biology 5

survival & response

• organisms increase chance of survival by responding to changes in the environment
• trophisms: response to a directional stimulus, in plants
• taxes: direction determined by stimulus
• kinesis: increase of random movements, a more unpleasent stumulus = more rapid movement & changes in direction

reflex arc

• stimulus --> receptor --> sensory neurone --> intermediate neurone -- > motor neurone --> effector --> response
• importance: protect body from harmful stimulus, invoulontary, fast

receptors

• in eye: rod-more at pheripery, high sensitivity, low acuity. cone-high acuity, low sensitivity, conc at foevea 

pacinian corpuscle: strech mediated Na channels - at resting potentialtoo narrow to allow Na+ in. permeability to Na changes when pressure is applied - channels widen & allow inflix of Na+, potential changes & causes generator potential

control of heart rate

autonomic nervous system: sympathetic & parasympathetic

sympathetic: stimulates effectors, speeds up activity

parasympathetic: inhibits effectors & slows activity

chemo receptors in cartoid arteries

• increased metabolic/muscular activity
• more CO2 produced by tissues - more respiration
• blood ph lowered
• chemical receptors increase frequency of impulses to medulla oblongata
• centre that increases heart rate increases frequency of impulses to SAN via sympathetic nervous system
• SAN increases heart rate
• increased blood flow, removes CO2 faster
• CO2 level returns to normal & ph returns to normal

principles

• neurones: nerve cells pass electrical impulses along their length - secrete neurotransmitters, give a short-lived rapid localised response
• hormones: stimulate target cells via blood, slow wide-spread long lasing response
• histamine & prostaglandins: local cheical mediators, released by some mammalian cells, affect only cells in immediate vicinity
• IAA in plants: diffuse down the plant & causes the elongation of cells, regulate growth in response to directional stimulation

1) Na+ actively transported out of axon by Na+/K+ pump

2) K+ actively transported in

3) Active transport for Na+ is greater than K+

4) Chemical gradient is established

5) Na+ diffuse in, K+ diffuse out

6) Most K+ gates open, fewer Na+ gates open so more K+ diffuses out than Na+ in

7) electrical gradient - as more K+ diffuse out so outside more positive

8) outward movement of K+ more difficult - attracted to negative state of axon

9) equilibrium when chemical & electrical balance, so there is no net movement of ions

1) at resting potential some K+ voltage gated channels open & all Na+ channels closed

2) energy from stimulus causes some Na+ channels to open, Na+ diffuses into the axon - triggers a reversal in P.D across the membrane

3) More Na+ channels open - greater influx of Na+

4) action potential at about 40mV established - Na voltage gated channels shut, K voltage gated channels open

5) electrical gradient reversed - K+ ions diffuse out, repolarising the axon

6) outward diffusion of K+ causes a temporary overshot of electrical gradient. inside of axon more negative. HYPERPOLARISATION. K+ channels close

7) resting potential established by Na+/K+ pump

1) at resting potential: conc of Na+ outside is higher relative to inside, conc of K+ inside is higher relative to outside

2) stimulus- depolarisation - influx of Na+ & a reversal of charge on axon

3) localised electrical circuits established: influx of Na+ cause Na channels to open further up axon. behind Na channels close and K channels open

4) action potential propagated along neurone

5) neurone repolarised

• myelin sheath
• diameter of axon - less leakage of ions
• temp - energy for active transport from respiration - respiration controlled by enzymes

refractory period

• limits the number of action potentials
• produces discrete impulses
• ensures impulse is in one direction

synapse

• unidirectionality pre-> post
• inhibition - on post synaptic membrane of some synapses, protein channels for Cl- may be open - post synaptic more negative - less likely a new action potential will be generated
• summation - temprol - single pre synaptic, releases neurotransmitter many times. spatial -many different presynaptic, release enough neurotransmitter to exceed threshold

1) arrival of action potential cases Ca2+ channels to open & an influx of Ca2+

2) vesicles migrate & fuse to membrane & release acetylcholine into synaptic cleft

3) migrate to post synaptic membrane & fuse to receptors on Na+ channels, Na+ diffuses along conc gradient

4) new action potential generated

5) acetyl cholinesterase hydrolyses acetyl choline to choline & ethanoic acid - diffuses back across synaptic cleft  & is reabsorbed. 

6) ATP from mitochondria recombine them. Na+ channels close

structure

• bundles: groups of muscle fibres surrounded by connective tissue, containing blood vessels & nerves
• Fibre: cells fuse together & form a very long strong multi-nucleated cell - it can withstand high tension
• myofibrils: each fibre contains many myofibrils within the sarcoplasm - exhibits a distinct striated pattern
• sacromere: banding pattern is cased by sacromeres - smallest contractive units - arranged end to end

protein filaments

• actin: thinner, 2 strands twisted round each other
• myosin: thicker & consists of long rod shaped fibres with bulbous heads
• light bands = I bands (actin & myosin don't overlap)
• dark bands = A bands (actin & myosin overlap)

1) increase in Ca2+ conc

2) tropomyosin molecules move away from actin binding sites

3) the ADP molecule attached to myosin heads means they can bind to actin

4) when attached, myosin heads change angle & pull actin along & release ADP

5) ATP attaches to each myosin head & causes it to detach

6) Ca2+ activates ATPase, hydrolysing ATP to ADP, the energy allows head to return to its original position

fast twitch fibres

• thicker & more numerous myosin filaments
• high conc of enzymes for anaerobic respiration
• store of phosocreatine
• contract more rapidly
• powerful contractions over short period of time
• intense exercise

slow twitch fibres

• contract slowly
• less powerful contractions over long period of time
• endurance work
• large store of myoglobin
• supply of glycogen
• rich supply of blood vessels
• numerous mitochondria

physiological control systems - maintain internal environment

importance of homeostasis:

• enzymes sensitive to changes in pH and temp - changes reduce efficiency/denature them
• changes in water potential may cause cells to shrink/burst - osmosis

temperature control: ectotherms reptiles

• temp controlled by behaviour: basking/seeking shade/from ground/ generating metabolic heat/colour variations

endotherms mammals

• internal metabolic activity
• producing heat: small SA to vol ratio/vasoconstriction/shivering/raising of hair - insulating layer/ decreased sweating
• loosing heat: vasodilation/increased sweating/lowering body hair/behavioural mechanisms

glucose= source of energy

if blood glucose low = less every / high & water potential of blood lowers

from diet, the breakdown of glycogen GLYCOGENOLYSIS, and production of new glucose GLUCONEOGENESIS

adrenaline increases blood glucose by inactivating enzyme synthesising glycogen from glucose & activating enzyme synthesising glucose from glycogen

NEGATIVE FEEDBACK

detect a rise in blood glucose conc

almost all body cells have glycoprotein receptors - insulin binds to them and causes:

• changes in tertiary structure
• increases the number of carrier molecules
• activation of enzymes: glucose --> glycogen + fat

blood glucose lowered:

• increased rate of absorption 
• glucose--> fat
• glucose --> glycogen
• increased respiratory rate

detect a fall in blood glucose

release hormone glucagon - only liver cells respond

activates enzyme - glycogen --> glucose 

increases conversion of amino acids + glycerol --> glucose GLUCONEOGENESIS

hormones: 2nd messenger model

• hormone 1st messenger - binds to specific receptors (hormone-receptor complex) on cell surface membrane
• activates enzyme inside cell that results in the production of a chemical
• series of chemical changes to produce required response

negative - restores system to original level - greater control

positive - greater deviations from norm - often associated with a breakdown in control systems

control of oestrus cycle

• FSH - ripening of a follicle
• Oestrogen - repair of lining
• LH - ovulation & development of corpus leuteum
• Progesterone - maintains lining

FSH stimulates OESTROGEN

OESTROGEN stimulates LH and inhibits FSH

LH stimulates PROGESTERONE

PROGESTERONE inhibits FSH and LH

the genetic code

• base triplets - code for specific amino acids
• universal
• non-overlapping
• degenerate
• RNA- pentose sugar, AUGC, phosphate group
• mRNA- single strand, triplet = codon
• tRNA - clover shaped, only carries a triplet of bases - anticodon. AA site

type I

• insulin 
• body unable to produce insulin 
• symptoms obvious

type II

• regulate diet & exercise & is age related
• glycoprotein receptors lose responsiveness to insulin
• may be unnoticed

transcription: production of mRNA

• DNA helicase binds to specific site on DNA strand --> breaks hydrogen bonds
• strands split
• RNA polymerase moves along DNA, adding free nucleotides
• A->U, T->A, C->G, G->C
• preRNA made
• DNA rejoins behind
• when RNA polymerase recognises a STOP codon it stops synthesis 

splicing: introns removed & exons joined together

• ribosome attaches to starting codon at end of mRNA
• tRNA with complimentary anticodon sequence joins to ribosome & pairs with triplet on mRNA
• tRNA carries AA
• another tRNA moves to ribosome & attaches to next triplet
• ribosome moves down mRNA
• using an enzyme & ATP, 2 AA joined together by peptide bond & releases 1st tRNA

substitution of bases

• mis-sense - a different amino acid coded for
• nonsense - base change results in a stop codon being formed - synthesis stops prematurely 
• silent - substitution still codes for same amino acid

deletion

• deletion at start causes more changes than deletion at end
• nucleotides are lost

causes

• spontaneous with no external influence
• radiation
• chemicals

proto-oncogens

• stimulate cell division
• growth factor attaches to receptor protein-->relay proteins--> 'switch on' genes for DNA replication
• can mutate into oncogens: receptor permanently switched on/growth factor produced in excessive amounts

tumour suppressor genes

• inhibit cell division
• if mutated: switch off and no longer inhibit cell division

Totipotent cells

• can mature into any body cell
• translate only part of DNA = cell specialisation 
• in mature plants: many cells remain totipotent: can develop into a plant/plant organ in the right conditions
• only occur for a limited time in mammalian embryos: multi potent cells in mature mammals - can divide into a limited number of different cell types
• can be used to treat some genetic disorders

transcription of target genes is stimulated only when specific transcriptional factors move from cytoplasm to the nucleus

oestrogen & transcription

• oestrogen switches on a gene to start transcription
• it binds to a receptor - causes it to change shape & releases the inhibitor
• transcriptional factor can bind to DNA & start transcription

SiRNA

• small double stranded RNA
• breaks down mRNA before it is translated
• can identify role of genes in a biological pathway & can prevent diseases caused by genes
• an enzyme cuts a large double stranded RNA to smaller sections-> SiRNA
• 1 of the strands combines with an enzyme & guides it to mRNA

gene cloning & transfer

• reverse transcriptase: mRNA-> cDNA. chose a cell that readily produces the protein, it contains large quantities of required mRNA- extract it. use DNA polymerase to make other strand, which is the required gene
• restriction endonucleases & recognition sequences: in vivo(uses a vector) restriction enzyme cuts DNA at a specific sequence of bases & leave 'sticky ends' (few single nucleotides long which can bing to any complimentary sequence, also with a sticky end)

PCR

• in vitro
• requires: DNA fragment, DNA polymerase from thermostable bacteria, primers, nucleotides, thermocycler
• separate DNA strand - heat to 95C 
• addition of primers - cooled to about 55C, primers join to complimentary sequence at ends of fragment = starting point for DNA polymerase
• synthesis of DNA - heat to 72C = optimum temp for DNA polymerase

in vitro

• extremely rapid
• doesn't require living cells

in vivo

• produces a transformed bacteria: can produce large quantities of gene
• no risk of contamination
• cuts specific genes
• able to introduce gene into living organism
• very accurate

animals: to induce resistance & to produce additional proteins in milk

plants: plants that produce plastics & disease/herbicide resistant crops

genetic modification

• increase crop yield
• vaccinations & medicines
• nutrient content in food increases
• crop plants tolerant to herbicides
• enzymes
• antibiotics: produced naturally by bacteria - genetic engineering increases quantity and rate of production
• hormones - insulin for diabetes

DNA probes & DNA hybridisation 

• probe radioactively/fluorescently labeled  
• DNA probe complimentary to gene
• DNA split into 2 strands
• DNA mixed with probe
• DNA hybridisation:- binds to complimentary bases on 1 strand
• site of probe can be identified & therefore site of gene

Gene therapy : supplementation- one or more copies of the health gene inserted to mask the effects of the recessive gene

DNA sequencing

• uses modified nucleotides that cannot be attached to further
• 4 test tubes each with: many single stranded DNA fragments, mixture of nucleotides, small quantity of 4 terminator nucleotides, primer & DNA polymerase
• new fragments vary in length
• separate the fragments by GEL ELECTROPHORESIS
• agar gel & fragments & voltage
• large fragments = slow
• photographic film shows the position of fragment

restriction mapping

• use different enzymes cut labeled DNA
• separate by GEL ELECTROPHORESIS
• restriction map is created by using size of fragments to determine locations of cut site

each organism's genome contains many repetitive non-coding base sequences - probability of 2 being the same repetitive sequences is very low.

• extraction - extract DNA from rest of cell & increase quantity by PCR
• digestion - DNA cut into fragments by restriction endonucleases
• separation - fragments separated according to size by gel electrophoresis
• gel immersed in alkali to separate the double strands - single strands transferred onto nylon membrane SOUTHERN BLOTTING
• hybridisation - radioactive/fluorescent DNA probes used to bind with core sequence
• development - x-ray film put over nylon membrane - film is exposed by radiation probes - series of bars revealed. pattern is unique to each individual

uses

• forensic science
• genetic variability
• medical diagnosis
• pedigree

only a portion of the bacterial vectors will take up the DNA fragment

gene markers

• antibiotic resistant markers - replica plating used to identify the plasmids with the new gene - uses the gene that was cut out of the plasmid to detect for resistance in the hybrid plasmid, without the gene the bacteria cannot produce the enzyme so won't have resistance to the antibody. cultures of bacteria can be grown on an agar plate and where the DNA has been taken up the bacteria won't survive. PROBLEM: kills cells with desired gene
• fluorescent markers - more rapid, gene from jelly-fish is transferred into the plasmid. gene to be cloned is placed in the centre of the jelly-fish gene. where DNA taken up bacteria won't fluoresce - these bacteria selected
• enzyme markers - gene that produces lactase turns a particular substrate blue. required gene is transplanted into the gene that produces lactase - cannot turn substrate blue as enzyme not prodced