Unit4notes.pdf

7/28/2019 Unit4notes.pdf

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Adam Clarke www.brain-freeze.co.uk

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Biology Unit 4 revision summary of processes

Photosynthesis

Photolysis decomposes H2O to O2, e-and H+

O2 air as waste product

e- PS2 to PS1 (via electron chain, energy released to transport protons into thylakoid

membrane, the concentration gradient causes protons to be released back into the stromagenerating energy which adds phosphate to adenine diphosphate generating ATP)

H+ used to reduce NADP (with electron from PS1)

Calvin cycle

RuBP (+CO2) > RUBISCO > GP [NADP+ATP] > GALP > GLUCOSE / RuBP

Primary Succession

Landslide / volcano

Empty inorganic surface bare rock / sand dune

Pioneer species algae/moss

Penetrate surface break it down into grainsOrganic material becomes trapped breaks down into humus

Humus + rock grains = soil

Grass/ferns can develop root systems die and add to soil

Larger plants can survive due to newer soil layers more water/nutrients stored

Plant/animal biodiversity increases until climax community

Secondary Succession

Fire/flood

Existing soil

Plants/animals present Increase in diversity until climax community

Experiment: Ecology

Random sample avoid bias [use water boatman from pond]

Frame quadrat / point quadrat populations

Line transect / belt transect / interrupted transect

Abiotic/biotic factors - measured

Repeat for reliability

Evolution

1) Individuals within a population show variation in their phenotypes

2) Predation disease and competition create a struggle for survival.

3) Individuals with better adaptations are more likely to survive reproduce and pass on theiradvantageous adaptations to their offspring.

4) Over time, the number of individuals with the adaptations increases so over generations

the adaptations become more common in the population through evolution.

Rigor mortis

Oxygen not being transferred throughout body

Lack of oxygen in cells leads to anaerobic respiration

ATP is used, lactic acid is produced

Acid reduces pH denatures enzymes - muscles stay contracted rigor mortis

Bonds between muscle proteins become fixed.

Lysosomes eventually break down cells


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Insect succession

Colonisers anaerobic bacteria (from the gut) spread over body

Blowflies lay eggs in bed / feed on tissue

Beetles eat maggots

Parasitic wasps lay eggs in fly/beetle larvae

Entomology life cycle

Blowflies lay eggs in corpses (in orifices / wounds) maggots hatch and feed on body until

they form a pupa new adult fly hatches

Based on what stage of the life cycle the blowflies are at determine time of death

Higher temperatures decrease in the length of life cycle.

Experiment: effect of temperature on organism (brine shrimp)

1) Determine range of temperatures to be used

2) Add sea salt to beaker

3) Add de-chlorinated water and stir until salt dissolves4) Place brine shrimp egg cysts onto paper

5) place paper into beaker

6) Incubate the beakers at different temperatures controlling extraneous variables

7) Each day use a light source to attract the larvae and count how many there are.

8) Evaluate any ethical issues that can arrive from using living organisms.

Protein synthesis

Transcription (nucleus)

DNA hydrogen bonds broken down by RNA polymerase

DNA template strand is transcribed to complementary mRNA antisense strand (formed with

RNA polymerase)Thymine is replaced with uracil

mRNA passes through pores in the nuclear membranes to cytoplasm then to surface of

ribsomes

Translation (cytoplasm / ribosomes)

tRNA carries anticodon carried to surface of ribosome

Each strand on mRNA has a start codon / stop codon

mRNA becomes attached to ribosome reads at the start codon

tRNA carries amino acids to the surface of the ribosome lining up its anticodon against a

complementary codon on the mRNA

Hydrogen bonds between tRNA and the ribosome bind it in place while enzymes link amino

acids together with peptide bonds forming proteins

tRNA finishes and returns to cytoplasm for more amino acids


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Experiment: Gel electrophoresis

DNA divided into fragments using restriction endonuclease

Gel electrophoresis chromatography

DNA fragments- agarose gel (containing dye that will be apparent under UV / buffer / known

DNA fragments)

Electric current is passed through DNA fragments move towards positive anode (negativecharge on phosphate groups)

Fragments move at varied rates dependent on mass/charge

Once electrophoresis is complete UV light is shone to display DNA

Southern blotting alkaline buffer added nylon filter paper placed over gel dry

absorbent paper used to draw solution containing DNA fragments to filter leaving them as

blots on the filter

Alkaline solution denatures DNA fragments strands separate base sequences observable

Experiment: Polymerase chain reaction

Mix DNA sample, primers (small sequences of DNA which must join to the beginning of the

separated DNA strands before copying can begin) and many of the four nucleotide basesinto a PCR machine

Mixture is heated to 90oC breaking hydrogen bonds and DNA strands

Mixture cooled to 55oC so primers bind to single DNA strands

Heated to 75oC optimum temperature for DNA polymerase to build complementary

strands of DNA

DNA profiling and identification of genetic relationships between organisms

1) 90% of DNA is made of introns - regions of chromosomes used for DNA profiling

2) Within introns there are short sequences of DNA repeated many times forming micro-

satellites (2-4 bases repeated 5-15 times) and mini-satellites (20-50 repeated 50-100 times).

3) The same micro/mini-satellites appear in the same positions on each pair of homologouschromosomes

4) Number of repeats of each satellite vary as different patterns are inherited from

mother/father

5) Many different introns with a huge variation in the number of repeats likelihood of two

individuals having same pattern of DNA is low.

6) More closely related individuals are more likely it is that similarities will be apparent in

DNA patterns.

Inflammation

1)Mast cells and damaged white blood cells release histamines

2)Histamines cause blood vessels to dilate, increasing blood flow

3)Raised temperature reduces effectiveness of pathogen reproduction

4)The walls of the capillaries also leak as the cells forming the walls separate slightly

(increase in permeability)

5)Fluid including plasma, white blood cells and antibodies are forced out of the capillaries

causing swelling and pain.


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The humoral response

Pathogen enters body

Macrophage engulfs pathogen vesicle containing pathogen fuses with lysosome

Enzymes in lysosome break down pathogen separates off the antigens

Inside macrophage antigens combine with MHCThese complexes move to surface of cell outer membrane

Macrophage + antigen/MHS on cell surface = antigen-presenting cell

CD4 receptors on the outer membrane of the T helper cell enable it to bind to specific

antigen of the antigen/MHC complex

T helper cell reproduce clone of the cells

New cells have same CD4 receptors as original T helper cell specific for original antigen

Cloned cells become active T helper cells

Some clone cells become T memory cells remain in the body to become active if same

antigen is encountered again.

Effector stage: T helper cells and B cells active

Different B cells which have immunoglobulins specific for antigen are presented by the

pathogenthey bind to it B cell then engulfs pathogen by endocytosis

Vesicle formed fuses with a lysosome Enzymes break down antigen leaving fragments of

processed antigen These become attached to MHC another APC forms

T helper cell from active clone recognises antigen displayed on MHC complex on B cell

Cytokines released from T helper cell stimulate B cell to divide and form a clone of

identical cells.

B effector cells and B memory cells

Cloning of b cells eventually forms correct antibodies clonal selection

B effector cells differentiate into plasma cell clones which produce antibodies (species

protein released into circulation- identical to immunoglobulin of original parent B cell)

Antibodies bind to specific antigens on pathogens which cause their destruction

Microorganisms agglutinate/clump together preventing their spread

Antigen-antibody complex readily engulfed and digested by phagocytes

Stimulate other reactions within body destruction of membrane release of histamine by

invaded cells causing inflammation

B memory cells

produced by divisions of B cell APC

Allow body to respond rapidly to second invasion by same antigen

Cell-mediated response

Pathogen digested surface antigens become bound to MHC forming APC

T killer cells present in blood complementary receptor proteins

Bind to antigen/MHC surface of body cell

T killer cells exposed to cytokines active T helper cell cell divisions clone of identical T

killer cells bind to infected body cells

T killer cells release enzymes pores appear in membrane of infected cells

Free entry of water and ions cells swell and burst

Any pathogens intact are labelled with antibodies produced by B effector cells destroyed


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TB

Bacteria inhaled into lungs multiply slowly for primary infection

Localised inflammatory response tubercule forms with dead bacteria and macrophages

8 weeks immune system controls the bacteria inflammation dies down lung tissue

heals. If it avoids the immune system it may survive primary infection stage

Bacteria thick waxy outer layer protects them from enzymes of macrophagesBacteria remains in tubercules dormantly growing - effective bacteria selected/ passed on

When immune system is not working well active tuberculosis is produced,

Bacteria multiply rapidly in lungs

Symptoms of TB fever, night sweats, loss of appetite, loss of weight.

Infection in lungs cough lung tissue damaged cough up blood

T cells targeted reduced production of antibodies

TB run a temperature denaturing enzymes

Insufficient oxygen/ organs fail due to lack of nutrition

HIV causes AIDS

1)HIV attaches to CD4 receptors on T helper cells and infects them2)Takes over host DNA and replicates

3) Viruses leave T helper cell and destroy it

4) Host T killer cells destroy heavily infected T helper cells reducing their number

5) Activation of macrophages and T killer cells doesnt occur

Normal functioning of T helper cells is lostimmune system cant fight off other pathogens

HIV/AIDS infection

Stage 1 acute HIV syndrome

Fevers, headaches, tiredness, swollen glands

3-12 weeks after infection HIV antibodies appear in blood HIV positive

Stage 2 asymptomatic /chronic - Infection established symptoms disappearVirus replicates infecting CD4 T helper cells

Secondary infections develop immune system overwhelmed

Stage 3 symptomatic disease immune system fails T helper cell count falls

Patients suffer HIV related symptoms

Weight loss, fatigue, diarrhoea, night sweats, thrush

Stage 4 advanced aids

T helper cell fall

Weight loss / dementia/ cancers/ TB

Experiment: Effects of antibiotics

1) Place some bacteria on an agar plate

2) Place discs of absorbent filter paper in different antibiotics / different concentrations of

the same antibiotic

3) Have one disc of absorbent paper in only ethanol (control)

4) Place the paper discs on the agar plate with the bacteria on it same conditions and same

time

5) Incubate the plate (cover it) to allow the bacteria to grow

6) Where the bacteria is prevented from growing there will be a clear area called the

inhibition zone

7) The larger the inhibition zone the more effective the antibacterial properties of the

antibiotic


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Glossary

Stroma matrix in chloroplast containing enzymes

Thylakoid chlorophyll molecules are found

Grana stacks of thylakoid

Photolysis decomposition of water to H+, e-and O2

Photophosphorylation the production of ATP using energy from sunlight

NPP = GPP - R

Biotic factors(living factors)- predation, mate-finding, territory, parasitism and disease,

competition

Abiotic factors (non-living factors) - light, temperature, wind and water current, water

availability, oxygen availability, soil structure

Carbon sink carbon is removed from the atmosphere and stored biotic: photosynthesis /

abiotic stored in rocks

Speciation the formation of two new species from one species

Reproductive isolationthe separation of one species into two populations that dont

interbreed

Pre-zygotic isolationfertilisation is prevented

Habitat isolationpopulations go into different habitats so they dont come in contact

during reproductive season

Temporal isolation populations out of reproductive time synchronisation

Mechanical isolation mutation resulting in physical barrier to isolation

Behavioural isolation may not recognise others as mating partners

Post-zygotic isolation failure to breed -

Low hybrid zygote vigour zygote (sperm fertilised egg) fails to develop properly

Low hybrid adult viability offspring fail to thrive/ grow

Hybrid infertility

offspring may appear healthy but are infertile

Antisense strand RNA strand as template of DNA

Allele frequency the relative proportion of different forms of a particular gene within a

gene pool

Triplet code sequence of three bases forming a codon

Virus structure capsid, capsomere, nucleic acid

Bacterial structure mitochondria, nucleic acid, mesosome, plasmid


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Pathogen invading microorganisms

Antigen substance that stimulates the production of an antibody

Antibody immunoglobulins fight antigens

Bacteriocidalantibiotics kills bacteria

Bacteriostatic antibiotics prevents bacteria from multiplying

Vaccination procedure through which people are immunised

Natural active immunity immune system of the body

Natural passive immunity antibodies from mother to baby providing it with temporary

immunity until its bodys immune system becomes activated.

Artificial passive immunity antibodies formed in one individual extracted and injected into

another.

Artificial active immunity some amounts of a weakened antigen are used to produce

immunity immune system produces antibodies against the antigen and memory cells form

so if real pathogen enters body it is prepared to destroy it immediately.

Independent/ dependent variables in an experiment e.g. where the effect of varying

temperatures on enzyme activity is measured, the independent variable would be the

temperature and the dependent variable would be enzyme activity.

Extraneous variable anything other than what is being changed that may affect the

outcome of the experiment e.g. if effect of changing light on plant growth was beingmeasured, volume of water available may be an extraneous variable.

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Unit4notes.pdf