Biology

exam revision

Speciation

The process by which one species splits into two or more separate species.

Steps of speciation:

1. Variation - must exist within population.
2. Isolation - different groups of the population are prevented from interbreeding.
3. Natural selection - each group must be exposed to different selection pressures.
4. Time - over generations, different alleles become more frequent in each group.

Barriers to evolution:

1. Geographical barriers
2. Prezygotic isolating mechanisms
3. Postzygotic isolating mechanisms

Geographical barriers

often leads to different environments, leading to different environmental pressures.

Sympatric speciation

When one species becomes two while still existing in the same geographical area

Allopatric speciation

When a barrier geographically seperates a population into two.

Prezygotic isolating mechanisms

physical or behavioural differences between species that prevents gametes from forming a zygote.

Temporal Isolation

created through species reproducing at different time of day or year.

Gamete isolation

gametes from different species are often incompatible, and if sperm survive and meets egg, biochemical differences prevent fusion

Behavioural isolation

operates through differences in species courtship behaviours.

Morphological isolation

structural differences in anatomy of reproductive organs prevents sperm transfer

Postzygotic isolating mechanisms

prevents any hybrid offspring from being reproductively successful

Hybrid unviability

once fertilisation has occurred, zygote is not viable. will either not start division or die shortly after birth.

Hybrid sterility

when two different species are able to reproduce, but offspring are sterile.

Hybrid breakdown

where the first generation of offspring are fertile but second generation are infertile.

Evolution

a gradual change in a gene pool in a population, over generations.

Microevolution

looks at the change in frequency of one allele within a single population.

Macroevolution

looks at the change in frequency and type of many alleles resulting in the formation of a new species.

Gene flow

movements of genes from one gene pool to another.

Genetic drift

changes to the gene pool that occur by chance and are not driven by selection pressures.

Bottleneck effect

occurs when a population is drastically reduced in size, for example by natural disaster. Alleles in surviving population may not be representative of original population.

Founder effect

occurs when a small number of individuals founds a new population. Alleles present in founding population may not be representative of original population.

Natural selection

the process where individuals with certain inheritable traits survive and reproduce more successfully than other individuals, leasing to evolutionary change in the population.

Variation

sum of all different alleles within a population’s gene pool

Selective agent

the environmental factor acting on a population.

Overpopulation

competition for limited resources and struggle for existence.

Struggle for existence

being able to survive long enough to reproduce and pass on alleles.

Artificial selection

process by which we choose parents to breed who have desirable characteristics in hope that their offspring will have these desirable traits.

Conservation programs

selectively breed to increase or maintain genetic diversity in endangered species.

Gene pools

the total collection of alleles that exist within a population.

Allelic frequencies

the proportion of alleles of a particular gene locus in a gene pool that are of a specific type.

Frequency of alleles in a population depends on:

mutation of an allele, immigration/emigration, different rates of reproduction of different individuals.

Frequency of a allele

number of copies of a allele/ total number of copies of the A gene

Genotypic frequencies

proportion of individuals in a population with a given genotype.

Frequency of AA genotype

number of individuals with AA genotype/ total number of individuals in a population.

Fossilisation

rare process that requires specific conditions to occur such as oxygen free environment to prevent decomposition, minerals to replace bones and shells. Preferably alkaline soils.

Issues with fossil record:

* Process of fossilisation is rare so not many species are preserved.
* Hard body parts more likely to be preserved than soft.
* Only part of an organism may have been preserved due to predation/scavenging.
* Fossil destroyed by weathering, erosion and human activity
* Difficult to get to fossils.

Relative dating

method of sequencing events in the order in which they happened. puts fossils in order of age without knowing true age. uses stratigraphy and fluorine dating.

Stratigraphy

Study of layers of strata. Principle of superposition states that rock layers at the bottom of a sequence of layers are older than upper layers, but is void if distortions in the earth’s crust have occurred, where rock layers have been flipped. Correlation of rock strata involves comparing rock sequences from two+ areas. Index fossils are preserved remains of organisms that were widely distributed but present on earth from limited period of time, used to compare data from different localities.

Absolute dating

method of estimating age of a rock sample in years via radiometric techniques.

Radiometric dating

takes advantage of the known rates of atomic decay. it determines the age of a rock/mineral by measuring the proportion of an original radioactive material and its decay product. the decay of radioactive isotopes occurs at a fixed rate. half-life is the time taken for half the quantity to decay.

Electron spin resonance

electrons trapped in a material gain magnetic force as a result of exposure to environmental radiation over time.

Luminescence techniques

measures the amount of light emitted from a material when heated.

Biogeography

the diversification of life from one species into the many that exist today forms the basis for the evidence of evolution. study of distribution of organisms and ecosystems across the world and time.

Fossil record

paleontology is the study of fossils; any preserved trace left by a previously living organism. organisms that have shells or calcified bones are more readily fossilized than soft body organisms like bacteria. Fossils of the simplest organisms found in the oldest rocks and fossils of more complex organisms are in the newest rocks. transitional fossils are the organisms that exhibit features that exist in between an ancestral form of a species and its modern ancestor. They provide evidence for the evolution of major groups of organisms.

Comparative genomics

where the differences in genomic DNA are compared. DNA hybridisation (used in past) is where DNA from 2 species was collected, denatured and combined into a hybrid molecule. the more similar the species, the more the bases match.

Mutation rate

Frequency of mutation in a single gene or species, can be used as a molecular clock to estimate divergence. different proteins mutate at different rates.

Similarity of mtDNA

provides estimate of closeness of the relationship through maternal ancestors. was used to trace migration routes of ancient peoples.

Comparative anatomy

the science of comparing the physical structures of a species with others

Homologous structures

evolutionary theory predicts that related organisms share similar structures that are derived from common ancestors that may or may not share same function. can result in adaptive radiation where one ancestral species has evolved to become many.

Analogous structures

features of organisms that have same function but different basic structures as they have evolved independently.

Vestigial structures

structures that cease to have purpose and become diminished. they are remnants of an ancestral form, where changing environments have left them useless.

Embryology

the study of development, structure and function of embryos. comparisons of vertebrate embryos show striking similarities in the early stage.

Evidence for natural selection

organisms that live in similar environments have similar characteristics, even if far apart.

evidence for speciation

many unique species occur on islands where there is isolation.

Gradualism

evolution occurs at a steady state. the divergence of species and lineages is occurring at an even pace. jumps in evolution are simply gaps in the fossil record.

Punctuated equilibrium

evolution can occur in bursts. species remain stable for long periods of time and then swiftly evolve due to changing environmental pressures. transitional forms only existed for short times and were not able to be fossilised

Divergent evolution

occurs as groups of organisms change over time, accumulating enough changes they become a different species. this is called speciation

Adaptive radiation

type of divergent evolution. the process where a single species rapidly diversifies into many taxa with differing adaptations to fill an available environment/niche where there is little competition.

Convergent evolution

occurs when different species evolve similar adaptations in response to similar environmental demands. structures that evolve are analogous structures.

Polymerase chain reaction (PCR)

technique used to produce large quantities of DNA identical to an original sample. Sample containing buffer solution (salts, pH and other chemicals that help polymerase to function) DNA to be replicated, free nucleotides, Taq polymerase and two primers.

Three stages to PCR: 

**Denaturing** (@ 95oC) - hydrogen bonds break and double strand of DNA separates into single strands.

**Annealing** (@ 50 – 60oC), Primers are able to attach to complementary DNA strands with newly formed hydrogen bonds. Forward primer (3'to5') and reverse primer (5'to3').

**Extension** (**elongation**) (@ \~72oC). - Taq polymerase attaches to DNA strand at primers and moves along template, putting all free nucleotides together to build new strands of DNA.

Process is repeated many times, each time number of strands of DNA is doubled.Occurs in a machine called a **thermal cycler** (thermocycler)

Gel electrophoresis process

uses a gel to separate molecules by moving them in an electric field, molecules are separated according to size. DNA that is placed in a gel electrophoresis is usually cut with a restriction enzyme to produce DNA fragments of various sizes, or only specific regions are amplified.DNA is negative due to phosphate groups in sides of the DNA ladder.An **agarose gel** is used to ‘run’ the DNA through.Gel is made with different concentrations of agarose, different densities of gel are used to separate different samples of DNA (thick gels for samples containing many small fragments of DNA, thin gels for samples containing large fragments of DNA) (Different gels generate different resolutions).The gel or the DNA samples contain a fluorescent dye making the DNA visible.Gels are submerged in a buffer solution that allows the flow of the electric current. DNA is placed in wells in the gel.Separation of DNA fragments is due to electrical charge and the size of the DNA fragments.Electrical current pulls DNA from the negative end of the gel to the positive end of the gel. Small pieces encounter less resistance to the gel and move faster hence move further in the same time. Molecular size markers (**Molecular ladders**) are used to determine the size of fragments in the samples in the gel. Molecular ladders are samples of DNA of known lengths.

DNA Sequencing

determining the exact nucleotide sequence of a gene/DNA fragment/genome. Can be used to compare genomes; intraspecific and interspecific. Can be used to create phylogenetic trees.

Sanger method 

similar to PCR but involves adding chain-terminating nucleotides (dideoxynucleotides), each labelled with a different colour of fluorescent dye.


1. The region of DNA to be sequenced is identified, cut and amplified, then heated till it denatures to separate the double strand.
2. Sample of DNA is divided into 4 test tubes with a forward primer (annealed), buffer, free nucleotides, TAQ polymerase and one of four dideoxynucleotides.
3. Elongation occurs through the attachment of complementary dNTPs. When a ddNTP is added to a DNA fragment, they inhibit Taq polymerase from adding any further nucleotides to a growing nucleotide chain. By performing four separate reactions, four separate sets of fragments are produced.
4. Following termination, heating denatures the double stranded molecules releasing the single stranded molecules of various lengths. Each of the samples is run through gel electrophoresis in separate lanes. The gel tells us the complementary sequence to the original DNA sample. By matching these bases with their complementary bases, the original nucleotide sequence can be determined. DNA sequence can be read from bottom of gel up.

DNA Profiling

process that is able to identify natural variations that exist within an individual's genome by using the polymerase chain reaction and gel electrophoresis. It is used to compare base sequences of two or more individuals to determine genetic relatedness.

DNA profiling uses **STR’s** (short tandem repeats, repeating sections 2-5 bases long) and **VNTR’s** (variable nucleotide tandem repeats, repeating sections >5 bases long).

DNA is cut into fragments at a specific base sequence using restriction enzymes. The reliability of DNA profiling depends on the number of restriction enzymes used on the sample. Fragment length will differ between individuals due to variable length of their short tandem repeats.

PCR allows very small DNA samples to be amplified and used for identification.

STR and VNTR vary even between homologous chromosomes.

DNA from individuals to be compared is run through PCR, with primers that attach to either side of the STR and VNTR.

DNA fragments are run through gel electrophoresis and separated. The different size repeats will move at different speeds creating different banding for each individual. The pattern of fragment distribution can be analyzed.

The larger number of repeats that are the same size the closer related the individuals, \[parents should share 50% of the STR’s and VNTR’s with children\].

Ethical considerations:

Identification for paternity/maternity

Procedures required to prevent cross-contamination of very small samples

DNA Extraction

Separate suitable cells from hair samples.

Break the cells open / lysis through a physical method.

Remove membrane lipids through use of detergent or surfactants.

Purify DNA by precipitation of alcohol.

Pure breed

a group of identical individuals that always produce offspring of the same phenotype when intercrossed.

Gene

a set of stored instructions for a protein, found on a specific locus on a chromosome.

Monohybrid cross

cross happening in the F1 ten offspring of parents differing in one trait only

polygenic traits

controlled by multiple genes

creating genetic variation:

\-crossing over (occurs in prophase 1 & metaphase 1)- process where homologous chromosomes pair up and exchange different segments of genetic material to form recombinant chromosomes.

\-non-disjunction - failure of homologous chromosomes to seperate properly during cell division. causes gametes to have an extra or only part of a chromosome.

\-random assortment - the way maternal and paternal chromosomes get organised into daughter cells during gamete formation.

\-random fertilisation - random event as there is no way of knowing what sperm cell will fertilise the egg.

mutations

occurs when there are mistakes during DNA replication where nucleotide sequence is changed and mistakes occur in making of proteins.

somatic mutations

occurs in cell of body after conception.

germ-line mutations

occurs in reproductive cells, are inheritable and affect entire organism

causes of mutations

\-physical factors such as x-rays, uv light

\-chemical mutations such as asbestos. tobacco tar, organic solvents.

\- biological agents such as viruses

Point mutations

when there is a change in a single base in a gene.

substitution mutation - a single base is swapped

* silent - substituted base codes for same amino acid
* missense - single amino acid is changed from original
* nonsense - premature termination of polypeptide

insertion

inclusion of an extra set of bases into the genome, leads to frameshift mutation

deletion

occurs when a base has been removed from genomic sequence, leads to frameshift mutations.

gene mutation

changes in the DNA sequence that make up a gene

chromosomal mutations

changes in structure of individual chromosomes

deletion

a piece of chromosome being lost

inversion

chromosome segment breaks off and flips around backwards before it can reattach.

translocation

part of one chromosome is transferred to another

duplication

occurs when a gene sequence is repeated.

chromosomal mutations

variations in chromosomal number

monoploid organisms

have one set of genes

polyploidy

acquiring additional set of chromosomes

aneuploidy

genome that has lost or gained one or just a few chromosomes