration
- Assuming- cells are turgid, more than 95% of the water
taken up is lost- transpiration
- Water vapour lost- leaves is replaced from water-
capillary tube

Precautions to ensure results are valid:
1
...
Ensure shoot is healthy
3
...
Cut stem at an angle to provide large surface area in contact- with the water
5
...
petroleum jelly at joints- airtight
7
...
3
...
Root pressure

• Action of endodermis moving minerals into medulla & xylem- active transport draws water
into medualla- osmosis
...
Transpiration pull

• Loss of water- evaporation- leaves replaced- water coming up from the xylem
• Water molecules attracted to each other by forces of cohesion- strong- hold molecules in a
long coloumn
• molecules are lost- top of the column- whole column is pulled up- creates tension in column-
xylem vessels lignified for strength & prevent it collapsing under tension
• mechanism- cohesion-tension theory
• water column is broken- in a xylem vessel- water column- maintained-via another vessel-
bordered pit





3
...
3
...
A- evaporation
Cacti – show other features to overcome arid/dry conditions

• Cacti are succulents- store water in stems-become fleshy & swollen- stem is ribbed- expand
when water available
• Leaves are reduced to spines- reduces total leaf SA- less water is lost by transpiration
• Roots are widespread- take advantage of any rain
Other xerophytic features:
• Closing stomata water availability- low reduces water loss & reduce need to take up water
• Some plants- low water potential inside leaf cells- maintaining a high salt concentration-
water potential gradient between cells & the leaf air spaces is reduced
• A very long tap root- reach water deep underground

Hydrophytes
plants adapted to live in water/wet coditions- oxygen in tissue- float–leaves in sunlight-
photosynthesis
Water lily adaptations include:
• Many large air spaces in leaf- afloat & absorb sunlight
• Stomata on upper epidermis- exposed to air- gaseous exchange
• Leaf stem- large air spaces- help buoyancy- allows oxygen to diffuse quickly to roots-
a
...
If water cannot leave the plant- transpiration stream stops- cannot
transport mineral ions up to the leave
• plants contain specialised structures at tips/margins of leaves- hydathodes
• release water droplets- evaporate from the leaf surface


3
...
7 Translocation

Translocation- phloem & is the movement of assimilates throughout the plant- sugars (sucrose) &
amino acids

Active loading
• Sucrose is loaded into sieve tube- active process –energy from ATP
• Energy- actively transport hydrogen ions out of the companion cells- increases
concentration outside cells & decreases inside companion cells- concentration gradient
• H+ diffuses back into the companion cells - special cotransporter proteins
• only allow movement of H+ into the cell only with sucrose molecules – cotransport
• concentration of sucrose- companion cell increases, diffuse through the plasmodesmata-
sieve tube
Movement of sucrose

• Movement of sucrose- phloem by mass flow; A solution of sucrose, amino acids &
assimilates- sap flows along the along tube up/down plant as required
• Flow is caused- difference in hydrostatic pressure between two ends of the tube
• Water enters tube increasing pressure at the source & it leaves tube at sink, reducing the
pressure
• sap flows from the source to the sink
The Source

• loads sucrose into the sieve tube element- water pot
...
Travel from one host to another (transmission- pathogen- infected individual to uninfected)
2
...
Reproduce
4
...
Direct physical contact- touching infect person/ contaminated surface
ü Hygiene- washing hands regularly- after toilet, disinfecting cuts, condoms
2
...
Droplet infection-tiny water droplet in air- carry pathogen
ü Cover your mouth- sneeze & cough – use tissue and dispose correctly
4
...
Callose- large polysaccharide that is deposited in sieve tubes-blocks flow- prevents
pathogen spread
2
...
High concentration of chemical– terpenes- toxic to pathogen
3
...
Cellulose cell wall- physical barrier & activate chemical defenses- pathogen detected
5
...
Lignin thickening of cell walls- waterproof and indigestible
7
...
Skin- Physical barrier- layer of dead cells
2
...
Goblet cells- (glands) secretes
mucus traps pathogens – cilia- tiny hair organelle- waft layer of mucus
3
...
Inflammation- swelling & redness of tissue- infection
...
Excess tissue fluid
drained into lymphatic system
...
Blood clot- abrasion- damage to skin- causes cascade of reactions- tissue exposed to air-
collagen fibers are exposed and platelets bind – releases clotting factors- calcium
...
Non- specific, attach to
variety of pathogenic cells

Phagocytes
• Phagocytes are not specific to a particular type of pathogen
...


Neutrophils
- They bind to opsonins attached to antigens of pathogen
- Pathogen engulfed by endocytosis- phagosome
- Lysosome fuse with phagosome- release lytic enzymes into it- digests and absorbs products
• Multilobed nucleus
• Made in bone marrow by stem cells
• Small
• Short lived
• Dead neutrophils gather around infection as pus
• A lot of lysosomes

Macrophages (Matured monocytes)
- When macrophage engulfs pathogen- isolates antigens fro pathogen- places it on plasma
membrane to be recognized by immune system- Antigen-presenting cell

• These are larger
• Long lived
• Large central nucleus
• They are made in the bone marrow and travel in the blood as Monocytes
...

These cells present parts of the pathogen membranes exposing the antigens of the
infectious pathogen
...
Clones of
lymphocytes develop into range of useful cells



Antibodies
Antigen- proteins/ glycoproteins- plasma membrane of pathogens and any molecules
Foreign antigens- detected by immune system- stimulates antibodies specific to antigen

Antibodies- attach to antigens- render them harmless

• 4 polypeptide chains
• variable region- specific shape to shape of antigen
• constant region- same on all antibodies- site for
easy binding of phagocytic cells
• hinge region- flexibility- allows molecules to attach
to more than one antigen
• disulfide bridge holds polypeptides together






• Opsonins- antibodies attach to antigens on pathogen- binding sites- easy binding-
phagocytic cells- not very specific- activate phagocytosis
• Agglutinins- antibodies causes pathogens to stick together
• Antitoxins- antibodies render toxins harmless

1
...
Secondary immune response: more rapid/vigorous response caused by subsequent
infection of same pathogen
B & T memory cells circulate in blood
- Higher peak
- Rate of antibodies produced is faster
- Concentration of antibodies remains in blood high

Vaccination

Vaccination: deliberate exposure to antigenic material- activates the immune system- provide
immunity
...
It provides resources for food, protection and breeding
• Range of habitats
• sand dunes, woodland, meadows, streams

Species Biodiversity:
Species: group of organisms that can freely interbreed to produce fertile off spring
• very similar in appearance, anatomy, physiology, biochemistry and genetics
• species richness &species evenness

Genetic biodiversity: differences between individuals belonging to same
species


Type of sampling
NonOpportunistic
Random



Stratified



systematic

Random

How sampling carried out
Sampling decisions based
on prior knowledge/ whilst
data collection
Pick areas with particular
species


Divide habitat into areas
that appear different
Sample each area separate

Samples taken at fixed
intervals across habitat
Line & belt transect

Use randomly generated
numbers as coordinates for
sample- select coordinates
via map or GPS (globalpositioning satellite)


Advantages
Easy and quicker than
random

Disadvantages
Biased- area with more
species maybe picked

Overestimate of
biodiversity

Ensure different areas
are sampled
Species not underrepresented by missing
areas (random)
Useful in habitats with
clear gradient in some
environmental factors
i
...
wet near a pond-
further away drier
Not biased

May lead to overrepresentation, of
some areas in sample


Sampling plants
Preparation: (for fieldwork)
• suitable clothing (suit weather conditions)
• suitable footwear
• apparatus need to carry out sampling
• clipboard, pen and paper- record observation
• appropriate keys to identify plants

Only species on the
line/belt recorded
Other species missed
out- underestimate of
biodiversity
May not cover all areas
Species with low
presence missed-
underestimate of
biodiversity

• smartphone- record specimen and grid location
At the site:
• If habitat is uneven
• Move sample sites into areas that appear different- Opportunistic (making decisions during
sampling) & stratified (divide habitat into areas that appear different)
• Cause very little disturbance as possible to habitat

Sampling plants
number of tree species- count individuals
small plant species- % cover using quadrats

Using random quadrat
• Quadrat: square frame- defines sample area (any size)
• Generate random numbers and use as coordinates, to place habitat
• In quadrat- identify plants found & calculate % cover
• Some quadrats have smaller squares (100) – to make a more accurate estimate
• Point frame with 10 needles held above quadrat, the needles fall, and touches a plant
...
Workout % of needles touched a
plant/100
...

Tulgren funnel:
• A device for collecting small animals from leaf litter
• Place leaf litter inside and turn on a light at the top
...

• Under the light is a reservoir of alcohol and eventually the moths and other insects tire and
fall into the alcohol
...


Mark and recapture technique
• a method for measuring populations of moving organisms e
...
birds, moths, sharks
• set a trap and catch sample of population
• count them (C1), mark them- with a tag (causes it no harm/caught by predator) and
release them
• set trap again (provide time for organism to back into their habitat) and catch a second
sample
• count number of individuals in the second sample (C2)
• count the numbers of marked individuals in the second sample (C3)
Estimate total number in population = C1 X C2/ C3

Calculating biodiversity

Estimating biodiversity:
Species richness (qualitative): measure of how many different species are present
More species, richer the habitat

Species Evenness (quantitative): measure of how evenly represented the species are
Habitat with an even number of individuals in each species- more diverse (habitat where one specie
outnumbers all other)

Simpson’s Index (D)
Ø used to calculate the biodiversity of a habitat

D (biodiversity index) = 1 – (Σ (n/N)^2 )
D= diversity of habitat
n = no
...
of individual’s present
Σ = sum of

• High Simpson’s index- diverse habitat – many organisms and species
• Habitat tends to be stable and withstand changes to a small change to the environment-
may only effect 1 species- small proportion of total number present
• Low value- habitat dominated by few species- small change (like disease) to environment-
affects one of those species- damage/destroy whole habitat

Genetic diversity
More than one allele for a particular locus- position of gene in chromosome- lead to variation- more
genetic difference between gametes by members of population
•

Genetic diversity = loci with more than 1 allele/total number of loci x 100
Polymorphic gene: a locus with more than 2 alleles- increase genetic diversity

proportion of polymorphic gene loci = total number of loci / number of polymorphic gene loci

What affects biodiversity?

Human population growth:
• -alter ecosystem to ourselves- food
• destroy habitats
• use more earths resources
• pollute atmosphere

Result of our activities- other species- directly/indirectly- perhaps extinction

Agriculture:
• Clear natural vegetation- reduce habitat size- population size less- reduces genetic
diversity of species
• species have less capacity to adapt to changing conditions- via evolution
• isolated and fragmented populations are too small to survive
• Monoculture- crop consisting of one strain of one species- limits genetic diversity as
single species are harvested to increase efficiency- e
...
Oil palm tree- to get palm oil

Selective breeding- reduces genetic diversity- farmers select particular traits- concentrates on
specific characteristics- declines genetic diversity

Genetic erosion- Specific breeds of domesticated plants and animals- other breeds become rare- die
out- varieties reduce genetic diversity of species

Climate change: significant, long-lasting changes in weather patterns
Species have migrated slowly to where climate suits them
...
Adapt to
climate change

Extinction: last living member of a species dies- species ceases to exist

Reasons to maintain biodiversity
Ecological:
Interdependence of organisms- all organisms in habitat linked to food chain/web (intra/inter-species
competition, prey & predator)
• 1 species number declines- affects other species
• higher species diversity- more stable than lower species diversity- withstand certain
amount of change
• keystone species: one that has disproportionate affect upon its environment relative t
its abundance
• decline in keystone species- dramatic effect on habitat
• deer population increase- vegetation gets all eaten- deer starve
• increase in certain plants- deep roots- transfer water from deep soil to shallow soil for
other plants, provides shade, provides sap- for insects to feed
...
e
...
By selective breeding- breed new
crops cope with climate change
...
Soil deposits in water

Conservation in situ
situ conservation- active management to maintain biodiversity- natural environment (preserve
specie and low human impact on natural environment)

Legislation: stop hunting and clearing land for development

Wildlife reserves: are set aside for the conservation of species/habitats
- How any species
- Large enough area for LR survival of species
- Full range of diversity in species
Marine conservation zones- 27 sites in UK coast- 2013- areas to conserve biodiversity of threatened
habitat and species in our seas

Advantages:
• species and habitats conserved in natural environment
• Larger population protected
• helps scientific research
Disadvantages:
• Difficult to control factors threatening species- like disease/climate change)
• May already have lost a lot of biodiversity
• Fragmented population may not survive- not big enough
Conservation ex situ


ex situ conservation: conservation outside normal habitat of the species (endangered)
Seed bank- collection of seed samples- aim to have seeds for every know species- viable for
decades- provide seeds for food crops- disease resistant cops for agriculture
Botanic gardens: seeds produce large numbers (little disturbance)- can be stored in large
amounts- bred asexually- increase number of individual plants rapidly via tissue culture
Zoos- wildlife parks- breeding endangered species- conducts research benefits speciesmodern reproductive technologies- freezing sperm/egg- preserve lot of genetic material

advantages:

• Organism protected from predation
• Health of individuals monitored and medical assistance
• Selective breeding- increase genetic biodiversity
Disadvantage:
• Organisms live outside their natural habitat
• Expensive to maintain suitable environment conditions
• Small population has a limited genetic diversity

Protection of species and habitats
CITES: convention on international trade in Endangered species, established in 1973
- Regulate and monitor International trade
- Ensure trade does not endanger species
- Prohibits trade of wild species for commercial
- Regulates permits of artificially propagated plants and less endangered species
Smuggling and black markets

Rio Convention on Biological Diversity (1992)
- Conserve biodiversity
- Share access to genetic resources
- Share scientific knowledge
- 150 members must adopt in-situ and ex-situ facilities
- All members must carry out their own Environmental Impact Assessment (EIA) before any
development

Botanical gardens: Swap genetic material to increase genetic diversity

Countryside Stewardship Scheme (CSS) 1991:
- Improve natural beauty & biodiversity of countryside
- Looking after wildlife, species and their habitats
- Opportunity for people to visit learn about countryside
- Protect historical features





















Biological classification

Binomial system: system using genes names and species name to avoid confusion when naming
organism
Classification: process of placing living things into groups
Classifying living things:
o see relationships between species
o easier to identify organism
o more convenient and manageable
Modern classification hierarchy: - system of classifications; eight taxonomic levels:
Taxonomy- study of the principle of classification
Domain: - highest taxonomic rank; Archaea, Eubacteria and Eukaryotae
Kingdom: - 5 main kingdoms; (eukaryotes- has a nucleus) Plantae, Animalia, Fungi, protoctisa and
prokaryotae (single-celled organisms- no nucleus)
Phylum: major subdivision of the kingdom; groups of organism with same body plan i
...
possession
of backbone
Class: group of organisms that possess same general traits i
...
same number of legs
Order: subdivision of class + additional info on organism i
...
class mammal- carnivore/herbivore
Family: group of closely related genera- carnivore family- cat and dog family
Genus: group of closely related species
Species: basic unit of classification: members in species show variation- essentially same
DO KEEP PENUS CLEAN OR FORGET GOOD SEX













Lower
the taxonomic groups- harder to separate closely related species (more detail needed on species in
order to differentiate)

The binomial naming system:
• Name: Homo-sapiens: Homo- genus and sapiens- species
• (start of genus name: Capital letter ‘Homo’ and species name: lowercase ‘sapiens’)
• Genus and species name must be underlined or in italics
• Latin name (universal name for species)- avoids confusion caused by common names, every
scientist uses same name
• Common names not used- translation of languages give different names, different common
names in different countries
Features used in classifications

• Species: a group of organisms that can freely interbreed to produce fertile offspring

•
•
•
•
•

Phylogenetic: group of organisms- very similar in appearance, anatomy, physiology,
biochemistry and genetics
Classification is the grouping of organisms into hierarchical taxa, including species, genera,
families, orders, classes, phyla, kingdoms
...

Phylogeny can be done without subsequent classification, but classification requires a
knowledge of phylogeny in order to make the taxa natural
...




Prokaryotae
Proctostisa
Fungi
Animilia
Plantae
No nucleus; loop of
Nucleus (linear DNA)
Nucleus (linear DNA) Nucleus (linear DNA) Nucleus (linear DNA)
naked DNA
Mostly single-celled
Can exist as singleMulticellular
Multicellular
No membrane bound
Various plant-like and celled
Cellulose cell wall
Cellulose cell wall
organelles
animal-like features
Mycelium-hyphae
Heterotrophic
Autotrophic nutrition
70s ribosomes
Both nutrition
Heterotrophic-
nutrition
Chlorophyll
smaller cells than
Cellulose cell wall
saprophytic nutrition Move around
80s ribosomes
eukaryotes
80s ribosomes
80s ribosomes
80s ribosomes
Murein cell well


Autotrophic nutrition- absorbs simple molecules and synthesises into larger molecules
Heterotrophic nutrition- digest large molecules into smaller molecules for absorption
Saprophytic: decays organic matter (extracellular digestion)

Evidence used in classification:

Convergent evolution: process whereby organisms not closely related, independently evolve similar
traits as a result of having to adapt to similar environments
Certain large biological molecules non-identical in every species- (respiration and protein synthesis)
Different versions of molecules seen today due to evolution
...


Cytochrome C- protein for respiration- in all respiring living things
• Not identical in all species
• Amino acids have different, different sequences
• Same sequence- 2 species closely related
• Different sequences- 2 species not so closely related
• More difference- less closely related the 2 species

DNA: genetic code- instructions for producing proteins
• Code is universal- same for all organisms
• Mutation- RANDOM changes in sequences of bases in DNA
• Classify species- DNA sequences

Classification and phylogeny

Phylogeny: study of the evolutionary relationships between organisms

Artificial classification:
• Based on few characteristics

•
•
•

Does not reflect evolutionary relationships
Provides limited info
Is stable


Natural classification:
• Biological classification – involves detailed study of the individuals in species
• Uses many characteristics
• Reflects evolutionary relationships
• Provides a lot of info
• Can change with advancing knowledge

Phylogeny:
• Evolutionary history- all organisms belonging to an evolutionary tree
• 2 species living today- common ancestor in past
• more recent common ancestors more closely related

Monophyletic- belonging to the same phylogenetic group

• Human and gorillas- share features- closely related
• All have common ancestors- recent past
• Human and gorillas- monophyletic and same taxonomic group
• Thrush more closely related to snake than mammals
• Common ancestor 2 more present day than 3
• All 6- monophyletic- evolved from same species

Evidence for natural selection:

Natural selection: explains how features of the environment apply a selective force on the
reproduction of individuals in population

Charles Darwin- naturalist- observed and studied living organisms
...
Clear variation between members of
same species on different islands
...
Offspring similar to their parents
2
...
Organism- ability- produce a lot of offspring’s
4
...
8% human DNA is the same as Chimpanzees
Molecular evidence:
• Cytochrome C
• Similarities in this molecule shows how closely related two species are

Variation:

Variation: Differences between individuals of the same or different species
...
















Continuous Variation: variation where there are 2 extreme values- full range of values in between
ü Most individuals- close to mean
ü Regulated by more than one gene
Discontinuous variation: distinct categories and intermediate values
ü Randomly/even distribution
ü Regulated by a single gene (not influenced by environment)

Genetic Variation: variation due to possessing different combination of alleles
• genes inherited from parents - defines our characteristics
...

• each gene there are multiple alleles
...

• Different alleles code for slightly different polypeptides -different phenotypes
• This is genetic variation

Environmental variation: variations due to response to environment

•
•
•

Many characteristics can be affected by the environment
skin colour in different light intensities
Hawthorn trees grow branches sideways in windy conditions


‘Genes load the gun; environment pulls trigger’
v changes in environment directly affects genes that are active
v small height family- even with good diet- unlikely to be tall- genes limits your height

Applying statistical techniques:

Standard deviation: measure of the spread around mean
Ø low st
...
dev- data has a larger range- less well grouped- less reliable

x= individual value
x(dash)= mean value
n= number of data points
s(st
...
6 s= +/- 8
...
62/93
...
63-93
...
Value of 1- perfect
correlation

D= difference between ranks
N= number of pairs of value(ranks)

Ø Use critical values to see if rs indicates a correlation
Ø Rs< critical value – no correlation (negative correlation)
Ø Rs> critical value- positive correlation (closer to 1)








Adaptation:

Adaptation: characteristic that enhances survival habitat

Behavioural Adaptations: Aspect of an organisms behaviour that enables it to survive in the
conditions it lives in
...
g Earthworm recoiling into it burrow, when touched (avoid being eaten)
• Marram grass- rolls leaf tighter- closes stomata, when shortage of water

Physiological Adaptations: An adaptation- biochemical or physiological which ensures the correct
functioning of cell processes
...

Evolution- selecting individuals with particular adaptions- survive & reproduce- pass on these
adaptations- from one generation to another

How natural selection works:
1
...
Intraspecific variation- genetic variation between species
3
...
Individuals with the advantageous characteristics survive and reproduce
5
...
The next generation higher proportion of individuals with successful characteristics- are
better adapted to the environment
Variation takes place before evolution
...

Ø This is an evolutionary arms race and medical researchers are struggling to develop new
effective drugs, but the bacteria are rapidly becoming resistant
...
CNS
• spinal cord and brain
• White matter- myelinated (outer region of spinal c), grey matter- non myelinated (central)
• spinal protected by vertebral column- between each vertebrate- action p enter/exit

2
...
heart rate/respiratory centre- rate/depth of breathing/
vasomotor centre- reg circulation/blood press

Reflex action
• response to external stimuli- doesn’t involve any processing- brain/unconscious
coordination

Blinking reflex

• cranial reflex
• receptor and effector same place- reflex arc
• optical reflex- sudden increase in light intensity- detected by retina& mediated by optical
centre in cerebral cortex
• Loud sounds/ sudden movements
corneal reflex
• foreign body touching eye- faster than optical- sensory neurone from cornea enters pons-
connects sensory to relay- passes action p
...

2
...

4
...


erector pili muscles- skin contract- hairs stand up- sign of aggression/look bigger/threating
input into sensory centres- cerebrum
cerebrum passes signal into association centres
threat recognised- cerebrum stimulates hypothalamus
increases activity- sympathetic NS- stimulate release of hormones- anterior pituitary gland
SNS- stimulates adrenal medulla- release adrenaline


hormones released from anterior pituitary
§ CRH
§ TRH

Controlling heart rate
§ Frequency of waves of excitation by SAN altered by the output of cardiovascular centre-
medulla oblongata- autonomic
§ action p
...
p sent down vagus nerve- releases acetylcholine- reduces heart rate
§ stretch receptors in muscles- send impulse to cardiovascular centre- need of more oxygen-
increase heart rate
-in carotid sinus- monitor blood press
§ chemo receptor in carotid arteries/aorta/brain monitor ph of blood- when exercise co2
produced- carbonic acid- reduce PH- detected by receptor- sends action pot
...
act pot arrives end of axon- opens Ca channels in mem- Ca ions flood into end of axon

2
...

4
...

6
...


vesicles of acetylcholine move and fuses with end of membrane
acetylcholine diffuses across gap and fuse with receptors on sarcolemma
opens Na channels- allow NA to enter muscle fibre- depolarisation of sarcolemma
wave of depolarisation spreads along sarcolemma & down transverse tubule into fibre
act pot carried to sarcoplasmic reticulum- stores CA- causes release of ion into sarcoplasm
ca ions bind to troponin- alters shape pulling the tropomyosin aside- exposes binding site on
actin
8
...
myosin head attaches to actin filaments- form cross bridge
2
...
after power stroke- ATP molecule attaches to myosin head- break cross bridge
4
...
Fred Sanger’s DNA sequencing
• Each of the 4 dish contains one modified versions of DNA bases- ATCG(labelled with
radioactive isotope) + DNA polymerase
• Once base is incorporated into complementary DNA strand- no more bases added
• Thousands of DNA fragments- varying length generated- passed through gel by
electrophoresis





•
•
•

Smaller fragments travel further- fragments sorted by length
nucleotide base at end of fragment read according to its radioactive label
time consuming and costly process

2
...

1
...

3
...

5
...


High throughout sequencing- pyrosequencing- synthesing
a long DNA to be sequenced cut by nebuliser – 300-800 bps
lengths degraded into single stranded DNA (ssDNA)- template strands- immobilised
Sequencing primer, DNA, DNA polymerase, ATP sulfurylase, luciferase
1 out of 4 nucleotides A/C/T/GTP is added at any ne time+ light generated is detected
GTP- dephosphorylates to Guanine (all bases)
APS+ pyrophosphate- ATP and in the presence of ATP- luciferase converts luciferin to
oxyluciferin
7
...
10 hour run- 400 million bases read


Bioinformatics- research to store data generated

Against genetic screening of population- high cost to gov/NHS, invasion of privacy/ discriminates
employer’s/insurance companies/anxiety future health, many diseases have no treatment

Applications:
• humans 99% of genes with chimpanzee
• FOXP2 gene in human, mice & chimpanzee- human one is mutated allows speech
• genetic similarities- track evolutionary relationships of species
• humans share 99
...
tandem repeats- noncoding-varies in people- similarities=resemblance


Applications:
• protein electrophoresis- identifies type of hb present- aid diagnosis of sickle cell anaemia
• STR fragments half comes from mother and other half from father
• identify victim’s body’s parts after crashes
• identify nazi war criminals hiding in south America

DNA profiling doesn’t involve reading of individual’s genes unlike sequencing

Gene sequencing

DNA is fragmented to smaller fragment- its too large and to increase accuracy

Polymerase chain reaction- amplify short lengths of DNA to millions of copies- range in different
lengths- for analysis/base sequence retained

- short sequences up to 10,000 base pairs
- primers- short single stranded DNA needed to start PCR/ sequencing
- Taq polymerase from Thermophilus aquaticus- stable at high temp
- any contamination will be amplified
- in cells primers are made by DNA polymerase/PCR- synthesise separately & added

1
...
mixture heated 95c- breaks H bonds between comp
...
Mixture cooled to 68c- primers anneal (H bond) to one end of each single strand- gives small
section of double stranded DNA at end of each single strand
4
...
Enzyme catalyses addition of DNA nucleotides to single stranded DNA- starting at end with
primer and proceed in 5’ to 3’ direction
6
...
Cycle repeats- increases 1-2-4-8-16-32

ü Tissue typing- donor and recipient tissue typed prior transplantation- reduce risk of rejection
ü Detection of oncogenes (tumour cells)- medication tailored to patient
ü Detecting mutation- analyse for presence of mutation- leads to genetic disease- parent’s
DNA- see if they carry recessive gene- during IVF embryo cell can be analysed before
implantation
ü Identify viral infection- detect small quantities of viral genomes in host cell DNA- verify-HIV



Electrophoresis- separate proteins/DNA fragments of different sizes

1
...
Agorose gel is made and poured into central tank & combs placed at one end- once gel has
set- buffer solution added- leaves wells at one end
3
...
once all wells loaded- electrodes connected to 18v battery- left to run 6-8 hrs/ higher
voltage pack for less time- do not use higher unless limited current- risk of severe electric
shock from electrodes/ gel
5
...
At the end buffer solution poured away & dye is added to gel- adheres to DNA & stains
fragments

DNA has negative charge- fragments move towards positive electrode
Agorase gel>agar- Neutral charge- interfere less with DNA structure

Separating proteins
- Charged detergent- SDS- equalises surface charge & allows proteins to separate as they
move across gel by mass
- diagnosis for Sickle anaemia

DNA probes- short single stranded length of DNA- complementary to DNA tested
- labelled by radioactive marker- in phosphate groups in probe strand- revealed by expose to
photographic film
- or fluorescent marker emits colour expose to UV light
- locate desired gene- for genetic engineering
- identify same gene on different organism
- identify presence/absence of allele- for diseases

Microarrays-
- place number of different probes on fixed surface- DNA microarray
- sample DNA binds to complementary fixed probes
- fluorescent marker reveals- scan

Genetic engineering- combining DNA from different organisms- recombinant DNA

Obtain gene
1
...
reverse transcriptase- catalyses formation of single strand of complementary DNA- uses
mRNA as template
3
...
Plasmid taken from bacteria
2
...
cut plasmid- exposed unpaired nucleotide bases- sticky ends- staggered cut- blunt ends
4
...
DNA ligase catalyses gene and cut plasmid binding

Vector into cell
1
...
ion reduces
repulsion as DNA is neg
...
Electroporation- high voltage- to disrupt membrane- permeable
3
...
Transfection- DNA inserted into bacteriophage- transfects host cell
5
...
Small piece if gold coated in DNA- shot into plant cells- gene gun

Grow in fermenter- multiply & reproduce- separate & reproduce

Bacteria & archaea- restriction enzymes- endonuclease (some need Mg ion-cofactor)

Prokaryotic DNA- protected by being methylated at recognition sites

Replica Plating

1
...
Dip a block covered with sterile velvet into colonies on Ampicillin agar and touch onto
surface of tetracycline
3
...
coli


-Contain more Zinc- cofactor in insulin
production/carbonic anhydrous
-Low meat diet- deficiency


- concerns- farmers- buy seeds yearly
- manufactures- free license to farmers to
keep/replant seeds
- reduce genetic diversity
- clone suffer from same disease
- rice don’t grown in all areas
-expensive

- fear artificially present DNA- harm our genes
- yet all food we eat- has genes-
enzymes/nucleotides
- Lytic enzymes digest DNA ingested

-Makes human insulin – treats all diabetes -escape & spread genes for antibiotic resistance-
- human growth hormone- treats children
affect ecosystem
with pituitary dwarfism
-they are modified- cannot synthesise an essential

nutrients-can’t survive outside lab
st
Soya bean: 1 gen
-Resistant to herbicide
-risk of gene for resistance pass into weeds- super
-Weeds competing with soya beans- killed weeds-
by herbicide
-not happened yet
Pathogen:
-Viruses GM- no harm- used to make
-GM- can increase risk of cancer/ interfere with
vaccines- still have antigens
gene regulation
-vaccine doesn’t make recipient ill
- used as vectors in gene therapy
Mice
-medical research- develop therapies for
- welfare concerns- medical/pharmaceutical testing
breast/prostate cancer
-UK- strict regulations govern welfare of animals
Gene therapy (gt)

Germ line gt- gt by inserting functional alleles into gametes/zygotes
- ensures all cells have a copy of it/ opposing may inherit foreign alleles
- illegal in humans
- concerns on how genes are inserted- could disrupt expression/ regulation of other genes
- increase risk of cancer

Somatic cell gt- gt by inserting functional alleles into body cells
- SMgt affects patient’s specific cells- not passed to offspring
- cystic fibrosis- inherit 2 faulty recessive alleles- for a gene
- Lack in functioning CFTR gene
- allele packaged into small sphere of lipid bilayer- liposomes
- aerosol inhaler- sprayed in nose- pass through plasma membrane of cell line in respiratory
tract
- pass through nuclear envelope- insert into host genome- express CFTR protein- Cl ion cannel

Problems of virus as gene delivery
• provoke immune response
• patient become immune to virus subsequent deliveries impossible
• insert allele into patient genome- disrupt gene in cell division regulation/ increase cancer/
disrupt regulation of other genes



Mutations of inheritance


mutagens- tar, ionising, radiation- UV, X rays, gamma
mutations with mitotic division- somatic & is not passed to offspring

Point mutation: - one base is substituted for another

1
...
Missense mutation- leads to different AA being incorporated in polypeptide chain
• sickle cell anaemia
3
...
coli metabolises glucose as respiratory substrate- if absent- disaccharide
lactose present induces:
- lactose permease- allow lactose to enter bacterial cell
- beta galactosidase- hydrolyse lactose into glucose & galactose

Lac operon- 6000 bp length of DNA
Operator region- Lac 0
structural genes- lacZ/Y- code for enzyme
P- promoter region- RNA polymerase binds to begin
transcription of lacZ/Y
regulatory gene I- codes for repressor protein LacI




Regulatory gene is expressed- repressor protein binds to operator- prevents RNA
polymerase binding to promoter region- prevents lacZ/Y being transcribed- enzymes for
lactose metabolism not made- genes switched off

Lactose is added:

1
...
lactose binds to LacI- repressor protein- alter shape- prevent it binding to operator
3
...
lactose induces enzyme needed to break it down


Transcription factors- protein/short non coding of RNA combines with specific site on a
length of DNA to inhibit/activate transcription of gene

Post-transcriptional gene regulation

-Introns- non-coding regions of DNA- not expressed
-Exons- coding regions of DNA
-All DNA transcribed- primary mRNA edited& split by endonuclease & RNA introns-
remaining mRNA exons are joined

Post- translational gene regulation

-requires activation of proteins- many enzymes are activated by being phosphorylated

cAMP- 2nd messenger in activation of enzymes
1
...
activates transmembrane protein- activates G protein activates adenyl cyclase
enzyme catalyses ATP-cAMP
3
...
activated PKA catalyses formation of phosphorylation of proteins & hydrolyses ATP
5
...
enters nucleus & acts as a transcription factor- regulates transcription

Genetic control of body plan development

Homeobox sequence- 180 bp (not introns)- found in genes- involved in regulating patterns
of anatomical development in animals/fungi/plant

- complex organism- hox clusters
- Homeodomain seq in a protein (transcription factors & act in nucleus)- folds into
particular shape & bind to DNA- regulate transcription of adjacent genes
- Homeobox genes- all multicellular organisms
- Hox genes- only in animals- formation of anatomical feature in correct locations of
body plan
- Hox genes also regulate development of embryos along anterior to posterior axis
- Hox genes regulated by gap/pair-rule genes regulated by maternal mRNA from egg
cytoplasm

Mitosis- homeobox & hox regulates cell cycle & ensures daughter cell contains full genome

Apoptosis- programmed cell death- hydrolytic enzymes

1
...

3
...

5
...
Small piece of plant tissue- explant- often meristem- Virus infection free or small leaf
2
...
explant- sterile growth medium-agar- nutrient rich- gluc/aa/phosphates & high conc of
growth hormone
4
...
placed in diff growth medium- 1
...
4:1 stimulate
shoots
6
...
Zygote- created by invitro fertilisation
2
...
Each small mass of cells- placed in uterus of surrogate mother

Somatic cell nuclear transfer
1
...
Adult somatic (normal body) cells removed
3
...
Shock also triggers egg cell to start developing- as if its been fertilised
5
...
young embryo placed into uterus of surrogate mother
7
...
g
...
Not operated all the time & slow growth rate
as nutrients decrease- easy set up
• Continuous- produce primary metabolites- everything continuously sterilised & added
continuously to maintain log phase- conditions are constantly monitored- operated all the
time- faster process- difficult set up

Importance if Asepsis

Asepsis- ensuring sterile conditions maintained as nutrient medium also supports growth of
unwanted micro
...


1
...
Inoculation- introducing micro
...
incubation
• petri dish labelled- taped using 2 strips of adhesive tape
• careful not to seal completely- can lead to anaerobic bacteria- pathogenic
• place in warm env- incubator- place upside down- condesnation drops o agar- prevents
dry out
• Do not open dish & must be sterilised before disposal & wash hands- mosture source of
infection

•
•
•
•
•
•


Liquid medium/broth- turns clear to cloudy when bacteria grown & placed onto agar plate- produces
visible colonies

Population growth- closed culture

liquid broth used to inoculate agar plate- too many colonies emerge- impossible to count- pop
...
of micro
...
1
• 1cm3 dilute broth 0
...
01 etc
• drop of each dilution used to inoculate agar plate
• record population & multiply by dilution factor

Growth curve
closed culture- no exchange of nutrients/gases with external env
...
growth- cell growth/synthesise
enzymes/switch on certain genes/take up water/pop- fairly constant

• Log phase-adjusted to env- enzymes to survive- sufficient nutrients to grow
rapidly & reproduce (exponential growth)

• Stationary phase- increasing no
...

growth

• Death phase- nutrients run out & concentration of waste products- lethal-
death rate exceeds reproduction- eventually all organisms die

Primary metabolites- produced by micro
...
Adsorption- attaches to insoluble surface- clay/resin- by ionic bonds/ hydrophobic
interactions- doesn’t affect rate & can be easily lost by leaking into reaction mixture
2
...
Entrapment- trapped in matrix- enzyme remain fully active- substrates needs to diffuse into
matrix & products out of it Eg
...
Membrane separation- semi permeable membrane around enzyme- small subrate pass
through & meet enzyme- limits rate

Industrial use

• glucose isomerase for the conversion of glucose to fructose
• penicillin acylase for the forma on of semi- synthetic penicillin (to which some penicillin-
resistant organisms are not resistant)
• lactase for the hydrolysis of lactose to glucose and galactose
• aminoacylase for production on of pure samples of L-amino acids
• glucoamylase for the conversion of dextrins to glucose
• nitrile hydrate- convert nitriles to amides
•

Ecosystems


Ecosystem: interactions between a community of living organisms and abiotic factors of their
chemical/physical environment

Small scale- single tree, medium- football field, large- African grassland

• Habitat- place where organism lives
• Population- all individuals of one species- live same place & time- breed together
• Community- all pop
...
- absorbed into body- mol
...
pioneer community- species begin process of succession- often colonising an area as the first
living things there- algae &lichen begin to live on rock
2
...
larger plants succeed small ones- climax community- final stable community exists after
succession occurs

secondary- takes place on previously colonised but disrupted/damaged habitat

1
...
Windblown sand builds up- around the base of these plant- mini sand dune- plants
die/decay- nutrients accumulate this dune- gets bigger
3
...
sand dunes & nutrients build up- other plants colonise- nitrogen converted to nitrate- more
species colonise- stabilise them further

Deflected succession- succession stops/interfered with grazing/mowing/burning
• results in subclimax- plagioclimax

Studying ecosystem


small proportion of habitat studied- representative for larger habitat

Quadrats:
• presence/absence of each species- distribution- 50% of plants need to be inside quadrat- to
count
• no
...
size
small

Log phase- high resources/ good conditions- reproduction quicker as rate of rep> mortality- size
increases quickly

Stationary phase- pop size levelled out to carry capacity (max pop size a habitat can be maintained
over a period in a specific habitat)- rate of rep= mortality- pop is stable

Limiting factor- factor whose magnitude slows down rate of a natural process

Density dependent-factor influences population more strongly as population size increases
§ availability of resources/oxygen/food/water/light/nesting sites/predation/parasites

Density independent- act strongly irrespectively of size of population
§ low temp kills same proportion of individuals in population irrespective of size

k- strategist- species whose population size determined by carrying capacity
§ limiting factors exert and a more significant effect on pop
...
to level out
§ birds/mammals/large plants- low reproduction rate/slow development/long lifespan/large
body mass/ late reproductive age

r- strategist- species whose population size increases so quickly- exceeds carrying capacity of habitat
before limiting factors start to effect size
§ mice/spiders/weed- opposite
§ Quick pop
...
predator pop
...
prey pop
...
size reduces
3
...
increases
4
...
can increases- cycle start again


Intraspecific:
§ stationary phase- slight fluctuation in size
§ pop
...
Krill
•
•
•
•



•

food for whales, seals, penguins, squids
make nutritional supplements- animal feed
advancement in tech- large krill pop
...
Protected areas
• International whaling commission- illegal to hunt & kill whales &monitoring whaling
activity needs to be maintained- ensure preservation
• current imitative to expand network of marine protected areas- Ross sea- high
biodiversity- attracts fish industry

3
...


Microscopes-


• take one cell thick onion epidermis- place onto slide- with a drop of iodine- soak excess with
paper towel
• cover section with coverslip
• stage micrometer to calibrate eyepiece graticule with objective lens(x10/40)
• examine cell- focus onto a few cells- draw 3/4 cells
• use eye piece graticule to calculate length
• use x40 obj lens to make high powered drawing- always used scale bar
• also use for plant root identify- xylem/phloem/endodermis/cortex/epidermis





v blood cells- own blood sample- disposed of in bleach
v haemocytometer- estimate conc of RBC in blood
v capillaries difficult to see- small diameter- thin walls- little material to take up stain
2
...


Species diversity


random sampling methods- determine species diversity- two contrasting areas
place tape measures (20m)- right angle to each other as X/Y axis
randomly generate no
...
x9
graph- %cover individual species- 2 areas, - calc Simpsons index biodiversity
D = 1 - E(n / N)2 (N = the total no
...
of organisms
of a particular species)
climax community- higher species diversity, diff food chains/loss of species- little effect on ecosystem
farmers reduce specie diversity- planting 1 crop- few habitats for other species/ pesticides/removal of
hedgerows- less habitat for species (hedgerows planted around field- increase species diversity
whilst data collection- note down current growing season/evidence of animal impact- grazing/ sketch
map of site- show key features
disrupt animals as little as possible & return back to original habitat
•
•
•
•
•
•
•

v
v
v
v


4
...



Calorimeter/photometer

• effect of temp against membrane permeability- beetroot cells (purple pigment- vacuole)
• 4 test tubes- 20°C, 40°C, 60°C and 80°C with 10cm3 water in each via syringe
• place in water bath- 5mins- equilibrate to correct temp- record temp
• cut beetroot cylinder- equal smaller ones with knife/ruler
• add one cylinder to each test tube- 15 mins- pour liquid into cuvette
• calorimeter (green filter) measure absorption- onto a graph- arbitrary units AU- graph
v Cell surface membrane/ tonoplast more fluid at high temp- phospholipid bilayer- progressively more
disaggregated- increase in KE increases movement of phospholipid molecules in membrane- proteins
become denatured- create spaces for pigment leakage by diffusion
v limitations- pigment present in diff amounts- diff parts of beetroot/ left in water for diff lengths of
time/age of beetroots varies/diff amounts of drying

A potometer measures the rate of water uptake by a leafy shoot
...
Set it up under water to make sure there are no air bubbles
inside the apparatus
9
...
Cut stem under water to prevent air entering xylem
11
...
Dry the leaves
13
...
scale on capillary tube


6
...
Microbiological techniques

Aseptic techniques:
• wash your hands, disinfect working area, bunsen’s burner- heat air- air to rise & prevent air bone
microorganism/ sterile air, open/close vessel- neck of bottle over flame to prevent bacteria into
bottle
• Lift lid of petri dish- just enough to allow intro of desired microorganism
• glass/ metal equipment- passed through flame- before and after contact- desired micro
...


5
...





Sterilisation
• nutrient agar medium &equipment sterilised-heating-autoclave- 121oc- 15 mins
• kills all living organisms- bacteria/fungal spores
• medium cooled and poured into sterile petri dish-left to set with lid kept on prevent infection
• all equipment must be sterilised with heating

Inoculation- introducing micro
...
Transport- cells

Serial dilutions- sequence of dilutions- reduces conc of a solution/suspension
• step wise dilution of broth culture/ sucrose solution
• 1cm3 of broth sample + 9cm3 of dilute h2o= dilute broth 0
...
1 + 9cm3 of dilute h2o= dilute broth 0
...
Qualitative testing

Test for carbohydrate:

Starch:-Iodine solution- positive result= orange-brown blue-black colour

Reducing sugars:
• All monosaccharides/some disaccharides including maltose & lactose are reducing sugars
1
...
reducing sugar present- solution turns blue- green- yellow- brick red ppt (Cu2O)
3
...
Test for reducing sugar to check there are none in first place
2
...
Cool solution and neutralize with sodium hydrogencarbonate solution
4
...
Add some of the test sample to ethanol and shake to dissolve
2
...
If a cloudy white emulsion forms in the water it indicates there was lipid present in the test

Test for proteins:
1
...
Protein present- colour change from light blue to lilac

• Biuret reagent made of a mixture of copper sulphate and potassium or sodium hydroxide

Calorimeter

• The colorimeter shines a beam of light through the sample
• A photoelectric cell picks up the light that is passed through the sample (on the other side)
• provides a reading of the amount of light- passed through – transmitted or absorbed
• more copper sulphate (benedict reagent) used- less light will be blocked/absorbed- more transmitted
...

• Use UV light-glows TLC plate except spots of mixture has travelled to
...
Polar solutes stick to surface travel slower, non polar solutes travel quickly

Urine tests for athletes- illegal drugs


Uv light, ninhydrin- binds to aa- visible brown spots
...
Data logger

• ph changes effect of lipase in milk
• spirometer/ECG
• temp affects lipase- over time more fatty acids/glycerol produced from triglyceride- increase ph
denature lipase- reaction stops





11

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