Brain and Nervous system

The cerebrum - what makes us human

• this is the largest part of the brain
• it is divided into two cerebral hemispheres, left and right
• these are joined by corpus callosum
• the outermost layer has a surface area of 2.5m^2 and it is folded
• it consists of a thin layer of nerve cell bodies known as cerebral cortex
• this area is highly developed in humans than in any other orgnisms
• The cerebrum contols the higher brain functions such as
• concious thoughts and emotional responses
• the ability to override some reflexes
• features associated with intelligence, such as reasoning and judgement

• Two areas of the brain (most found in the left cerebral hemisphere) are associated with understanding language and speaking
• these a Broca's area and Wernicke's area. Damage to these cause problems with understanding language.
• damage to Bronca's area will result with an inability to speak
• damage to Wenicke's area causes trouble understanding language.
• they are connected by a bundle of neurones
• if broke - unable to speak but understand the language
• visual sensory and association - Wernicke's area
• hearing sensory area - Broca's area

The cerebellum - movement and postures

• the concious decision to move voluntary muscle is initiated by the cerebral hemispheres
• the fine control of muscular movements requires a significant level of non-concious operation and involves the cerebellum e.g. walking and riding a bike
• examples - responding to changes in the body position to remain balanced and upright
• judging the position of objects and limbs
• tensioning of muscles in order to manipulate tools effectively
• feedback information on muscle position, tension and fine movement
• Neurones in cerebellum carry impulses to the motor areas so that motor output the effectors can be adjusted appropriately
• often feels like we are on 'auto-pilot' some activties become programmed into the cerebellum e.g. catching  a ball
• the cerebellum contains over half of the nerve cells in the brain

Key role in balance and fine movement

• the cerebellum processes sensory information from
• the retina
• balance organs in the inner ear
• joints
• specialised fires in muscles called spindle fibres which relay information about muscle tension

Hypothalamus

• controls the body's homoeostatic mechanisms
• temperature regulations - input from thermoreceptors
• osmoregulation - input from osmoreceptors
• controls much of the endocrine function because it regulates pituitary gland

Medulla oblongata

• controls non-skeletal muscle eg. cardiac muscle, smooth muscle of the gut
• effectively in control of autonomic nervous system
• contains regulatory centres such as cardiac centre and the respiratory centre
• contains reflex centres for vomiting, coughing sneezing and swallowing

RESPONDING TO THE ENVIRONMENT

• The CNS (central nervous system) is a way of connecting sensors with effectors
• this is significant if living things are to escape predation, control balance and regulate temperature
• the nervous system is made up of the CNS and peripheral nervous system

CNS

• the central nervous system is made up of the brain and spinal cord
• it is made up of grey matter and white matter
• grey matter has billions on non-myelinated nerve cells
• white matter has longer, myelinated axons and dendrons

Peripheral nervous system

• relays impulses from sensors to the CNS
• it then relays impulses from CNS to effectors (motor neurones)
• this peripheral nervous system is divided into sensory and motor systems

Motor system

• the motor system is divided into
• somatic motor neurones - impulses from the CNS to skeletal muscle which are under voluntary concious control
• autonomic motor neurones - impulses from the CNS to cardiac muscle, smooth muscle in the gut to glands, involuntary (subconscious) control

Somatic v Autonomic

• Autonomic neurones are non-myelinated
• Somatic neurones are myelinated
• Autonomic connections to effectors consists of two neurones (connect at a ganglion)
• somatic connections to effectors consist of one
• autonomic
• independent of concious control
• controles homoeostatic mechanisms
• autonomic motor neurones occur in 2 types
• sympathetic
• dilates pupils
• no effects on tears glands
• accelerates heart, constrict arterioles
• dilates bronchi
• relaxes bladder
• most active in times of stress
• the neurones of a pathway are linked at a ganglion just outside the spinal cord. pre-ganglionic neurones are very short
• post-gaglionic neurones secrete noradrenaline t the end of the synapse etween neurone and effector 
• parasympathetic
• constricts pupil
• stimulates tear glands
• inhibits heart, dilates arterioles
• constricts bronchi
• contracts bladder
• most active in sleep and relaxation
• the neurones of a pathway are linked at a ganglion within the target tissue. pre-ganglionic neurones carry considerable in length
• post-ganglionic neurones secrete acetyl-choline at the synapses between neurone and effector

Why plants respond to the environment?

Plants responds to a stimuli

• When a plant responds to a directional stimulus by a growth movement it is known as tropism
• If growth is towards the stimulus it is known as positive tropism
• if growth is away from the stimulus it is described negative tropism

Tropisms

• Light
• response: phototropism: eg. shoots grow towards a light source (positively phototropic)
• Gravity
• Geotropism: e.g. shoots grow away from gravity (negatively geotropic) but roots grow in the direction of gravity (positively geotropic)
• Chemicals
• Chemotropisim: e.g. pollen tubes grow down style attracted by chemicals
• Water
• hydrotropism: e.g. roots grow towards water (positive hydrotropic)

Hormones

• Auxins e.g. IAA
• promote cell elongation
• inhibit growth of side shoots
• inhibit lead abscission (leaf fall)
• Cytokinins
• promotes cell division
• Gibberellins
• promotes seed germination and growth of stems
• Abscissic acid
• inhibits seed germinationa nd growth
• causes stomatal closure when plant is stressed due to low water availibility
• ethene
• promotes fruit ripening

Growing regions

• Growth only happens in particular places in plants called meristems
• where there a groups of immature cells capable of dividing
• apical meristems - located at the tip/apex of roots and shoots, lengthening growth
• lateral bud meristems - found in the buds, could give rise to side shoots
• lateral meristems - found in a cylinder near the outside of roots and shoots widening growth

voluntary muscle - skeletal muscle brief notes

• muscles attach to bones by tendons - which are made of collagen
• bones to bones = ligaments
• muscles work in pars - oppose each other - antagonistic 

complex joing e.g. wrist has whole range of movement you need a complex series of muscles = synergist
if a join does a lot of movement it needs to be lubricated - use synonial fluid - made by the synorial membrane

skeletal of voluntary muscle

muscle is made up of bundles of muscle fibre and each muscle fibre is a giant cell with many nuclei

each muscle fibre is made up of bundles of myofibrils each myofibril is made off bundles of myofilaments which are proteins, myosim and actin

became myofils are inside giant fibre they can be called organelles

how muscles contracts - sliding filament theory and power stroke

Actin = globular protein which join together like string of heads

2 actins twist around each other - they have binding sites to the myosin head

troponin has 3 binding sites: 1 to troponin and actin and ca^++

POWER STROKE

• nervous impulse arrives at the neuromuscular junction an releases acetyl-choline 
•  DEPOLARISES 
• sarcolemma going into the centre of cells to T tubes - releases calcium ions from sarcoplasmic reticulum
• calcium ions binds to the troponin 
• troponin moves tropomyosin exposing thebinding sites on the actin
• myosin head flips through 45 degrees = power stroke
• pulling the actin
• ATP binds to the head - head = ATPase - ATP > ADP + phosphate > eergy
• energy unbinds the head to the binding site in ATP - head flips back to bind to next binding site
• this continues to happen power stroke is the flipping of the head
• actin is made to slide over myosin
• sarcomere - Z - Z shortens from 2.5 um to 2 um
• after contraction calcium ions move back to sarcoplasmic reticulum by active transport

• when myosin head binds to the actin band is known as cross link
• as the muscle contracts the A band always stays at thesame length
• H band gets shorter and may disappear
• I band - actin on its own will get shorter
• Z-Z = sarcomere shortens

Fight - flight - scared

• e.g. heart rate increase, breathing rate increases, depth increases, pupils dilate
• release endorphins in brain (natural pain killers)
• stressor - stimulus that causes stress
• humans are intelligent - so we can percieve stress e.g. when OFSTED come we know theyre not going to kill you
• percieve by cererum
• sends mpulse to the hypathalamus
• sympathetic nervous system stimulated release of adrenaline from adrennal medulla
• hypathtlamus releases a hormone aka CORTICOTROPHIN RELEASING FACTOR into the pitutitary - pituitury release adrenocorticotrophic hormone
• this makes adrenal cortex release more corticotrophic hormones

Hypathalaus - nervous tissues - release hormones

• lots of ways to animal deals with threats/stress
• animals deal w/ stress in different ways
• e.g. snakes place dead so they wont be eaten by the eagle
• some reptiles camouflage
• stress/hurting/digestion - are interlinkes
• stress-stomach ulcer

a2 biology: muscles

Muscles - three types

1. cardiac muscle cell
2. skeletal muscle cell
3. smooth muscle cell

Structure

• they are made up of elongated cels called fibres
• contraction is possible because the fibres contain filaments
• these filaments are made up of the proteins actin and myosin.

Involuntary muscle (smooth)

• this muscle is innervated (distrubution of nerves to an organ or body part) with neurones
• these neurones are from the autonomic nervous system
• as a result they are not under voluntary (concious) control

Types of smooth muscles

• Walls of intestines
• arranged in circular and longitudinal bundles
• Peristalsis - moves food along the intestines
• Iris of the eye
• circular and radial bundles
• controls the intensity of the light entering
• contraction of radial muscles dilates the pupil
• contraction of circular muscle constricts the pupil
• Walls of arteries and around arterioles' wall and cervix of uterus
• circular bundles
• important in temperature regulation, regulation of BP and redirecting blood flow
• contraction narrows vessel diameter
• relaxation causes dilation

Smooth muscle cells

• They are not striated like voluntary and cardiac muscle
• they are described as being 'spindle shaped'
• they contain small bundles of actin and myosin and a single nucleus
• when relaxed they are 500 µm and 5µm wide
• contraction is slow but the muscle tires very slowly

CARDIAC MUSCLE

• these are three types of cardiac muscle
• atrial
• ventricular
• specialised excitatory and conductive muscle fibres
• it contracts continuously, powerfully and without fatigue
• contraction of atrial and ventricular muscle is similar to skeletal muscle but for longer
• the excitatory and conductive fibred contract feebly
• they conduct electrical impulses and control the rhythmic heartbeat
• some cardiac muscle is myogenic
• capable of stimulating contraction without a nerve impulse
• cardiac cycle
• initiation of this rhythm comes from a patch of specialised excitatory and conductive muscle fibres in a small part of the right atrium
• this is called sino-atrial node (S.A.N)
• waves of electrical activity spread out rapidly over oth atria.
• the atrioventricular septum between the atria and the ventricles does not conduct the cardiac impulse from SAN
• another node made of specialised excitatory and conductive muscle fibres, the atrioventricular node (AVN) and t picks up atrial impulse
• this is transmitted along a bundle of modified cardiac fibre in the inerventricular septum
• this bundle of fibres is called the bindle of His
• when the impulse reaches the apex of the heart it spreads rapidly up the ventricular walls in a network of conductive fibred called the purkyne fibre

Role of autonomic nervous system

• neurones of the autonomic nervous system can carry impulses to the heart and regulate the rate of contraction
• sympathetic stimulates an increase
• parasympathetic stimulates a decrease
• Intercalated discs
• these are areas where adjacent cardiac muscle cells meet
• they are cell membranes with gap junctions with free diffusion ions
• this allow action potentials to pass easily and quickly

Voluntary (skeletal/striated) muscle

• Result in the movement of the skeleton at joins
• muscle cells form fibred about 100µm in diameter
• these contains several nuclei
• Each fibre is surrounded by a cell surface membrane called sarcolemma
• muscle cell cytoplasm is called sarcoplasm
• contains following organelles
• many mitochondria
• extensive sarcoplasmic reticulum
• a numer of myofibrils
• Myofibrils
• these are contractile elements
• each consists of a chain of smaller contractile units called sarcomeres
• this is the smallest contractile unit of a muscle
• within myofibrils there are two types of myofilaments
• thin actin
• thick myosin

The sarcomere

• the span from Z-line to the next is the sarcomere
• relaxed its around 2.5µm and shorter when contracted
• Z line gets closer durig contraction

Actin

• thin filaments are two strands
• mainly actin couled around each other
• each strand is made up of actin sub units
• tropomysin coils around actin to reinforce it
• a troponin complex is attached to the tropomyosin
• each troponin consist of 3 polypeptides (binding sites) for
• actin
• tropomyosin
• calcium ions

Myosin

• thick filaments arranged as bundles of protein
• each molecule is made up of a tail and two heads
• each filament consists of many myosin molecules with heads sticking out from opp ends

Succession

• Primary succession
• Begins in a place without soil
• sand dunes
• sides of volcanoes
• landslides
• flooding/land left after glaciation
• Starts with the arrival of living things such as LICHENS that do  not need soil to survive (called PIONEER SPECIES)
• Lichens - mutualistic relationship between algae and fungus
• algae photosynthesis - fungus absorbs water and minerals and cling onto rocks
• Soil starts to form as lichens and the forces of weather and erosion help break rocks into smaller pieces
• when lichens die, they decompose, adding small amounts of organic matter to the rock to make soil
• simple plants like mosses and ferns can grow in the new soil
• the simple plants die adding ore organic material
• the soil layer thickens and grasses and windflowers and other plants begin to take over
• these plants die thus more nutrients added to the soil
• shrubs and trees can survive
• insects smalls birds and mammals have begun to move in
• what was once a bare rock now supports a variety of life
• Secondary succession
• begins ina place that already has soil and was once a home of living organisms
• occurs faster and has different pioneers species than primary successin
• eg. after forest fires
• Climax community
• a stable group of plants and animals that is the end result of succession pricess
• does not always mean big trees
• grasses in prairies
• cacti in deserts

Galapagos islands - effects of human activities

• Charles Darwin visited the Galapagos island in 1835
• Native species of Galapagos
• Darwin's finches
• Giant tortoises
• Land iguanas
• Galapagos are the best conserved and have the highest number of native species.
• For these reasons, they are a world heritage site since 1978.
• Unfortunately, 50% of vertebrates and 25% of plant species are endangered.
• The population of Galapagos has grown in response to developing tourist trade
• Effect of human activities on the animal and plant population in the Galapagos Islands
• Habitat disturbance
• increased population has place demands on water, energy and sanitation
• more waste pollution
• demand for oil has increased
• an oil spill in 2001 had adverse effect on marine and coastal ecosystems
• increased pollution, building and conversion of land to agriculture have caused destruction. (Forests of scalesia trees and shrubs has been eradicated for agriculture)
• Over exploitation of resources
• harvesting whales and seals to sell internationally
• giant tortoises een killed and eaten (200, 000 tortoises taken in less than half a century)
• fishing for exotic species in 1990s have depleted population
• depletion of sea cucumber population has a drastic effect on under water ecology
• demand for shark fin had led to death of 150 000 sharks each year
• introducing new species
• deliberately brought in
• humans
• goats
• one of the most damaging species
• eats Galapagos rock purslane
• out competes tortoise for grazing and trampling on their food supply
• changes habitat reduced tortoise nesting sites
• cats
• fruits and veg
• unintentionally brought in
• insects
• diseases (malaria, bird flu etc)
• Charles Darwin research centre adopted strategies to prevent the introduction and dispersion of introduced species
• they have instigated a quarantine system, they search boats for foreign species
• natural predators have been exploited e.g. ladybirds to control a scale insect
• culling wild goats and pigs
• educating local people
• 
  

A2 biology: Ecosystem

Ecosystem - an interacting community of organisms, and the environment in which they live and with which they interact.  (Can be larger, e.g. African grassland, or small, e.g. pond)

Habitat - a place where an organism lives (e.g. an oak tree)

Population - a group of organisms of the same species which live in the same place at the same time and can interbreed with each other.

Community - all the populations of different species wo live in the same place at the same time and can interact with each other e.g. the woodland made up of a community with different trees, plants and animals etc.

Niche - the role o the organism in the ecoystsem. e.g. oak tree, produces O2, provides food a shelter for organisms, takes in CO2

Ecosystems are dynamic

• Ecosystems are constantly changing
• physical changes e.g. temperature
• changes in population due to predation disease etc
• human interferance
• pollution
• changes in soil condition
• Biotic and abiotic factors are constantly chnaging, a change in one factor can affect others

A2 Biology: Cloning

Cloning

• Genes cellsor whole organisms carrying identical genetic material
• Occurs naturally in
• identical twins
• plans which reproduce asexually
• bacteria replicating though binary fission

Asexual reproduction

• Prokaryotes divide by binary fission
• the DNA replicated and the cell divides
• Two cells are genetically identical 
• The basis of asexual reproductions in nearly all eukaryotes is mitosis
• the genetic material replicated to separated to form two nuclei
• the nuclei contains exact copies of the original DNA
• the cells splits to produce two daughter cells that are cloned offspring
• Advantages
• quick - reproduces rapidly - take advantage of the environment
• alternative if sexual reproduction fails or is not possible
• all offspring have the genetic information to enable them to survive
• Disadvantage
• it does not produce genetic variation
• therefore if the environment changes or a new disease is introduce then they are all equally susceptible.

Artificial vegetative propagation 

• taking cuttings
• section of a stem is cut between the leaf joints
• end treated with plant hormones
• plnted = forms ne plants
• grafting
• shoots section is joined to an already growing root and stem
• the graft grows and is genetically identical to the parent plant, but rootstock is genetically different
• advantages
• plants with useful features are identified for growth
• some have to be grown this way - bananas have to be cloned because cultivaed bananas are sterile
• farmers know what features the plant will have - yield, taste, disease resistance etc
• cost reduced because all the crop can be harvested at the same time
• faster
• disadvantages
• plants equally susceptible to new pests or disease
• crops are grown in specific areas and are divided by a certain distance to limit this effect

CLONING ANIMALS

• a cloned animal is one that has been produced using the same genetic information as another animal
• such an animal has the same genotype as the donor organism
• nuclear transfer - dolly the sheep

• splitting embryos
• an embryo can be genetically manipulated
• IVF using the sperm and egg of high value ales and females
• +ve
• high value animals produce in large numbers
• rare animals cloned and preserved
• genetically modified animals can be quickly reproduced
• -ve
• high value animals not produced with animal welfare in mind
• genetic uniformity reduced ability to cope with changes in the environment
• it is unknown how the process effect the long term health of the animals

Non-reproductive cloning

• this is the use of cloned cells to regenerate cells, tissue and organs to replace those that become damages
• +ve
• no rejection by the immune syste
• cloning and cell culture could end the wait for transplantation
• cloned cells are totipotent - generate any cell type (some diseses cannot be treated by transplant)
• likely to be less dangerous
• possibilities include:
• regeneration of heart tissues after a heart attack
• repair or nervous tissues destroyed by diseases such as multiple scleorosis
• repairing the spinal cord
• 
  

A2 Biology: Biotechnology

Biotechnology involved the exploitation of living organisms or biological processes to improve agriculture, animal husbandry, food science, medicine and industry

Food production

• Yoghurts and cheese
• produced by bacterial growth in milk
• this chnages the texture and flavour
• the bacteria prevent the growth of those bacteria that caue spoilage
• this helps preserve ood
• 'Qourn'
• produced by the growth of a fungus 'Fusarium'
• The fungal mass (mycelium) is processed and shaped into food
• Soy Sauce
• Roasted soya beans are fermented with yeast of fungus such as Aspergillus.

Drugs and pharmaceuticals

• Penicillin
• this is a product of the growth of a fungus called Penicillium.
• It is a by-product of the organisms metabolism
• this is isolated from the growth medium and is used as an antibiotic
• Insulin
• Bacteria such a E.coli are genetically modified to carry human insulin gene
• they secrete insulin as they grow

Bioremediation of waste products

• a variety of bacteria and fungi use organic waste in the water as nutrients and make wast harmless
• e.g. Fusarium grown on corn steep liquor, a waste product of the corn milling industry.

Why use bacteria and Fungi?

• grows rapidly in favourable conditions
• can produce chemicals or proteins that are released into the surrounding medium and ce be harvested
• can be genetically modified to produce specific products
• grow well at relatively low temperatures
• can be grown anywhere in the world - not climate dependant
• generated products that are in a pure form than those generated via chemical processes
• can often be grown using nutrient materials that would otherwise useless or even toxic to humans

GROWTH CURVE

What is a culture?

• it's a growth of micro-organisms
• it may be pure culture (single species) or mixed culture (mix of species)
• they can be cultured in liquid broth or solid nutrient agar gel.

Lag phase - organisms adjusting to conditions, cells active but not reproducing. Population is fairly constant

Log phase - population size doubles each generation. plenty of space and nutrients to reproduce.

Stationery phase - nutrients level decrease, waste products builds up. Death rate = production rate

Death phase - nutrients exhaustion, increased level of toxic waste products. Death rate > reproduction rate.

FERMENTATION

• Fermentation refers to the culturing of micoorganisms
• they could grow both aerobically and anaerobically in tanks called fermenters

Fermenters

• growth of an microorganism on an enormous scale
• begins with a 'start culture' a small pure culture from whicl all microorganis will grown
• conditions
• temperature
• type and tie of addition of nutrients
• O2 concentration
• pH

• Batch culture
• microorganisms mixed with specific quantity of nutrients then grown for a fixed period, no further nutrients added
• advantages and disadvantages
• growth rate slower
• easy to set up and maintain
• if contaminated, one batch is lost
• lless efficient - not operating all the time
• useful for producing secondary metabolites
• Continuous culture
• microorganisms mixed with nutrients and nutrients are added continuously  with products removed continuously throughout the process
• advantages and disadvantages
• growth rate higher
• difficult to set up and maintain
• if contaminated, huge volumes lost.
• ore efficient, operated continuously
• useful fro primary metabolites.
• Aseptic technique - asepsis
• unwanted micro-organisms can contaminate the fermentation process
• to avoid this, aseptic technique ensures contamination of the culture does not occur
• contamination may result in products being unsafe
• unwanted micro-organisms
• compete with culture micro-organisms for nutrients and space
• reduce the yield of the product
• may cause spoilage, produce toxic chemicals or destroy the culture micro-organisms

Metabolism and metabolites

• Metabolites include:
• chemicals such as hormones and enzymes
• waste products e.g. CO2, urea and O2
• these can be nutrients required by other organisms
• primary metbolites
• these are produced by organisms as part of its normal growth
• amino acids
• proteins
• enzymes
• ethanol
• lactate
• secondary metabolites
• these are produced by the organism and are not part of its normal growth
• antibiotic chemicals
• produced y a small number of microorganisms

Industrial enzymes

• Commercial use of enzymes
• Pectinase can be used in fruit juice extraction
• Metabolic enzymes in the bacteria A. niger produce citric acid used in detergents
• Downstreaming
• isolated enzymes can be produced in large quantities through biotechnology
• their extraction from the fermentation medium is known as downstream processing
• this is their separation and purification
• Immoilising enzymes
• when using enzymes in industry they need to be removed after they have served their purpose
• this can be a costly process
• it is possible to immobilise enzymes and prevent them from mixing
• immbolisation
• this is a technique were enzyme molecules are held, separated from the reaction mixture
• substrate molecules can bind to the enzymes and the products are formed go back into the reaction leaving the enzymes in place
• methods
• adsorption
• covalent bonding
• entrapment
• membrane separation 

A2 Biology: Roles of genes and environment in evolution

• The Hardy-Weingberg equation is used to show that population changes over time. (they evolve)

Environmental resistance: combined action of biotic and abiotic factors that limits the growth of a popuation.

Selection pressure: 

• environmental actor that confers greater chances of surviving and reproducing on some members of the population than others
  e.g. Rabbits that are well camouflaged are more likely to escape predation, survive, reproduce and pass on favourable (camouflaged) genes to offspring.
• Selection pressure in this case is predation
• it reduces the chances of white or black coat being passed on
• this keeps the population stable = stabilising selection
• If the environment changes - becomes colder, ore snow - rabbits with white fur would have selective advantage. White rabbits are more likely to survive, reproduce and pass white alleles to the next generation.
• frequency of white alleles would increase  = directional selection
• leads to evolutionary change.

Types of selection

• Driving force behind evolution is natural selection and this occurs in three main ways
• stabilising selection
• most common
• a response to a stable environment
• e.g. birth weight
• under weight babies are less likely to survive
• overweight babies are likely to get stuck during birth killing not only themselves but also their mothers.
• The result is that the population graph gets narrower and taller as selection agaisnt mutations takes place
• bottle neck event - occurs when a population is reduced to just a few breeding individuals (e.g. cheetahs)
• though the total population may later recover, they will all be descendants of the few originals and so will have a much smaller gene pool than the original population.
• directional selection
• results ina population of new trait
• takes place whenever a change occurs in the environment
• an evolutionary force of natual selection
• e.g. resistance. Wararin resistance in rats, DDT resistance in mosquitoes or antiiotic rsistance in bacteria. Resistant individuals soon become the dominant type within the population
• disruptive selection
• less common
• results in two distinct populations
• eventually these two forms may become so distinct they become new species

Isolating mechanism

• A large population of organisms may be split into sub groups that are prevented from interbreeding by
• geographical barriers e.g. rivers, mountain range
• seasonal/temporal barriers e.g. climate
• reproductive mechanism

Genetic drift

• change in allele frequency in a population, as some alleles pass to the next generation and some disappear
• large changes in small populations
• as the size of the population decreases the degree of fluctuation increases

SPECIES

Basic classifcation system

• Domain          Eukaryotes
• Kingdom        Animalia
• Phylum          Chordates
• Class              Vertebrata
• Order             Mammalia
• Family            Primates
• Genus            Great Apes
• Species           Home sapiens

Biological species concept

• a group of similar organisms that can interbreed and produce fertile offspring
• problems with this definition
• some species do not reproduce sexually
• some members of the same species look very different  (e.g. gender)

Phylogenetic species concept

• a group of organisms that have similar
• morphology
• physiology
• embryology
• behaviour
• and occupy the same ecological niche
• Closely related organisms will have similar DNA
• DNA analysis is carried out to compare particular base sequences (haplotype)
• Any differences  in bases is expressed a % divergence
• A clade is a group of all the organisms that share a single common ancestor and therefore have the similar DNa and features. 
• aka a monophyletic group e.g. A single ancestor and all its descendants

Cladistics

• based on evolutionary ancestry (phylogentic relationships)
• it does not use a fixed number of level such as kingdom, phylum and class
• whereas taxonomic classification focuses on similarities between organisms
• it include both monophyletic and paraphyletic groups

• Use molecule analysis e.g. DNA/RNA sequencing
• computer programs to represent evolutionary tree of life
• makes no distinction between extinct and existing species
• the cladisitic approcach has often confirmed the Linneasen classfication of orgnanisms but has sometime sled to organims being reclassified

Paraphyletic groups

• includes most recent ancestors but not all of its descendants e.g. reptiles
• Class: Reptilia. Reptiles are cold blooded vertebrates which unlike amphibians possess thick, impermeable skin covered y scaled. They have lungs, not gills and usually a three chambered heat. Their eggs are watertight shells. - Paraphyletic as it excludes birds which are descendants of reptiles
• The cl

A2 Biology: Variation

Interspecific variation - it's easy to see how one species of organism varies from another. e.g. elphant from a kangaroo.

Intraspecific variation - less obvious is the distinction between the two individuals of the same species but nevertheless there are small differences (thus no two elephants are found to be identical)

Cause of variation

• variation is the result of either genetic differences or the influence of the environment
• in many cases its a combination of both genetic and environmental factors

Genetic differences

• are due to different genes each individual possesses
• genetic variations arises as a result of
• mutations
• these sudden changes to genes and chromosomes may or may not be passed onto the next generations
• meiosis
• this special form of nuclear division forms the gametes - this mixes up the genetic material before it is passed on to the gametes all of which are therefore different.
• fusion of gametes
• in sexual reproduction the offspring inherit some characteristics of each parent and are therefore different from both of them
• which gametes fuses with which at fertilisation is a random process adding to the variety of the offspring.

Discontinuous variation

• Qualitative difference between phenotypes
• Some characteristics of organisms grade into one another; there are no separate categories but a complete range of values.
• examples
• ear lobe shapes
• ability to role tongue
• blood type
• gender
• due to
• influence of one or more genes
• if greater than one they behave epistatically
• if only one gene then its called monogenic
• different alleles at a single gene locus have large effects on the phenotype
• different gene loci have different effects on the phenotype
• e.g. codominance 

Continuous variation

• due to
• more than one gene - polygenic
• genes provide an additive effect to the phenotype
• different alleles at a gene locus have a small effect
• genes found on different chromosomes
• environmental influences
• affect the way the organisms' genes are expressed.
• the genes set limits but its largely the environment that determines where within those limits the organism lies
• e.g.
• temperature
• rainfall
• soil conditions
• pH
• food availability 
• Variation and selection
• variation and selection is necessary within  population
• selection can be natural or artificial.

Genetic Diagrams

Conventions

• Start by showing parental phenotypes then genotypes then gametes.
• A gene is represented by a single letter, upper case for dominant and lower cas for recessive
• Where a gene has more than two alleles, the gene has an upper case letter and the alleles are denoted in supercript.
• Where this is codominance the same convention applies

MONOHYBRID CROSSES

P1

Trait: Seed shaoe

Alleles: R- Round | r - Wrinkles

Cross: Round seeds x Wrinkles seeds

                  RR       x       rr

They would all be Rr

Genotype: Rr

Phenotype: Round

Genotypic ratio: all alike

phenotypc ratio: all alike

• homozygous dominant x homozygous recessive
• offring all heterozygous (hybrids)
• offspring called F1 generation
• genotypic and phenotypic ratio is all alike

F1 monohybrid cross

Traits: Seed shape

Allels: R- Round | r - Wrinkled

Cross:     Rr       x       Rr ( round seeds x round seeds)

Result:

RR                                   

Rr

Rr

rr

Gentotpes: RR, Rr, rr

Phenotype: Round and wrinkled

G ratio: 1:2:1 (RR:Rr:rr)

P.ratio: 3:1 (3 are rounded and 1 is wrinkles)

SEX LINKAGE

• a characteristic is sex linked if the gene that codes for it is found on one of the sex (X and Y) chromosomes

Convention

• when dealing with sex-linked characteristiccs in humans, the genotype of the male is XY (heterogametic) the female XX (homogametic)
• the sex linked allele is then denoted in supercript

Haemophilia A

• several factors are needed for blood to clot
• one of these is factor VIII - found on the X chromosome
• in it s recessive form the allele produces a non functional protein, blood takes longer to clot
• male only have on X chromosome
• if this has the recessive allele they will have haemophilia
• only having on allele for a characteristics is aka hemizygous

X^H= allele for normal factor VIII

X^h = allele for non functioning factor VIII

Cross between a carrier female and normal male
Results:

X^HX^H - normal female

X^Hy - normal male

X^HX^h - carrier female

X^hy - male with haemophilia

Duchenne muscular dystrophy (DMD)

• gene for muscle protein, dystrophin is on th X chromosome
• it is needed in muscular contration
• boys with te disease develop muscle weakness in early childhood and are usually wheelchair bound by age 10
• death often occurs due to complications of muscle degeneration (skeletal and heart uscle) by the early 20s

CODOMINANCE 

• this means thatthe homozygous dominant (AA) and the heterozygous dominant (Aa) both have the same phenotype = look the same
• however, in many cases when considering a pair of characters
• two alleles of a gene have an effect when they are present together
• when choosing symbols to represent co-dominant alleles it would be misleading to use a capital and lower case letters as this would suggest that the one with the cap was dominant
• instead, a capital letter is chosen to represent the gene and then two different superscript to represent the co dominant alleles
• a good example on incomplete dominance is found in snapdragons with respect to flower colour 

SICKLE CELL ANAEMIA

• the beta-strands of haemoglobin differ by 1 amino acid at position 6 (glutamic acid instead of valine)
• abnormal haemoglobin is de oxygenated and insoluble
• this deforms RBC making them inflexible and often sickle shaped
• they are unable to squeeze through capillaries
• after many oxygenated and de oxygenation cycles the RBC can be irreversibly damaged and sometimes destroyed
• when lodged in capillaries they can block the blood flow
• eventually organs esp heart lungs and kidneys become damage 

Sickle cell heterozygotes

• these individuals produce RBC with half of their haemoglobin normal and half sickled
• normal haemoglobin prevents sickling
• thus heterozygotes are symptomless carriers and at whole organism level this condition is considered to be recessive
• however, a molecular and cellular level because both alleles contribute to the phenotypes as observed in RBC it is co dominant

• Normal genotype: H^A H^A
• Sickle-cell gentoype: H^S H^S
• Symptomless heterozygous: H^A H^S

DIHYBRID INHERITANCE

• inheritance of two pairs of contrasting characters is known as dihybrid inheritance
• in pea plants:
• round seeds are dominant to wrinkled seeds
• yellow seeds are dominant to green seeds
• Y = allele for yellow seed coat
• y = allele for green seed coat
• R = allele for round seed shape
• r = allele for wrinkled seed shape
• when pure breeding plants with round, yellow seeds are crossed with plants that have wrinkled green seeds, all of the F1 generation had round yellow seeds
• These plants were allowed to self fertilise or were cross with each other and the resulting seeds were examined
• The expected ratio of 3 dominant to 1 recessive was found for both seed colour and for seed shape
• also, the inheritance of seed colour is independent of the shape of the seed and that nw combo of the characters appear in the F2 generations as well as the parental combination of the charcters

• Dihybrid inheritance is concerned with the inhereitences of the two genes at different loci
• genes that are on difference chromosomes (unlinked) are separated independently, and all combinations of two pairs of genes are possible
• a ratio of 9:3:3:1 is common when two factors are controlled y two independently sorted genes

EPISTASIS

• there are cases where different genes on different loci interact to affect one phenotype
• where one gene masks or suppresses the expression of another gene it is called epistasis
• they may either
• work antagonistically resulting in masking
• the homozygous presence of a recessive allele e.g. aa. may prevent the expression of another allele at a second locus.
• alleles at the st locus are epistatic to the alleles on the 2nd locus these are hypostatic
• work together in a complementary fashion
• recessive epistasis
• this can be seen in the inheritance of flower colour in salvia where two gene loci A/a and / on different chromosomes are involved
• a ration of 9:3:4 is observed
• this ration indicated recessive epsistasis
• the homozygous aa is epistatic to both alleles of gene B/ neither the allel or combiniion for purple  BB/b or the allele combination for pink b can be expressed i there s no dominant allele A present

Apoptosis

Events of apoptosis

• enzymes breaks down the cell cytoskeleton
• cytoplasm becomes dense with organelles tightly packed
• the cell surface membrane changes and small bits called blebs form.
• chromatin condenses and nuclear envelope breaks. DNA breaks into fragments
• the cells breaks into vesicles that are taken up by phagocytosis. the cellular debris is disposed of and does not damage any other cells or tissues

How it's controlled

• Apoptosis is controlled by cell signalling
• some from the inside the cell and some from outside
• these include cytokines made by cells of the immune system, hormones, growth factors and nitric oxide
• nitric oxide works by making the inner mitochondrial membrane more permeable to hydrogen ions
• it would prevent the formation of the proton gradient needed for ATP synthesis
• proteins are released into the cytosol
• these proteins bind to apoptosis inhibitor proteins and allow the process to take place

Apoptosis and development

• apoptosis is an important part of the tissue development. Extensive division and proliferation is followed by pruning through apoptosis. 
• Excess cells undergo apoptosis and their components are reused. Different tissues use different signals to induce it.
• Examples:the removal of ineffective or harmful T lymphocytes during the development of the immune system

How often does apoptosis take place?

• In children between 8-14 years old, 20-30 billion cells per day undergo apoptosis.
• in a year this is equivalent to the total body ass
• in adults the figure is around 50-70 million cells per day
• the rate of cell death should = the rate of mitosis
• however, not enough apoptosis leads to the formation of tumours. 
• too much leads to cell loss and degradation
• cell signalling helps maintain the right balance

Mutations - in depth

A mutation is change in the amount of or arrangement of the genetic material in the cell. They can be chromosomal mutations which involves changes to parts or whole chromosomes. Or, they can be DNA mutations which are changes to the nucleotide base sequences.

What causes mutations?

• During the process of replication, DNA is normally copied exactly so that the genetic material remains the same from generation to generation. However, occasionally changes can occur so that an organism may inherit altered DNA.
• The sudden change that can occur may produce an individual which is obviously different from the rest of the population. e.g. bacteria resistant to penicillin.
• Altered DNA molecules replicates the changed sequences so that the mutant genes are passed on to successive generations. - Such inherited changes are known as mutations.
• Mutation is another source of genetic variability n a population and it can occur spontaneously. 
• Mutant genes tend to be recessive but are transmitted in the normal way
• most mutations are harmful to the organism but some can be useful
• spontaneous mutations are essential for providing a new variation necessary for survival in a changing environment; in other words, it proves raw materials for evolutionary change
• The frequency with which one allele mutates to another is known as the mutation rate or mutation frequency and is measured by their occurrence in a population 
• mutations tend to be rare but the mutation rate can be speeded up by certain factors called mutagens or mutagentic agents which include x-rays, gamma rays and UV light which can damage DNA in various ways
• mutagens also include certain chemical substances which alter DNA by adding or deleting one or more bases in a sequences
• chemical mutagens include nitrous acid and 5-bromouracil

DNA mutations

• during protein synthesis, the sequence of ases in DNA is transcribed into a complementary sequence of bases in RNA which is then translated into a sequence of amino acids
• each sequence of three bases is a code for a specific amino acid, so that if the code is altered, this may result in an incorrect sequence of amino acids
• these changes would therefore result in non-functional proteins or proteins with a different function

Types of DNA mutations

• Point mutations - one base replaces another - also called substitutions
• Insertion/deletion mutations - one or more nucleotide pairs are inserted/deleted from a  length of DNA which causes frameshift
• A gene mutation in which a nucleotide is left out is called a deletion and a mutation in which a nucleotide is gained is called an insertion. 

• The effect on the sequence of amino acids from this small change in the DNA base is great.
• Every amino acid after the change ight be replaced by a different amino acid.
• both base deletion and base insertion have resulted in a shift so that all subsequent codons are altered.
• it is not surprising that mutation can result in the synthesis of a totally different protein

SICKLE CELL ANAEMIA

• The kind of point mutation that causes sickle cell anaemia is called substitution
• this is because the mutation is due to the substitution of one base for another just one place in the DNA molecule (thymine is replaced by adenine)
• the result of this is that the beta-chains of haemoglobin contains the amino acid valine at position 6 instead of glutamic acid
• Effect
• the haemoglobin is less soluble than normal haemoflobin and causes the RBC to become distorted into a sickle shape.
• this has many effects including severe anaemia and a clumping of cells which may lead to heart failure
• sickle-cell anaemia is often fatal before middle age

CYSTIC FIBROSIS

• 70% of the cases if cystic fibrosis the mutation is the deletion of a triplet base pair
• this deletes one amino acid out of a chain of 1480 in the normal polypeptide
• cystic fibrosis produces extra thick and very sticky mucus
• this can accumulate in the lungs and pathogens would normally be removed in the mucus by cilia  but the cilia are unable to move the mucus and thus causing infection - physiotherapy is required to get rid of it

ONCOGENES

• growth- promoting genes called protooncogenes
• these can be changed to oncogenes by point mutation so they cannot be turned off
• oncogenes promote unregulated cell division so this can lead to tumour. 

HUNTINGTON DISEASE

• Huntington disease results from an expanded triple nucleotide repeat
• the normal gene has a repeating CAG sequence above a certain threshold the protein alters sufficiently to cause the disease
• the symptoms are see later in life and include dementia and loss of motor control

Mutations w/ a neutral effect

• A change in the base sequence may produce no change in the organism if
• the mutation is a non-coding region of the DNA
• is a silent mutation - the change in the base does not alter the amino acid sequence
• the change in the organism is not seen as an advantage or disadvantage e.g. taste

Harmful/Beneficial effects:

• Early humans in Africa almost certainly had dark skin
• the pigment melanin protected them from the UV light
• they could however, still synthesise vit D from the action of intense sunlight on their skin
• humans with mutations resulting in paler skin would have been burned or suffered skin caner
• as humans migrated to more temperate areas sunlight was not intense enough to produce sufficient vit D by those with dark skins
• those with the pale mutations would have had an advantage (as a lack of vit D leads t rickets, narrow pelvis etc.)
• the Inuit peoples have not lost all their skin pigments although they dont live in an area with intense sunlight
• however, they eat a lot of vit D rich fish and seal meat.

Homeobox genes

All vertebrates looks very similar in the early stages of their embryonic development. All animals have the same body plan.

Drosophila melanogaster (fruitfly)

• The early steps in fruitfly developments are influenced by chemical gradients within the zygote.
• the gradients are generated by the synthesis of proteins in the eggs before fertilisation
• this uses information from the maternal effect genes
• a (bicoid) protein is most intense at the future head end of the fruitfly embryo
• at this stage, the fruitfly embryo is different from other embryos in that
• as the zygote divides, no cell membrane form
• so the nuclei are free in the cytoplasm rather than being contained within distinct cells forming syncytium
• however, soon the plasma membrane fold inwards around the nuclei in forming single layer of out cells
• After the initial steps in pattern formation have been taken under the guidance of the gradients, the homeotic genes take over the next more detailed stage (stage of development)

• homeotic genes that are amazingly similar in structure and function in all animals = genes that direct the building of bodies according to definite body plans
• homeotic genes code for proteins known as transcription factors which then contol the activity of other genes nearby 
• all of these genes contain identical sequence of 18 nucleotides called the HOMEOBOX which codes for 60 amino acids
• the proteins they code for are able to bind with DNa
• all the genes containing this sequence are called homeoox genes
• a peculiarity of these is that they are arranged along the chromosomes in the same linear order as the region of the embryo they are controlling
• since the discovery f Drosophila homeobox genes have been found in many other species incl humans
• it seems that homeobox genes arose early in evolutionary history and have been guiding embryonic development in animals and plants ever since.

HOX CLUSTERS

• homeobox genes are arranged in clusters called HOX clusters
• Nematodes have 1 HOX cluster, Drosophila have 2 HOX clusters and Vertebrates have 4 HOX clusters
• Increase in number of HOX clusters were probably due to mutations
• this allowed more complex body plans to develop
• by controlling the transcription in the cells, homeobox HOX genes act as aster switches determining cell growth and devlopment

Retinpoic acid and birth defects

• Vitamin A > Retanoic acid > Activates homeobox genes in vertebrates
• Retanoic acid is a MORPHOGEN - a substance that controls the pattern of development
• too much Vitamin A in the 1st month of pregnancy interferes with normal expression of genes and can result in birth defect including cranial deformities.

Mutations

Mutations:

• the arrangement of bases in an individual gene = DNA mutations
• the structure of the chromosome (changes the arrangement of the genes) = chromosome mutations 
• a change in a cell which changes a trait - usually a change in a gene sequence e.g.
• ...AACTAGGGACATTTACG
• ...AACTAGGGCAATTTACG
• can also be gene loss

Causes of mutations:

• radiaition e.g. to UV
• Chemicals e.g. cigarette smokes
• spontaneously 

Types:

• In body cells - can lead to cancer
• In sex cells - can lead to new traits in offspring

• Mutations can occur in gametes and somatic cells
• chance of mutations is between 2-30x10^-7
• faulty DNA can be repaired by specific enzymes
• unrepaired mutations will affect new proteins being synthesised

Point mutations are caused by changes in an individual gene due to miscopying of one or more nucleotides.

Deletion or insertion of a nucleotide result in a frame-shift.

Substitution mutation result in a change of one base

Some mutations can be harmful, beneficial or neutral.

e.g.

Dark skin

- in Africa protects against UV light - less chance of skin cancer

- however, prevents limited amount of UV light reaching skin cells to synthesise vitamin D - could lead to rickets, narrow pelvis (difficulty in child birth) and increased risk of hear disease and cancer

Translation of the Genetic Code: Protein Synthesis

• Messenger RNA is made in the nucleus by transcription from a DNA molecule. 
• A ribosome on the rough endoplasmic reticulum (RER) attaches to the mRNA molecule.
• A transfer RNA molecule arrives and brings an amino acid to the first three bases (codon) on the mRNA.
• The three unpaired bases (anticodon) on the tRNA link up with the codon.
• Another tRNA molecule comes into place bringing a second amino acid
• Its anticodon links up with the second codon (next three bases) on the mRNA
• A peptide bond is formed between the two amino acids
• The first tRNA molecule releases its amino acid and moves off into the cytoplasm
• The ribosome moves along the mRNA to the next codon
• Another tRNA molecules bring in the next amino acid into place
• A peptide bond joings the second and third amino acid to form a polypeptide chain
• The process continues - polypeptide chain gets longer, this continues until termination (stop) codon is reached then the polypeptide is complete