3.4.7 Investigating diversity

Genetic diversity within, or between species, can be made by comparing:

• the frequency of measurable or observable characteristics
• this is based on he fact that each observable characteristic is determined by a gene/genes
• it has limitations because a large number of them are coded for by more than one gene (they are polygenic) so they are not discrete but actually vary continuously. It is therefore often difficult to distinguish one from another.
• the base sequence of DNA 
• we can do this because of DNA sequencing
• we can measure the genetic diversity of a species by sampling the DNA of its members and sequencing it to produce a pattern of coloured bands (as each base is tagged with a fluorescent dye). Analysis of these patterns allows us to compare one species with another/the individuals of the same species.
• the base sequence of mRNA
• mRNA is coded for by DNA
• it follows that, since we can measure genetic diversity with DNA, we can measure it with mRNA.
• the amino acid sequence of the proteins encoded by DNA and mRNA
• the amino acid sequence is coded for by mRNA which is coded for by DNA.
• Genetic diversity can therefore be measured by comparing the amino acid sequences of organisms proteins.

Quantitative investigations of variation

Random sampling
There are several reasons why measurements might not be representative of the population. These include:

• sampling bias
• the selection process may be biased
• chance
• individuals by pure chance may not be representative

The best way to prevent sampling bias is to eliminate any human involvement in choosing the samples. This can be achieved by random sampling. For example:

• divide the area into a grid (e.g stretch two tape measures perpendicular to each other)
• use a random number generator to obtain a series of coordinates
• take samples at the intersection of the coordinates

We can minimise chance by:

• using a large sample size
• analysing the data collected using statistical tests

It is important to understand that gene technology has caused a change in the methods of investigating diversity. E.g DNA differences from measurable/observable characteristics has been replaced by direct investigation of DNA sequences.

3.4.6 Biodiversity within a community

Okay so first it's probably a good idea for us to learn some terms:

• species diversity is the number of different species and the number of individuals of each species within any one community
• genetic diversity is the variety of genes possessed by the individuals that make up a population of a species
• ecosystem diversity refers to the range of different habitats from a small local habitat to the whole of the Earth

A good measurement of species diversity (the number of different species and the number of individuals of each species within any one community) is species richness. Species richness is a measure of the number of different species in a community. One way of measuring species diversity is to use the equation:

d = (N(N-1))/(Σn(n-1))

NOTE:
d = index of diversity
N = total number of organisms of all species
n = total number of organisms of each species

An index of diversity describes the relationship between the number of species in a community and the number of individuals in each species.


Efforts to provide enough food for the human population at a low cost has led to a reduction in biodiversity. This is because basically as natural ecosystems develop they become complex communities with a high index of diversity. However, agricultural ecosystems are controlled by humans and farmers often select species for particular qualities to make the farms more productive. Any particular area can only support a certain biomass. If most of the area is taken up by the desirable species there is smaller area for the other species and the other species must out-compete one another for the small area. Furthermore, pesticides exclude species that compete for light/mineral ions/water/food required by the farmed species.

We need to know about the balance between conservation and farming. Certain practices that have (directly) reduced species diversity include:

• removing hedgerows
• creating monocultures
• draining marshland/filling in ponds
• over-grazing of land

Practices that have indirectly reduced species diversity include:

• the use of pesticides/inorganic fertilisers
• escape of effluent from silage stores/slurry tanks into water courses
• absence of crop rotation

A number of management techniques can be applied to increase species diversity without largely raising food costs/lowering yields. These include:

• maintaining hedgerows
• planting hedges as boundaries instead of fences
• maintaining ponds
• planting native trees
• using organic fertilisers
• reducing the use of pesticides
• using crop rotation that includes a nitrogen-fixing crop
• creating natural meadows

3.4.5 Species and taxonomy

Okay so we sorta need to know a bit about how organisms are classified and named etc (naming system isnt rly important but it sort of is good to know so i'll put it in, just skip to the next paragraph if you cba to read it)...

We use the binomial naming system. The first name is the generic name (this is the name of the genus, think GENeric=GENus). Next is the specific name (this is the name of the species, think SPECIfic=SPECIes). For example, Homo sapiens (us). This tells us that we belong to the homo genus and sapiens species.

A species is a set of organisms that are able to breed to produce fertile offspring.


Courtship behaviour
Individuals can recognise members of their own species by the way they act (the behaviour of members of the same species is more similar than that of different species). Reproduction is necessary for a species to survive (duh). It is important that mating is successful as it will lead to maximum chance of species survival. Courtship behaviour enables individuals to:

• recognise members of their own species
• identify a mate that is capable of breeding (e.g is sexually mature)
• form a pair bond
• synchronise mating
• become able to breed

Courtship behavior is often used by males to determine which females are at the receptive stage (in most species, females only produce eggs for a short amount of time). 

Classification

The grouping of organisms allows better communication between scientists and avoids confusion. Classification is the grouping or organisms. there are two main types of classification:

• Artificial classification
• this divides organisms according to things that are useful at the time (e.g colour, size, etc). These features are described as analogous characteristics where they have the same function but not he same evolutionary origins (e.g butterfly and bird wings originated differently but are both used for flight).
• Phylogenic classification
• this is based upon evolutionary relationships between organisms and their ancestors. it arranges the groups into a hierarchy in which the groups are contained within larger groups with no overlap.
• it attempts to arrange species into groups based on their evolutionary origins and relationships
• Each group is called a taxon (plural taxa)
• one hierarchy comprises the taxa:
• domain
• kingdom
• phylum
• class
• order
• family
• genus
• species. 

NOTE: The theory and practice of biological classification is taxonomy.

3.4.4 genetic diversity and adaptation

Genetic similarities and differences between organisms can be defined in terms of variation in DNA. This is because if is differences in DNA that lead to genetic diversity.

It is important to understand that al members of the same species have the same genes, which phenotype they express depends on which alleles they possess. Organisms of the same species differ in alleles (not genes!).

Genetic diversity is the total number of different alleles in a population (a population is a group of individuals of the same species in the same habitat at the same time). A species consists of one or more populations, The greater the number of different alleles that all members of a species possess the greater the genetic diversity of that species. This is important as it increases the chance of survival with environmental change as there is a greater probability that an individual will possess a characteristic that suits it to the new environment.

I must add that it is not equally likely that all alleles of a population are to be passed on. This is because not all individuals are reproductively successful so not all pass on their alleles. Differences between the reproductive success of individuals affects allele frequency within populations because:

• within any population of a species there will be a gene pool containing a wide variety of alleles
• random mutation may result in a new allele
• in certain environments the new allele might give its possessor an advantage over the other individuals
• this individual is better adapted so more likely to survive in their competition with others
• these individuals therefore have a better chance of successfully breeding and producing offspring
• only individuals that reproduce successfully will pass on their alleles to the next generation
• over time the frequency of the 'better' allele will increase whilst the 'worse' allele will decrease

This is the principle of natural selection. Natural selection results in species that are better adapted to the environment they live in. these adaptions may be:

• physiological
• to do with like inside stuff (e.g oxidization of fat rather than carbohydrate produces more water in kangaroo rats)
• behavioural
• to do with behaviour
• anatomical
• to do with anatomy

Types of selection

Directional selection

Process covered in 3.7.3

We need to know an example of this by antibiotic resistance in bacteria:

• A spontaneous mutation occurs in the allele of a bacterium that enables it to make a new protein
• this protein is an enzyme that breaks down an antibiotic before it's able to kill the bacterium
• the antibiotic was used to treat an individual and the bacterium was present
• the mutation gave the bacterium an advantage and it was not killed (unlike the rest of the population
• the bacterium that survived reproduced by binary fission and a built up a population of antibiotic-resistant bacteria
• the populations normal distribution curve shifted in the direction of a population having greater resistance to the antibiotic

Stabilising selection

Process covered in 3.7.3

The example we need to know of this is human birth weights. There is a much greater risk of infant mortality if the baby is born outside the 2.5-4.0kg range

3.4.3 Genetic diversity can arise as a result of mutation of during meiosis

Gene mutations involve a change in the base sequence of chromosomes. They can arise spontaneously during DNA replication and include base deletion and base substitution. Due to the degenerate nature of the genetic code, not all base substitutions cause a change in the sequence of encoded amino acids. Mutagenic agents can increase the rate of gene mutation. Mutations in the number of chromosomes can arise spontaneously by chromosome non-disjunction during meiosis.

Meiosis
Meiosis produces four daughter cells each with half the number of chromosomes as the parent cell. It is important as it (usually) produces gametes which have half the number of chromosomes which means the chromosome number of offspring does not double when two gametes fuse. During meiosis homologous pairs of chromosomes separate so only one chromosome from each pair enters a daughter cell (the haploid number). when two haploid gametes fuse during fertilisation the diploid/full number of chromosomes is restored. Meiosis involves two nuclear divisions (it's a bit like mitosis, but twice if you get me):

1. meiosis 1: homologous chromosomes pair up and their chromatids wrap around each other. Equivalent portions of these chromatids may be exchanged in a process known as crossing over. By the end of the is division the homologous pairs have separated with one chromosome from each pair going into one of two daughter cells
2. meiosis 2: the chromatids move apart and form 2 new cells. At the end of meiosis 4 cells have formed each with a diploid number of chromosomes

Meiosis also produces genetic variation among the offspring which may lead to adaptations that improve survival chances. It brings about genetic variation in the following ways:

• independent segregation of homologous chromosomes
• during meiosis 1 each chromosome lines up alongside its homologous partner at the equator, this arrangement is random. Which pair goes into each daughter cell with which other pairs depends on how they are lined up in the parent cell. Since the line up is random the combination of chromosomes that go into each cell is a matter of chance. This is called independent segregation.
• To further this, the alleles of each member of a homologous pair may differ. The independent assortment of these chromosomes produces new genetic combinations
• new combinations of maternal and paternal alleles (crossing over and recombination)
• after each chromosome lines up alongside its homologous partner the chromatids of each pair become twisted around one another. During this time tensions are created and portions of the chromatids break off. They then rejoin with the chromatids of its homologous pair. In this way new genetic combinations of maternal and paternal alleles are produced.
• If there is no recombination by crossing over only two different types o cell are produced. If recombination occurs four different types are produced. This means that crossing over further increases genetic variety.

As we know, homologous pairs line up at the equator during meiosis 1. Each of one pair can pass into each daughter (independent segregation) so there is a large number of possible combinations of chromosomes in any daughter cell. we can use the formula 2ⁿ where n is the number of pairs of homologous chromosomes to determine the number of possible combinations of chromosomes for each daughter cell.

Variety further increases through the random pairing of male and female gametes. We can calculate the number of combinations using the equation (2ⁿ)².

NOTE: It is important to realise that these calculations are based on chromosomes that do not undergo crossing over. If recombination occurs it will greatly increase the number of possible combinations in the gametes.

3.4.2 DNA and protein synthesis

3.4.2 DNA and protein synthesis 

The genome is the complete set of genes in a cell and the proteome is the full range of proteins that a cell is able to produce. 

We need to be able to recall and talk about the structure of mRNA and tRNA.

RNA overall:

• pentose sugar (ribose)
• A, U, C, G
• a phosphate group
• a polymer made up of repeating mono nucleotide sub-units
• single stranded

mRNA:

• small enough to leave the nucleus through clear pores to enter the cytoplasm
• it contains coded information to determine the sequence of amino acids in the proteins which are synthesised
• a codon is a sequence of three bases on mRNA that codes for a single amino acid
• long strand arranged in a single helix (1,000s of nucleotides)
• base sequence determined by the base sequence of a length of DNA (transcription)
• associated with ribosomes in the cytoplasm
• acts as a template for protein synthesis

tRNA:

• relatively small (around 80 nucleotides)
• single stranded chain folded into a clover-leaf shape with one end of the chain extending beyond the other
• an amino acid can easily bind to this extending part (there are many different types of tRNA, each is specific to a different amino acid)
• on the other end is an anticodon (sequence of three bases) this binds with the codon during protein synthesis (the codon and anticodon are complimentary).

Transcription

This is the process of making pre-mRNA from DNA (the DNA acts as a template):

• an enzyme acts on a specific region of the DNA causing the two strands to separate exposing the nucleotide bases in that region
• the nucleotide bases on one of the two DNA strands (this is the template strand) pair with complimentary free nucleotides by complimentary base pairing
• RNA polymerase moves along the strand joining the nucleotides together forming a pre-mRNA molecule
• the DNA strand rejoins behind the pre-mRNA strand
• when the RNA polymerase reaches a particular sequence of bases (a stop triplet code) it detaches and the production of pre-mRNA is complete

Splicing

In prokaryotes transcription results directly in the production of mRNA from DNA. In eukaryotic cells transcription results in pre-mRNA which must be spliced to form mRNA. The DNA of a gene of eukaryotic cells is made up of sections known as exons (coding) and introns (non-coding). Introns prevent polypeptide synthesis, so we must remove these and join the exons together. This process is known as splicing. The mRNA molecule now leaves the nucleus via a nuclear pore.

Translation

• A ribosome becomes attached to the start codon at one end of the mRNA molecule
• the tRNA molecule with the complementary anticodon moves to the ribosome and pairs up with the codon on the mRNA. This tRNA carries a specific amino acid
• A tRNA molecule with a complementary anticodon binds to the next codon
• the ribosome moves along the mRNA bringing together the two tRNA molecules
• the two amino acids are joined by a peptide bond using ATP which is hydrolysed to provide the energy required
• the ribosome moves onto the next codon and the first tRNA is released from its amino acid (simultaneously)
• this tRNA is now free to collect another amino acid
• this continues until the ribosome reaches a stop codon
• here the ribosome, mRNA, and last tRNA molecule all separate and the polypeptide chain is complete

3.4.1 DNA, genes and chromosomes

Eukaryotic and prokaryotic organisms have different DNA. Eukaryotic organisms hold genetic information in their nucleus, mitochondria and chloroplasts (remember only plant cells have chloroplasts). In the nucleus, the DNA is long, linear, and histone associated (histones are a type of protein - histone associated DNA is known as a protein). Mitochondria and chloroplasts of eukaryotic cells also contain DNA. This is more like prokaryotic DNA in that is is short, circular, and not protein (histone) associated.

Chromosomes become visible during prophase (the first stage of nuclear division). They appear as two threads (chromosomes) joined at the centromere. Each thread is called a chromatid and they are identical as the DNA has already replicated (during interphase). The chromosome structure is held in place by histones (see above, a type of protein). Since the DNA is highly coiled around histones a considerable length of DNA can be found in each cell.

A gene is a section of DNA that codes for a polypeptide sequence. It technically first codes for an mRNA strand, so a gene is also a section of DNA that codes for a functional RNA. The position of a gene on a section of DNA is known as the locus. An allele is one of a number of alternate forms of a gene (e.g a gene will code for eye colour, so an allele will code for blue and an allele will code for brown etc etc).

A gene can code for a polypeptide sequence because each DNA triplet (sequence of three DNA bases) codes for a single amino acid. This is known as a degenerate code. It is important to realise that the triplets are read in one direction only, each base is only read once (triplets are non-overlapping), the start of a gene always codes for the same amino acid (methionine), and stop codons do not code for an amino acid (they mark the end of the sequence). There are 64 possible triplet combinations but only 20 regularly occurring different amino acids. This means that some triplet codes code for the same amino acid. The code is also universal meaning each triplet codes for the same amino acid in (pretty much) every organism.

That being said, there also a few other reasons why a DNA sequence may not code for an amino acid (along with stop codons). In eukaryotic organisms, between genes there are non-coding parts of the DNA . Furthermore, within genes there are sections that are non-coding. These are known as introns. The coding parts are known as exons.

As I mentioned earlier, genes can also code for RNA sequences. RNA stands for ribonucleic acid. It is single stranded and made up of a phosphate group, ribose sugar, and a nitrogenous base. The two RNA molecules that are used to for proteins (polypeptide sequences).

• mRNA
• longer stranded
• arranged in a single straight helix
• base sequence determined by the base sequence of the length of DNA is was transcribed from
• tRNA
• smaller than mRNA (only around 80 molecules long)
• clover-leaf shaped
• one end extends beyond the other (this is the bit where an amino acid attaches)
• On the opposite side of the tRNA molecule is the anticodon (this is complimentary to codons on the mRNA molecule
• Each tRNA molecule is specific to one coding triplet, and therefore one amino acid