# Biology unit 4 AQA

covering most topics in unit 4

• Created by: Emma
• Created on: 11-06-12 21:50

## Ecosystems

More or less a self contained funtional unit in ecology made up of all interacting biotic (living) and abiotic factors (non living)  in a specific area. Two major processes to consider:

- flow of energy througfh the system

- cycling the elements within the system

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## populations

A group of interbreeding organisms of one species in a habitat at the same time.

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## Community

the organisms of all species that live in the same area

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## Habitat

the place where an organsism normally lives, which is characterised by physical conditions and the species of other organisms present. Within these habitats are microhabitatswhich are smaller units that consist in a habitat.

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## ecological niche

all conditions and resources required for an organism to survive, reproduce and maintain a viable population .

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Three factors to consider using quadrats:

1) size of quadrat - depends on size of plants or animals being counted and how they are distributed within the area.

2) number of sample quadrats to record within the study area - the more quadrats the more reliable the results. The greater the number of species present in the area the greater amount of quadrats are needed.

3) the position of each quadrat within the study area -random sampling must be used.

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## Random sampling

1) lay out 2 long tape measures at a right angle along two sides of the study area

2) Obtain a series of numbers generated by a computure

3) place the quadrats on these coordinates and record the species within it.

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## Systematic sampling along transects

Sometimes better to measure the abudence of distrobution using a systematic rather than random manner.

A line transect is a string or tape stretched across a straight line, any organism that crosses it is recorded.

A belt transect is a ***** ( aprox a metre wide) marked by putting a second line parallel to the first. The species occuring within the belt are recorded.

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## Measuring abundance

Abundance is the number of individuals of a species in a given space. Can be measured in several ways:

- frequency the likelihood of a particular species occuring in a quadrat for example if a species occurs in 15 out of 30 quadrats the frequency of occurance is 50%. A useful method if the species is hard to count, it gives a quick idea of the distrobution of species within the area. However does not provide information on the density and detailed distrobution of a species

- percentage coverage an estimate of the area within a quadrat that a particual plant species covers. useful when the species if diffcult to count or is abundant. Advantages - data collected fast, individual plants dont need to be counted. disadvantages- less useful when where an organism occur in several overlapping layors.

To make reliable sample size must be large. the larger number of samples the more representitive the data will be

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## Mark release recapture techniques

A known number of species are caught, marked in some way, and thern released back into the community. later a given number of individuals is collected randomly and the number of marked individuals is recorded.

estimated pop size = total number of individuals in 1st sample x total number of indivduals in 2nd sample / number of marked individuals recaptured.

technique relies on:

- the mark or label is not lost or rubbed off

- there a few deaths or births within the population

- popultation has a definate boundry so no imigration or emigration

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## population growth curves

a natural population has three phases:

1) a period of slow growth as the initially small number of individuals reproduce slowly.

2) a period of rapid growth where the ever increasing individuals continue to reproduce.

3) a period when the population growth declines until the size remains more or less stable. decline may be due to food supply or increased predidation

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## abiotic factors

temperature, light,  pH, water, humidity

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## intraspecific competition

occurs when individuals of the same species compete with one another for resources such as food, water, breeding sites, ect. it is the avalability of these resourses that determines population size.

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## interspecific competition

occurs when different species compete for resouces such as food, light, water. whre 2 species occupy the same niche one will normally have a competitive advantage over the other. the pop size of this species will increase whilst the other decreases. if conditions remain the same it will lead to removal of the species - competitive exculsion principle

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## predation

Occurs when on organism is consumed by another. in a nature situation the area over which the population can travel is great and therefore prey population falls to a low level but rarley becomes extinct

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## effect of predator prey relationship on population

- predators eat their prey, reducing prey population size

- with less prey avaliable, predators are in greater competition with each other

- predator population is reduced

- with less predators, fewer prey are eaten

- prey population size increases

- with more prey now avaliable as food, the predator population in turn increases

predator prey relationships are not the only reasons for fluctuations in pop size, these pop crashes are important in evolution as they create a selection pressure whereby only those individuals who escape predators and disease reproduce creating a population better adapted to the conditions

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## human population and growth rate

human population like any other organisms has for most of our history been kept in check by food and disease however recent events have lead to the explosion of the human population:

- development of agricultuire

- development of manufacturing and trade that created the industrial revolution

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## factors affecting the growth and size of human pop

-birth rate and death rate

immigration- individuals join population from outside

emmigration - where individuals leave a population

population growth = (births + immigration ) - (deaths +emigration)

percentage population growth rate ( in a given period)  = population change during a period / population at ther start of the period x 100

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## factors affecting birth rate

• economic conditions - countries with lower incomes tend to have higher birth rates
• cultural and religious backgrounds - some countries encourage larger familes and are opposed to birth control
• social pressures and conditions - some countries larger families means increased social standing
• birth control
• political factors - influence through education and taxation policies

birth rate = number of births per year / total population in the smae year x 1000

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## factors affecting death rate

• age profile
• life expectancy at birth
• food supply
• safe drinking water and effective sanitation
• medical care
• natural disasters
• war

death rate = number of deaths per year / toatl population in same year x 1000

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## population structure

age population pyramids:

• stable populations - where birth and death rates are in balance
• increasing population - birth rate high giving a wider base at the bottom of the pyramid and very narrow at the top. countries with less economically developed
• decreasing populaiton - where there is a low birht rate ( narrow base ) and lower morality rate leading to more elderly people (wider apex). usually cxountries which are ecomically developed such as Japan
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## life expectancy

avedrage life expectancy is at the age where 50% of the individuals in a particualr population are still alive.

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## what is energy?

defined as 'the ability to do work'

- takes a variety of different forms eg light, heat, sound, electrical, magnetic, mechanical, chemical and atomic energy

- it cannot be created or destroyed

- it can be changed from one form to another

- measured in joules (j)

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## why do organisms need energy?

• metabolism
• movement
• active transport
• maintenance, repair and devision of cells
• production of substances used within an organism eg enzymes or hormones
• maintenance of body temperature in bird and mammals. these organisms are endothermic and need energy to replace that lost as heat to the environment
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## Energy and metabolism

flow of energy through living systems occurs in three stages:

1) light energy from sun is converted by plants into chemical energy during photosynthesis

2) the chemical energy from photosynthesis, in the form of organic molecules, is converted into ATP during respiration in all cells

3) ATP is used to perform useful work

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## how ATP stores energy

ATP has three phosphate groups. the bonds between these phosphate groups are unstable and so have a low activation energy meaning they are easily broken. when they break they release energy. in living cells it is usually on the terminal phosphate that is removed:

ATP+H20 ----> ADP + Pi + E

Adenosine triphosphate + water ----> adenosine diphosphate + inoganic phoshpate + energy

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## synthesis of ATP

Conversion of ATP to ADP is a reversable reaction therefore energy can be used to add an inorganic phosphate to ADP to re-form ATP. As water is removed in this process it is called a condensation reaction.

The synthesis of ATP from ADP involves the addition of a phosphate. it ocuurs in 3 ways:

1) phosphorylation - takes place in chlorophyll- containing plant cells during photosynthesis

2) oxidative phosphorylation - occurs in mitrocondria during the process of electron transport

3) substrate level phosphorylation - occurs in plant and animal cells when phosphate groups are transferred from doner molecules to ADP to make ATP e.g: formation of pyruvate

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## structure of the leaf

- large surface area- collects as much sunlight as possible

- thin -  most light is absorbed in first few milimetres + diffusion pathway kept short

- transparent cuticle and epidermis - lets light through to mesophyll cells beneath

- long, narrow, upper epidermis cells packed with chloroplasts to collect sunlight

- numerous stomata for gaseous exchange

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## structure of chloroplasts

the grana - stscks of up to 100 disc like structures called thylakoids where the light dependent stage of photosynthesis take place. within these are chlorophyll

the stroma a fluid filled matrix where the light independent stage takes place. within in it are other structures such as grains

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## oxidation

described in three ways

1) loss of electrons

2) loss of hydrogen

3) gain of oxygen

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## reduction

described in thrre ways

1) gain of electrons

2)gain of hydrogen

3) loss of oxygen

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## making of ATP - light dependent reaction

When chlorophyll absorbs light energy it boosts the energy of 2 electrons within this chlorophyll molecule. - Said to be in an excited state. the electrons then leave the chlorophyll molecule and are taking up by a molecule called an electron carrier. Having lost a pair of electrons the chlorophyll molecule is said to be oxidised.

The electrons then pass along a number of electron carriers in a series of oxidation - reduction reactions. these electron carries form a transfer which is in the membrane of the thylakoids. Each new carrier has a slightly less energy than the previous one in the chain and so the electrons loss energy at each stage. This lost energy is used to combine an inorganic molecule to ADP to make ATP.

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## photolysis of water

the loss of electrons from the chlorophyll leaves it short of electrons. if the chlorophyll molecule is to continue absorbing light it must replace the electrons. the electrons are replaced by water molecules which are split using light energy. this photolysis of water also yields hydrogen ions

2H2O ---> 4H+  + 4e-  + O2

Water ----> protons + electrons + oxygen

these hydrogen ions ( protons) are taken up by NADP. the NADP therefore becomes reduced and enters the light independent reaction along with the electrons from the chlorophyll molecule.

The reduced NADP is important as it is a source of chemical energy for the plant. The oxygen by product is used in respiration or is diffused out of the leaf as a waste product.

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## site of light dependent reaction

takes place in the thylakoids.

thylakoid membranes provide large surface area for attachment of chlorophyll, electron carriers and enzymes

a network of proteins in the grana hold the chlorophyll in a precise manner - allows maximum absorption of light

grana membranes have enzyme attached to them

chloroplasts contain both DNA and ribosomes so can quickly and easily manufacture proteins needed for light dependent stage.

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## Calvin cycle

1) CO2 diffuses into the leaf through stomata and dissolves in water around the wall of the mesophyll cells. it then diffuses into plasma membrane, cytoplasm and chloroplast membranes into the stroma of the chloroplast.

2) in the stroma CO2 combines with a 5 carbon compound ribulose bisphosphate (RuBP) using an enzyme

3) the combination produces two molecules of the 3 carbon glycerate 3 carbon

4) ATP and reduced NADP are used to reduce the glycerate 3 carbon to triose phosphate

5) the NADP is reformed and goes back to the LDR, To be reduced again.

6) some triose phosphste molecules are converted to useful organic substances such as glucose

7) most of the triose phosphate molecules are used to regenerate ribulose bisphosphate using ATP from LDR

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## Site of Light dependent reaction

takes place in stroma of the chloroplasts

- fluid of stroma contains all enzymes needed

- the stroma fluid surrounds the grana and so the products of the LDR can easily diffuse into the stroma

- contains DNA and ribosomes so quickly and easily manufacture some of the proteins needed.

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## limiting factors of photosynthesis

light - as light intensity increases the rate of oxygen produced and the rate of CO2 absorbed increases until a point in which it is exactly balanced by the oxygen absorbed and CO2 produced. At this point there is no net exchange of gases in or out of the plant. Known as the light compensation point. a point will be reached where light will have no effect of the rate of photosynthesis due to other limiting factors

CO2 - effects enzyme activity, in particular the enzyme that catalysis the combination of ribulose bisphosphate with CO2 in LIDR.

Temperature - providing no other limiting factors the rate of photosynthesis is directly proportional to the temperature. photosynthesis increases as temperature increase until optinum temperature and then enzymes start to become denatured so rate of photosynthesis decreases.

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## Glycolysis

1) activation of glucose by phosphorylation -before glucose can be split into 2, it must be made more reactive by adding 2 phosphate molecules (phosphorylation) the phosphate molecules come from the hydrolysis of 2 ATP molecules to ADP.

2) Splitting of the phosphorylated glucose- each glucose molecule is split into two 3 carbon molecules known as triose phosphate

3) oxidation of triose phosphate - hydrogen is removed from each of the two triose phosphates and transferred to a hydrogen carrier molecule known as NAD to form reduced NAD

4) the production of ATP - Enzyme controlled reactions convert triose phosphate into another 3 carbon molecule called pyruvate. in the process two molecules of ATP are regenerated from ADP

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## Energy yields from glycolysis

the overall yield from one glucose molecule undergoing glycolysis:

• 2 molecules of ATP (4 molecules of ATP are produced but 2 were used up in the phosphorylation of glucose.
• two molecules of pryruvate
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the pyruvate molecules are actively transported into the matrix of the mitrocondria. it then undergoes a series of changes:

• the pyruvate is oxidised by removing hydrogen. this hydrogen is accepted by NAD to form reduced NAD, which is later used to produce ATP
• the 2 carbon molecule called an acetyl group that ids thereby formed combines with coenzyme A to form a compound called acetylcoezyme A
• A carbon dioxide molecule is formed from each pyruvate

pyruvate + NAD + CoA ---> acetylCoA + reduced NAD + CO2

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## Krebs cycle

•  the 2 carbon acetyl CoA forms the link reaction. it combined with a 4 carbon molecule to produce a 6 carbon molecule.
• this 6 carbon molecule loses carbon dioxide and hydrogens to give a 4 carbon molecule and a single molecule of ATP produced as a result of substrate level phosphorylation
• the 4 carbon molecule can now combine with a new molecule of acetylCoA to begin the cycle again
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## What is produced

• reduced coenzymes such as NAD and FAD. These have the potential to produce ATP molecules and are therefore the important products of the krebs cycle.
• one molecule of ATP
• 3 molecules of carbon dioxide

as 2 pyruvate molecules are produced for each original glucose, the yield for a single glucose molecule is double the quantities above

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## co enzymes

FAD - important in krebs cycle

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## significance of krebs cycle

• it breaks down macromolecules into smaller ones e.g pyruvate into carbon dioxide
• produces hydrogen atoms that are carried by NAD to the electron transport chain for oxidative phosphoryilation. this leads to the production of ATP that provides metabolic energy for the cell.
• it regenerates the 4 carbon molecule that combines with acetylcoenzyme A, which would otherwise accumulate
• source of immediate compounds used to make fatty acids, amino acids and chlorophyll
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## the electron transport chain and mitrocondria

mitrochondria is the site of the electron transport chain. attached to the cristae are enzymes and other products needed in the ETC.

As mitrochondia play a vital role in respiration and the release of energy. they are in greater numbers in the metabolically active cells such as liver. the mitrochondria in these cells have a more densely pack cristae and so provide a large SA for the attachment of enzymes and proteins

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## the electron transport chain

• the hydrogen ions combine with NAD and FAD, which are on the cristae
• The reduced FAD and NAD donate the electrons of the of the hydrogen ions to the 1st molecule in the ECT
• This releases the protons of the hydrogen atoms which are then actively transported across the inner mitochondrial membrane
• the electrons meanwhile pass along the electron transport carrier molecules through a series of oxidation - reduction reactions. t
• the electrons loss energy as they pass down the chain and some of this is used to combine ADP with an inorganic phosphate to make energy. The remaining energy in released in the form of heat.
• the protons accumulate in the space between the 2 mitochondria membrane before they diffuse, through a protein channel, into the matrix
• at the end of the chain the electrons combine with the protons and oxygen to form water
• oxygen is therefore the final acceptor in the chain
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## importance of oxygen being the final acceptor

without it the protons and electrons would 'back up' along the chain and respiration would come to a halt. this is illustrated by the effect of cyanide ( a poison ) it is lethal because it is a non competitive inhibitor if the final enzyme in the ECT. the enzyme catalyses the addition of hydrogen ions and electrons to oxygen to from water. it inhibition causes hydrogen ions and electrons to accumulate on the carries. causing respiration to halt.

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## anaerobic respiration in plants and some micro-org

occurs in organisms such as some bacteria and fungi e.g yeast as well as some higher plant cells, for example root cells under water logged conditions

the pryuvate molecule formed at the end of glycolysis loses a molecule of C02 and excepts hydrogen from reduced NAD to produce ethanol

this has been exploited by humans in the brewing industry. in brewing ethanol is an important product. yeast is grown in anaerobic conditions in which it ferments natural carbohydrates such as grapes into ethanol

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## production of lactate in animals

in the absence of oxygen gylcolysis would usually stop due to reduced NAD accumulates. if gylcolosis is to continue to produce some energy reduced NAD must be removed. To do this each pyruvate molecule produced takes up 2 hydrogen atoms from the reduced NAD produced in glycolysis to form lactate

at some point lactate must be oxidised back to pyruvate - this can either be further oxidised to release energy or form glycogen. - happens when O2 is available again lactate causes cramp and fatigue in muscles.

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## energy yields from anaerobic and aerobic respirati

Energy from cellular respiration is derived in two ways:

• substrate level phosphorylation in glycolysis and krebs. direct linking of inorganic phosphate to ADP to produce ATP
• oxidative phosphorylation in the ECT - indirect linking of inorganic phosphate to ADP to produce ATP using hydrogen from glycolysis and krebs that are carried on NAD and FAD. Cells produce most of their ATP this way
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## Genotype and phenotype

GENOTYPE is the genetic make up of an organism. It describes all of the alleles that the organism contains. Any change in the genotype due to a change in the DNA is called mutation and may be inherited if it occurs in the fromation of gametes

PHENOTYPE is the observable characteristics of an organism -result of the interaction between the expression of the genotype and the enviroment. The enviroment can alter an organisms apperance. Any change in the phenotye that does not change the genotype is calld modification.

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## Genes and alleles

A gene is a section of the DNA ( a sequence of nuleotides bases) that usually determines a characteristic. does this by coding for particular poly peptides. These make up the enzymes needed in the biochemical pathway that leads to the production of the characteristics. The position of the gene on the DNA is called the locus.

An allele is a different form of a gene for example, the gene for the shape of the pea seeds has two alleles one for 'round' and one for 'wrinkled'. only one allele of a gene can occur at the locus of any one chromosome.

in sexually reproducing organisms the chromosomes occur in pairs calledhomologous chromosomes. Therefore 2 loci that can carry each allele of a gene. If the alllele of on each of chromosomes is the same the organism is said to be a homozygous for the character. if 2 alleles are different then the organism is said to be hetrozygous for the characteristics..

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## Genes and alleles continued ...

• The allele of the heterozygote that expresses itself on the phenotype is said to be dominant, while the one that is not is said to be recessive. A homozygous organism with 2 dominant alleles is called a homozygous dominant, whereas one with 2 recessive alleles is called a homozygous recessive.   The effect of a recessive allele is apparent in the phenotype of a diploid organism (when a nucleus contains 2 sets of chromosomes) only when it occurs in the presence of another identical allele.
• in some cases both alleles contribute to the phenotype - said to be co dominant. in these cases the phenotype is either a blend of both alleles or displays both on its phenotype
• sometimes a gene has more than one allelic form, said to have multiple alleles for the character. However there is always only 2 chromosomes in a homologous pair, it follows that only 2 of the 3 or more alleles in existance can be present in a single organism. Multiple alleles occur in the human ABO blood grouping system
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## sex inheritance in humans

unlike in other organisms, sex is determined by chromosomes rather than genes. in humans:

• as females have 2 x chromosomes all the gametes are the same in that they contain a single X chromosome
• as males have one X and one Y chromosome they produce 2 different types of gametes - half an X or half a Y chromosome
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a gene carried on either the X or Y chromosome is said to be sex linked. However the X chromosome is longer than the Y, meaning that for most of the length of theX there is no equivalent homologous portion of the Y. Those characteristics that are controlled by ressecive alleles on this non homologous portion of the X chromosome will appear more frequently in the male. Because there is no homologous portion on the Y chromosome that may have the dominant allele, in the prenence the recessive allele would not express itself

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## Haemophilia

• in which the blood clots slowly and so can lead to internal bleeding - lethel if not treated. ( a relatively rare condition). Although some females has haemophilia it mostly occurs in males because ..
• it is a recessive allele (in most cases) with altered DNA nucleotides and therefore do not code for the correct protien.
• As males only obtain their Y chromosomes from their father it follows that their X chromosome is from their mother. if the mother does not suffer from the disease she may be hetrozygous for the character. Such females are called carriers because they carry the allele without showing any signs of the charater in the phenotype.
• As males pass the Y chromosome on to their sons they cannot pass haemophilia onto them however will be able to pass them onto their daughters.
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## Pedigree charts

one way to trace the inheritance of sex linked characters is to use predigree chart in these:

• a male is represented by a square
• a female is represented by a circle
• shading within each shape indicated the presence of a character such as heamopphila, in the phenotype
• a dot within the circle signifies a women with a normal phenotype but who carries the defective allele
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## Co dominance

in which both alleles are equally dominant. Example: snapdragon plant - if these flowers showed an usual pattern one dominant and one recessive allele then the flowers would only contain 2 colours red and white. As they are co dominant however 3 colours are found:

• in plants that are homozygous for the first allele, both alleles code for the enzyme, and hence pigment, production. These plants have red flowers
• in plants that are homozygous for the other allele, no enzyme and therefore no pigment, These plants are white
• Heterozygous plants with their single allele for the functional enzyme, produce just sufficient red pigment to produce pink flowers.

if snapdragon with red flowers is crossed with one with white flowers, resulting seeds gives a rise to plants with pink flowers

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## geographical isolation

• individuals of species X form a single gene pool and freely interbreed
• climate changes lead to drier conditions which reduce the area of forest and sepertate it into 2 regions that are many miles apart
• furether climate change causes one forest region (a) to become much cooler and wetter than forest region (b)
• in region A phenotypes become more suited to cooler conditions whereas region B become more suited it warmer conditions
• the type and fequency of alleles in each region become increasingly different
• in time the differences in the gene pools are so great they become different species.
• futher climate change can lead to the species being reunited but will not be a able to interbreed
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Really good notes! One thing I noticed however is that on slide 27, should number 1 be photophosphorylation rather than just phosphorylation? Found these notes really useful though, thanks! :)

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sick as balls

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really useful, thanks :)

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great, thanks!

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Amazingly useful notes thanks! :)

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Good, but there are many punctuation and capital letter mistakes that are annoying me.

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penis and also dicke and balls

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