9.

3 Blueprint of Life

1. Evidence of evolution.

Evolution through natural selection

The theory of evolution attempts to explain how species have changed from very simple forms to much more complex organisms Both Darwin and Wallace concluded that species are not fixed but change over time Darwin introduced the idea of evolution through natural selection. The mechanism of natural selection is: Organisms produce many more offspring than are needed Due to natural variation the offspring will differ from each other in small ways. Some of these differences will be inheritable and will offer the organisms that have them a slight advantage over the others. These organisms will be better fit to survive and reproduce in that habitat. Their offspring will inherit those traits and, over time, will become more numerous in the population. A number of these gradual changes will make the new organisms sufficiently different from the original that they can no longer produce viable offspring, should they mate. At this stage they can be considered a new species.

A model of natural selection

For this experiment you will need a number (20-30) toothpicks which have been dyed three or four different colours (not real bright ones) You will need to work in pairs. One of you will be the prey and the other the predator. You will need to work outside in an open area of about 100 sq m. Record the colour and number of the starting population. The prey goes outside first and, while the predator has their eyes covered up, he/she disseminates the 20 toothpicks in strategic areas some where the colours blend-in and some where they stand out. Next, the predator is given a fixed time, say 1 minute, to 'hunt' for as many toothpicks as he/she can see and counts and records the colour and number of the victims The prey goes out again and retrieves all the 'survivors'. The survivors are now allowed to reproduce (each colour's number is tripled) This procedure is repeated a few times (5 or 6) and then the final population is compared to the starting population.

Changing conditions
If a species has become adapted to a particular habitat there will still be many variations in its population. If none are particularly favoured, then the species will remain relatively unchanged over time However, if the conditions in the habitat were to change so that some of the different traits in the population are significantly favoured over others then the species will change over time. This change is called becoming adapted to the new environment. If none of the variations are favoured in the new environment and the species cannot adapt , then it may become extinct Conditions on Earth have changed a lot over millions of years and many more species of organism than are alive today have gone to extinction, it is part of the way life has evolved and space is made for new species Changes in the habitat can be Physical, chemical or competitive.

Effect of physical changes

Physical changes in an environment include changes in climate (temperature, rainfall, humidity, etc), amount of light, materials for shelter (rocks, logs etc), flooding and drought. An example of this, are the types of plants that we find in Australia, as we move from a temperate coastal climate to an arid one . Both areas contain similar species of trees but the ones in an arid environment are much better at retaining water and minimizing water losses. Sometimes the organism changes its habitat because of better food supply or to minimize predator encounters or maybe conditions in its original environment have changed. An example of this is the evolution of whales: their original ancestor was a wolf-looking coastal predator, which must have spent more and more of its time in the water. Over millions of years it evolved into a fully aquatic species: its anatomy changed radically because of the physical differences (buoyancy, streamlining, breathing etc) between the two habitats.

Effect of chemical changes

Sometimes the changes in an environment are related to the chemicals in it, which maybe toxic or harmful or beneficial. An example of this is the on-going war between insects and plants: as a plant develops an new toxin, the insects feeding on it develop resistance to it and the plant has to develop new toxins. A more visible example, one that we can observe happening, is the ability of insects or bacteria or rats have to become resistant to the poisons we develop to exterminate them. It's a war that they are winning by continuously evolving. As agents of evolution we are breeding super-pests!

Effect of competition
An important concept in evolutionary theory is that of adaptive radiation. Adaptive radiation is where a number of species, evolved from a common ancestor, have over time successfully adapted to new niches in their environment (via natural selection). When Charles Darwin visited the Galapagos islands, he noticed the wide variety of finches that existed on each of the islands. Originally, the finches occupied the South American mainland as ground-dwelling seed-eaters. Somehow they managed to colonise the Galapagos islands, over 600 miles away. At first they occupied the new habitat with little competition. But, as the population began to flourish, resources on the islands were squeezed and would not have sustained the population for long.

As competition grew, the finches managed to find new ecological niches, by adapting to new food sources. They evolved away from the original ancestor changing beak shapes, feeding habits, plumage etc.
The finches had adapted to their environment via natural selection, due to a competition for resources

Evidence for Evolution

Since the time when Darwin and Wallace published their theory of evolution, a lot of evidence supporting the theory has been obtained. The amount of evidence is much too great to deal in here, but a few important examples follow. It is important to note that he evidence does not come from one area of science alone, but it comes from a number of diverse fields: paleontology; anatomy; embryology; bio-geography and biochemistry. Little or no evidence has been found for the competing theories of Lamarkism, Creationism (in a short time span); Spontaneous generation or Intelligent Design. Some of the evidence for evolutionary theory may point at different mechanisms than those suggested by Darwin (e.g. punctuated equilibrium) but none of the evidence, to date, has contradicted the basic theory.

This type of evidence is based on the extensive fossil record that has been left behind by previously living organisms. A careful study of fossils highlights a steady increase in the complexity of organisms. The gradual development of specialized morphology is clearly illustrated in countless examples. A very good example of this gradual change is the evolution of horses . Fossils that are on the cusp of a major morphological change are known as transitional forms. A very familiar example of a transitional form are the fossils of archaeopteryx. They clearly show some reptilian and some birdlike structures, all in the same animal. Could monotremes, the Australian egg laying mammals, be living transitional forms between mammals and egg laying reptiles?

Paleontology

Comparative Anatomy (homology)

Comparing the anatomy of similar organism often highlights body parts that are similar in structure and function, suggesting a common ancestor. A good example is the vertebrate limb. The similarity in bone structure is evident in the vertebrate limbs shown here This example is often referred to as 'homologous structures in the vertebrate pentadactyl limb' Similar studies of other homologous structures in other classes of organisms yield the similar results: common ancestors (e.g. wings in insects) The concept of common ancestorship is one of the main concepts in Darwin's Theory of Evolution .

Vertebrate limbs
Print this slide Identify the forelimbs and hind limbs in each of the skeletons shown Colour-in the homologous structures on them using the same colours Deduce reasons why they are similar and why they are different from each other.

Comparative Embryology
Embryology is the study of the developmental stages of an organism from fertilized egg to birth. A comparison of vertebrate embryos illustrates their strong relationship and developmental similarity. Early-on in their development, an expert biologist would be required to distinguish between them. For example, they all go through a stage where vestigial tails and gills are present. Eventually, they develop into different structures depending on the species concerned (e.g. gills become ears in human embryos).

Bio-geography
Bio-geography deals with how organisms, that can be shown to share a common ancestry, differ from each other because they have occupied different habitats. The finches of the Galapagos Islands are an obvious example of biogeographical evidence, as they show significant differences among themselves and with the mainland South American finches. The evolution of Australian macropods ('big-feet': kangaroos and wallabies) can also be related to bio-geography. The common ancestor (about 25 mya) of all macropods is thought to have been an ancient tree-dwelling marsupial (Balbaridae). With the continent becoming more and more arid macropods evolved and adapted to different energy-poor habitats where food was sparse and the landscape had less and less suitable trees. Some had to evolve an extremely efficient way of covering large distances - hopping to it!.

Biochemistry
Biochemistry is the study of the chemicals that are important in living things. This includes proteins, fats carbohydrates, enzymes, DNA, RNA and many, many others. All living thins on earth use the same amino acids to build their proteins. Just 20 amino acids out of thousands possible amino acids. All living things use DNA or RNA to transmit genetic information, they all use the same genetic code, for the same amino acid The changes in the DNA of organisms can be studied and mapped so that evolutionary relationships become clear. For example, is has been shown that human DNA is 98% identical to chimpanzee DNA. Suggesting a recent (5 or so mya) common ancestor The metabolism of vastly different organisms is based on the same or very similar complex biochemical compounds. The protein cytochrome c, essential for aerobic respiration, is one such universal compound. The universality of cytochrome c is evidence that all aerobic organisms probably descended from a common ancestor that used this compound for respiration.

Divergent evolution

Divergent evolution is the term used when closely related organisms have evolved in different environments and as a result have developed different characteristics. Given a sufficiently long period of separation, the accumulation of differences between groups will lead to the formation of new species. Divergent evolution accounts for the different species of closely related organisms. For example, from one ancestral mammal, divergent evolution has resulted in all the mammal species. All are closely related (mammary glands, hair/fur, etc) but also vastly different (mouse and whale) A recent divergence, which has actually been observed: The normal host of the Apple Maggot Fly is the Hawthorn tree. Sometime during the nineteenth century it began to infest Apple trees. Laboratory studies have shown that flies from apple trees take about 40 days to mature, whereas flies from hawthorn trees take 60 days to mature. Now there are two distinct species, one that reproduces when the apples are ripe, and another that continues to infest the native hawthorn.

Convergent evolution
Convergent evolution is a term that is used to describe the evolution of relatively unrelated species into similar organisms that have similar structures, physiology and/or behaviours This parallel evolution is in response to similar environments. The organisms may not only have quite different ancestry but may also live in completely different times and may have evolved in different epochs, but because the habitat conditions were very similar, the evolutionary solution to survival was similar. Adjacent are some notable examples.

A case studyenvironmental change

Koala fossils are quite rare, but some have been found in northern Australia dating back to 20 million years ago. During this time, the northern half of Australia was rain forest. The Koala's ancestors did not specialize in a diet of eucalyptus until the climate cooled and dried, eucalyptus forests replaced rain forests. Its origins are still unclear, however, since its pouch opens backwards instead of forwards as would be expected in a tree-climbing marsupial. It has been theorised that Koalas may have evolved from a burrowing marsupial. The thinning of the forest probably made the koala an easier prey for carnivores like the marsupial lion (Thylacaleo Carnifex) which lived up to 200,000 years ago. The koala survived predation by adapting to an entirely arboreal existence. The species also shifted its distribution further south in the continent, following locations where eucalypts were the dominant plant species.

Evolution and society

When you consider the effect of Evolutionary Theory on society you should discuss some of the following points: The difference between faith and fact. The misunderstanding by lay people of the meaning of the term theory as is used in Science (e.g. Gravitational Theory, Theory of Relativity). The over-abundance of evidence supporting evolutionary theory, form many sources and many different disciplines. The strange notion that God may have placed all this evidence for us to find as a trap. The probable fact that most scientists have no vested interest in proving the evolution of life one way or the other. But that they do have an interest in only what is supported by evidence. All the DNA evidence that is piling up on a daily basis in support of evolutionary theory. The philosophical problem that you generate if you decide to ignore evolutionary evidence. Because this evidence is based on our knowledge of physics, chemistry, biochemistry, geology, biology and astronomy, if one discounts evolutionary evidence then the whole foundation of Science must also be discounted. An impossible position to support while availing one self of all the technology that very science has developed. Evolutionary theory has been a divisive influence on society because it has collided with people's belief systems. However, the past has shown that unsupported belief will eventually yield to scientific evidence (e.g. the fall of the belief held for thousands of years that the Earth was the centre of the universe or that the Earth was flat).

Advances in technology - DNA

Darwin's theory has been improved and modified in many ways, but the central concepts stand firm. Studies in molecular biology, in particular of DNA (unknown in Darwin's time) have supported the theory of evolution in many ways.
The ability to sequence the DNA molecule has made it possible to use genes to reconstruct the evolutionary history of organisms. Mutations change the DNA make-up over time and it has been found that the more closely related two organisms are, the less different their DNA will be. Genes change at different rates as mutation is a random event. But, some proteins are much more tolerant of changes than others proteins, and hence will change more rapidly. The average rate at which a particular kind of gene or protein evolves gives rise to the concept of a "molecular clock." Molecular clocks are useful for two reasons: they show evolutionary relationships among organisms, and they give an indication of the amount of time since two or more species started to diverge from one another. Another type of DNA based evidence supporting evolution involves the DNA of special genes called "pseudo-genes." . They are 'pseudo' because they are remnants of genes that no longer function but continue to be carried along in every species' DNA. Pseudo-genes also change through time. When comparing the functioning DNA from two similar organisms (e.g. dog and wolf) their similarity could be explained as a consequence of living and behaving in similar habitats and not from having a common ancestor. However, because pseudo-genes are non-functioning this explanation would not work and a common ancestor becomes the only viable option. The more remote the last common ancestor of two organisms, the more dissimilar their pseudogenes have been found to be.

Revision questions- 1
1) Outline the impact on the evolution of plants and animals of: changes in physical conditions in the environment; changes in chemical conditions in the environment and competition for resources 2) Describe, using specific examples, how the theory of evolution is supported by the following areas of study: paleontology ( including fossils that have been considered as transitional forms); bio-geography; comparative embryology; comparative anatomy and biochemistry 3) Explain how the Darwin / Wallaces theory of evolution by natural selection and isolation accounts for divergent evolution and convergent evolution 4) Describe a first-hand investigation you performed to model natural selection 5) Describe using a named example how an environmental change can lead to changes in a species 6) Describe a first-hand investigation you performed to observe, analyse and compare the structure of a range of vertebrate forelimbs

7) Analyse, using a named example, how advances in technology have changed scientific thinking about evolutionary relationships
8) Assess social and political influences on the historical development of theories of evolution

2. Inheritance of characteristics

Mendel's work
Experiments on Plant Hybridisation was presented in 1865 by Gregor Mendel at two meetings of the Natural History Society of Brnn, in Moravia. It was the result of more than 29 000 experiments and 11 years of studying genetic traits in pea plants. Mendel compared seven discrete characters of pea plants in his study of inherited characteristics: Colour and smoothness of the seeds (grey and round or white and wrinkled) Colour of the cotyledons (yellow or green) Colour of the flowers (white or violet) Shape of the pods (full or constricted) Colour of unripe pods (yellow or green) Position of flowers and pods on the stems (terminal or axial) Height of the plants (short ~1 ft or tall ~ 6 ft) In 1866 Mendel published his work on heredity in a little known journal (Proceedings of the Natural History Society of Brnn or Verhandlungen des naturforschenden Vereins Brnn). Not surprisingly, it had little or no impact. His ideas and findings were revolutionary but his writing style was tedious, complex and detailed it was not understood even by influential people in his field . He did make some attempt to contact scientists abroad by sending them reprints of his work but this was an uphill struggle for an unknown author, writing in an unknown journal, in a difficult language. It was not until 1900 that his work was 'rediscovered' by de Vries and Correns. But, it was not until the early 1920's that the full significance of his work was recognised, in particular, its significance to evolutionary theory.

Mendel's genius - 1
Mendel worked very hard performing thousands of experiments. He was successful because, he: Used very large sample numbers (lots of plants) Chose a plant (the pea) that was easy and quick to grow (he could study a number of generations) and a plant that would allow selffertilization. Observed traits that were easy to see and he studied one of them at a time Kept a close control over the whole experiment and especially the fertilization step Used his knowledge of math and statistics to analyze his results Kept accurate records of all his methods and results Ensured the reliability of his results by repeating each experiment a great number of times.

Mendel's genius - 2
Mendel began by ensuring his plants were all 'true-breeding' plants (homozygous).
As a botanist he knew that he must control fertilization Self-fertilization was controlled by covering the flowers to make sure their pollen (from the stamens) landed on the stigma of the same flower. Controlled cross-fertilization was ensured by cutting off the stamen from a flower before pollen was produced, then dusting the stigma of the flower with pollen from the plant he intended to use. Cross contamination from other flowers was strictly avoided

He let the plants self-fertilize to produce offspring identical to the parents numerous times.
Mendel cross-fertilized two true-breeding plants for one trait. Then he allowed the offspring to self fertilize or cross-fertilize producing second and third generations.

In each case, he found that the first generation always showed the phenotype of one of the parents, he called this a dominant trait and the other a recessive trait. Further fertilization experiments always produced the same simple ratios of traits, now known as Mendelian ratios or as Mendelian inheritance.

A Genetics glossary
Allele an alternative form of the same gene

Genetic engineering a form of biotechnology used to modify organisms by altering their Artificial pollination fertile stigmas are dusted with genes. pollen harvested from selected plants.
Chromatid one of the two daughter strands of a replicating chromosome that are joined by a centromere. Chromosome structures in the nucleus that become visible before cell division and contain all the cell's DNA Crossing over the exchange of chromosomal material between a pair of homologous chromosomes during meiosis. Cross-pollination transfer of pollen from one flower to the stigma of another. Genotype genetic make-up of an organism. Haploid having only half of a pair of chromosomes as in sex cells or gametes. Heterozygous having two different alleles for a genetic trait. Homozygous having two alleles that are identical for a genetic trait Hybrid offspring Mutation a change in the genetic material Phenotype Observable trait(s) of an organism.

Diploid containing two of each type of Random segregation the process by which pairs of chromosome. As in body cells (except gametes) homologous chromosomes are distributed between separate gametes during meiosis DNA deoxyribonucleic acid. Carries all genetic information in units called genes Recessive a gene that is expressed only in a homozygous genotype. Dominant a gene that is expressed equally in homozygous or heterozygous genotype Sex-linked inheritance determined by genes located on the sex chromosomes (usually the X ) Gene Part of the DNA molecule that codes for a polypeptide (protein). Different forms of the Zygote A diploid cell resulting from fertilization of same gene are called alleles. an egg by a sperm cell.

Monohybrid crosses

A Monohybrid cross considers only one trait or gene at a time. The flow diagram adjacent shows a monohybrid cross where green cotyledons are dominant. It shows the homozygous (true-breeding) parents (P1); the first filial generation (F1) and the second filial generation (F2). The F1 offspring are all heterozygous and have a genetic make-up (genotype) of Gg and they are all green (phenotype) because green is dominant (note: the letter chosen to show each allele is usually the capital of the dominant trait, the lower case letter is used for the recessive allele) The F2 generation genotype is in the ratio of 1:2:1 for GG:Gg:gg and a phenotype of 3:1 for green:yellow. These are the Mendelian ratios. Monohybrid crosses of this type always produce off-spring in these probability ratios.
(a large number of crossings are needed to actually get offspring in theses ratios. It is similar to tossing a coin - it takes many tosses to achieve the expected probability of 1:1= heads:tails)

Examples of monohybrid crosses

In fruit flies a normal wing has been found to be dominant over a short wing. Derive the expected ratios of genotypes and phenotypes for each of the following crosses: i. ii. Homozygous normal x short; Heterozygous normal x heterozygous normal ii.

Genotype: 1: 2 : 1 = NN : Nn : nn Phenotype: 3 : 1 = Normal : short winged

iii. Heterozygous normal x short

iii.

The best way to answer this type of question is by using Punnett squares:
Let N = normal allele and n = short allele

Genotype: 1 : 1 = Nn : nn

Phenotype: 1 : 1 = Normal : short winged

Genotype: all Nn Phenotype: all normal wings

Family trees (or pedigrees)

A family tree can be used to trace the occurrence of inherited traits in parents and offspring through a number of generations. Dominant traits are characterized by: One parent and offspring both affected Heterozygous individuals will be affected Two affected parents can produce an unaffected child (both parents would be heterozygous) Recessive trait is characterized by: the offspring is affected but neither parent is. Heterozygous parents will be unaffected Two affected parents will always have an affected child. Pedigrees are used in genetic counseling. They allows identification of the genetic disease and on the probability of couples having affected children.

Some Family trees

In each case decide whether the trait is dominant or recessive; work out the genotype and phenotype of each member in the family tree and determine whether the question-marked individual will be affected

Hybridisation
In biology, hybrid has two meanings. In the first meaning, a hybrid is the result of interbreeding between two organisms of different species within the same genus. These hybrids are often sterile (e.g. the mule and the hinny are sterile hybrids of breeding horses with donkeys). In this second meaning, a hybrid refers to hybridisation within a species and between different breeds or strains. It is used in plant and animal breeding. (e.g. breeds of cats and dogs, farm animals, crops) In these cases, hybrids are commonly produced and selected because they have desirable characteristics of both parents. Most agricultural animals and plants are the result of hybridisation. Sterile hybrids would be a negative in a crop such as wheat (growing a crop which produces no seeds would be pointless), but it is an attractive attribute in some fruits. Bananas, seedless watermelon, seedless grapes for instance, are intentionally bred to be sterile so that they will produce no seeds making them easier and more pleasant to eat.

Example: Warmblood Horses A warmblood horse is the result of hybridisation between pure-blooded horses such as English thoroughbreds and heavier farm horses to produce a horse for a specific function and purpose such as show-jumping or dressage. Careful breeding programs are carried out to produce a horse ideally suited to the breeders' needs.

Revision questions - 2
1) Outline the experiments carried out by Gregor Mendel 2) Describe the aspects of the experimental techniques used by Mendel that led to his success 3) Describe outcomes of monohybrid crosses involving simple dominance using Mendels explanations 4) Distinguish between homozygous and heterozygous genotypes in monohybrid crosses 5) Distinguish between the terms allele and gene, using examples 6) Explain the relationship between dominant and recessive alleles and phenotype using examples

7) Outline the reasons why Mendels work and its importance were not recognised until some time after it was published
8) Describe an investigation you performed to construct pedigrees or family trees, trace the inheritance of selected characteristics and discuss their current use 9) A black rat is paired with a white one. The F1 offspring are all black. Some of the F2 offspring are black and some are white. Explain, using Punnett squares, and deduce the likely ratio of black to white rats in the F2 generation 10) Describe an example of hybridisation within a species and explain the purpose of this hybridisation.

3. Chromosomes

Chromosomes
Mitosis and meiosis were discovered in the early 20th Century. At that time it was also realised that the nucleus of the cell contained the material responsible for inheritance. In 1903 Walter Sutton (1877-1916) and Theodore Boveri (1862-1915) while studying gamete formation (independently) concluded that it was the chromosomes that carried the inheritance material. They noticed that in normal body cells chromosomes came in pairs, but that in gametes they were no longer in pairs. This led to the "Chromosomal Theory of Inheritance," which states that chromosomes carry hereditary units, and that the sperm and egg have half the number of chromosomes found in the typical cells of the resulting offspring.

The chromosome
When the cell is not in the process of dividing chromosomes are invisible. Just prior to cell division, the DNA in chromosomes becomes more tightly packed and the chromosomes become visible under a light microscope. When they are stained with special dyes they become 'banded (the banding is used to recognise each individual chromosome). Chromosomes are made of about 40% DNA and 60% DNA-bound proteins, which serve to package the DNA and control its functions. The word chromosome comes from the Greek chroma (color) and soma (body) due to their property of being very strongly stained by particular dyes. In eukaryotes, DNA is packaged by proteins into a condensed structure called a chromatin. This allows the very long DNA molecules to fit into the cell nucleus. Chromosomes may exist as either duplicated or as single chromatins. Duplicated chromosomes (copied at the start of cell division) contain two copies joined by a centromere. (the classic four-arm structure) Human cells have 22 different types of autosomes, each present as two copies (diploid), and two sex chromosomes (46 in total). The DNA in a chromosome is divided into: functional (coding DNA) and non-functional (noncoding DNA) . A gene is a region of functional DNA that controls the base sequence used in the production of a specific polypeptide or RNA. A human chromosomes may contain from 500 genes (Y chromosome) to more than 4000 genes (chromosome 1). A gene can be as short as 1000 nucleotides to as long as several hundred thousand nucleotides.

DNA
Deoxyribonucleic acid (DNA) is a polymer made up of nucleotide units. Each nucleotide is made up of a phosphate group joined to a sugar molecule which is joined to an organic nitrogenous (containing Nitrogen) base. The main role of DNA molecules is the long-term storage of genetic information. The backbone of the DNA strand is made from chemically joined, alternating phosphate and sugar molecules. The sugar in DNA is a five carbon sugar: 2-deoxyribose. ( the sugar ribose is found in RNA) The DNA double helix is held together by hydrogen bonds between the bases attached to the sugar molecules on each of the two strands. The four bases found in DNA are adenine (A), cytosine (C), guanine (G) and thymine (T) (the base uracil replaces thymine in RNA). Each one of the four bases can only form hydrogen bonds to its complementary base: A only joins with T; G only joins with C (mnemonic: A 'T' on the Golf Course) It is the sequence of these four bases along the backbone that is the code for all life on Earth (some viruses use RNA).

Meiosis
Meiosis is the cell division that produces sex-cells or gametes. Meiosis and sexual reproduction produce genetic diversity. When a diploid cell divides to produce gametes each of the four daughter cells is genetically unique. The uniqueness arises partly from the independent assortment of chromosomes as each cell randomly receives either the maternal or paternal homologue of each paircalled random segregation. And partly from the process known ascrossing over of chromosomes. This produces chromatids that have unique combinations of genetic material from both parents. This shuffling of genetic material produces unique gametes that during fertilization combine with other unique gametes to produce unique offspring having the natural variation in traits and characteristics which are fundamental to evolutionary theory.

Use Petri dishes and plasticine of different colours to construct this model

Sex-linked inheritance
T H Morgan (1866 1945) was an American geneticist and embryologist. Following the rediscovery of Mendelian inheritance in 1900, Morgan's research moved to the study of mutation in the fruit fly (Drosophila melanogaster). In his famous fly-room at Columbia University, Morgan was able to demonstrate that genes are carried on chromosomes and that they are the mechanical basis of heredity. in 1910 Morgan noticed that when white-eyed male flies were bred with a red-eyed female, their progeny were all red-eyed, while a second generation cross produced white-eyed males: he had discovered sex-linked inheritance In a paper published in Science in 1911, he concluded that (1) some traits were sex-linked, (2) the trait was probably carried on one of the sex chromosomes, and (3) other genes were probably carried on specific chromosomes as well. He was awarded the Nobel prize in 1933 for his work in genetics

A sex-linked recessive trait e.g. colour-blindness

Codominance
In codominance, neither allele is recessive. Instead, the heterozygous individual expresses both phenotypes. A common example is the ABO blood group system. The gene for blood types has three alleles A, B and O. A and B are codominant and form blood type AB (both alleles are given capitals). O blood type is recessive to both A and B. A codominant genetic disease in humans is 1-antitrypsin deficiency, A roan horse has codominant follicle genes, expressing individual red and white follicles. Roan Shorthorn cattle also express codominant alleles red and white. Camellia flowers show codominance between red and white alleles. (note: pink carnations show a different process called 'incomplete dominance')

Effect of environment on phenotype

The environment may affect the expression of a gene. Mendel was able to get reproducible results with phenotype expression because he ensured identical growing conditions. Had his tall plants received a different fertilizer regimen than his short plants, his results would not have been as clear cut. Plants grown in different conditions will develop differently. Identical twins, separated at birth and brought up in different environments may develop differently in height, weight and even IQ. A visible example of the effect of environment on phenotype is the colour of Hydrangeas: blue, pink and purple flowers can grow from the same plant. A soil that is basic causes the blooms to be pink. If the soil is more acid, then the blooms are blue. Hydrangeas are easy to grow or purchase already established and could form the centre of your first hand investigation on the effect of environment on phenotype: Plant 3 plants in 3 different pots, add lime to the soil of one plant, add aluminum sulfate to the soil of another and to the third plant's soil add both. Make sure each receives the same amount of light and water.

Exceptions to Mendelian ratios

The ratios of phenotype and genotype obtained by Mendel were only possible because the allele relationship for each gene he studied was a straight forward dominant-recessive one Since Mendel, many more complex relationships in gene expression of alleles have been found. For example: codominant alleles and sex linked inheritance. Other exceptions are: lethal alleles, Incomplete or semi-dominance, pleiotropy and others

Revision Questions - 3
1) Outline the roles of Sutton and Boveri in identifying the importance of chromosomes 2) Describe the chemical nature of chromosomes and genes 3) Describe the structure of DNA 4) Explain the relationship between the structure and behaviour of chromosomes during meiosis and the inheritance of genes 5) Explain the role of gamete formation and sexual reproduction in variability of offspring 6) Describe the inheritance of sex-linked genes, and genes that exhibit co-dominance and explain why these do not produce simple Mendelian ratios 7) Describe the work of Morgan that led to the identification of sex linkage

8) Explain the relationship between homozygous and heterozygous genotypes and the resulting phenotypes in examples of codominance
9) Outline ways in which the environment may affect the expression of a gene in an individual 10) Describe a model that demonstrates meiosis and the processes of crossing over, segregation of chromosomes and the production of haploid gametes 11) A woman falls pregnant while seeing two men. Her blood type is A, the first man's blood type is B and the second's is O. The baby's blood type is also O. Show that this does not exclude the first man from being the true father. Under what circumstances would the first man definitely not be the father? Explain using Punnett squares. 12) Describe a first-hand investigation you performed to demonstrate the effect of the environment on phenotype

4. DNA

Franklin vs. Wilkins & Watson & Crick Part 1

In 1951 James Watson, a biologist and Francis Crick, a physicist, were working at the Cavendish Lab in Cambridge, England on the structure of DNA. Maurice Wilkins, a physicist at King's College had, in 1951, taken the first X-ray pictures of DNA. These lead him to suggest the DNA structure might be a helix Rosalind Franklin was a 30 year old English chemist who was doing brilliant work in a X-ray crystallography lab in Paris, France in 1951. She was head-hunted by J.T. Randall, Director of King's College biophysics labs, to create an X-ray unit and work on DNA. She arrived at the King's College lab also in 1951. Randall did not clearly delineate a chain of command. He had hired Franklin as director of the x-RAY lab, without informing Wilkins, who was away on holidays. On his return the startled Wilkins (a man in a man's world), believed himself to be in charge and Franklin to be a glorified lab assistant! Franklin, a renown feminist, and just as qualified as Wilkins, did not regard him as her superior. Randall's lack of communication was the main cause of the friction between Wilkins and Franklin and their lack of cooperation in their research efforts. Previously, a Swiss chemist (Signer) had isolated some quality DNA, which he gave in a "jelly jar" to Wilkins sometime in 1951. But it was given to Franklin by Randall, another cause of resentment. Franklin discovered that Signer's DNA produced X-ray patterns which indicated 2 forms an A form and a B form. Franklin's efforts often included X-ray pictures that took over 100 hours of exposure . At a Conference attended by Watson, she suggested that B-DNA was helical. Watson and Crick began at once to build a model, upon its completion they asked Wilkins and Franklin to view the model. Rosalind did not hesitate in pointing out that it was completely wrong! (The model had the phosphate-sugar backbone placed inside the molecule with the bases on the outside. As a chemist, she knew that it had to be on outside the molecule in order to give DNA its hydrophilic properties). In May of 1952 Franklin took the famous photograph #51 of the B-form, but she set it aside, spending all her efforts on the A-form pictures because they were contradictory.

Franklin vs. Wilkins & Watson & Crick Part 2

By 1953, conditions at King's had gotten so unsociable that Franklin decided to leave. She had reconciled her conflicting data on the A-form and had started to write a series of three draft manuscripts, two of which included a double helical DNA backbone. Two of her manuscripts reached Acta Crystallographica in Copenhagen in March 1953. Wilkins had been as frustrated by Franklin's lack of 'cooperation'. Unfortunately, Wilkins expressed some of his frustration to his friends Watson and Crick (they were competitor researchers at Cambridge University), maybe naively supplying them with crucial data from Rosalind Franklins work. When he showed them Rosalinds best DNA photograph (#51), Watson immediately saw its significance and it was enough to start them on the correct solution to DNA. Wilkins also told them about a report containing a summary of Rosalinds latest findings, including all essential molecular size calculations. The two 'rogues' managed to obtain a copy from Max Perutz. The report was not confidential, but it was private. Perutz passed the report on to Crick without asking Randall or Franklins permission, and they used it without her permission or acknowledgement ! Watson and Crick now had all Franklins data which showed that DNA was a multiple helix. Crick, who had worked on proteins, soon realised that Franklins data implied an anti-parallel double helix. Upon learning of Watson and Cricks model, Rosalind innocently rewrote her own draft manuscript as a supportive paper to theirs, to be published in the same April 1953 issue of Nature. She never knew that her data had been so essential to Watson and Crick. Rosalind's photo #51 was a pivotal moment in the discovery of the double helix. At 37 Rosalind Franklin died of ovarian cancer, probably due to constant exposure to X-rays. Four years later, Francis Crick, James Watson, and Maurice Wilkins shared the Nobel Prize but she was not included (the Nobel Prize is not awarded posthumously). Strangely, only Maurice Wilkins, with whom she'd fought for so long, acknowledged her contribution in his acceptance speech. The other two did not mention her valuable and essential help to their work, even though, over the years, she had formed a lasting friendship with Francis Crick and his family.

...DNA replication... DNA replication...

DNA replication is complex, fast and very accurate. It takes place in three, almost simultaneous, steps: (1) unzipping and uncoiling (2) adding nucleotides and (3) forming the two new backbones The process is helped by enzymes, proteins and RNA. The two new strands are formed in opposite directions and replication occurs at a number of different points on the huge molecule at the same time (~30 000 points for human DNA)

Why replicate?
DNA molecules code for the synthesis of every enzyme, protein and RNA molecule used by the cell every second of its life. When the cell divides (growth or replacement) the information must be passed on and it must be an exact copy or the wrong enzymes, proteins etc. will be made and the daughter cells will be unable to function. All organisms reproduce, this would not be possible if the DNA molecule did not replicate exactly. The offspring would most likely not be viable and if viable would not be the same as the parents making the propagation of the organism's species impossible. Without DNA being able to replicate life on Earth would not have existed and evolved as we know it, if at all.

Effect of changes in DNA

If just one amino acid in hundreds is in the wrong location, the protein or enzyme will not be able to fold properly and function properly, if at all.

This means that whatever processes the protein or enzyme is used for will not occur, or at best will occur less efficiently. i.e. cell function will be affected
For example: sickle cell anemia is caused by glutamate amino acid being substituted by valine amino acid in the haemoglobin molecule. As a result the haemoglobin molecule is no longer globular in shape but is fibrous. The red blood cells in sickle-cell anaemia have a different shape, which does not flow through capillaries very well and painful circulation problems arise On the other hand, people with this disease are malaria resistant. The flow chart shows how this could happen if just one base pair is changed on the coding DNA molecule

Polypeptide synthesis -1
Transcription starts as the DNA is "unzipped" by the enzyme helicase. RNA polymerase reads the DNA strand and synthesizes a single strand of m-RNA This single strand of m-RNA leaves the nucleus through nuclear pores, and migrates into the cytoplasm.

*Note: In RNA the base Uracil substitutes for Thymine

Polypeptide synthesis - 2

Translation is the process of converting the m-RNA codon sequences into an amino acid polypeptide chain. A ribosome attaches to the m-RNA and starts to code at the START codon (AUG*). t-RNA brings the corresponding amino acid (which has an anti-codon that identifies the amino acid as the corresponding molecule to a codon) to each codon as the ribosome moves down the m-RNA strand. The synthesis ends when the ribosome reads the STOP (UAA, UAG, or UGA) codon, and the polypeptide chain is released.

Polypeptide protein enzyme ?

The term peptide refers to the type of chemical bond between adjacent amino acid, poly means many . Both proteins and enzymes are made of polypeptide chains. Enzymes act as biological catalyst in metabolic reactions. Proteins can be made up of more that one polypeptide and are more involved with structure and function e.g. muscle tissue, haemoglobin, hair etc Beadle and Tatum studied mutations in red bread mould caused by irradiation with X-rays. They found a mould that was unable to grow unless a specific amino acid was added. They found that a single gene was mutated, which resulted in the lack of a single enzyme In this way they demonstrated that genes control metabolic processes. By coding for the enzymes necessary for the specific metabolic process. Beadle and Tatum, who won the Nobel prize for their work, demonstrated that genes code for specific polypeptides. Hence: 1 gene => 1 polypeptide*
*Note: the human genome project has since shown that one gene may code for many
polypeptides, as we have only 20,000 (or so) genes, but there are many more polypeptides in the body.

Mutations
A mutation is a change to the nucleotide sequence of an organism's DNA. Most mutations are neutral or repaired quickly or harmful, very few are beneficial to the organism. Mutations can be caused by chance, by chemicals, by viruses or by radiation. If the mutation is present in a sex cell, it will be passed on to the offspring as a new allele (which may or may not be functioning). Mutations in sex cells may cause miscarriages, stillbirths, congenital defects, death in the first year of life, chromosomal abnormalities and cancer in later life. If the mutation occurs in a somatic cell it will be present in all descendants of that cell (certain mutations can cause the cell to reproduce out of control and thus cause cancer) In 1927 H J Muller published research showing the genetic effects of radiation as a mutagen. In 1946 he was awarded the Nobel prize for his findings. Marie Curie discovered Radium and worked with ionizing radiation, she received the Nobel Prizes for both physics and Chemistry but died of radiation induced cancer. Rosalind Franklin co-discoverer of the structure of DNA worked extensively with X-rays. She died of ovarian cancer before she could receive her Nobel prize Long term studies of the Chernobyl disaster have reported an unusually large number (1,800) thyroid cancers in children from contaminated areas and in many birth defects. In the late 50's and early 60's, more than 10,000 children in 46 countries were born with severe deformities. The Australian obstetrician, William McBride, showed that the unfortunate mutations were caused by a drug called thalidomide if taken during pregnancy (it was an effective tranquiliser and painkiller). A chemical or an agent that causes mutations is known as teratogen

Variation
Genetic variation is the basic mechanism of evolutionary change. Mendelian genetics, the processes that occur during meiosis, the structure and function of DNA all supply ways through which variation in a species is ensured. There are three main sources of genetic variation: Meiosis produces genetic variation by the processes of crossing over and random segregation, it has the major effect on variation in a population.
Mutations are changes in the DNA which can result in changes in the alleles of genes and can have a large effect. Gene flow is the movement of genes from one population to another and can have a significant effect on genetic variation. G. L. Stebbins, Jr. (1906 2000) was an American botanist and geneticist who is widely regarded as one of the leading evolutionary biologists of the 20th century. He summarized the importance of variation: In brief, evolution is here visualized as primarily the resultant of the interaction of environmental variation and the genetic variability recurring in the evolving population

Natural selection

Some modern examples of observable natural selection are: the increasing resistance of bacteria to antibiotics and the resistance of insects to insecticides. Antibiotic resistance is the ability of a microorganism to survive and reproduce in the presence antibiotics. Antibiotic resistance evolves via natural selection acting upon a random mutation. Once such a gene is generated, bacteria can then transfer the genetic information between individuals by plasmid exchange. Staphylococcus aureus (Staph infection) is one of the major resistant pathogens. It was the first bacterium in which penicillin resistance was found just four years after the drug started being mass-produced (1947). MRSA (methicillin-resistant S. aureus) was first detected in Britain in 1961 and is now "quite common" in hospitals (MRSA was responsible for 37% of fatal cases of blood poisoning in the UK in 1999) Half of all S. aureus infections are now resistant to penicillin, methicillin, tetracycline and erythromycin.

Punctuated equilibrium

Gradualism (Darwin's suggestion) and punctuated equilibrium (first suggested In 1972 by paleontologists N. Eldredge and S. Gouldare) are two of the ways in which the evolution of species is thought to occur. It is believed that species with a shorter evolution evolved mostly by punctuated equilibrium, and those with a longer evolution evolved mostly by gradualism. Some species may have used both mechanisms at different times. Gradualism is selection and variation that happens gradually over a long time. Change is slow, constant, and consistent. In punctuated equilibrium, change comes in spurts. There is a longer period of time when there is little change. Followed by a sudden major change . Darwin saw evolution as being "steady, slow, and continuous". Paleontologists have found fossils that show gradual change but also fossils that appear on the scene without any evidence of gradual change. When dating the fossils, results showed that these large changes had occurred in a relatively short time

Revision questions - 4
1) Describe the process of DNA replication and explain its significance 2) Outline, using a simple model, the process by which DNA controls the production of polypeptides 3) Explain the relationship between proteins and polypeptides 4) Explain how mutations in DNA may lead to the generation of new alleles 5) Discuss evidence for the mutagenic nature of radiation 6) Explain how an understanding of the source of variation in organisms has provided support for Darwins theory of evolution by natural selection 7) Describe the concept of punctuated equilibrium in evolution and how it differs from the gradual process proposed by Darwin 8) Describe a first-hand investigation you performed to develop a simple model for polypeptide synthesis 9) Outline the evidence that led to Beadle and Tatums one gene one protein hypothesis and to explain why this was altered to the one gene one polypeptide hypothesis 10) Construct a flow chart that shows that changes in DNA sequences can result in changes in cell activity 11) Explain a modern example of natural selection 12) Describe and analyse the relative importance of the work of: James Watson; Francis Crick; Rosalind Franklin and Maurice Wilkins in determining the structure of DNA and the impact of collaboration and communication in scientific research.

5. Reproductive technologies.

Current reproductive techniques

Artificial insemination is the injection of selected male sperm into a selected female of the same species. It reduces variation and prevents natural selection. It is normally carried out by animal breeders to instill certain wanted traits into the offspring e.g. in race horses the ability to sprint or stay in races. Artificial pollination is the transfer of pollen from one selected flower to another. It again defeats natural selection and variation. It is carried out by agriculturists to promote certain traits in the fruit, grain, flower or vegetable being grown e.g. Mendel's work. Cloning is the development of new individual organisms from body cells, hence they are genetically identical to the parent cells. All bacteria and single celled organisms, some insects or plants reproduce asexually and hence produce clones of themselves. Cloning again produces no variation and reduces biological diversity in the species. The worlds first cloned animal was Dolly the sheep, created in 1996 in Scotland. In all three cases genetic variability within the species will be been reduced.

Cloning

There are two main types of cloning: cellular cloning and organism cloning. Cellular cloning is to derive a population of cells from a single cell. In the case of unicellular organisms such as bacteria and yeast, this process is simple, however, in the case of cell cultures from multi-cellular organisms, cell cloning is an arduous task as these cells will not readily grow in standard media Somatic cell nuclear transfer can be used to create a clonal embryo. The most likely purpose for this is to produce embryos for use in research, particularly stem cell research. Organism cloning refers to the procedure of creating a new multicellular organism, genetically identical to another. This process entails the transfer of a nucleus from a donor adult cell (somatic cell) to an egg from which the original nucleus has been removed. If the egg begins to divide normally it is transferred into the uterus of the surrogate mother. Dolly was cloned by this method at the Roslin Institute in Scotland and lived there until her death (aged 6), she was born after 277 eggs were used to create 29 embryos, which only produced three lambs at birth, only one of which lived. Some other species that have been cloned successfully are: Mice(1986); Rhesus Monkey(2000); Mule (2003) and Horse (2003)

Transgenic species
Transgenic animals are made when a gene or genes are transferred from a donor species to a host species (the inserted genes are called transgenes). The foreign genes must be inserted into sex cells, so that every cell of the offspring will contain the same modified genetic material, which will be inherited by future generations. There are three basic methods of producing transgenic animals: Embryonic stem cell-mediated gene transfer: DNA Micro-injection: Retrovirus-Mediated Gene Transfer Gene transfer by micro-injection is the predominant method used to produce transgenic farm animals. Since the insertion of DNA results in a random process, transgenic animals are mated to ensure that their offspring acquire the desired trans-gene. Some transgenic animals are produced for specific economic traits. e.g. transgenic cattle were created to produce milk containing particular human proteins for the treatment of human emphysema. Other animals are made to exhibit disease symptoms so that effective treatment can be studied, e.g. transgenic mice were produced that would catch polio, to study possible cures for human use (polio cannot infect normal mice)

Ethics of transgenesis
Genetically modified bacteria are used to produce the protein insulin to treat diabetes. Similar bacteria have been used to produce clotting factors to treat haemophilia. Transgenesis in Salmon has resulted in dramatic growth enhancement . These fish have been created for use in the aquaculture industry to increase meat production and, potentially, reduce fishing pressure on wild stocks. Transgenic plants have been engineered to possess several desirable traits, including resistance to pests, herbicides or harsh environmental conditions and increased nutritional value Some of the ethical questions that need to be debated might be: Is human welfare the only consideration? What about the welfare of other organisms? Should the focus be on in vitro transgenic cells rather than on live animals ? Will transgenic animals change the direction of evolution, which may result in drastic consequences for nature and humans alike? Could transgenic organisms give rise to new diseases for which we have no cure? Could transgenic animals contaminate wild stocks and cause ecological disasters? Should transgenic animals be produced for profit or for entertainment (e.g. fluorescent gold fish or rabbits)? Should there be an internationally agreed protocol for the production of transgenic species?

Impact
In 1900, the global population was approximately 1.6 billion. It will explode to 10 billion by 2030. Using biotechnology to increase the productivity of our animals is a variation on the age-old practice of selective breeding. Genetic modification of animals by humans has already created all of our domesticated livestock and companion animals Now genetic engineers are taking the next step and developing transgenic animals to provide solutions for disease treatment, organ transplant shortage and food production. Increased public demand for seafood and dwindling natural marine habitats have encouraged the study of ways that biotechnology can increase the production of marine food products The benefits of transgenic fish like salmon include increased growth rates and improved disease resistance. Transgenic salmon grow faster than other salmon but the offspring of these fish have a high and early mortality rate: genetically engineered fish are three times more likely to die prematurely than wild fish. The growth gene that gives these super fish reproductive advantage could spreads through the native population quickly, genetic diversity would be minimized and because of the high mortality native fish populations could dwindle and eventually become extinct. To reduce the chance of contaminating wild stocks with transgenic genes, only sterile all female transgenic salmon should be farmed. But what controls could be enforced locally and world wide?

Revision questions - 5
1) Identify how the following current reproductive techniques may alter the genetic composition of a population: artificial insemination; artificial pollination; cloning 2) Describe a methodology used in cloning 3) Outline the processes used to produce transgenic species and include examples of this process and reasons for its use 4) Identify examples of the use of transgenic species and discuss the ethical issues arising from the development and use of transgenic species 5) Discuss the potential impact of the use of reproduction technologies on the genetic diversity of species using a named plant and animal example that have been genetically altered