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VCE Biology Summary Book 2013 Samantha Tierney

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CONTENTSSAC 1ProteinsDNA Structure and protein synthesisEnzymesCellular respirationPhotosynthesisExperimental Design

SAC 2CarbohydratesLipidsNucleic acidsOrganic and inorganic compoundsWaterComposition of membranesProcesses molecules use to cross membrane

Important termsDifferent ways animal and plant cells respond to osmosis and water balance

Adaptations of some organisms to osomoregulateMovement across membranes in circulatory and digestive system

SAC 3Signal transductionNervesPl

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PROTEINS Sub units:

Amino acids

Protein stages:

Stage Bond Diagram

Primary Peptide

Secondary Hydrogen

Tertiary Ionic anddisulphide (specific

h )

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Common proteins used in the cell: RNA polymeraseDNA polymeraseProtein channelsEnzymes (to catalyse chemical reactions)

Two types of proteins: Fibrous proteins (strength, structure and support)Globular (eg. enzymes) have a very specific shape (active site) for their very

specific function.How proteins transported and manufactured in the cell: Produced via protein synthesis

o Transcription (nucleus) During Transcription RNA polymerase reads the DNA template strand to

produce a complimentary strand of pre mRNA. Post transcription modificationoccurs and Introns are spliced out and exons are re-joined. A methyl cap(5')

and poly A tail(3') are added to the mRNA. This forms mature mRNA, whichthen leaves the nucleus via a nuclear pore.

o Translation (cytoplasm) During Translation the Ribosome reads the mRNA, one codon (3 bases) at a

time. tRNA with the complimentary anticodon then binds to mRNA and drops offa specific amino acid. Peptide bonds form between adjacent amino acids toform a polypeptide chain.

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Differences between DNA and RNA:

DNA RNA

Double stranded (double helix) Single stranded

Thymine Uracil

Stays in the nucleus Can leave the nucleus

Contains deoxyribose sugar Contains Ribose sugar

Start codon:Start codon is the message that starts a certain protein being synthesized. For allproteins this is the nucleotide sequence "AUG" and this codes for the amino acidmethionine.Stop codon: The stop codons are the messages that tells the cell that the protein is made andthat they should stop adding more amino acids to the polypeptide. The stop codonsdo not have amino acids. They are:UAA (You are annoying)UAG (You are gross)UGA (You Go away)

When a base on DNA is changed: Codes for incorrect amino acid

R l i i i

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EnzymesDefinition: Protein that catalyses chemical reactions in living organisms. An enzymehas a highly specific shape for its specific function. They can be used over and overagain.

Protein structure: GlobularHighly specific active siteQuarternaryHighly specific for specific function

Lock and Key theory:Where the shape of the active site of the enzyme and the substrates arecomplimentary. (SE not ES complex)

I d d fi

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pH: Due to charges in surface of enzyme, it interacts with solution it's dissolved inLarge changes result in denaturingSmall changes result in reduced activityOptimum pH determined by pH enzyme is usually found in

Competitive inhibition: Molecule (not substrate) binds to active siteStops enzyme acting as catalyst for desired substrate

Non Competitive inhibition: Molecule binds to another part of enzymeNew bond changes active site or obstructs it

Amount of substrate: Increase in substrate increases enzyme activityUntil Enzyme saturation is reached (then it has no effect)

An enzyme is saturated when the active sites of all the molecules are occupied mostof the time. At the saturation point, the reaction will not speed up, no matter howmuch additional substrate is added.

Can you pick the enzyme substrate and product in a chemical reaction?Yes for example lipase breaks down lipids into fatty acids and glycerol.

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Enzyme graphs:

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Cellular RespirationStages:

Glycolysis-CytosolKrebs Cycle-MatrixElectron transport chain-Cristae

Products of Glycolysis: 2 Pyruvate molecules (aerobic)

Lactic acid (anaerobic)

Mitochondria: Matrix: Fluid nutrient component of mitochondriaCristae: Inner membrane of mitochondria

NADH and FADH 2: Loaded acceptorsCarry electronsCarry Hydrogen

Chemical formula: C6H12 O 6 + 6O 2 enzymes-> 6CO 2 + 6H 2O + 36/38 ATP

Fermentation:

l h l b d d ( l )

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Can you apply oxidation and reduction to NAD and FADH? Accepting H - ReductionDonating H - Oxidation

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PhotosynthesisLight dependant: Light is absorbed by chlorophyll. Water is split. NADP binds with hydrogen-NADPHand ADP binds with Pi ATP. Oxygen produced.H2O --> O 2 + H +

Light independent: CO2 enters stroma. It combines with H ions during a metabolic reaction to produce

glucose.H+ + CO 2 -> C 6H12O 6 + H 2O

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Chloroplast:

Light dependant-GranaLight independent-Stroma

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Experimental DesignDependent variable:

Is the measure of the independent variable. Therefore it depends on theindependent variable.

Independent variable: Is the variable which you change in an experimentYou can only have 1 variable that can change in an experiment

More than one independent variable will result in an unfair experiment.Example:

An experiment looking at the growth of trees in no sunlight, low sunlight, a lotof sunlight.The independent variable is the amount of sunlight on the plants, because thisis what is being changed.The dependent variable may be the height of the plants, which is determinedby the independent variable (amount of sunlight on the plants)

Controlled Variables: The factors that stay the same in the experiment.

Controls: A standard (reference) treatment that helps to ensure that the othertreatments are being acted upon by the dependent variable and that the

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CarbohydratesStructure:

General formula C nH2nO n eg. C 6H12 O 6 Names end in 'ose'Contain many hydroxyl groups and one carbonyl group.Classified by number of carbons eg. Glucose is a pentose sugar as it has 5carbons.Composed of monosaccharides joined by glycosidic bonds.

Function: Store energyUsed as fuel for cellular workUsed as raw material for synthesis of other substances such as amino acidsand fatty acids

Synthesis of Carbohydrates: Dehydration reaction where water is lostGlycosidic bonds form

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Common Carbohydrates:

GlycogenFound in animalsSynthesised in the smooth ERWhen in excess they are converted into lipidsUsed for energyMonomer: Alpha Glucose

StarchFound in plantsStores energyMonomer: Alpha Glucose

CelluloseFound in plant cell wallsStrong bonds (due to cross bonds)Monomer: Beta Glucose

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LipidsSynthesis of lipids:

Condensation reaction where water is lost (one per fatty acid tail)Synthesised in smooth ER

Subunits: Fatty acids

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5 common lipids:

TriglyceridesContains 3 fatty acid tails.Form due to condensation reaction.Sometimes referred to fats and oils.Used as energy source and insulator.Provides protection for organs.Glycerol and fatty acids

PhospholipidsPrinciple major component of cell membrane2 fatty acid tails that are water hating therefore insoluble therefore nonpolar.

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SteroidsHas a four ring structure that looks like a carb.

They are lipids made in smooth ER.Two main types: cholesterol gives strengthHormones involved in cell to cell recognition and can act as transcriptionfactors and cause growth.

GlycolipidsCarbohydrate attached to lipid.2 fatty acids and lipids. In cell membraneCell to cell identification, communication and cohesion.

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Nucleic Acids

DNA (DeoxyriboNucleicAcid)

Monomer: Nucleotide

Polymer: Consists of many monomer unitsDouble helix structureWound and coiled to form chromosomeFound in nucleus (and mitochondria/chloroplast)

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RNA (RiboNucleicAcid)

Monomer: Nucleotide

Polymer: Single strandedContains uracil instead of thymineMany monomer units

Polymerisation: Condensation reaction

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Organic and Inorganic Compounds

Organic Compounds Are compound that are large and contain carbon in complex forms. They also havecarbon-carbon bonds. Important organic compounds are:

CarbohydratesProteinsLipidsNucleic acids

Vitamins

Inorganic Small and not containing carbon (so they cannot have carbon-carbon bond).

OxygenSodiumPotassiumPhosphorus

Water

The role of water in organisms:Used in cellular respiration

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Composition of MembranesMembrane structure:

hospholipid bilayer(lipids, protein, carbs, cholesterol) Hydrophilic on the outside to let molecules in/out Hydrophobic on inside

Membrane function: Encloses contents of the cell

Controls movement of substances into and out of the cell.Permits selective control of molecules coming in/out Active environment for chemical reactionsEstablish compartments within the cell(separating hereditary material, cytosol, lysosomal enzymes, secretoryproducts of cell, energy processing materials in mitochondria/chloroplast)Restrict movement of substances between one part of a cell and another,thereby permitting regulation of the many enzymatic pro cesses that takeplace within the cellHave protein receptors involved in intercellular communication (directlybetween adjacent cells, and by hormones and nerves)Involved in cell cell recognitionProduce electrical activity in excitable cells.

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Proteins: Provide channels for water soluble molecules

Facilitated diffusion

Carbohydrates: Often linked to protruding proteins

Involved in recognition/adhesion btw cellsRecognition of antibodies, hormones and viruses

What can go through where?

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Processes Molecules Use to Cross Membranes

Definition What uses thisprocess

Why is it importantin human cells?

Diffusion Movement ofsubstances froman area of highconcentration to

an area of lowconcentration. Noenergy required

Gases (oxygen,carbon dioxide)

Water molecules(rate slow due topolarity)

Lipids (steroidhormones)

Lipid solublemolecules(hydrocarbons,

alcohols, somevitamins) Small non

chargedmolecules (NH 3)

Cell respiration

Alveoli of lungs

Capillaries

Red Blood Cells

Medications: time-release capsules

FacilitatedDiffusion

Passive diffusionthrough selective

Ions+ + -

Cells obtain foodfor cell respiration

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ActiveTransport

Movement ofsubstancesagainst theconcentrationgradientthat requiresenergy. Occursthrough selectiveprotein channels.

Certain water solublemolecules (some ions,amino acids,monosaccharides)

Bring in essential

molecules: ions,amino acids,glucose,nucleotides

Rid cell ofunwantedmolecules (Ex.

sodium from urinein kidneys)

Maintain internalconditions differentfrom theenvironment

Regulate the

volume of cells bycontrolling osmoticpotential

Control cellular pH Re-establish

concentrationgradients to run

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Important TermsHypertonic:

Solutions that have a higher solute concentration than a suspended cell.

What happens if you place a cell into this solution? The cell will lose water and shrink. (Red blood cells = crenation)In plant cells, the central vacuole will shrink and the plasma membrane willpull away from the cell wall causing the cytoplasm to shrink called plasmolysis

Hypotonic:Solutions that have a lower solute concentration than the suspended cell.

What happens if you place a cell into this solution? The cell will gain water and swell.If the cell bursts, then we call this lysis. (Red blood cells = hemolysis)In plant cells with rigid cell walls, this creates turgor pressure.

Isotonic:Solutions that have the same concentration of solutes as the suspended cell.

What happens if you place a cell into this solution? The cell will have no net movement of water (goes in and out at same rate)and will stay the same size.

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Different ways animal and plant cells responds to

osmosis and water balanceOsmosis in different solutions:

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Adaptations of some organsisms to osomoregulate

Contractile vacuoles gather excess water and expel it to the outside of the cell(sponges and freshwater protozoans)By pumping ions such as sodium and potassium across cell membranes,creating a concentration gradient that causes water to follow by osmosis.

Movement across membranes in the circulatory anddigestive system

Circulatory system: In the lungs diffusion is used for gas exchange of carbon dioxide and oxygen.In the capillaries, oxygen diffuses into the bloodstream, while carbon dioxidediffuses out.Without diffusion we would not acquire enough oxygen to got to the heart andcirculate throughout the body.Nutrients and waste will move in/out of blood/extracellular fluid.

Digestive system: In the small intestine nutrients diffuse into across the microvilli (increasedSA/V for maximum diffusion)

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Signal transduction

Signal Transduction: Chemical process by which an extracellular message isconverted to an intracellular message to cause cell change.

Ways signalling molecules travel: Endocrine: Blood streamParacrine: Neighbouring cells

Autocrine: Within itself

Exocrine: Outside body

4 Main signalling molecules

Pheromones: Chemical released by an animal that acts as asignal to other animals of the same speciesFunction: Used for communication between organisms of the same species

Affect matingMark feedingMark territorySignal presence of foodSignal presence of predator

Animal Hormones: Chemical substance produced in one part of the organism(animal) and sent to another to initiate signal transduction.

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Protein Hormone

1. Bind externally2. Activates G Protein3. Secondary messenger4. Cyclic AMP (cAMP) is a common

secondary messenger.5. Results in further reactions in the

Signal Transduction Pathways

Steroid Hormone 1. Able to move through the membrane so

receptor is inside.2. Binds to receptor.3. Often then act as transcription factors.4. Help switching on genes.5. Results in protein formation.

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Neurotransmitters: 1. Impulse converted from electrical message to chemical message

2. Neurotransmitters are released from axon terminal via exocytosis3. They diffuse across synaptic gap4. They bind to receptors on dendrites of neighbouring neuron5. Sodium gates open and sodium ions rush in6. If this stimulus reaches threshold an action potential is generated and the

impulse ia passed on

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Transcription Factors: Molecule that binds to specific receptor on DNA to initiatetranscription.

Homeostasis: The maintenance of a relatively stable internal environment within anarrow range.

Animal Adaptions to Maintain Homeostasis:

Physiological: Extended loop of henle

Increases water uptake back into the bodyCounter current heat exchange

Regulates temperature

Behavioural:Panting

Cools blood down when animal does not have sweat glands

Shade seeking behaviour to reduce radiation exposureMigration

to move to more suitable climates

Apoptosis 1. Signalling molecule binds to death receptor stimulating response apoptosis2. Many different enzymes are activated within the cell and at the same time

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Importance in body Essential for feature development

Balances out with mitosis (must be balanced)

To much apoptosis Causes neurodegenerative diseases

AlzheimerHuntington

Not enough apoptosis Leads to production of cancersLeads to autoimmune diseases

Negative feedback mechanisms:

GAS REGULATION (pH)

Chemoreceptors in theHypothalamus

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WATER CONCENTRATIONIN BLOOD

Osmoreceptors in theHypothalamus

-Posterior pituitary gland(stimulated) releaseshormone ADH

-Posterior pituitary gland(inhibited) does not releasehormone ADH

Low waterin blood

High waterin blood

-ADH binds to specific receptoron the loop of henle (in kidney)stimulating (water gates open)

-ADH not secreted therefore itcannot bind to its specificreceptor and the water gates in

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TEMPERATURE REGULATION

Thermoreceptors in the skin andHypothalamus

-Skeletal muscles (contract)-Pilli muscles (contract)-Smooth muscles surroundingblood vessels (contract)-Sweat glands (inhibited)-Thyroid gland (stimulated)

-Skeletal muscles (relax)-Pilli muscles (relax)-Smooth musclessurrounding blood vessels(relax)-Sweat glands (stimulated)-Thyroid gland (Inhibited)

Low corebody temp

High corebody temp

-Shivering: increases metabolicrate therefore increases heatproduction

-No shivering: decreasesmetabolic rate thereforedecreases heat production

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GLUCOSE CONCENTRATION IN BLOOD

Pancreatic receptors

-Alpha cells (in islets oflangerhans) of pancreasproduce and secrete hormoneglucagon

-Beta cells (in islets oflangerhans) of pancreasproduce and secretehormone insulin

Lowglucoselevels

Highglucoselevels

-Glucagon binds to its specificreceptor stimulating thebreakdown of glycogen toglucose

-Insulin binds to its specificreceptor on liver cells andmuscle cells stimulating theactive uptake of glucose and

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Nerves

Stimulus: The change from ideal or resting conditionsReceptor: The cells or tissue which detects the change due to the stimulusTransmission: A form of chemical communication that occurs between two nervecells or between a nerve cell and an effector cellEffector: The cells or tissue (usually muscles or glands) which cause responseResponse: Change in an organism due to a stimulus

Neurohormones:Hormones produced in the hypothalamusStimulating/releasing hormones

Neurosecretory cells Located in hypothalamus (but continue into anterior pituitary)Produce and secrete neurohormones

Common glands and what they secrete

Thyroid Gland:ThyroxineSpeeds up metabolic rate

Parathyroid Gland:

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Pituitary Gland: Secretes neurohormones such as oxytocin

Oxytocin: causes uterine contractions and stimulates milk secretion inmammary glands Adrenocorticotropic hormone (ACTH): Stimulates secretion of cortisol andaldosterone by adrenal cortex

Antidiuretic hormone (ADH): Stimulates reabsorption of water by kidneysFollicle stimulating hormone (FSH): (ovaries/testes): Stimulates production ofovum/spermGrowth hormone (GH): Regulates development of muscle and bonesLuteinizing hormone (LH): Stimulates production of progesterone andoestrogen production; initiates ovulation in females; stimulates testosterone inproductionProlactin (PRL): Stimulates milk production in breasts during lactationThyroid stimulating hormone (TSH): Regulates secretion of thyroid hormones(thyroxine and thyroidthyronine)

Neurons Neurons are nerve cells (specialised for transmission of impulses)

Are not replaced after initial developmentOnly carry signal in one direction

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Sensory: Afferent as they carry signal towards CNS

Detects stimulusCell body in the middle

Motor: Efferent as it carries signal away from CNSStimulates effector (muscle/gland)

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Reflex Arc Controls rapid autonomic involuntary responses to keep the body out of

dangerDoes not involve the brain (making the response faster)Stimulus travels from sensory to spinal cord to motor neuron

Action potential +

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Transmission Can only move in one direction

In order for the impulse to take place the stimulus must reach or pass thethreshold

Signal transduction across the synapse

Action potential (charge) stimulates calcium gates to openCalcium ions diffuse into the axon terminalStimulates vesicles to release neurotransmitters (EG.Acetylcholine) via

exocytosisNeurotransmitter diffuses across synaptic gap (synapse)Neurotransmitter binds to specific receptors (Sodium channels) on thedendrites of the neighbouring neuronNa channels stimulated to open (by Neurotransmitter) and Na rushes inmaking cell slightly positive. If this stimulus reaches threshold action potentialis initiated.Enzyme breaks bond btw neurotransmitter and receptor. Neurotransmitter

goes back into cell and is repackaged ready for next stimulus

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Feedback: The consequence of the response on the stimulus. This can be

positive or negative.Negative feedback: Homeostatic mechanisms where the response diminishesthe original stimulus.Positive feedback: Homeostatic mechanisms where the response enhancesthe original stimulus.

Plants

Important hormones: IAA, GBA, ABA, Ethylene, Cytokinin

Hormone Function

IAA (auxin) -Promotes growth -causes cell elongation- promotes apicaldominance -prevents lateral growth

GBA -Promotes germination -breaches dormancy ABA -inhibits germination -initiates dormancy -stimulates closure

of the stomata -promotes abscission

Ethylene -Ripens fruit -leaf/flower abscission

Cytokinin -Breaches dormancy -stimulates lateral buds -enhancesstomata opening - promotes cell division

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Opening and closing of the stomata

Opening:Increased turgor results from an influx of water into the guard cells, causing them toswell in the only direction possible, lengthwise. Because they are attached at theirends, this buckles the guard cells and opens the stoma.Closing:Water rushes out of the guard cells decreasing turgor pressure and allowing theguard cells to go back to their normal shape and close stomata

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Plant adaptations

Desert Plant Adaptations Some plants, called succulents, store water in their stems or leaves; Some plants have no leaves or small seasonal leaves that only grow after itrains. The lack of leaves helps reduce water loss during photosynthesis. Leaflessplants conduct photosynthesis in their green stems. Long root systems spread out wide or go deep i nto the ground to absorb water; Some plants have a short life cycle, germinating in response to rain, growing,flowering, and dying within one year. These plants can evade drought. Leaves with hair help shade the plant, reducing water loss. Other plants haveleaves that turn throughout the day to expose a minimum surface area to the heat. Spines to discourage animals from eating plants for water; Waxy coating on stems and leaves help reduce water loss. Flowers that open at night lure pollinators who are more likely to be active duringthe cooler night. Slower growing requires less energy. The plants don't have to make as much

food and therefore do not lose as much water.Tropical Rainforest Plant Adaptations Drip tips and waxy surfaces al low water to run off, to discourage growth ofbacteria and fungi Buttresses and prop and stilt roots help hold up plants in the shallow soil Some plants grow/climb on others to reach the sunlight Flowers on the forest floor are designed to lure anima l pollinators since there is

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Plant defenceThorns, spines and micro needles: discourage animals from eating them

Barriers such as waxy cuticle, bark and resins: resist penetration by virusparticles, bacteria, and the spores of fungi. Barks also provide some defenceagainst insect jaws and stingers. Thick barks provide fire protection.Covering epidermis, leaves, stem, roots, with a contact poison to defendagainst herbivores. Poison ivy, poison oak

Triggered by attackWhen being eaten some plants can produce substances that act on theanimal eating themMany plants produce volatile signal-chemicals that attract the natural

predators of their attackers.Eg corn plants:

Attracts tiny wasps which home in on the signal and sting the caterpillar then laytheir eggs in itIt tells nearby corn plants to activate their defences.

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DNA Structure

DNA's 4 nitrogenous basesBase Pair Pyrimidine/Purine

Adenine T Purine

Guanine C Purine

Cytosine G Pyrimidine

Thymine A Pyrimidine

Pyrimidines have a single ring structure.Purines have a double ringed structure.

Double HelixTwo DNA strands form a helical spiral, winding around a helix axis in a right-handed spiralThe two polynucleotide chains run in opposite directions (antiparallel)5'end- with the 5th carbon on sugar exposed, 3'end- with the 3rd carbon onsugar exposed.The sugar-phosphate backbones of the two DNA strands wind around thehelix axis like the railing of a spiral staircaseThe bases of the individual nucleotides are on the inside of the helix, stacked

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DNA ReplicationProcess

DNA helicase unwinds the double stranded DNADNA is copied in a 3' to 5' direction therefore the leading strand is copiedcontinuously where complimentary bases join to the parent strandThe lagging strand is copied in fragments discontinuously where DNApolymerase binds to primers and synthesises short otzaki fragmentsThe otzaki fragments are joined by DNA ligaseThe final product is two identical DNA strands that are semi conservative.

(double stranded semi conservative DNA)

DNA template strandGenerally from 5' end to 3' endStrand on which a new strand is synthesisedBoth strands act as template strand3'-5' is lagging strand

Semiconservative: When the product contains one parent and one daughter strandof DNAPurpose: It limits the amount of mutations that would occur.

Primer: Marks binding site for DNA polymerase during DNA replication.

Otzaki Fragment: Short fragment of DNA synthesised on the lagging strand during

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Transcription

Operon: A group of genes or a segment of DNA that functions as asingle transcription unit. It is comprised of an operator, a promoter, and one ormore structural genes that are transcribed into mRNA.

Operator: A segment of DNA where the repressor binds to, thereby preventing the transcriptionof certain genes.

Promoter Region: A site in a DNA molecule at which RNApolymerase and transcription factors bind to initiate transcription of mRNA.

TRANSCRIPTION: Nucleus-RNA polymerase binds to promoter region and initiates translation. It moves alongthe DNA template strand (5' to 3'direction)-Using complimentary free floating nucleotides it synthesises a complimentary

strand of pre mRNA-Post Transcriptional Modification occurs. Introns are spliced out by a splicosome

and exons are joined together. A methyl cap is added to the 5' end and a poly-A tailis added to the 3' end. Mature mRNA is produced.

Intron: Non coding regions of a geneExon: Coding regions of a gene

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TranslationTRANSLATION: RibosomeInitiation-mRNA binds to the ribosome and the ribosome reads one codon (3 bases)at a time. It begins at the start coon (which codes for methionine). Each codonspecifies for a specific amino acid.Elongation-tRNA with the specific complimentary anticodon brings the specific aminoacid as specified by the mRNA to ribosome (occurs at ribosome site A). Amino acids

join by forming a peptide bond (site P) and the tRNA exits the ribosome (site E)Termination- A stop codon is reached. This indicates that the production of the

polypeptide chain is complete. A stop codon does not code for an amino acid. Apolypeptide is produced.

-During transcription the mRNA moves through the ribosome. The ribosome staysstill.

Transfer RNA (tRNA): RNA molecules responsible for bringing specific amino acidsto the ribosome for incorporation into a polypeptide during translation.

Anticodon: 3 bases located on tRNA which are complimentary to an mRNA codon.

Ribosome: Is an organelle consisting of rRNA and protein. It is the site ofTranslation. It translates the mRNA code to call for specific amino acids to make apeptide chain.

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The coding of DNA determines the mRNA code. The codons of mRNA specify for aspecific amino acid. These amino acids form specific bonds that determine the

shape of the protein. If a DNA base is changed, the mRNA codon is changed and inturn the amino acid sequence of the polypeptide produced. This means that differentbonds form and a different shaped protein is produced.

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Genetic Engineering

Restriction Enzymes: Enzymes that cut DNA at a specific recognition site togenerally produce sticky ends. They are named after the bacteria they are isolatedfrom.Eg.

Enzyme Bacteria/Source Recognition Site

EcoRI Escherichia coli RY 13 GAATTC

BamHI Bacillus amyloliquefaciens H GGATCC

HindIII Haemophillus influenza Rd AAGCTT

DNA Ligase: Type of enzyme that joins DNA segments with sticky ends. It aids theformation phosphodiester bonds between nucleotides.

Reverse Transcriptase: An enzyme naturally found in retroviruses used to makecDNA from mRNA. It is used for gene cloning.

Gel Electrophoresis Add dye to the marker DNA and all samples (so that they are visible at theend of the process)Load Marker and samples into the wells of the gel

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Gene Probes: Single stranded DNA (can be RNA) that binds complimentary to DNAunder investigation to enable it to be seen or visualised.

They are used in gel electrophoresis to see if a particular allele is present in asample.

STR: Short tandem repeat. Non coding segments found between genes. Theyrepeat themselves many times and are between 2-6 bases long. There are manydifferent alleles for STR's and it less likely for people to have the same STR allelesthat coding segments of DNA. This makes them more useful for DNA fingerprinting.

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1. Heat DNA of interest to 95 0C to break the hydrogen bonds between bases.2. Cool to 50 0C to allow primers to anneal the 3' end of DNA strands.

3. Heat to 720

C. Add Taq polymerase and nucleotides to extend the primers.4. Repeat many times

Taq Polymerase: An enzyme which is used to extend primers in PCR. It synthesisesDNA at high temperatures.

Primers: Indicate the starting point for enzymes (in this case Taq polymerase.

DNA Sequencing: Determining the order of bases of a segment of DNA

Plasmid: A ring like structure that holds non essential DNA, found in bacteria. Theycan replicate on their own, they are double stranded and easily manipulated.

General Structure of Bacteria:Prokaryotic, therefore no membrane bound organellesCell wall made of peptidoglycanCircular DNADoes not have a true nucleus

Transformed Bacteria: Bacteria that have taken up a recombinant plasmid.

Recombinant Plasmid: A plasmid that has had a foreign gene inserted into it.

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Agrobacterium Tumefaciens: Bacteria that is a pathogen of plants. It can be used asa gene delivery system by taking out its pathogenic genes and inserting other genes

(such as growth promoters) and infecting the plants with it.

GMO

Advantages Disadvantages

-figuring out how to cure geneticdiseases, like sickle-cell anaemia- Producing larger animals/crops sothat farmers get more money forthem- cloning animals that are about toextinct

-Raises ethical/religious issues-Expensive process-GMO's escaping. eg The big fish thatgot out and started eating the little fishof the same species.

Cell ReplicationBINARY FISSION

1. Cell replicates its DNA2. Cell elongates and DNA moves to either pole3. Cell wall and membrane begin to form4. Cell wall forms completely

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MITOSIS

1. G1, G2 and S phase. Where DNA replication occurs and ischecked. Centriole move to either pole

2. Chromosomes thicken, nuclear membrane breaks down andspindle fibres begin to form

3. Homologous chromosomes line up linear single file.4. Centromeres are divided and pulled to either pole. Sister

chromatids are separated at their centromere and pulled toeither pole.

5. Nuclear membrane reforms6. Separation of the cytoplasm

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Population Genetics and Evidence of Evolution

Process of natural selection 1. VARIATION must exist between members of the species2. SELECTION PRESSURE causes a struggle for survival3. There is a SELECTIVE ADVANTAGE. Those that are most fit are able to respond an

pass on their alleles4. Favourable traits ae INHERITED and over many generations allelic frequencies will

change

Two examples1. Darwin's finches. Small populations moved to the Galapagos islands. On each islandthere were different selection pressures, in terms of food source, which meant differentbeaks were favourable. The finches with the favourable beaks were able to then mateand pass on their trait. Over generations a specific beak type became higher infrequencies.

2. Resistant Bacteria. There are some bacteria in a population that are resistant to aparticular antibiotic. When the population is exposed to this antibiotic there is a strugglefor survival. Those with the resistance are most fit for this environment and survive sothat they may replicate thus increasing the number of bacteria in the population thatare resistant.

Evolution: The changes that occur in the genetic makeup of a population over time.

Mutation and migration are the only factors that bring about variation in an asexualpopulation. The law of independent assortment and crossing over do not apply as asexualorganisms do not undergo meiosis.

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Asexual reproduction, genetic variation is restricted to Mutation: A change in that organisms DNA which is then passed on to its daughter

cells (eg bacteria) Migration: By chance organisms that migrate may have variation in a phenotype due to

environmental influencesSexual reproduction, genetic variation is brought on by

Mutation: A change in that organisms DNA Migration: By chance organisms that migrate may have variation in a phenotype due to

environmental influences Sexual reproduction: Brings about the most variation by the following processes Crossing over: The exchange of genetic material between homologous chromosomes. Independent assortment: The alleles of a gene controlling one trait assort

independently of alleles of another gene controlling a different trait.

Selection Pressure: Environmental conditions leading to differential fitness based on thevalue of a particular trait

Adaptation: Inherited characteristic that increases the likelihood of survival andreproduction of an organism

Artificial Selection: When an organism seeks a mate with a particular phenotype

Selective Breeding: The intentional breeding of organisms with desirable trait in an attemptto produce offspring with similar desirable characteristics or with improved traits

Experimental Design (example) Corn is grown on many farms. It was found that corn plants grown on one farm were always

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SpeciesProcess of Speciation

1. A species becomes isolated by a geographic barrier therefore no gene flow can occur.2. The two populations are exposed to different selection pressures and agents. Natural

selection occurs thus changing the allelic frequencies of that population.3. The two populations become reproductively isolated.4. They can no longer interbreed to produce fertile and viable offspring.

Eg. There is a land bridge between north and south America. On either side there aresnapping shrimp. The two groups are phenotypically similar but when brought together they

snap at each other. They are considered to be two different species.Explain how the differences between the shrimp could have arisen.1. The population is separated into two groups by the geographic barrier of the land

bridge, therefore no gene flow can occur.2. The two populations on either side of the land bridge are exposed to different selection

pressures. Natural selection occurs thus changing the allelic frequencies of thepopulation.

3. The two populations are reproductively isolated and will not mate4. Therefore they cannot produce fertile viable offspring and are considered different

species.

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Extinction The dying out of a species or a group of species.

A species is considered extinct when they cannot be released into the wild. For example ifthere still remains an organism of a particular species, but it lives in a zoo and cannotsurvive on its own in the wild, the species is considered extinct.

THE TWO FORMSOF GENETIC DRIFT ARE: Bottle Neck When a large population is reduced to a small population due to a random catastrophicevent and the surviving individuals have different allelic frequencies that the originalpopulation. When the population increases the new population is genetically different to theoriginals.

North elephant seals went through a bottleneck when they were hunted so much that theirpopulation was reduced to only twenty individuals. The population grew back to tens ofthousands after the species was listed as a protected animal. However, all the seals todayare identical for 24 genetic loci examined so far.

Founders Effect When a small population becomes isolated from the original large population and the allelefrequencies in the founding population is different from the original population

An example of this is when a small group of Amish people moved from the main populationto Pennsylvania. The small group had a large number of people with polydactyl, where asthe large population only had a few, therefore allelic frequencies were different.

Genetic Drift: Change in the gene pool of a population over generations by chance

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Analagous features: of organisms have the same function but do not have the samestructural similarity. They are evidence of Convergent evolution.

Parallel Evolution: When related species are exposed to similar environmental conditionsafter speciation evolving similar features independently

Ancestor: A species from which another species evolved.

Selection Pressures: All the abiotic and biotic components of the external and internalenvironment of an organism that influence population change over time.

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Methods of finding evidence of Evolution

DNA Hybridisation 1. DNA from two species of the same gene is obtained2. Heat is used to separate the DNA3. The two strands from the different species is mixed together and allowed to cool4. The strands are heated again until separated5. The higher the melting temperature (T m) the closer the species are related (as there

are more complimentary base pairings with each other)

Linkage Groups This is a group of genetic loci close together on the same chromosome.These are used in immunological studies to see how similar genes from certain speciesare.

1. Blood from a human (containing proteins but no cells) is injected into a rabbit.2. The rabbits immune system recognises this as non self and produces antibodies

against human blood.3. A sample of the rabbits blood is taken and the anti-human antibodies are extracted.4. These antibodies are then added to samples of other species blood.5. The more similar the sample is to human blood, the more precipitate is likely to form.

Biochemistry Similarities between species can be determined by examining their amino acid sequences,and therefore their nucleic acid sequence.

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DNA Barcoding Scientists look at the CO1 gene of the species and create a 'barcode' of that speciesnucleic acid sequence. As most eukaryotic cells require Mitochondrial DNA, scientists cancreate barcodes for most species. They then use these barcodes to identify which species aplant animal or fungus belongs to by comparing the similarity between the barcodes.

Pseudo Genes A segment of DNA that is part of the genome of an organism, and which is similar to a genebut does not code for a gene product.

Phylogenetic Tree

A tree diagram showing the evolutionary relationship between species that have a commonancestor.In the diagram below the pine and rose are more closely related than the pine and the moss.

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FossilsConditions for fossilisation

Organism undergoes rapid burial by sediments-Organism is trapped and therefore protected from erosion and scavengers. The lackof oxygen reduces activity and therefore slows rate of decay.Organism is in the bottom of a deep lake-Lack of movement and low temp reduce scavenger activity and therefore theorganism is less likely to decay and more likely to fossilise.Organism dies in a cave

As it is not disturbed by scavengers and wind the rate of decay is slowed.

Organism trapped in ice or glacierLow temp and low oxygen slow decay.

Types of fossils BonesTeethShellsFootprintsMoulds

AmberPollen grains

Abundance of fossils Could be because:

the area was inhabited by a large number of that organismThe conditions were optimal for fossilisation at this location

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Radioisotope dating The amount of a particular isotope left in an organism can determine the approximate age ofa fossil (by using half-lives). Different isotopes in organisms will break down at different ratesand therefore can only be used within a specific timeframe.

EG. Carbon Dating (carbon to nitrogen) can be used if the fossil is between 40,000 to 60,000years oldUranium to lead-1,000 to 1,000,000 years old.

Hominid Evolution

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APES HUMANS HOMO ERECTUS AUSTRALOPITHECUSAFERENSIS

FORAMENMAGNUM

Back of head Centre of head Centre of head Centre of head

SHAPE OF DENTALARCH

Box shaped

Parabolic arch

CANINES /DIASTAEMA

have large canines withdiastaema

small canines without a gaparound them (diastaema)

Small but not as small as homosapiens

Large

BRAIN SIZE Small Largest Smaller than homo sapiens butlarger than apes andaustralopithecines

Medium

SHAPE OF PELVIS longer pelvis is found in treedwelling primates as it is used asan anchor point for skeletalmuscles

shorter more rounded pelvis

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ANGLE OF KNEEJOINT

Similar to modern humans

SLOPE OF FACE

BROW RIDGES Prominent Slight Less prominent Prominent

ZYGOMATICARCHES (cheekbones)

Large/Very pronounced Far less pronounced Less promounced Large/Very pronounced

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AUSTRALOPITHECUS

Graciles Robust

More slender

Includes: A. anamensis A. afarensis (Lucy) A. africanus (Taung Child)

Possible ancestors of our line

Rounded top of skull with no crest

More robust

Includes: A. robustus A. boisei A. aethiopicus

Cousins of our line

Bony crests on skull

Time of living

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GROUPACTIVITYFeature

Pan troglodytes

(Chimp)

a. Afarensis

(lucy)

A. Africanus (taungbaby)

Homo Habilis

Years ago The great apes, including thechimpanzee and humans, spilt off

from the lesser apes about 20mya

3.9-2.5 mya 3.0 2.3 2.3 1.5

Cranial capacity 320-480 cubic centimetres (cc) - 430-440ml 400ml 480ml 630 800ml

Physique - males larger than females- arms and shoulders that enablethem to swing from branch tobranch

- long curved finger and toebones to grip tree branches andknuckle walking; walking onknuckles.

- light build some apefeatures- long arms curved fingersand toes

- females grew to only alittle over one metre inheight (105 110centimetres) and maleswere much larger at about150 centimetres in height-rib cage was cone-shapedlike apes

Light build more likehumans than afarensis,longer arms

Legs were relatively short,providing this species witharm and leg proportions thatwere relatively ape-like.

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Skull shape

(Images)

Front

Side

Underneath

Apelike face, low forehead,bony brow ridge flat nose,no chin

Brow ridges lessprominent, higherforehead shorter face

Beginnings of slight forehead

Small, arched brow ridgesmaller and shorter thanearlier ancestors

Hole for the spinal cordlocated in centre of skullbase, therefore bipedal

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Teeth and jaw Long pointed canine teeth andlong jaws

Human like teeth, smallerthan apes,, larger thanhumans. Large jaw shape

Canine teeth furtherreduced. Shape of jawfully parabolic.

Smaller narrow molars,thinner jaw.

Use of tools Sticks, twigs and stones Simple tools; sticks, non-durable plant material,stones.

Includes core tools,choppers and smallerflakes used as scrapers.

Use of sticks, also rocks wereused but no evidence ofshaping the rocks.

Use of fire

Ceremonies Complex social groups; 10-100individuals that often divide intosmall foraging groups ofconstantly changing membershipof about 3-10 individuals.

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Feature Homo erectus Homo floresiensis Homo Neanderthal- Homo sapien (modern)

Time ofliving

This species lived between 100,000and 1.6 million years ago, although

some estimates extend this tobetween 35,000 and 1.8 millionyears ago.

The human remains date fromabout 38,000 to 18,000 years old,

but archaeological evidencesuggests H. floresiensis lived atLiang Bua from at least 95,000 to13,000 years ago. -

Between 28,000 and300,000 years ago

300,000 years ago topresent

(archaic Homo sapiens from300,000 years ago,modern Homo sapiens fromabout 160,000 years ago)

Cranialcapacity

800-1100ml 417 cc Neanderthals : 1,200 1,900 cc (73 120 cu in)

Humans : 1,000 1,900 cc(61 120 cu in)

Phisique The body tended to be shorter

and stockier than those ofmodern humans.

Brainshowed an increase in size overearlier structure of the brain wassimilar to that of modern humans

Limbs

were like those of modern humansalthough the bones were thicker,suggesting a physically demandinglifestyle

similar to early humans than

modern humans

characteristic bipedal foot thatincludes a big toe aligned withother toes and a lockingmechanism on the middle of thefoot

Several primitive features include

a relatively long foot for its bodysize, a flat arch lacking the spring-like mechanism used to store andrelease energy during running,

generally shorter and

had more robustskeletons and muscularbodies than modernhumans

males averaged about168 centimetres in heightwhile females wereslightly shorter at 156centimetres

Modern humans now have

an average height of about160 centimetres in femalesand 175 centimetres inmales

Slender trunks and longlimbs. As well as stockierbuilds

http://en.wikipedia.org/wiki/Neanderthalhttp://en.wikipedia.org/wiki/Neanderthalhttp://en.wikipedia.org/wiki/Humanhttp://en.wikipedia.org/wiki/Humanhttp://en.wikipedia.org/wiki/Humanhttp://en.wikipedia.org/wiki/Neanderthal

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and a short big toe.

unusual low twist in the upper armbone, wide leg bones, relativelyshort and curved clavicle,

shoulder moved forwards slightly.

They lack features that evolvedwith the ancestors of modernhumans at least about 800,000years ago

Skull -face was large with a low, slopingforehead, a massive brow ridge anda broad, flat nose

-skull was broad and long with sharpangles at the rear,-bones of the skull were very thickand formed a small central ridge,known as a midline keel, along thetop of the skull

cranial shape is long and low andcloser to that of H.erectus than H. sapiens receding and small foreheadthick bones within the range of H.erectus and H. sapiens flat facebrow ridges over each eye that donot form a continuous brow ridgeas in Indonesian H. erectus narrow nose

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Teeth andJaw

Jaw was large and thick without apointed chin

Molar teeth had large roots but were

decreasing toward a more modernsize

lacks the bony point on the chinfound in modern humans

relatively large jaw and teeth that

resemble H. erectus but withmore primitive featurespremolar roots different from H.sapiens

-jaws were larger andmore robust than thoseof modern humans andhad a gap called the

retromolar space, behindthe third molars (wisdomteeth) at the back of the

jaw.

-jaws are short which resultin an almost vertical face-usually no gap between thelast molar teeth and the jaw

bone-lightly built and have aprotruding bony chin foradded strength. Homosapiens is the only species

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small post-canine and canineteethparabolic or V-shaped dentalarcade typical of Homo bony shelf at the front of the lower

jaw which is a primitive featurenot seen in H. erectus

-jaw lacked theprojecting bony chin thatis found in Homosapiens.-teeth were larger thanthose of modern humans

to have a protruding chin.-Shortened jaw resulted in aparabolic shape-Teeth are relatively smallcompared with earlierspecies.-Front premolar teeth in thelower jaw have two equal-sized cusps

Use of tools Advanced tools for choppingscraping and cutting

Stone tools were found in anumber of different layers datingfrom 90,000 to 13,000 years ago.Tools include simple flakes,points, perforators, blades andmicroblades which were possibly

hafted as barbs.

Similar to the blade toolsof Homo sapiens but lessadvanced.

-Homo sapiens made stonetools such as flakes,scrapers and points thatwere similar in design tothose made by theNeanderthals

-wider range of materialsincluding bone, ivory andantler were used-very small blades(microliths) that were oftenused in composite toolshaving several parts

Use of Fire Burnt stones and animal bones,charcoal and ash deposits indicatethese people may have used fireabout 500,000 years ago but it isdifficult to prove whether this usewas controlled.

There is evidence of the use offire in Liang Bua cave. Theremains of numerous juvenileStegodon have charred bones,possibly indicating that H.floresiensis was able to control

The Neanderthals builthearths and were able tocontrol fire for warmth,cooking and protection

Sophisticated control of fire,including complex hearths,pits and kilns

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fire for cooking.

Ceremonies There are no traces of pigments,ornaments or deliberate burials inthe layers associated with H.floresiensis all of whichcharacterise the modern humanlevels from the upper parts of thecave.

The dead were oftenburied, although there isno conclusive evidencefor any ritualisticbehaviour. However, atsome sites, objects havebeen uncovered thatmay represent gravegoods.

Burials were infrequent andvery simple prior to 40,000years ago and then beganto become more elaboratewith the inclusion of valuedobjects such as tools andbody adornments. Redochre was sprinkled overmany of the bodies prior toburial.

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Out of Africa Theory Suggests that Homo erectus evolved into Homo sapiens in Africa, and then venturedout of Africa and dispersed to all around the world.

Mitochondrial DNA indicates that the out of Africa Hypothesis is most likely

Regional Development TheorySuggests that Homo erectus ventured out of Africa and then evolved into modernman in several different locations through out the world.

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Biological Evolution: Slow change over time due to mutations and genetic changesdue to natural selection acting on phenotypes.

An example is Darwin's finches changing beak shape.

Cultural Evolution: The passing on of ideas, knowledge, beliefs and language fromone generation to another. This is rapid and deliberate.

Examples include; teaching how to use fire or communicate via speech.

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Genetic Screening Is the systematic testing of individuals in a population for genetic disorders that haveyet to be expressed or are in the early stages of development.

EVOLUTIONARY CONSEQUENCES-Decisions which individuals make on the basis of the results of genetic screeninghave the potential to change the human gene pool.-A person who knows they are a carrier of a detrimental trait may choose not to havechildren.-Parents may choose to terminate a pregnancy if the foetus is shown to have genetic

abnormalities or inherited diseases.-Screening prior to the implantation of embryos leads to fewer offspring with geneticdiseases.

DNA ProfilingIs determining all alleles of an organism

EVOLUTIONARY CONSEQUENCES-Decisions which individuals make on the basis of the results of DNA profile have thepotential to change the human gene pool, if parents chose not to have a child if theypossess a specific trait.-Can lower genetic diversity if certain traits are not kept within the population

Bacterial TransformationIs when bacteria take on a plasmid and are used to produce certain proteins.

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Apoptosis: Programmed cell death (is an example of signal transduction)

Signal Transduction: Chemical process by which an extracellular message isconverted to an intracellular message to cause cell change .

Apoptosis 1. Signalling molecule binds to death receptor stimulating response apoptosis2. Many different enzymes are activated within the cell and at the same time

messages go out to nearby phagocytes.3. All cells that have received the death signal begin to break down and develop

small lumps (blebs) on the surface.4. Organelles (except nucleus and mitochondria) are usually preserved as cell

breaks down into membrane enclosed fragments.5. Fragments bind to receptor on phagocytic cell that have responded to message

from dying cell.6. Phagocytes engulf fragments and release cytokines to inhibit inflammation so

that nearby cells are not damaged by necrosis.

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What it is Why scientists use it How it works How it interveneswith evolution

Issues

IVF and AI Process by whichegg cells arefertilised by sperm

outside the womb

-So that couples unableto naturally reproducemay have children

-Egg is removed fromwoman and placed ina culture medium

-Sperm is extractedfrom semen andplaced in the culturemedium with the eggin an incubator-Egg is fertilised-Embryo istransferred into thewoman's uterus

-Maintains variabilitywithin the populationby allowing more

people to pass ontheir alleles

Legal-If embryos are frozenand the parents do not

wish to use them, theymust be destroyed ifthat is what they want.There can be issues ifthe medical practitioneruses them without thepermission of theparents.

Cloning The production of anew organism froma cell nucleus ofanother organism.The clone isgeneticallyidentical.

-To protect endangeredspecies from extinction-To understanddiseases and testmedicines (therapeuticcloning)-To test new medicineson cells taken fromthe embryos beforetrying the medicines onanimals and real people-To replace body parts

EMBRYOSPLITTINGCells of an earlyembryo are artificiallyseparated. Eachsingle cell is thenplaced into asurrogate mother fordevelopment tocontinue. Allorganisms producedare identical.NUCLEARTRANSFEREgg ell is enucleated.

-Leads to loss ofgenetic variability-Should animalcloning becomewidespread,decreased diversitymay result-Cloning may beused for medicalpurposes to provide atreatment to adisease thusmaintaining unfitalleles within thepopulation

Environmental-By creating herds ofcloned animals thathave the same geneticcomposition, thediversity of thoseanimals is reduced. Asa consequence, clonedanimals and herds maybe more susceptible todisease and less ableto withstand anoutbreak.

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The nucleus from acell of the organismto be cloned istransferred into theegg cell. The egg cellis now fused with thesomatic cell of theother organism. It isgiven an electricpulse whichstimulates celldivision.

Stem cells Are undifferentiatedcells that have thepotential to developinto a variety ofcells.

-Use it for research-Patients' own adultstem cells have beensuccessfully used totreat a number ofconditions, likeParkinson'sdisease and multiplesclerosis-Used forcloning/therapeuticcloning

-Egg is fertilised-Cell multiplies andturns into a blastocystStem cells areremoved from theblastocyst (or can betaken from bonemarrow/cord blood)-Stem cells arecultured in the lab-used to producebone cells, nervecells, skin cells andblood cells

-Maintains unfitalleles within thepopulation byallowing sick peopleto reproduce andpass on their allelesto their offspring-Frequencies of thealleles may beincreased within thepopulation

Ethical-The blastocyst fromwhich the stem cells areextracted is consideredby some people to be afoetus and somebelieve it is killing thefoetus.

Genetherapy

involves theinsertion offunctional allelesinto an individual

-To increase the lifespan of people with fataldiseases

-Functioning allele isplaced into a vector,such as a virus-The virus is then

-Maintains unfitalleles within thepopulation byallowing sick people

Economical-Gene therapy is a veryexpensive process

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who has a non-functional allelewhich causes ageneticdisease/disorderthis enable theorganism toproduces thefunctional protein.

injected into thepatients bloodstream-The virus attaches toits specific receptoron its target cell andinjects the functionalallele into the cell-The cell starts toproduce the proteincoded for by thefunctional allele

to reproduce andpass on their allelesto their offspring-Frequencies of thealleles may beincreased within thepopulation

-Patients may not beable to afford it-Patient numbers maybe too small to supportcommercialdevelopment

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SAC 4 Summary

SAMANTHA TIERNEY

Biology 2013

SAC4 SUMMARY

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Pathogen or Pathogenic Agent:Is any infectious agent that is capable of

causing disease to an organism.

Cellular Non Cellular

Protozoans:Are unicellulareukaryotic organismsclassified on the basis

of their locomotion.They are usuallyendoparasitic.

Fungi:Are eukaryotic sporeproducing organisms.They are heterotrophic

and their cell wall ismade of chitin. (Theyproduce penicillin)

Bacteria:Are prokaryoticorganisms that have acell wall made of

peptidoglycan ormurein. They do notcontain membranebound organelles (eg.Nucleus). They may bemotile eg. Have flagella.

Viruses:Are non-cellularpathogens that caninfect all types of

organisms. They areclassified as non-livingas they require cellmachinery of the hostto reproduce. Theycontain either DNA orRNA which issurrounded by aprotein coat.

Worms:Are multicellularorganisms that come intwo forms; flat or

round. They areendoparasitic and havehooks or suckers toattach to the host.

Prions:Are pathogenscomposed of proteinonly which replicates

via host cell (thereforenon-living). It infectsthe nervous systemonly (degenerative).Transmission viainheritance oringestion. It consists of:sPrP-scarpie prionprotein and nPrP-Normal prion protein

Structure of the lymphatic system:The lymphatic system is composed of lymph nodes, spleen, thymus, lymph vessels andbone marrow.

o Lymph Nodes: centre for production of white blood cells. Contain mature T-cellsand B-cells

o Spleen: Like a giant lymph node with blood. It purifies the blood and lymph fluidthat flows through it

o Thymus: organ where T-cells matureo Lymph Vessels: Carry lymph fluid from cells to lymph nodeso Bone Marrow: Contains tissue that produces red blood cells, T-cells and B-cells

Function:1. Transportation of lipids (lipids can cause blockage in arteries)2. Returns nutrients into the blood stream3. Defends against disease

SAC4 SUMMARY

Samantha Tierney 2013

Binary Fission: Optimal Living Conditions:Must be living in anenvironment with sufficientnutrients, specifictemperature and pH at which

Mode of reproduction:Can be asexual/sexualEg in wheatWhen fungi infects host it

d h l d h

Diseases:To prevent diseases from fungi youshould kill fungi to preventspreading/reproduction, wear

i l hi ( h i

Disease:To prevent disease fromthis parasite avoid effectedwaters and consumption ofuncooked/infected foods

Optimal living conditions:In the gut of animals where theyhave a surface to latch onto thehost and can obtain sufficient

i i

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temperature and pH at whichthey function at their optimallevel.

Prevention of disease andtreatment:Bacterial diseases (eg. choleraand pneumonia) can betreated with antibiotics in

extreme cases chemo can beused. Prevention of bacterialdiseases comes in the form ofvaccines and antibiotics.Other methods can be takensuch as usin heat to killbacteria in food (cell wall) orby using disinfectants to kill

produces haploid spores. Theyfertilise and grow into a fruitingbody. This then releases morespores and those infect otherplants.

Optimal living conditions:Warm and moist environments.

Main distinguishing feature:Fungi are eukaryotic organisms.Their cell walls are made ofchitin. They are spore producingheterotrophs.

protective clothing (eg shoes inshower) to prevent direct contact anduse antifungal powders. If you dobecome infected with a fungal disease(eg. Tinea-Humans or Ringworm-Plants) antibiotics and antifungalpowders can be used. They will notcure this disease though.

Reproduction:

The different segments of the worm contain male/female reproductive organs. Fertilisation occurs between the different segments. Each segmentmatures into bag of eggs and breaks off. They are excreted with faeces. Animals eat it and become infected. When humans eat the animal meat theytoo become infected.

uncooked/infected foods.There are a number ofdrugs available to treatdieases cause by worms(eg scabies)

nutrients to survive.

Main distinguishing feature:They are multicellular organisms that are either flat or round. Theyare endoparasitic and have hook/sucker to attach to host

Reproduction: Asexual reproduction of protozoans occurswhen the cell divides in half by binary fission. Someprotozoans reproduce sexually as well. This can happen whentwo protozoans carrying half of their regular genetic materialfuse together and form a new cell.

Prevention and treatment of disease: Prevent breeding of infected vector,revent vector from acsessing human, vaccines and preventative drugs.Treatment involves drugs which kill the parasite.

Main distinguishing feature: They are eukaryotic organisms that canbe motile. Part of Protista family.

Optimal living conditions:Environment with nutrients and water as well as having the right temp, pHetc.

Malaria life cycle:

Other disease life cycle:African sleeping sickness

Reproduction: Main distinguishing feature:Viruses are non-cellular andinfect all types of organisms.They require cell machinery of

Ideal living environments:Where there is anabundance of host cells

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Prevention of disease:Avoid direct contact withinfected individuals,ensure you do notconsume infectedfood/water and there arevaccines.

They require cell machinery ofhost cells to reproduce(therefore they are nonliving).Their nucleic acid issurrounded by protein coat,they only have DNA or RNA.

Treatment:As viruses do not have the structures that are usually thetargets of antibiotics treatment is difficult. Most effectivestrategies involve interfering with protective coat & preventingassembly/release of viral particles. An example of a viralinfection is chicken pox.

Prevention of diseas:Avoid consumption of infected foodandmaintain strict quarantine processes.There is no treatment for prion diseases.

Reproduction:Prions consist of a protein, called PrP ( Pr ion P rotein). There is normal PrP and disease-causingPrP (scrapie PrP). The amino acid composition of the two forms is similar however their tertiarystructures are different. Contact between scrapie PrP and normal PrP causes the normal PrP to flipinto the disease shape. In an infected mammal the nervous system accumulates large amounts ofscrapie PrP and slowly degenerates.

Types of prion disease:

-Cruetzfeldt-Jakob Disease (effects People) -Kuru (effects People) -Scrapie(effects sheep)-Mad cow disease -All caused by prions that led to spongi-form Encephalopathy

Optimal living conditions:As they are a protein their optimal livingconditions would be their specific pH andtemperature.

Main feature:

-Composed of protein only -Replicates via host cell -Infects nervous system (degenerative) -Consists of:sPrP-scarpie prion proteinnPrP-Normal prion protein -Genetic or inherited form

o Pathogen: An organism that can produce disease in another organismo Ectoparasite: A parasite that lives on the outside of the host.o Endoparasit e: A parasite that lives on the inside of the host.o Infectious disease: caused by pathogenic organisms or agents.

Tetanus bacteria

PreventionVaccine and booster shot.

TreatmentAntibiotics and vaccination.

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enters the body

Second line of defence:Is a form of nonspecific (innate) immunity, meaningthat it recognises and responds to a pathogen in ageneric way. It is not long lasting but is immediate.

Third line of defence: .It is the reaction of lymphocytes to specific antigenresulting in the production of specific antibodies andthe production of memory cells. It is a form of specificimmunity

Chemical:Lysosomes: Burst bacteriacells.Sweat: High salt contentdries up microbes. Digestive enzymes: Breakapart components onpathogen.

Urine: Changes pH, changingtheir environment (so theycannot function as they arenot in optimal conditions)

Barriers:Skin: Is a physical barrier. Itsglands secrete sweat andfatty acids to inhibit bacterialgrowth.Natural secretions: Such asstomach acid to kill bacteria.Lysosomes in tears and

saliva burst bacteria cells.Natural flora: Preventsinfection by pathogenicbacteria, by taking nutrientsand being competition.Mucus: lines therespiratory/digestive tracttrap bacteria.Cilia: sweep them upward tothe back of the throat to beremoved by swallowing,blowing your nose orsneezing.

First Line of defence:Is a form of nonspecific (innate) immunity, meaningthat it recognises and responds to a pathogen in ageneric way. It is not long lasting but is immediate.

Physiological:-Fever-Inflammatory response

-Blood clotting

Chemical:-Cytokines-Interferons-Histamine

-Compliment proteins

Cellular:-Phagocytosis-Natural killer cells-Mast cells-Basophils-Platelets

Cell mediated:It is a specific immuneresponse wherecytotoxic T-cells andmemory cells areproduced against aspecific antigen. It actson infected cells, tissue

transplants, eukaryoticparasites andtumour/cancer cells.

Humoral:Is a specific immune response toa specific antigen where specificantibodies and memory cells areproduced. It fights disease in theextracellular fluid.

It is also known as antibody

mediated.Involves B-cells.

Vaccination & Immunisation (Vaccination is when a vaccine is administered to youImmunisation is what happens in your body after you have the vaccination )Contains an attenuated (weakened), dead or synthetic form of th eantigen/pathogen that cause an i mmune response.

Primary Immune response:The first encounter with a specific antigen which causes an immune response whereantibodies and memory are produced. Takes about a week.

Secondary Immune response:Second encounter with a specific antigen which produces a more intense and rapidimmune response producing large amounts of antibodies. The response lasts longer.

Firs vaccination causes A booster vaccine causes

CELLULAR SECOND LINE DEFENCE

http://www.nps.org.au/medicines/immune-system/vaccines-and-immunisation/for-individuals/what-is-vaccinationhttp://www.nps.org.au/medicines/immune-system/vaccines-and-immunisation/for-individuals/what-is-vaccination/what-is-immunity-and-how-does-it-workhttp://www.nps.org.au/medicines/immune-system/vaccines-and-immunisation/for-individuals/what-is-vaccination/what-is-immunity-and-how-does-it-workhttp://www.nps.org.au/medicines/immune-system/vaccines-and-immunisation/for-individuals/what-is-vaccination

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Phagocytosis

Phagocytes are types of white blood cells that engulf, ingest and digest (with the use of powerful enzymes) foreign substances. It has no memory and isinnate.

Natural Killer cellsIs a type of white blood cell. It is a type of lymphocyte that givesprotection by killing infected cells by releasing cytokines. They have nomemory.

BasophilsAre granular white blood cells that contain histamine and serotonin.

Mast cellsAre white blood cells located in the smooth muscles and connective tissue. Thathave vesicles containing histamine (signalling molecule) and their function is topromote the inflammatory response.

Dendritic cellsAre a type of phagocyte that breaks down pathogens and becomes anAPC

Granules are small packets of enzymes and other substances - for exampleinflammatory chemicals like histamine - that are made by the white blood cells thathelp them perform their function. For those white blood cells that are phagocytic(they eat bacteria and waste chemicals) the enzymes in the granules (vesicles) willbe released onto the eaten material and break it down into its component pieces -bacteria are killed in this way. The enzymes have to be kept in these vesiclesbecause if they were free inside the white cell they would destroy it from theinside.

CHEMICAL SECOND LINE OF DEFENCE

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Types of Immunity

Naturally induced: Whenantigens naturally enter anorganisms body

Artificially induced: Anorganism is given an injectionof attenuated, dead orfragments of an antigen.

Naturally induced: When anorganism gains its antibodiesmaternally

Artificially induced: Whenantibodies are introduced tothe body by injection (eg.Against snake bite)

Active: Is when a specificimmune response occurs andproduces antibodies andmemory. Longer lasting

Passive: Is when an organismis given specific antibodiesand does not producememory

ComplementInvolves 20 different proteins. Once activated it will coat pathogens making them sticky(therefore easier to phagocytose) or it can lyse the cell wall of the pathogen andstimulate phagocytes to the area. It also stimulates the release of histamine.

Signalling molecules

CytokinesAct as messengers between cells. There are many different types ofcytokines. They are the signalling molecules of the immune system.

InterferonsAre a type of cytokine. They are antiviral chemicals produced in the cellinfected by a virus that interfere with the reproduction of virus particles.They send messages to nearby cells and stimulate macrophages to thearea.

HistamineIs a signalling molecule released from Mast cells. It binds to its specific receptorsin the

smooth muscle/blood vessel. The blood vessel dilates and becomes slightly morepermeable. This causes the inflammatory response and compliment to occur and attractsphagocytes to the area.

Triggers the release of

Stimulates release of

PHYSIOLOGICAL SECOND LINE OF DEFENCE

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Fever:When the core body temperature is reset to destroy pathogens.

4-Interleukin-1 stimulate hypothalamus resetsbodys thermostat top a higher temperature

roducin fever.

3-Interleukin-1 is released into blood stream andtravels to hypothalamus.

2-The pathogen is digested in a vacuole bypowerful enzymes. This causes the release ofendotoxins which induce the macrophage torelease interleukin-1 (a cytokine).

1-A macrophage engulfs and ingestspathogen.

Crisis phase: Finally all pathogens consumed,therefore decrease in interleukin-1, thereforethe thermostst has been reset.

Chill onset Fever onset

1-Dilation of blood vessels Increases blood flow

Pain caused by odema andcertain substances releasedby injured tissue

Odema (swelling)

Antibodies, complement,interferon can pass intoaffected area

3-Increased permeability ofblood vessel walls allowsfluid to leave circulationand enter tissues

Phagocytes can reach andenter affected tissues

2-Histamine produced andattracts phagocytotic cells

Inflammatory response starts withinvasion of tissues by pathogen

Phagocytosis. Phagocytes releasechemicals (interleukin) to controltemperature via hypothalamus (fever)

Allows antimicrobial factors (egphagocytes , antibodies,complement, interferon) inblood to reach infected site.

Heat-denatures proteins in pathogen

Redness

Toll Like Receptors (TLRs) Are protective immune guards that sensePAMPs. They induce the secretion of inflammatory cytokines via signaltransduction.

Blood Clotting:The biochemical process to minimise blood loss and damage

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The biochemical process to minimise blood loss and damagefrom an organism

Injured tissue and platelets release clotting factor(prothrombin activator) and calcium ions.

Blood prothrombin >converted to> thrombin >splits fibrinogen> fibrin

Fibrin fibres form a mesh cover over woundtrapping platelets and red blood cells

Bleeding stops and the clot hardensand becomes smaller

New cells grow to repair wound site

Enzyme plasmin is released anddissolves clot

n s e d i n a l

l

g a n i s m

. I t

s e

l f f r o m

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T H I R D L I N E

O F D E F E N C E : C E L L M E D I A T E D R E S P O N S E

V i r u s I n

f e c t s c e

l l s

I n f e c t e d c e

l l s p

l a c e a n t i g e n i n M H C c l a s s 1

M a c r o p h a g e e n g u

l f s ,

d i g e s t s a n

d

p r o c e s s e s a n t i g e n

( w i t

h t h e u s e o

f

p o w e r

f u l e n z y m e s

) a n

d b e c o m e s a n

a n t i g e n p r e s e n t i n g c e

l l .

A P C p r e s e n t s a n t i g e n t o T - H e l p e r c e

l l s

a n d s t i m u l a t e s i t w i t

h i n t e r l e u k i n 1

.

T - H e l p e r c e

l l s t i m u

l a t e s c o r r e c t

T - C e l

l w i t

h i n t e r l e u

k i n - 2

T h e s t i m u

l a t e

d T - C e l

l p r o

l i f e r a t e s

,

d i f

f e r e n t i a t e s a n

d d i v i d e s

( m i t o s i s )

T C b

i n d t o i n

f e c t e d c e

l l s a n

d r e

l e a s e t h e c y t o

k i n e p e r

f e r i n

, w h i c h

l y s e s t h e i n

f e c t e d c e l l s m e m

b r a n e . T h e y a l s o r e

l e a s e o t h e r

c y t o

k i n e s t o a l e r t p h a g o c y t e s a n

d s t i m u

l a t e c o m p

l i m e n t

( t o

m a k e t h e c e

l l s s t i c

k y f o r p

h a g o c y t o s i s )

M C H -

P r o t e i n m a r

k e r s e x p r e s s

c e l l s t h a t a r e s p e c i f i c t o a n o r g

e n a

b l e s c e

l l s t o

d i f

f e r e n t i a t e

n o n s e

l f .

u c e &

d i e s

h u n t i

l

d i v i d e

b o

d y . T

h e y

u l a t e

c t

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T H I R D L I N E O F D E F E N C E : H U M O R A L

A P C p r e s e n t s t o T h

M a c r o p

h a g e e n g u

l f s ,

d i g e s t s a n

d p r o c e s s e s

a n t i g e n a n

d p

l a c e s i t o n M H C 2

C l o n a l s e

l e c t i o n o c c u r s : s

p e c i

f i c a n t i g e n

d e t e r m i n e s c o r r e c t B - c

e l l . T h i s B - c

e l l

u n

d e r g o e s c l o n i n g

A n t i g e n s e

l f a n

d n o n s e

l f

T h e

b o

d y i s a b

l e t o

d i s t i n g u i s

h i t s o w n c e

l l s ( s e l

f )

f r o m

f o r e i g n m a t t e r

( n o n s e l

f ) b y s h a p e s o

f

a n t i g e n

. M H C 1 = S e

l f a n t i g e n P A M P = f

o r e i g n

T h s

t i m u

l a t e s B - c

e l l w i t

h t h e c o r r e c t a n t i

b o d y ( i m m u n o g l o

b u

l i n

a n t i g e n r e c e p t o r )

T h e B - c

e l l t h e n p r o

l i f e

r a t e s ,

d i f

f e r e n t i a t e s a n

d d i v i d e s

b y m i t o s i s

i n t o B - m

e m o r y a n

d B - p

l a s m a c e

l l s

B - P

l a s m a : r a p i d

l y p r o

d u

s e c r e t e s p e c i f i c a n t i

b o d

B - M

e m o r y : r

o a m

l y m p

h

s e c o n

d e n c o u n t e r a n

dd

q u i c k

l y .

A n t i

b o

d i e s a r e s e c r e t e d i n t o t h e

b

t h e n

p r e c i p i t a t e

, a g g

l u t i n a t e , s t i m

c o m p

l i m e n t , n e u t r a l i s e a n

d a t t r a c

p h a g o c y t e s .

Autoimmunity:when self-cells recognise other self-cells ads non-self and attack them.

Multiple Sclerosis (MS) is when the myelin sheath isrecognised as non-self and is therefore attacked.

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Diabetes type 1 is when the beta cells in the pancreas arerecognised as non-self and are therefore attacked.

Allergen (anything that causes a specific immuneresponse and the production of IgE antibodies) entersthe body

Allergic Response:Considered as an inappropriate immune response.Treatments for allergies include antihistamines andepi pens with adrenalin

The more frequent contact, the more severeeach response is. It can eventually lead tohypersensitivity, which is when the allergicresponse affects the whole body and can beenough to cause death.

Plasma cells become sensitised andproduce and release IgE antibodies.

IgE antibodies bind to mast cell (insteadof allergen)

Mast cell secretes histamine and causesinflammation (which is the allergic response)

Tissue rejection

Transplant is placed into the body

If immunosupressants are given the immunesystem is slowed and almost shut down.

If immunosupressants are not given the immunesystem functions as normal.

New self cells grow over the non -self cells intransplant. Therefore the antigen (MCH ofother organisms cell) on transplant is notdetected or attacked.

There is not enough time for self cells to growover non -self cells. They are detected andattacked via cell mediated response.

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PLANT DEFENCE

Mechanical Barriers Chemical Barriers Plant Diseases

Epidermis layer/waxycuticle resists penetrationby virus particles, bacteriaand the spores of fungi.

Bark /resin providesdefence against insectsthat may be vectors for

pathogens.

Soft rot: Bacteria enterplant and attack thefleshy storage organs oftheir hosts, but they alsoaffect succulent buds,stems, and tissues.

Honey Fungus : Honey fungus is thecommon name given to severaldifferent Armillaria fungi that attackand kill the roots of many woodyand perennial plants. The mostcharacteristic symptom of honeyfungus is white fungal growthbetween the bark and woodusually at ground level.

-Plant antibodies to kill/destroy pathogen.-Sticky substances trap pathogen to stop it fromreproducing and spreading.-Phenols (Phyltolexins) destroy a range ofpathogens.-Toxins kill animals and pathogens.-Stop aerobic respiration in an infected area, sealit off and induce abscission.

Thorns preventherbivores from eatingthem.

Galls encapsulatepathogen to prevent itfrom spreading.

Epidermal layer (acts as skin) provides a barrier betweenplant and pathogen. The thicker, the better. Fungi

-Biggest plant killer-Xylem: when infected plant dries and wilts-Phloem: plant becomes discoloured as it cannot send food tomake pigment-Hyphae: are branch filaments extending from fungi

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PROTOMICS

Molecular Biology: The study of biochemistry of cells, particularlyDNA and genes

Genome: The sum total of all genes in a functioning organismProteome: The sum total of all proteins found in afunctioning organism

Molecular Biology can be used to create vaccines based onknowledge gained from studying the structure of antigens.

Rational drug design

1.Finding out the infective agents work against a cell:Find the shape(structure) of the active site (or biological target) that aids in the cause ofthe illness.

2.Then using this information to design drugs to prevent the infective agent being able todo what it does.Design a drug that is complimentary to the active site thereby inhib