AQA A2 Biology Unit 5

Stimulus- A detectable change in the internal or external environment that an oranism produced a                 response to. Organisms need to respond to stimuli to increase their chances of                           survival.

Taxis- directional movement in response to a stimulus. 

Kinesis- non-directional (random) movement in response to a stimulus. 

Tropisms- A growth movement of a plant in response to a directional stimulus  in its environment.

Receptors- Detect stimuli. Can be cells or proteins on cell surface membranes. E.g.                                       baroreceptors detect blood pressure changes.Receptors communicate with effectors                     via the nervous system or hormonal system.

Effectors- Cells that bring about a response to a stimulus, to produce an effect. Effectors                             include muscle cells and cells found in glands (e.g. pancreas).

Reflex Arc:       Stimulus ----> Receptors ----> CNS ----> Effectors ----> Response                                   Sensory- transmit electrical impulsese from receptors to CNS.                                                   Relay- transmit electrical impulses between sensory and motor neurones.                                   Motor- transmit electrical impulses from CNS to effectors.                                        When electrical impulse reaches end on neurone, chemicals called neurotransmitters take    information across gap (synapse) to the next neurone.

Spinal Cord:                                                                                                                                                                     

Autonomic Nervous System:                                                                                                                    Sympathetic nervous system- stimulates effectors and is like an emergency                                                 controller and helps us cope with stressful situations on our body.                            Para Sympathetic nervous system- inhibits effectors and so slow down activity,                                           control activities under normal conditions.

Control of heart rate: The heart is controlled by a region of the brain called the medulla                                               oblongata. It is linked to the SAN which can increase and decrease heart                                   rate. whether the heart rate is increased or decreased is due to receptor                                       which detect chemical and pressure changes in the blood.

Chemoreceptors: These receptor detect pH changes that are due to CO2 concentrations in the                               blood and is the pH is to low (acidic) the heart rate is increased and vice versa.

Pressure Receptors: When blood pressure is high, heart reate is decreased and wen blood                                         pressure is low, heart rate is increased.

Pacinian Corpuscle: When pacinian corpuscle is stimulated, the corpuscle is deformed and presses on a sensory nerve ending. This opens stretch-mediated sodium channels in sensory neurones cell membrane. This allows sodium ions to diffuse into cell, creating a generator potential.

 Receptors are specific and only detect one particular stimulus.Receptors in the nervous system convert the energy of the stimulus into the electrical energy used by neurones, this is called a generator potential(cell membrane becomes excited and more permeable, allowing more ions to move in/out of the cell- altering the potential difference).

Action potential: If generator potential is big enough, an action potential is triggered (electrical impulse along neurone). Action potential only triggered if generator potential reaches threshold level. An action potential resets the receptor to resting potential (Inside of cell is negatively charged relative to the outside).

The Eye:Rods are very sensitive to light(low visual acuity) as many rods join one neurone, so                     many weak generator potentials combine to reach threshold and trigger action potential,               however that can only give info in black and white.Cones are colour receptor which need               high light  intensities to create an action potential.

The hormonal system: hormones are transmitted in blood plasma to cells which they stimulate.                                     These stimulation's are often longer-lasting and widespread.

Chemical mediators: chemicals that are released from cells,& effect cells in immediate vicinity.                                   Two examples of these are Histamines, found in white cells are released                                     in response to allergens, and prostaglandins, found in cell membranes                                       and they cause dilation or constriction of small arteries and arterioles.

Plant growth factors: plant growth is affected by light, gravity and water. They react to these                                         factors through indoleacetic acid (IIA).    

Control of Tropisms by IIA:                                                                                                                                             1) cells in tip of shoot make IIA which is then transported down the                                                  shoot.                                                                                                                                2) Light causes IIA to move to one side of shoot.                                                                        3)Greater concentration of IIA on shaded side causes shoot to bend                                                towards light.

Sensory neurone: transmit nerve impulses from receptor to intermediate or motor neurone.

Motor neurone: transmit nerve impulse to an effector such as a gland or muscle.

Intermediate neurone: transmit nerve impulse between neurones.

The resting potential (-70mV): outside of membrane is positively charged compared to inside- so membrane is polarised. Resting potential created & maintained by sodium-potassium pumps in neurone's membrane. Pumps use active transport to move 3Na+ out of neurone for every 2K+ moved in.                                                                                      1. Pumps move Na+ out of neurone, but membrane not permeable to Na+ so cannot diffuse          back in. Creates gradient as there are more +ve sodium ions outside cell than inside.          2. Sodium-potassium pumps also move K+ into the neurone                                                3. When at rest, most K+ channels open. This means membrane is permeable to K+, so              some diffuse back out through K+ channels.

Action Potential: 1. Stimulus excites cell membrane, causing Na+ channels to open, Na+                                     diffuse into neurone gradient. Inside of neurone now less negative            2. Depolarisation- If potential difference reaches thresshold (-55mV), more Na+ channels open,      so more Na+ diffuse into the neurone.                                                  3. Repolarisation- Na+ channels close and K+ channels open. K+ diffuse out of the neurone.  4. Hyperpolarisation- K+ channels are slow to close so slight 'overshoot' where too many K+        diffuse out of neurone. Potential difference becomes more negative than resting potential.      5. Resting potential- Pump returns membrane to resting potential & potential maintained until        another stimulus. Refractory period ensures action potentials are unidirectional.

Three factors affect speed of conduction of action potentials:

1. Myelination: some neurones have a myelin sheath which is an electrical insulator. It is made of a type of cell called a Schwann cell. Between the Schwann cells are tiny patches of bare membrane called the nodes of Ranvier. Na+ channels are concentrated at the nodes of Ranvier

Saltatory conduction: in myelinated neurones, depolarisation only happens at nodes of Ranvier- impulse 'jumps' from node to node. This is called saltatory conduction and is very fast. In a non-myelinated neurone, the impulse travels as a wave along whole length of axon membrane. This is slower than saltatory conduction.

2. Axon diameter: Action potentials are conducted quicker along axons with bigger diameters as there is less resistance to flow of ions than in cytoplasm of smaller axon.

3. Temperature: Speed of conduction increases as temperature increases as ions difuse faster.

                                                                               Effect of an action potential: Action potential reaches end of neurone. Neurotransmitters    released into synaptic cleft Diffuse across to postsynaptic membrane and bind to specific    receptors. May trigger an action potential, cause muscle contraction or cause hormone to be  secreted.                                                                                                              Receptors only on postsynaptic membrane, so impulses are unidirectional. Neurotransmitters  are removed from the cleft so response does not keep happening  

 1. Action potential arrives at synaptic knob of presynaptic neurone. The action potential                    stimulates Ca2+ channels in the presynaptic neurone to open. Ca2+ diffuse into the synaptic        knob                                                                                                                                  2. Influx of Ca2+ causes synaptic vesicles to fuse with presynaptic membrane. The vesicles              release acetylcholine (neurotransmitter) into the synaptic cleft by exocytosis                    3. Acetylcholine diffuses across synaptic cleft & binds to specific receptors on postsynaptic              membrane, causing Na+ channels in postsynaptic membrane to open. Influx of Na+ causes          action potential on the postsynaptic membrane. Acetylcholine removed from synaptic cleft so        response does not keep happening. It is broken down by acetylcholinesterase and the                  products are reabsorbed by the presynaptic neurone and used to make more acetylcholine.     -------------------------------------------------------------------------------------------------------------------------------------------Excitatory neurotransmitters- depolarise the postsynaptic membrane, making it fire an action                                                    potential if a threshold is reached

Inhibitory neurotransmitters- hyperpolarise the postsynaptic membrane preventing it from firing                                                 an action potential

Structure: Contain bundles of thick and thin myofilaments that move past each other to make muscles contract. Thick myofilaments are made of myosin and the thin are made of actin.

Under a microscope a myofibril will have dark (myosin) and light (actin) bands.

Myofibril made up of many short units called sarcomeres. Ends of each sarcomere are marked with a Z-line. In the middle of each sarcomere is an M-line (middle of myosin filaments). Around M-line is H-zone (only contains myosin filaments).

  Slow-twitch: contract slowly and so can work from a longer period of time, addapted to aerobic                       respiration.                                                                                                   Fast-twitch: contract rapidly and give powerful contractions but can only do this for a                                      short period.

Neuromuscular Junctions: A specialised cholinergic synapse between a motor neurone and a     muscle cell.                                                                                                       Neuromuscular junctions use acetylcholine which binds to cholinergic receptors called nicotinic     cholinergic receptors.                                                                                                           They work in the same way as cholinergic synapses but have a few differences:

• Postsynaptic membrane has lots of folds that form clefts which store acetylcholinerase
• Postsynaptic membrane has mre receptors than other synapses
• When a motor neurone fires an action potential, it always triggers a response in muscle cells. This is not always the case for a synapse between two neurones

Sliding Filaments:Myosin and actin filaments slide over one another to make the sarcomeres                                  contract. The myofilaments themselves do not contract. The simultaneous                                  contractoin of lots of sarcomeres means the myofibrils and muscle fibres                                    contract. Sarcomeres return to their original length as the muscle releases.

Contration of Muscle after Stimulation:                                                                          1) Ca ions bind to tropomyosin, causing it to change shape and reveal binding site on the actin.    2) The myosin binds to binding site on actin, forming actin-myosin cross bridge. Ca ions also            activate ATPase which breaks down ATP to produce energy needed for muscle contraction.      3) ATP used to detach myosin from actin and reattach it  to the next actin in a "rowing" motion.        ATP also provides energy to break actin-myosin cross bridge. 

Homeostasis: maintenance of a constant internal environment.

Temperature-Rate of metabolic reactions increases with temp. More heat = more kinetic energy so more enzyme-substrate complexes. If temp too high, H-bonds in tertiary structure break, changing shape of active site & enzyme is denatured. If temp too low enzyme actvity reduces, slowing the rate of metabolic reactions.                                                                    pH- If blood pH is too high/low enzymes become denatured.                                                    Blood glucose concentration- if too high,water potential of blood reduced so water diffuses out   of cells into the blood and cells to shrivel up  and die. If too low, cells unable to carry out normal   activities as not enough glucose for respiration to provide energy. 

Control Mechanisms: Receptors detect when level has changed, and info is communicated via nervous/hormonal system to effectors which counteract change- bringing level back to normal. This is called a "negative feedback mechanism", there are lots of these as this gives more control over  changes to internal environment.                                                                            Positive feedback mechanisms amplify the change. Effectors further increase level away from  the  normal level. Positive feedback is not involved in homeostasis because it does   not keep  internal  environment constant. It is useful to rapidly activate process in the body.

Mechanisms of heat control:                                                                                                        Heat loss- sweating, Hairs lie flat (erector pili muscles relax so hairs lie flat. Less air trapped,                        so skin is less insulated and heat can be lost more easily) Vasodilation.                      Heat production- shivering (muscles contract in spasms &heat produced from increased                                   respiration), hormones (adrenaline & thyroxine released. Increase metabolism.        Heat conservation- Less sweat, Hairs stand up (erector pili muscles contract so stand                                               up. More air trapped, prevents heat loss), Vasoconstriction.

Ectotherms- can't control body temp internally. Controlled by behaviour. Internal temp depends on external temp. Have a variable metabolicrate so unable to keep internal temp constant. Generate little heat themselves. Activity level depends on external temp, more active at higher temp.

Endotherms- control body temp internally, as well as altering their behaviour. Internal temp less affected by external temp. High metabolic rate as can keep internal temp constant. Generate heat from metabolic reactions. Activity level of largely independent of external temp.         

Body temp controlled by Hypothalamus. Info recieved from thermoreceptors and hypothalamus  sends impulses along motor neurones to effectors (muscles and glands).

Blood glucose conc monitored by cells in pancreas. Conc rises after eating food containing carbohydrate, falls after exercise as more glucose used in respiration to release energy.        Control: Hormonal system controls blood sugar using insulin and glucagon which are secreted                 by cells in pancreas called 'islets of Langerhans', these contain beta and alpha cells.                   Beta cells secrete insulin, alpha cells secrete glucagon.                                                Insulin: lowers blood glucose conc. Binds to receptors on cell membranes of liver & muscle cells              & increases permeability of cell membranes to glucose, cells take up more glucose.                    Insulin activates enzymes that convert glucose to glycogen (glycogenesis). Liver and                    muscle cells store glycogen in cytoplasm as an energy source.                                    Glucagon: raises blood glucose concentration when low. Binds to receptors on cell membranes            of liver cells & activates enzymes that break down glycogen to glucose(glycogenolysis).           Glucagon also promotes formation of glucose from glycerol & amino acids (gluconeogenesis).  -ve Feedback: Rise in blood glucose conc- Pancreas detects change. Insulin secreated and                  glucagon secretion stops. Liver & muscle cells respond & take up glucose,                                  glycogenesis is activated & cells respire.                                                                     Fall in blood glucose conc:Pancreas detects change. Glucagon secreted and insulin secretion          stops. Liver cells respond & glycogenolysis & gluconeogenesis activated, cells respire less.

Cycle lasts 28 days in humans. It is a cycle of physiological changes in which the female body prepares for reproduction.

Menstrual hormones:                                                                                                                           Follicle-stimulating hormone (FSH)- stimulates the follicle to develop                                           Oestrogen- stimulates the uterus lining (endometrium) to thicken                                                  Luteinising hormone (LH)- stimulates ovulation and stimulates corpus luteum to develop                Progesterone- maintains thick uterus lining, ready for implantation of an embryo

Cycle:                                                                                                                                          FSH anf LH are secreted by the anterior pituitary gland in the brain. Oestrogen and                                      progesteroneare secreted by the ovaries.                                                                  FSH stimulates follicles to develop and oestrogen causes endometrium to thicken.                      LH causes ovulation, progesterone maintains a thick endometrium and remains high during                          pregnancy. It decreases when there is no pregnancy.                                                  Progesterone and oestrogen inhibit FSH. Progesterone has a negative feedback mechanism                           to FSH and LH. LH has a positive feedback mechanism to oestrogen.

Genes: sections of DNA found on chromosomes. Genes code for proteins (polypeptides). Order of bases in gene determines order of amino acids. Each amino acid is coded for by sequence of three bases (triplet) in a gene. Sequence of bases in a section of DNA is a template that is used to make a protein during protein synthesis.

DNA molecules found in nucleus of cell. Ribosomes synthesise proteins and are found in cytoplasm.

RNA: Sugar in RNA nulceotides is ribose sugar, single polynucleotide strand, Uracil replaces thymine as a base.                                                                                                                             mRNA: single strand made in the nucleus during transcription. mRNA carries the genetic                 code from the DNA in the nucleus to the cytoplasm, where it is used to make a protein                 during translation. In mRNA, groups of three adjacent bases are called codons.                       tRNA: single polynucleotide strand folded into a clover shape. H-bonds between specific                    base pairs hold molecule in this shape. Every tRNA molecule has a specific sequence                  of three bases at one end called an "anticodon", They have an amino acid binding site                  at the other end. tRNA is found in the cytoplasm where it is involved in translation.                        It carries the amino acids that are used to make proteins to the ribosomes.

Transcription is the first stage of protein synthesis. An mRNA copy of a gene is made in the nucleus:

1. RNA polymerase attaches to DNA- enzyme attaches to DNA double helix. Hydrogen bonds between two DNA strands in gene break, separating the strands. One strand used as template to make mRNA copy

2. Complementary mRNA is formed- RNA poolymerase lines up free nucleotides alongside template strand. T base replaced by U. Once RNA nucleotides have paired up with their specific bases on the DNA strand they are joined together, forming an mRNA molecule

3. RNA polymerase moves down the DNA strand- RNA polymerase moves along DNA, separating strands and assembling mRNA strand. Hydrogen bonds between uncoiled strands of DNA re-form back into double helix

4. mRNA leaves nucleus- when RNA polymerase reaches a particular of sequence of DNA called a "stop signal", it stops making mRNA and detaches from DNA. mRNA moves out through the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm

Translation is the second stage of protein synthesis. It takes place at ribosomes in the cytoplasm. During translation, amino acids are joined together by a ribosome to make a polypeptide chain (protein):

1. mRNA attaches itself to ribosome and tRNA molecules carry amino acids to the ribosome.

2. tRNA molecule, with an anticodon that is complementary to the first codon on the mRNA,             attaches itself to the mRNA by specific base pairing. A second tRNA molecule attaches itself       to the next codon on the mRNA in the same way.

3. The two amino acids attached to the tRNA molecules are joined by a peptide bond. The first         tRNA molecule moves away, leaving its amino acid behind.

4. A third tRNA molecule binds to the next codon on the mRNA. Its amino acid binds to the first       two and the second tRNA molecule moves away. This process continues, producing a chain of     linked amino acids (polypeptide chain), until there is a stop signal on the mRNA molecule.

5. The polypeptide chain (protein) then moves away from the ribosome and translation is                   complete.

Nonsence Mutation- change of a base result in the formation of a 'stop' codon.

Mis-sence Mutation- change of a base results in a new codon being formed.

Silent Mutation- change in a base that results in no change to the codon formed.

Deletion Mutation- when a base is deleted from a sequence, causing a'frame-shift'.

Causes of Mutation: radiation, chemicals that alter DNA structure or interfere with transcription.

Genetic control of cell division: Proto-oncogenes stimulate cell division, and tumor                                                                 suppressor genes slow down cell division. 

Role of proto-oncogenes: when these genes are mutted they can cause excessive cell division                                           (form cancerous cells).

Role of tumor suppressor genes: when mutted they can become inactive and therefore will not                                                       slow down cell division cycles.

All cells contain the same DNA but in different cells different genes are expresses or 'switched-on'. some genes may be permanently switched on or off or only temporarily expresses or not.

Totipotent cells: These are cells which can mature into any form of body cells, such as                                         embryonic stem cells where all genes have the potential to become active.                                   Once cells have matured and specialised they can no longer develop into other                             cells and so lose their totipotency; the only cells which are still totepotent in                               mature animals are adult stem cells.

Stem cells: stem cells are undifferentiated dividing cells that occur in adult animal tissues ans                       need to be constantly replaced. They are found in teh inner linign of the small                               intestine, in the skin and in the bone marrow, which produced red and white blood                         cells.

Effect of Oestrogen: Oestrogen is a hormone that can affect transcription by binding to a                                            transcription factor called an oestrogen receptor & forming an oestrogen-                                     oestrogen receptor complex.                                                                                                     The complex moves from cytoplasm into nucleus where it binds to specific                                   DNA sites near start of target gene.                                                                                           The complex can act as an activator or a repressor & this depends on the                                   type of cell and the target gene. So, the level of oestrogen in a particular                                     cell affect the rate of transcription of target genes.

siRNA can interfere with both the transcription and translation of genes. siRNA affects translation             through a mechanism called "RNA interference":                                                                       Their bases are complementary to specific sections of a target gene and the mRNA that is            formed from it.                                                                                                                        How: In the cytoplasm, siRNA and associated proteins bind to the target mRNA.                                 Proteins cut up the mRNA into sections so it can no longer be translated.                                   So, siRNA prevents the expression of the specific gene as its protein can no longer                            be made during translation.

Reverse transcriptase-mRNA is used as a template to make lots of DNA.                                               -reverse transcriptase makes DNA from an RNA template -> the DNA produced it called                          complementary DNA (cDNA.)                                                                                         -DNA is isolated & mixed with free DNA nucleotides and reverse transcriptase.                            - reverse transcriptase forms cDNA. double stranded DNA formed using DNA polymerase                          and free nucleotides.

Restriction Endonucleases: some sections of DNA have palindromic sequences -> restriction                                                enzymes recognise these patterns.                                                              - DNA sample incubated with reverse transcriptase -> cuts DNA at specific sites.                        - leaves sticky or blunt ends.

Polymerase Chain Reaction (PCR): make millions of copies in a few hours                              - reaction mixture set up containing; DNA sample, free nucelotides, primers, DNA polymerase      - heated to 95oc to break hydrogen bonds between strands of DNA                                            - cooled to 55oc so primers bind to strand                                                                                - heated to 72oc so DNA polymerase lines up free floating nucleotides along template strand        - complementary strand formed.

In vivo cloning: - DNA fragment isnserted into vector & vector is cut open using same restiction                                    enzyme as fragement, mixed together with DNA ligase forms recombiant                                    DNA.                                                                                                                               - vector transfered into host cells,  vector containing recombinant DNA                                                encouraged to take up vector, host cells that take up vector are said to be                                     transformed.                                                                                                                  - identify transformed host cells by marker genes, only genes containing the                                         marker gene will survive and grow.

Recombinant DNA: Produces organisms which have been transformed to benefit humans.

Benefits: agriculture- produce high yielding crops, more nutrious & help combat malnutrition and                                  famine.                                                                                                                 industry- some processes use biological catalysts, these can be transformed to                                        produce large quantities for less.                                                                               medicine- drugs and vaccines produced from transformed organisms so they are                                          produced in large quantiies and quickly, reduces costs. 

Concerns: agriculture- monoculture, vulnerable to disease, possibility of 'superweeds' (resistant                                      to herbicedes).                                                                                                    industry- people don't have a choice whether they want to consume food thats                                          genetically engineered or not.                                                                                      medicine- companies that own techniques may limit its use, prevent people from                                         saving others lives, designer babies.

Involves altering defective genes (how depends on whether its caused by a dominant or recessive allele) by new alleles are inserted using vectors e.g. plasmids.

2 types of gene therapy:                                                                                                                    somatic- altering alleles in body cells, therapy targets epithelial cells lining the lungs                   Germ line- altering alleles in sex cells, means every cell of the offsrping will be effected                                 by the therapy so they won't suffer from the disease.

advatanges:                                                                       Disadvantages:

- prolong lives of people suffering from diseases             - effects of treatment short lived

- better quality of life                                                    - need multiple treatments

- people can have offpsring without disorder                   - difficult to get allele into specific gene

- decrease number of sufferers                                     - trigger immune response against allele

DNA probes: used to locate genes or to see if a person contains a mutated gene.                                            -short strands of DNA - specific base sequence thats complementary to target                             gene binds/anneals to target gene, if present in a sample DNA probe is labelled so                       it can be detected.

Restriciton Mapping: (most genes too long to sequence -> so cut into sections and then put back together) uses restriction endonucleases to sequence parts of DNA.                                               1) different restriction enzymes used to cut labelled DNA into fragments                                       2) DNA fragments separated using elctrophoresis                                                                       3) size determines relative cut locations                                                                                     4) resrtiction map of original DNA made

Gene sequencing: used to determine order of bases using the chain termination method.         1) reaction mixture set up containing; DNA template, DNA polymerase, primer, terminators              & free nucleotides                                                                                                             2) tubes undergo PCR: strands are different lengths as they terminate at different points.           3) DNA fragments are separated using electrophoresis.                                                             4) complementary base sequence can be read from the bottom up.

Used to find human diseases are caused by gene mutations e,g. Sickle cell anemia (caused by mutation of heamoglobin gene, alters shape of red blood cells & makes them concave).  However people who have this mutation are protected from malaria -> advantageous in Africa where its common.

DNA probes & genetic screening (used to look for genetic disorders):                                                1) Probe is labelled and used to look for a single gene in a sample of DNA.                                  2) probe used as part of a DNA microarray, screens multiple genes at the same time.                            -glass slide with microscopic spots containing different labelled probes.                                        - sample of human DNA washed over, any attach to probes are seen as flourescent                         when under UV light this means they contain that mutated gene

Genetic counselling- advise patients and relaives about risks of certain genetic disorders,                                             explain what positive results mean and possible methods of treatment

Genomes contain repetitive non coding sequences of DNA, different for each person, these can be compared to other individuals to determine genetic relationship. Used in forensic science and medical diagnosis.

Electrophoreis:                                                                                                                      -sample of DNA obtained from individual & PCR used to make multiple copies of repeated                sequences.                                                                                                                         -end up with DNA fragments where the length corresponds to the number of repeats at a specific       region.                                                                                                                               -flourecent marker added to DNA fragements so they can seen under UV light.                            - DNA mixture placed in the agrose gel (conducts electricity).                                                    - electrical current passed through gel, DNA fragments are -ve charged so they move towards the        positive elctrode.                                                                                                                - small fragments move further as they travel faster.                                                                    - 2 genetic fingerprints can be compared to see genetic relationship.