paper 2

• LDR:

  • photons hit chlorophyll, excite its electrons
  • photolysis of water, into 4 protons, 4 electrons and 1 oxygen, oxygen diffuses away, electrons replace the missing ones in chlorophyll, protons move into stroma
  • electrons move down chain of proteins by a series of redox reactions, releasing energy, used to pump protons from stroma to thylakoid, then electrons combine with protons to form hydrogen, used to reduce NADP to form reduced NADP
  • conc of protons in thylakoid > stroma, protons move across membrane by fac. diff. through an ATP synthase channel, catalysing formation of ATP from ADP and Pi
• LIR:

  • carbon dioxide diffuses in through the stomata and is fixed with 5-carbon ribulose biphosphate RuBP, this reaction is catalysed by the enzyme rubisco, and forms two molecules of 3-carbon glycerate-3-phosphate GP
  • reduced NADP reduces GP to two molecules of triose phosphate TP, using energy supplied by ATP, this reforms NADP which can be re-used
  • most TP is used to regenerate RuBP, using energy supplied by the rest of the ATP
  • two molecules of TP combine to form hexose sugars such as glucose
• glycolysis:

  • glucose is phosphorylated to glucose phosphate, making it more reactive, using phosphate molecules from ATP hydrolysis
  • 1 glucose phosphate is split into 2 triose phosphate molecules
  • triose phosphate is oxidised, hydrogen is removed from each triose phosphate and transferred to NAD which reduces it to NADH
  • enzyme-controlled reactions convert triose phosphate into pyruvate, producing 2 molecules of ATP from condensation
  • overall yield is 2 ATP, 2 NADH and 2 pyruvate, so there is a net gain of ATP
• link reaction:

  • 2 molecules of pyruvate are actively transported into the mitochondria
  • pyruvate is oxidised to acetate, by losing 1 carbon dioxide and 2 hydrogens
  • hydrogen reduces NAD to form NADH
  • acetate combines with coenzyme A to produce acetyl coenzyme A
• krebs cycle:

  • acetyl coenzyme A combines acetate with a 4 carbon molecule to make a 6 carbon molecule
  • the 6 carbon molecule loses 2 carbon dioxide and 2 hydrogens through a series of reactions, releasing 1 ATP, becoming a 4 carbon molecule
  • the H reduces NAD and FAD to NADH and FADH
  • the 4 carbon molecule can repeat the cycle
• oxidative phosphorylation:

  • NADH and FADH donate the electrons of the H to the first electron acceptor, and release the H+ as protons
  • electrons pass down the chain through a series of redox reactions
  • as electrons flow, they release energy, used to pump protons across the inner-mitochondrial membrane into inter-membranal space
  • protons build up, creating a concentration gradient, so diffuse back into the matrix through ATP synthase channels in the membrane
  • at the end of the chain, electrons combine with protons and oxygen to form water, so oxygen is the final electron acceptor
• nitrogen cycle:

  • ammonification, sapro. bact. break down matter to ammonia, proteases break down proteins into amino acids, deaminases remove amino groups, decomposition products are used for respiration
  • nitrification, nitrifying bact. convert ammonia to nitrite then nitrate ions by oxidation, plants can absorb
  • denitrification, denitrifying bact. convert nitrate ions to nitrogen gas, wasteful
  • nitrogen fixation, n-f bact. fix nitrogen gas into compounds by reducing it to ammonia which dissolves into ammonium ions
• phosphorus cycle:

  • erosion causes ions in sedimentary rocks to be dissolved in soil + water
  • absorption of ions from soil + water by plants
  • feeding and digestion of ions in plants by animals
  • excretion of excess ions by animals causes ions to be dissolved in soil + water
  • excretion and decomposition of wastes and remains cause ions to be in guano, bones + shells
  • erosion of guano, bones + shells causes ions to be dissolved in soil + water
  • deposition of guano, bones + shells causes ions to be in sedimentary rocks
  • sedimentation of ions in soil + water causes ions to be in rocks
• eutrophication:

  • nitrate ions are limiting factor
  • leaching causes increased ion conc.
  • plant/algae populations increase, causing algal bloom
  • algal bloom prevents light from reaching the bottom, light becomes limiting factor for deeper plants/algae, they die
  • saprobiontic bacteria feed on dead plants/algae
  • saprobiontic bacteria require oxygen for respiration, oxygen becomes limiting factor for aerobic organisms, they die
  • anaerobic organisms have less competition, increase in population size
  • anaerobic organisms decompose dead material, releasing more nitrates + toxic waste, water becomes putrid
• phototropism in shoots:

  • cells in the tip of the shoot produce IAA which is transported down the shoot
  • IAA is initially transported evenly throughout
  • light causes the movement of IAA from the light side to the shaded side
  • a greater concentration of IAA builds up on the shaded side than the light side
  • as IAA causes elongation of shoot cells and there is a greater concentration of IAA on the shaded side, the cells on the shaded side elongate more
  • the shaded side of the shoot elongates faster than the light side causing the shoot tip to bend towards the light
• gravitropism in roots:

  • cells in the tip of the root produce IAA which is transported along the root
  • IAA is initially transported evenly throughout
  • gravity causes the movement of IAA from the upper side to the lower side of the root
  • a greater concentration of IAA builds up on the lower side than the upper side
  • as IAA inhibits elongation of root cells and there is a greater concentration of IAA on the lower side, the cells on the upper side elongate more
  • the upper side of the root elongates faster than the lower side causing the root tip to bend towards gravity
• pacinian corpuscle process:

  • at resting potential, the stretch-mediated sodium channels are too narrow to allow sodium ions to pass along them
  • when pressure is applied, the pacinian corpuscle is deformed and the membrane around the neurone becomes stretched
  • the stretching widens the sodium channels in the membrane, sodium ions diffuse into the neurone
  • the influx of sodium ions changes the potential of the membrane, it becomes depolarised, producing a generator potential
  • the generator potential creates an action potential which passes along the neurone to the central nervous system
• the SAN stimulating the heartbeat:

  • a wave of excitation spreads from the SAN across the atria, making them contract
  • non-conductive tissue stops the wave from crossing to the ventricles
  • the wave of excitation enters the AVN
  • the AVN, after a short delay, conveys the wave of electrical excitation between the ventricles along purkyne tissue fibres, which make up the bundle of His.
  • the bundle of His. conducts the wave to the base of the ventricles, branching into smaller fibres
  • the wave is released from the fibres making the ventricles quickly contract from the bottom upwards
• the control of blood pH:

  • when blood has high CO2 concentration, pH is low
  • chemoreceptors detect this and increase the frequency of nerve impulses to the centre in the medulla oblongata which increases heart rate
  • the centre increases the frequency of nerve impulses to the SAN via the sympathetic nervous system
  • this increases the rate of production of electrical waves by the SAN so heart rate increases
  • increased blood flow leads to more CO2 being removed by the lungs, so the concentration returns to normal levels
• the control of blood pressure:

  • pressure receptors increase the frequency of nerve impulses to the centre in the medulla oblongata that decreases heart rate
  • the centre decreases the frequency of nerve impulses to the SAN via the parasympathetic nervous system
  • this decreases the rate of production of electrical waves by the SAN so heart rate decreases
• establishment of resting potential:

  • 3 Na+ ions are actively transported out of the axon by the sodium-potassium pump
  • 2 K+ ions are actively transported into the axon by the sodium-potassium pump
  • both ions are positive and more Na+ ions move out than K+ ions move in so an electrochemical gradient is created
  • voltage-gated sodium channels are closed so few Na+ ions diffuse back into the axon
  • voltage-gated potassium channels are open so K+ ions diffuse out of the axon
• action potential:

  • at resting potential some K vgc are open but all Na vgc are closed
  • some Na vgc open so Na+ ions diffuse into the axon along their electrochemical gradient
  • Na+ ions are positive, so potential difference across the membrane is reversed
  • as Na+ ions diffuse in, more Na vgc open, until a threshold is reached, then Na vgc close and K vgc open
  • as K+ ions diffuse out, more K vgc open, this starts repolarisation of the axon
  • resting potential is restored
  • K vgc close slowly, causing hyperpolarisation
  • sodium-potassium pump reverses hyperpolarisation
  • resting potential is restored
• cholinergic synapse transmission:

  • ap arrives at pre-n., causes Ca vgc to open, Ca2+ ions enter sk by facilitated diffusion
  • synaptic vesicles fuse with the pres-m, releasing acetylcholine into the sc
  • acetylcholines diffuse across the sc, bind to receptors on Na vgc in the post-m
  • this causes Na vgc to open, Na+ ions diffuse into the post-n
  • this generates a new ap in the post-n
  • acetylcholinesterase hydrolyses acetylcholine into ch and ea, which diffuse back across the sc into the pre-n
  • ea and ch are combined into acetylcholine using ATP
  • Na vgc close due to no acetylcholine in their receptors
• muscle stimulation:

  • action potential reaches neuromuscular junctions
  • Ca vgc open, Ca2+ ions diffuse into the synaptic knob
  • Ca2+ ions cause synaptic vesicles to fuse with presynaptic membrane and release acetylcholine into the synaptic cleft
  • acetylcholine diffuses across the cleft, binds with receptors on the muscle cell-surface membrane, causing depolarisation
• muscle contraction:

  • ap travels into muscle fibre through series of T-tubules
  • Ca2+ ions actively transported from sarcoplasmic reticulum to sarcoplasm
  • ap opens Ca vgc, Ca2+ ions diffuse in
  • Ca2+ ions cause tropomyosin blocking binding sites on actin to pull away
  • myosin heads bind to actin using ADP molecules, forming cross-bridges
  • myosin heads change angle, pulling actin along, releasing the ADP molecule
  • ATP attaches to myosin, myosin detaches from actin
  • Ca2+ ions activate ATPase, ATP is hydrolysed, energy is used to return myosin to original position
• muscle relaxation:

  • when stimulation stops, Ca2+ ions are actively transported back into sarcoplasmic reticulum
  • tropomyosin reblocks the binding site on the actin filament
  • myosin heads are unable to bind
  • force from antagonistic muscles can pull actin from between myosin slightly
• second messenger model:

  • adrenaline/glucagon binds to a transmembrane protein receptor in the cell-surface membrane of a liver cell
  • this causes the protein to undergo a conformational change
  • this activates the enzyme adenyl cyclase
  • adenyl cyclase converts ATP to cyclic AMP
  • cyclic AMP acts as a second messenger which binds to the enzyme protein kinase
  • protein kinase catalyses the conversion of glycogen to glucose
  • glucose moves out of the liver cell by facilitated diffusion and into the blood
• glomerular filtrate + PCT:

  • blood enters by renal artery, which divides into the afferent arteriole then glomerulus
  • podocytes have gaps between to allow filtrate to move out into proximal convoluted tubule
  • pressure gradient is created as afferent arteriole diameter > efferent arteriole diameter
  • water and soluble components are forced out, except proteins as they are too large
  • glomerular filtrate moves to proximal convoluted tubule, all glucose must be absorbed into the blood but not all waste
  • glucose is reabsorbed by co-transport from epithelial cells to blood capillaries
• loop of henle + DCT:

  • loop of Henle acts as counter-current multiplier
  • sodium ions are transported out of the ascending limb using ATP
  • low water potential created in the interstitial space
  • ascending limb is impermeable to water, water only moves out of the descending limb by osmosis into interstitial space due to water potential gradient
  • water enters capillaries in the interstitial space by osmosis
  • water potential is lowest at the hairpin as sodium ions move out
  • water moves out of distal convoluted tubule and collecting ducts by osmosis
  • ion concentration increases going down medulla
• osmoreceptors and ADH:

  • when osmoreceptors detect a fall in water potential, they shrink, causing the hormone ADH to be released
  • ADH passes to the posterior pituitary gland, and is secreted into the blood
  • when ADH reaches the kidney it combines with receptors on the surface of the collecting duct and activates the enzyme phosphorylase
  • this causes vesicles containing aquaporins to fuse with the cell surface membrane, increasing water and urea permeability
  • the increase in water and urea permeability causes urea and water to leave the collecting duct, and be reabsorbed into the blood
• natural selection:

  • there is a variety of phenotypes in a population
  • an environmental change occurs, causing the selection pressure to change
  • some individuals have advantageous alleles so are more likely to survive and reproduce
  • advantageous alleles are passed down to offspring
  • frequency of alleles changes over time, leading to evolution
• predator-prey relationships:

  • when prey are eaten, the prey population falls and the predator population rises
  • once the levels of prey fall to a certain point, the predator population falls as there is not enough food to support them
  • there are fewer predators so the prey population rises
  • this cycle repeats itself over and over
• mark-release-recapture method:

  • known number of organisms are captured and marked in a way that does not decrease their chance of survival
  • marked organisms are released into the same area they were caught in
  • after a length of time long enough for organisms to redistribute randomly, capture another known number of organisms, record the percentage of these that were marked
  • use population size = (no. in first sample)*(no. in second sample)/(no. of marked recaptured)
• succession:

  • pioneer species specially adapted to harsh conditions colonise an environment that is inhospitable to others
  • as pioneer species such as lichen die, they are decomposed by microorganisms
  • this creates soil and eventually releases enough nutrients, changing the environment in a way that makes it more suitable for another species
  • the new species outcompetes the old species
  • this process repeats until a balanced equilibrium is reached, called a climax community
• oestrogen starting transcription:

  • oestrogen is lipid-soluble so freely diffuses across the cell membrane into the cytoplasm
  • oestrogen binds to a receptor site on a transcription factor
  • this causes a conformational change in the shape of the DNA binding site on the transcription factor, making it able to bind to the DNA
  • the transcription factor enters the nucleus via a nuclear pore, and binds to DNA
  • this stimulates transcription
• siRNA switching off genes short-term:

  • siRNA binds to complementary sequence of mRNA
  • mRNA should be single-stranded but the cell detects this sequence as double-stranded
  • the sequence is labelled as abnormal and broken down by enzymes
  • this prevents translation as ribosomes are unable to bind
• PCR:

  • DNA sample, primers, free nucleotides and DNA polymerase are added to a vessel in the thermocycler
  • mixture is heated to 95 degrees to break the hydrogen bonds and separate the two strands
  • this denatures the DNA
  • mixture is cooled to 55 degrees
  • primers bind to the strands
  • this prevents the separate strands from rejoining and provides the starting sequence for DNA polymerase to attach nucleotides to
  • mixture is heated to 72 degrees
  • DNA polymerase binds complementary nucleotides along each of the DNA strands
  • this produces two identical strands of DNA
• using DNA probes to identify alleles:

  • a probe is made which has a complementary base sequence to the base sequence of the allele
  • the double-stranded DNA that is being tested is treated to separate it into two strands
  • the separated DNA strands are mixed with the probe
  • the probe binds to the complementary sequence if it is present
  • the sample is viewed using x-ray film or UV light depending on the labelling of the probe
• determining whether someone possesses an allele:

  • determine the base sequence of the allele
  • produce a fragment of DNA with the complementary base sequence
  • amplify the fragment using PCR
  • attach a marker to create a DNA probe
  • extract DNA from the person
  • denature the DNA
  • anneal the DNA in a mixture containing the DNA probe
  • wash out the vessel containing the sample
  • test using x-ray film or UV light
• gel electrophoresis:

  • if too large, DNA is cut into fragments using restriction endonucleases
  • DNA fragments are placed on agar gel
  • a voltage is applied across it
  • DNA is negatively charged so moves towards the positive end
  • the larger the DNA molecule, the slower it moves due to the resistance of the gel
  • if fragments are labelled, they can be detected using x-ray film or UV light
• genetic fingerprinting:

  • a sample of DNA is extracted from a cell
  • DNA is cut into fragments using restriction endonucleases, leaving the minisatellites intact
  • gel electrophoresis separates the fragments by placing them on a gel and passing a current through the gel
  • the gel is immersed in alkaline solution, separating the two DNA strands
  • nylon is used as a cover to absorb DNA
  • DNA is fixed to the nylon using UV light
  • probes with markers, which are complementary to VNTRs are added
  • areas with the probe are identified using UV light or x-ray film