You are on page 1of 29

o VCE Biology GA 3 is a 90 minute examination of the work covered in Unit 4 VCE Biology.

The questions in the exam will not be only factual recall questions. There will be many questions where the principles covered in Unit 4 are presented in a new context. You are expected to identify the relevant biology in such questions and use your understanding to answer the questions asked. o Other questions may ask you to make predictions, or to interpret the results of a biological experiment. You should be aware that correct spelling of biological terms is expected in exams. If spelling is incorrect, markers are instructed not to award any marks. o You also need to know that markers are instructed that if, within the one response, a student provides both correct and contradictory incorrect information, there is no mark awarded for the correct part of the response. Basically this means that unless you are certain it's correct, don't offer extra information in an answer. o The best method of preparation for GA 3 is to make sure that you have a good grasp of the facts, then do as many practice exams as you can find. Correct these practice exams yourself, and ask your teacher to explain any answers which you do not understand.
About these Notes

Unit 4 Exam NOTES

The notes are a summary of the main ideas of the 'dot points' in the previous VCE Biology Study Guide. Those dot points outlined the ideas which were examined in GA 3. If you use these notes as a 'skeleton' upon which to build your revision of each topic you can face the exam well prepared. The notes are adaptations of a website formerly maintained by Jenny Herington, who was then at La Trobe Uni. All of the pages at the VCE Biology Students' site were copyright Biochemistry, LaTrobe University.

Area of Study 1
Chromosomes

Chromosomes, Genes and DNA


Chromosomes are structures within a cell which contain the genetic information that is passed on from one generation to the next. In prokaryotes, there is usually a large circular chromosome. In addition, there may be several smaller circular chromosomes called plasmids. None of these is enclosed in a membrane, they merely drift around within the cytosol of the prokaryote cell. In eukaryotes, most chromosomes are located in the cell nucleus and are composed of protein and DNA. Smaller chromosomes exist in mitochondria and chloroplaststhese tend to regulate activity solely within the organelle in which they occur. Chromosomes only become visible through a microscope just prior to cell division. Before they are able to be seen, the DNA has been duplicated and coils tightly around proteins. The two strands of DNA so formed are called chromatids and are still joined by a protein disk at a point called the centromere. Human cells other than gametes (= somatic cells) contain 46 chromosomes. This represents 22 pairs of autosomes and a pair of so called sex chromosomes. When a cell has a set of paired chromosomes, as in a somatic cell, it is described as diploid. The chromosomes in each autosome pair (= homologous chromosomes) look very similar in length, position of the centromere and staining reactions. And when the genetic information on a pair is examined it is found that the genes match up perfectly although the proteins for which they code may have important differences. The sex chromosomes may or may not be homologous. In a human female, each somatic cell has two copies of the X chromosome as well as the 22 autosome pairs. The human male has 22 pairs of autosomes and one X chromosome and one Y chromosome. The Y chromosome is physically smaller than an X chromosome and only some of the genetic information on an X chromosome has matching information on the Y chromosome. Other species have different numbers of chromosome pairs in their somatic cells. It is this difference in size and arrangement of chromosomes which, at the molecular level, separates one species from the other.
Karyotype

It is possible to stain the chromosomes of a dividing cell and view them under a microscope. If the image is then photographed and enlarged, the individual pictures of the chromosomes can be cut up and sorted. This is known as a karyotype. Examination of an individual's karyotype may reveal information about gender or the presence/absence of the correct number of chromosomes. For this reason karyotype analysis is sometimes performed on cells from unborn babies.
Genes

A gene is a section of a chromosome. A gene carries coded information within a sequence of chemicals. When appropriate, a section of this information is decoded and used to provide the recipe for protein synthesis within the cell. The proteins synthesized may affect the way the cell interacts with its environment. This, in turn, may affect the way the whole organism responds to its environment. Since the genes directly control the functioning of cells, it is hardly surprising that (almost) all cells contain chromosomes. When cell reproduction occurs (as in growth or tissue repair) it is therefore necessary to reproduce the chromosomes in such a way that each new cell has its full quota of the DNA needed to ensure the cell's survival.

Mitosis

The process of mitosis ensures that each new (daughter) cell in the organism's body inherits the correct amount of DNA. This is described in more detail under New proteins, Cells and Individuals on page 3. Similarly, new individuals need a supply of DNA in order to exist. If these individuals are generated by asexual reproduction, they are provided with a copy of the same chromosomes and genes as the parent from which they arise. Individuals which are the product of sexual reproduction, however, gain half of their DNA from each parent. A different type of cell reproduction is called for in preparation for sexual reproduction if the cells of the offspring are not to be overloaded with too many chromosomes.

p.

VCE Unit 4 Chapter Summaries

Meiosis

The process of meiosis results in gametes with half as many chromosomes as a normal body cell (a somatic cell). Gametes from two parents unite in sexual reproduction to form a zygote with the correct amount of DNA. This is also described in more detail under New protein, Cells and Individuals.
DNA structure

Deoxyribonucleic acid (DNA) is the chemical which carries the genetic code. DNA is composed of subunits called nucleotides which themselves are composed of sub-units: a sugar molecule (deoxyribose), a phosphate group, and one of four possible nitrogen bases. The nucleotides in a single strand of DNA are linked together by chemical bonds between the phosphate group of one nucleotide and the deoxyribose of the next. In this way, a backbone of deoxyribosephosphatedeoxyribosephosphatedeoxyribosephosphate is formed with the bases attached to each deoxyribose. In 1949, it was discovered that there is always the same amount of adenine and thymine in DNA and there is always the same amount of cytosine as guanine. From this observation, in 1953, Watson and Crick (and others) deduced the structure of DNA to be two single strands, wound around each other, and linked together with weak chemical bonds between the bases on each strand. The specific base pairing was found to always occur between adenine:thymine and guanine:cytosine, thus accounting for the constant ratios observed earlier. The arrangement of two strands of DNA, linked by the base pairs and twisted together, is described as a double helix. Because of the special relationship between the bases of one strand of DNA with the bases on the opposite strand, the two chains of the double helix are described as complementary to each other.
DNA replication

When cells prepare to divide, either for growth or for repair, the chromosomes become visible microscopically, as duplicated threads, the chromatids. For chromatids to form, the DNA of the original chromosomes needs to be reproduced so that each new cell will ultimately possess the correct genetic information to function appropriately. DNA replication occurs when the complementary strands of DNA break apart and unwind. This is accomplished with the help of enzymes called helicases. Additional enzymes and proteins attach to the individual strands, holding them apart and preventing them from coiling upon themselves. The point at which the double helix separates is called the replication fork, because of the shape of the molecule. At this site, enzymes called DNA polymerases move along each of the separated DNA strands, adding nucleotides to the exposed bases according to the base pairing rules. The deoxyribose-phosphate bonds form between the new nucleotides to hold the new strand together. The process continues until the original double helix is completely unwound and two new double helices have been formed. Each new double helix is composed of one old DNA strand and one new strand. This is described as semi-conservative replication. During replication, there are occasionally errors made in the insertion of the complementary bases in the new DNA strand. Usually these are repaired by special DNA polymerases, but a few remain (increasing in frequency with the increasing age of the organism). These errors in the DNA may or may not have an effect on the functioning of the cell lines in which they then appear. Errors or alterations in the base sequence of DNA are called mutations.
The DNA code

One of the most important discoveries in Biology was the realisation that genes are responsible for the production of proteins. George Beadle and Edward Tatum, working at the California Institute of Technology in the 1940s, are credited with this discovery, although, of course, they were working on extending ideas that had been published earlier by other scientists. Then it was Alfred Hershey and Martha Chase who, in 1952, published the results of their experiments that convinced scientists that DNA is indeed the carrier of hereditary information. So how does the DNA carry the 'recipe' for all the proteins, structural and functional, that an organism needs? The answer is in the four bases, Adenine, Thymine, Cytosine and Guanine (learn how to spell these!). These four bases on the DNA chain in the double helix can be thought of as 'letters' which are used to build the total possible range of three letter 'words'it's a simple maths exercise to realise that this gives a possible 'vocabulary' of 64 (=4x4x4) words. Since there are only 20 amino acids that are used, in various combinations, to make proteins, it is possible to give each amino acid a DNA code 'word'. For example, the DNA triplet code CGA will lead to the insertion of the amino acid alanine into a protein. But there are still 'words' left over to have duplicates for many of the amino acids (CGG, CGT and CGC also code for alanine) and 'special words' to tell where a gene stops (e.g. ATT does this). The term for the DNA bases in their groups of three is codons, and it is these codons, grouped together as genes, which hold the information for the accurate production of all the cells' proteins.

New Proteins, Cells and Individuals


Introduction

Exactly how does the DNA in a portion of a chromosome (i.e. the DNA in a gene) determine an individual's characteristics? The answer is, in fact, to be found in the proteins which are coded for by the DNA. Different proteins do different things: structural proteins determine the organisms physical form; functional proteins determine how the cells, tissues, organs and indeed the whole organism survives in 3 VCE Unit 4 Chapter Summaries p.

its environment; and regulatory proteins act as switches, where appropriate, to direct metabolic responses as needed. How, then, does DNA determine the nature of a protein?
Transcription

Transcription is the formation of RNA from a DNA template. The RNA formed may be rRNA (ribosomal RNA), tRNA (transfer RNA) or mRNA (messenger RNA). The functions of rRNA and tRNA are discussed elsewhere. At present, we will concentrate on the formation of mRNA by the process of transcription. A flow chart will summarise the steps involved, but you should read this in conjunction with a series of good quality diagrams which illustrate the process. Inside the nucleus of a eukaryotic cell, an enzyme, RNA polymerase , binds to a specific sequence of bases on the DNA of the gene to be expressed. This starting sequence is the promoter. Then the DNA begins to unwind and the strands begin to separate and the RNA polymerase begins to move along one strand of the exposed DNA (the sense strand), linking ribonucleotides together in order specified by the sequence of bases on the DNA. (Ribonucleotides are similar to the deoxyribo nucleotides which are the building blocks of DNAthe differences are that the sugar section is slightly changed and, whilst cytosine guanine and adenine are still used as bases, the fourth base is uracil.) Base pairing occurs as follows:
BASE ON DNA SENSE STRAND Adenine Thymine Cytosine Guanine COMPLEMENTARY BASE ON mRNA Uracil Adenine Guanine Cytosine

Transcription (literally "rewriting") continues until the RNA polymerase reaches a "stop" message on the DNA (a terminator), after which the unzipped DNA closes back up, the enzymes drop off and the messenger RNA is released into the nucleus prior to the next stage in the production of a protein.
Introns and Exons

Before leaving the nucleus, the mRNA is modified so that only the sections of it necessary for the "recipe" of the required protein are retained. This is necessary because the DNA of a eukaryotic gene seems to contain large lengths of "junk" information, called introns, which interrupt the sections which will ultimately be expressed, the exons. (In DNA from prokaryotes, this is not the case. There is very little, if any, intron material in bacterial genes). Both introns and exons are transcribed onto mRNA, but enzymes cut out the introns and rejoin the exons into the final molecule of mRNA which leaves the nucleus. The mRNA leaves the nucleus, via nucleopores, and travels in the cytoplasm to a ribosome.
Ribosomes, rRNA and tRNA

It is at the ribosome that the base sequence code of the mRNA is translated into the string of amino acids which will ultimately form a protein. This translation is possible because the sequence of the bases on the mRNA is "read" in groups of three. Each group of three bases on the mRNA is called a codon. Each codon is specific for the insertion of one amino acid into the growing protein on the ribosome. This was described under Chromosomes, Genes and DNA on page 1. Ribosomes are made up of two subunits, a large one and a smaller one. Each ribosome consists of ribosomal RNA (rRNA) and proteins (about 70 different types). Ribosomes are either found attached to the cell's internal membrane system (rough endoplasmic reticulum) or free in the cytoplasm. Transfer RNA (tRNA) is also involved in the synthesis of proteins. This substance is a single strand of RNA that loops back on itself. At one of the free ends, there may be an amino acid attached to the tRNA. At the central loop, there are three bases (the anticodon) exposed. There are different tRNAs for each of the 20 amino acids. The sequence of the three bases in the anticodon determines which amino acid a particular tRNA will carry.
Translation

mRNA binds to the two subunits of a ribosome. The initiator codon on mRNA (AUG) binds to first anticodon of tRNA (UAC). This tRNA carries the amino acid methionine. The next codon on the mRNA determines the next tRNA anticodon which binds with it and so the next amino acid in the polypeptide. A peptide bond forms between the amino acids. (The tRNA detaches from the ribosome and returns to the cytoplasm to pick up another amino acid.) The process continues, with codons matched by appropriate tRNA anticodons and peptide bonds forming between the amino acids. Eventually a STOP codon is reached on the mRNA. The ribosome releases the mRNA and the newly formed polypeptide. (Further processing of the polypeptide may occur to make it functional).
Mitosis

Mitosis is the process by which the nucleus of a cell is divided into two nuclei, each with the same number and kinds of chromosomes as the parent cell. Mitosis is the process by which all of an organism's body cells (the somatic cells) are reproduced. The process of mitosis is divided into phases in which particular events take place. The acronym IPMAT can be used to remember the phases in order. * Interphase is the period between cell divisions. During this time the cell grows, develops and carries out its normal function. At the end of interphase DNA replication takes place.
p.

VCE Unit 4 Chapter Summaries

* Prophase begins when the chromosomes become visible (using a light microscope) within the cell's nucleus. Each chromosome consists of two sister chromatids joined at the centromere. The centrioles of animal cells separate and move to positions opposite each other at the poles of the cell. Spindle fibres form from the centrioles. Near the end of prophase the nucleolus disappears and the nuclear membrane breaks down. * Metaphase is when the chromosomes line up across the centre, or equator, of the cell. The chromosomes attach to the spindle fibres at their centromeres. * Anaphase begins when the centromeres split. The sister chromatids part and are now individual chromosomes. Still attached to the spindle fibres, the chromosomes move until they are in two groups near the poles of the cell. When chromosome movement stops anaphase is complete. * Telophase sees the two groups of chromosomes uncoiling into tangles of chromatin and new nucleoli forming in each region which will from a nucleus. Nuclear membranes form and the spindles break apart. Mitosis is technically complete. * (Cytokinesis occurs to divide the cell contents between the two daughter cells. Mitochondria, ribosomes, cell proteins, membranes and cytoplasm are all divided and a dividing membrane is synthesized. As the daughter cells grow, the cytoplasm and organelles are replicated as needed.) The cell cycle is the period from the end of one mitosis to the end of the next. During a cell cycle, a cell grows, prepares for division (the S phase), continues to function for a while, then divides to form two daughter cells, each of which begins the cycle for itself. The time to complete one cell cycle varies considerably with different cells. Most human nerves and muscle cells do not divide once formed, but the cells lining the digestive tract may pass through a complete cell cycle every six hours.
Meiosis

Meiosis is the process that produces haploid gametes from diploid cells. This process reduces the number of chromosomes in the gametes to half of that in the normal somatic cells. During meiosis the homologous chromosomes which exist in diploid cells are separated. In humans this means that sperm and ova contain 23 chromosomes (the haploid number) but somatic cells contain 46 chromosomes (the diploid number). The desirability of this becomes apparent when fertilization is considered. The phases of meiosis can be remembered as IPMAT-PMAT. Whilst the names of the phases of meiosis seem to be the same as those of mitosis, there are some very important differences in the details of meiosis compared with mitosis. When reading the stages which follow, you are advised to have a detailed diagram of meiosis available as an additional reference. * During interphase the gametocyte (gamete-producing cell; spermatocyte or oocyte) grows and matures until the appropriate hormone level stimulates gamete production. DNA replication occurs to produce joined chromatids ready to begin meiosis. * Prophase I sees the condensation of the chromatids into visible chromosomes. The chromosomes then seek out and align with their homologous partner. Thus a tetrad (four homologous chromatids) is formed. It is while these tetrads are in the cell that crossing over may occur (see later). * During metaphase I the tetrads move to the cell's equator and attach to the spindle fibres. * Anaphase I sees the two chromosomes of the tetrads (but NOT the individual chromatids) separate from their homologous partner and move towards the poles. The assortment of the chromosomes at this point is random. The "maternal" and "paternal" chromosomes are shuffled between the two poles, so the two cells which form have sets of chromosomes (and genes) that are different from each other. The combination is also different from that which was in the original cell. * Telophase I completes the first stage of meiosis as two cells form around the poles of the original cell. Nuclear membranes surround each cell's chromosomes. * Prophase II begins without further DNA replication, since the chromosomes already exist as chromatid pairs. Nuclear membranes again disappear and the chromosomes are again visible. * Metaphase II sees the chromosomes line up across the cells' equators and attach to the spindles at the centromeres. * As before, anaphase II is when the chromatids (now individual chromosomes) separate and move towards the cells' poles. Again, the assortment of these chromosomes is random. Therefore, if crossing over has rearranged some of the genetic information these rearranged chromosomes are randomly assigned to one or the other pole. * During telophase II the two cells become four cells, each with a nuclear membrane surrounding the single set of chromosomes which gives each gamete its haploid number.
Chromosome crossover

At the start of meiosis, during prophase I, the pairing of the homologous chromosomes means that the four chromatid strands can become intertwined. At this time the strands may be exposed to pressure at points of overlap (called chiasmaplural chiasmata) and breaks may occur. Enzymes quickly repair these breaks, but often the "wrong" strands are rejoined, leading to new combinations of genetic information in the repaired chromatids. This process is known as crossing over and it can result in either more or less desirable combinations of genes in the gametes which are eventually formed and contain the new gene combinations. This, in turn, leads to individuals with new characteristics which may make them better or worse suited to sur5 VCE Unit 4 Chapter Summaries
p.

vival. The resulting variation amongst individuals in a population is a major contributor to the explanation of Natural Selection (more about that later).
Genotype

The genotype of an individual refers to that individual's genetic makeup. It is the total of all the genes that person possesses on his/her chromosomes. Often, in discussing inheritance, we consider only a few of the individual's genes and then the term genotype refers to the particular combination of these genes of interest that the individual possesses. Because somatic cells have two copies of each chromosome (the homologous pairs), each gene is represented twice in each cell. Normal homologous chromosomes always have the same gene at the same position (the locusplural loci). But mutations may have, over many generations, caused slight differences in the base sequences of the genes in different individuals (and in the gene products), so that the gene may exist in two or more different forms. These different forms of a gene are termed alleles. The alleles of any particular gene are often represented by letters. If there are only two possible alleles, capital and lower-case letters are used. So for a gene with two alleles, we could label the alleles A and a. If the individual has two alleles the same, either genotype AA or aa, this is described as being homozygous. An individual with different alleles has genotype Aa and is heterozygous. (Some texts use the term hybrid as a synonym for heterozygous, but this can lead to confusion and should be avoided.) Some alleles are found to be dominant over their alternative allele. This means that if an individual has either one (genotype Aa) or two (AA) copies of the allele its effects will always be seen. A dominant allele is always assigned a capital letter, hence it is A in the example given. The alternative allele (a), is said to be recessive. The effects of the recessive allele are only observed when no dominant allele is present, that is in an individual who is homozygous for the recessive allele.

p.

VCE Unit 4 Chapter Summaries

Phenotype

The observable effects of the alleles an individual possesses are called the phenotype of that individual. Depending on the nature of the genes in question, the phenotype may be structural (some particular visible characteristic, e.g. fur colour), functional (something to do with the organism's metabolism, e.g. ability to digest lactose) or behavioural characteristics (the ability to do something, e.g. make sexy movements which attract many mates). Clearly, different methods need to be used to 'observe' the different phenotypes described above, but the important point is that the differences can, with appropriate methods, be observed. In the simplest cases, only one gene, and its alleles, controls a particular characteristic (or trait). An example of this is the famous tall and short pea plants studied by Mendel. But in many cases, a number of genes (and all of their possible alleles) have an effect on a particular trait. This is polygenic inheritance and is responsible for the continuous variation seen in some traitsfor example human height. This is discussed further under Real-world Genetics on p. 11.
The influence of the environment on phenotype.

Whilst the genotype of an individual determines what that individual can become, it is not the only factor in determining the individual's phenotype. For example, with inadequate nutrition and exercise, a person with the genetic potential to be an Olympic heavyweight weightlifting champion may end up as a proverbial "90-pound weakling". Similarly, when an apparently healthy population of individuals moves from one location to another location with markedly different conditions it may be found that some individuals possess previously unknown abilities to survive in the new conditions whilst others rapidly deteriorate. This relationship between an individual's genotype, the environment in which he/she/it lives and the observed phenotype is often summarised in the following "equation":
Genotype interacting with Environment Phenotype

In discussing the relationship between genotype and phenotype the influence of the environment of the individual must not be overlooked.
Mutation and Mutagens

A mutation is a change in the genetic material in a cell. That is, the sequence of bases in a part of the cell's DNA is altered in some way. Since the processes of duplicating genetic information and passing it on to either the next generation of cells or the next generation of individuals are complex, it is hardly surprising that mistakes sometimes occur. These mistakes lead to the changes which are mutations. Not all mutations are harmful. Many mutations have no effect or cause minor harmless effects in the organism. Occasionally a mutation may be beneficial to the organism. Sometimes, however, mutations are harmful or even lethal. The effect of a mutation is entirely dependent on the amount and location of the DNA which it alters. Chromosomal mutations involve segments of chromosomes, whole chromosomes, and even entire sets of chromosomes. There are four types of chromosomal mutations: * Deletions involve loss of part of a chromosome. * Duplications (or additions) are where a portion of a chromosome is repeated. * Inversions occur when a portion of a chromosome becomes oriented in the reverse direction. * Translocations occur when a portion of one chromosome breaks off and attaches to another, non-homologous chromosome. (These usually occur in pairs, so both of the chromosomes involved lose a piece and gain another, wrong, piece.) Nondisjunction is the cause of chromosomal mutations which involve whole chromosomes or sets of chromosomes. This is the failure of homologous chromosomes to separate properly during meiosis (see above). The resulting gametes will have more or fewer chromosomes than they normally would. Nondisjunction of human chromosomes can lead to a number of disorders. Sometimes it is fatal, depending on the particular chromosomes involved. When all the homologous chromosomes fail to separate during meiosis the gametes which are formed are not haploid. Depending on the other gamete involved in fertilization, the resulting offspring may be triploid (3N) or tetraploid (4N). This condition is known as polyploidy and is almost always lethal in animals. Polyploid plants, however, are often larger and hardier than normal plants. Gene mutations involve individual genes. The smallest gene mutation is a point mutation where only one base is affected. If this is just a change to a different base, the effect may be minimal, although if the change causes a change in the amino acid sequence of a polypeptide the effect may be major. However, if a single base is added to or deleted from a gene, the whole sequence of bases is altered and so the codons become changed. This is a frameshift mutation and it can completely change the polypeptide product of the gene. The extent of the change in the polypeptide product depends upon where, in the gene, the frameshift mutation occurs. The consequences of this, in terms of the functioning of the organism can be disastrous. A somatic mutation is one which occurs during mitosis in an individual's body cell. This type of mutation will be passed on to all cells in the cell line in which it arose. If there are still plenty of normal cells surrounding the mutated cell/cells, the normal cells may continue to provide enough normal gene product that the affected cells do not influence the functioning of the organism. 7 VCE Unit 4 Chapter Summaries
p.

Mutations also occur in mitochondrial DNA. These are similar to somatic mutations since mitochondrial DNA (mtDNA) reproduces by a mechanism similar to mitosis. Since this mechanism does not allow for 'crossing over' and the mixing of genes seen in meiosis, changes accumulate much more slowly in mtDNA than in chromosomal DNA. Also, since mitochondria are inherited along the maternal side of any population (think about the structure of the ovum and the sperm and the details of fertilisation to explain this), this too slows the rate of accumulation of mtDNA mutations in a population. Mitochondrial DNA mutations are of interest to scientists in establishing 'relatedness' between individuals, especially in attempting to determine evolutionary links between and within species. Mutations which affect the ability of cells to regulate their own growth and reproduction may cause cancer. In this case tumours may form and the normal functioning of tissues may be so severely impaired that death occurs. A mutagen is a substance or agent which increases the frequency of mutations in organisms. Many different chemicals (such as nicotine) are known to be mutagens as are many forms of radiation (e.g. x-rays). A mutagen which causes cancer is known as a carcinogen. This information was current at 15 August 97 and might have changed subsequently.

Gregor Mendel's Legacy


Introduction

Whilst these notes have started with some of the molecular biology of the gene that is known now, the discovery of the gene and its role in inheritance of characteristics came well before the structure and function of DNA was discovered. Since it would be almost impossible to find a student course of genetics which does not mention the scientific history behind this area of biology, we should not let this be ignored here.
Gregor Mendel

Gregor Mendel, an Austrian monk who experimented with breeding experiments in the garden pea, Pisum sativum, is credited with being the "father" of the science of geneticsheredity. He did not know about chromosomes or DNA, nor did he know about genes as we do today. However, he performed many experiments in which he controlled the breeding of his pea plants. By observing the number and types of phenotypes in the offspring plants he developed the rules of inheritance known today as Mendel's laws.
Mendel's Laws

* The law of segregation states that members of each pair of alleles of a gene separate when gametes are produced in meiosis. * The law of independent assortment states that pairs of alleles separate independently of each other during gamete formation. We now know that this is only true for genes located on different chromosomes.
Mendel's Experiments

Mendel's experiments usually involved three steps: 1. Mendel allowed the peas to self pollinate (pollen from the plant was used to fertilise the flowers of the same plant) for several generations. He continued this until he obtained pure breeding plants for the trait he was investigating. (Pure breeding plants produce offspring identical to themselves every time.) Mendel chose these plants as the parents of the next step, therefore he called them the P generation (P for parental). 2. Mendel cross pollinated (took pollen from one plant and used it to fertilise a different plant) two varieties from the P generation that exhibited contrasting phenotypes (eg purple/white flowers). He called the offspring of this cross the first filial generation, the F1 generation. (filial= "brothers and sisters") 3. Finally, he allowed members of the F1 generation to self pollinate. The offspring of this breeding were called the F2 generation. He counted the numbers of offspring with each of the parental phenotypes in this generation. For each of the hundreds of experiments that Mendel performed, using a variety of traits, he found that the F1 generation always had offspring displaying only one of the parental traits. However, the F2 generation was seen to display both of the parental traits in a ratio, which was calculated over many thousands of plants, of 3:1 . Mendel described the trait which was always seen in the F1 generation as dominant. This was also the most frequently observed phenotype in the F2 generation. The trait which disappeared in the F1 generation, but appeared in 25% of the F2 generation, he called recessive. Putting together these observations of Mendel's and what we now know about chromosomes, genes, alleles and meiosis, it becomes possible to understand these basic genetic experiments. It is important to remember that predicting the outcomes of genetics experiments is based on probability, and that if enough repeats are performed the theoretical outcome becomes more likely. However, chance is just that, and the theory and result do not always match very well!
Monohybrid Crosses

A simple monohybrid cross is one in which data about one gene with two alleles is obtained. For a simple Mendel's pea experiment, using pure breeding tall (genotype TT) and short (tt) plants as the P generation, the theoretical outcomes for the F1 and F2 generations can be calculated:
P generation: Phenotypes: Tall X Short p.

VCE Unit 4 Chapter Summaries

Genotypes: TT X tt Gametes: (T or T ) X (t or t)

This shows us the possible offspring genotypes (in the F1 generation) from the gametes of the parents:
F1 generation: Phenotypes: 100% Tall Genotypes: 100% Tt

Using members of the F1 generation to breed the F2 generation, the same process is used to predict the outcome:
F1 generation: Phenotypes: Tall X Tall Genotypes: Tt X Tt Gametes: (T or t) X (T or t)

This shows us the possible offspring genotypes (in the F2 generation) from the gametes of the F1 generation:
F2 generation: Phenotypes: 75%, or , are Tall; 25% or are Short Genotypes: 25% or are TT; 50% or are Tt; 25% or are tt

9 VCE Unit 4 Chapter Summaries

p.

Remember that: * TT would be described as homozygous dominant, * Tt would be described as heterozygous (NO dominant or recessive needed here!) * tt would be described as homozygous recessive. In the phenotype and genotype statistics,the numbers can also be expressed as ratios. In the above example, the ratios are:
Phenotype ratios: Tall : Short = 3:1 (as Mendel found); genotype ratios: TT:Tt:tt = 1:2:1

Exam questions sometimes ask for predictions of numbers or ratios of offspring in a genetic cross. Many students lose marks because they get the arithmetic wrong! Take care with this, and show all your working, especially Punnett squares, when arriving at your answer. This way, you should get most of the marks, even if you do mix ratios, fractions and percentages! And PLEASE do lots of examples of monohybrid cross problems when you study this section.
ONE MORE TIP: When you hand-write the genotypes in a question involving two alleles, it is often easy for upper- and lower-case letters to ook very similar. The letters W/w, S/s are M/m are examples. If an exam script marker cannot distinguish between them, you will get no marks! So make an effort to write very clearly in questions such as these, or your knowledge and good work may be wasted. Lethal Genotypes

Occasionally, "tricks" can appear in apparently straightforward monohybrid cross questions. The most common of these is that the expected ratios in the F2 generation are not observed. This is almost always explained by one of the homozygous combinations being lethal. This means that individuals with the lethal genotype fail to develop and they die as embryos or perhaps they die immediately after birth. Let's consider this possibility for the genotype and phenotype ratios of the F2 generation in the previous example:
If TT was lethal? (That is, the TT offspring are all dead!) Phenotypes: Tall:Short = 2:1 OR 66.6% Tall, 33.3% Short OR 2/3 tall, 1/3 Short Genotypes: Tt:tt = 2:1 OR 66.6% Tt, 33.3% tt OR 2/3Tt, 1/3tt If tt was lethal? (Here the tt offspring don't survive) Phenotypes: All offspring (100%) are Tall Genotypes: TT:Tt = 1:2 OR 33.3%TT, 66.6% Tt OR 1/3TT, 2/3Tt Dihybrid Crosses

A dihybrid cross involves two pairs of contrasting traits. In the simplest dihybrid crosses, it is assumed that the genes for the traits are located on different chromosomes and so Mendel's laws are true for them. Predicting the results of a dihybrid cross is rather more complicated than a monohybrid cross because one needs to consider all the possible combinations of the two alleles for the two traits in each parent's gametes and then all the possible gamete combinations at fertilization. A Punnett square is again used and if you recognise that the most complex dihybrid cross requires a 4x4 (16 cell) Punnett square for the offspring, with plenty of practice all possible dihybrid cross questions become easy. The following example illustrates this. In guinea pigs the allele for short hair (S) is dominant over the allele for long hair (s). (Note that although short hair is "little hair" the allele symbol is "big S" because it's dominant.) The allele for black hair (B) is dominant over the allele for brown hair (b). Suppose two guinea pigs, both heterozygous for both traits, mate. What are the theoretical types and ratios of the phenotypes and genotypes of the offspring? (This is the most complex possible dihybrid cross!) Parents: Phenotypes: short black hair X short black hair Genotypes SsBb X SsBb Gametes SB, Sb, sB, sb X SB, Sb, sB, sb (There are two genes and their alleles to consider in producing these gametes, the S/s gene is on one chromosome, the B/b gene is on a different chromosome. There are 4 possible ways the alleles for these genes can combine during meiosis and be segregated into the gametes.)
SB SB Sb sB sb SSBB SSBb SsBB SsBb Sb SSBb SSbb SsBb Ssbb Sb SsBB SsBb ssBB ssBb sb SsBb Ssbb ssBb ssbb

Now comes the (tedious) task of counting all the genotypes and assigning phenotypes! Offspring: p. 10 VCE Unit 4 Chapter Summaries

Genotypes SSBB 1/16 + SsBB 2/16 + SSBb 2/16 + SsBb 4/16 SSbb 1/16 + Ssbb 2/16 ssBB 1/16 + ssBb 2/16 ssbb 1/16

Phenotypes 9/16 will have short black hair 3/16 will have short brown hair 3/16 will have long black hair 1/16 will have long brown hair

After doing several of these problems, you will immediately recognise the phenotype ratios of 9:3:3:1 as the theoretical outcome of a heterozygous dihybrid cross. Please do lots of examples of dihybrid cross problems. These questions on Biology GA 3 exams have been answered poorly in the past, so here is a chance to pick up some marks that others may not get! But you'll need plenty of practice to become an expert at these!
Incomplete- and Co-dominance

The relationships between genes and their alleles are not always as simple as the dominant/recessive independently assorted traits described so far. Most of the time, genes show more complex patterns of heredity. In some organisms, heterozygous individuals display a phenotype somewhere between the two homozygous phenotypes. An example of this is in snapdragon flowers:
GENOTYPE RR (or better, R'R') Rr (or better, R'R) rr (or better, RR) PHENOTYPE Red flowers Pink flowers White flowers

This is a case of incomplete dominance, where the heterozygous individual shows neither one nor the other of the homozygous phenotypes, but is somewhere in between. The pink petals of the heterozygous plants' flowers can be demonstrated to have less of the red pigment in them than is found in red flower petals. Petals of white flowered plants have no red pigment at all (and are therefore white). It is wise in this case NOT to use the symbols R/r for the alleles, because, as we have defined them earlier, this notation implies dominance (R) and recessiveness (r). Therefore, the symbols R' for having red pigment and R for no pigment are a better choice. It is still best to retain the same letter, and distinguish between the alleles with absence/presence of a superscript ( i.e. R and R'). The introduction of another letter (such as R for red and W for white alleles of the pigment gene) can lead to confusion about whether it is one gene with two alleles or two genes. In other cases, two dominant alleles are expressed at the same time. This also results in a mid-way phenotype in the heterozygous individual but for slightly different reasons. The roan coat of horses illustrates this:
GENOTYPE R'R' R'R RR PHENOTYPE Red hairsred coat Red hairs AND white hairsroan coat White hairswhite coat

This phenomenon is known as co-dominance. Sometimes it is difficult to distinguish between incomplete dominance and co-dominance as the heterozygote in both cases can appear to be somewhere between the two homozygote extremes. But if the heterozygote is "blended", (as in pink flowers) the inheritance is usually described as incomplete. But if the heterozygote clearly shows both of the homozygotes features (as in red-and-white striped carnations with genotype R+R-, or in the blood group phenotype AB which corresponds to the genotype IAIB), then it is co-dominance. This concludes the basic genetic theory for Area of Study 1. But, as in all areas of biology, genetics can get far more complicated than this. The final section in Area of Study 1 is covered in the next section, called Real-world Genetics. [Note: This next section was last updated on 15 August 97, so is now quite dated in parts.]

Realworld Genetics
Multiple Alleles

Some traits have genes with more than two alleles. These are called multiple alleles, but any one individual can still have only two alleles for any gene (one on each of the homologous chromosomes). A human blood group gene provides an example of this, as well as an interesting dominance relationship. There are three A,B O blood group alleles, usually given the symbols IA, IB and i. IA and IB are codominant to each other, but are both dominant to i . Since any individual only has two alleles, there are four possible blood group phenotypes but nine possible genotypes.
Polygenic Inheritance

11 VCE Unit 4 Chapter Summaries

p.

When several genes influence a trait, such as the genes for height or weight, it is difficult to determine the effect of any one of these genes. Such traits, with many genes influencing them, are examples of polygenic inheritance. Assuming that the genes are on different chromosomes, we know that they will segregate independently during meiosis. Polygenic inheritance then becomes a genetic problem of at least the complexity of a dihybrid cross (for two genes) and possibly much more complex (if more than two genes are involved). The resulting variety of possible genotypes can give a large number of phenotypes, and when the influence of the environment is also considered, it is hardly surprising that almost every possible variety of phenotype can be observed in a large population. This is termed continuous variation.
Linkage Relationships

If the chromosomes in a gamete-producing cell are not broken up or rearranged during meiosis, it would be expected that all the genes on a particular chromosome would be transferred together into whichever gamete gets that particular chromosome. That is, the genes are linked together on their chromosome. Linked genes (i.e. genes on the same chromosome) would be expected always to be inherited together unless something happens during meiosis to separate them. In a classic experiment using Drosophila (fruit flies) the geneticist T.H. Morgan demonstrated this linkage. The results of this experiment follow:

p. 12

VCE Unit 4 Chapter Summaries

G = grey wings, g = black wings AND W = normal wings, w= small wings Parents:
Phenotypes Genotypes Gametes Grey normal wings GgWw (GW+Gw+gW +gw) X X X black small wings ggww all gw

These gametes assume that the genes for wing size and colour are on different, independently assorted chromosomesi.e. that this is a dihybrid cross between a parent heterozygous for both traits and a parent homozygous recessive for both traits. So we'll work out the EXPECTED genotypes and phenotypes in the offspring:
GW all gw GgWw Gw Ggww gW ggWw gw ggww

Now compare the expected results (from the Punnett square above) with the results T.H. Morgan obtained:
Genotype GgWw ggww Ggww ggWw Phenotype grey, normal wings black, small wings grey, small wings black, normal wings Theoretical % 25 25 25 25 Actual % 41.5 41.5 8.5 8.5

This seemingly odd result can be understood if it is assumed (correctly) that the genes for wing colour and size are actually on the same chromosome, but fairly widely separated. In this case the genes are usually inherited togetherfor example gametes of the first parent would mostly have GW or gw genotype unless crossing over swapped the ends of the chromosomes to (rarely) give the recombinants gW and Gw. So instead of all four gamete types being equally likely, and the 1:1:1:1 ratio of phenotypes being observed in the offspring, the apparently odd results are explained. The percentage of the recombinant offspring in a test cross such as this (a cross of the heterozygote with a homozygous recessive individual) gives an estimate of the distance between the linked genes. It is more likely that crossing over, and separation of the linked genes, will occur if the genes are widely separated on the chromosome. These types of linkage experiments are widely used by geneticists to build up chromosome maps. Chromosome maps, sometimes called linkage maps, are maps or diagrams of individual chromosomes on which lines are drawn to represent the genes known to be on that particular chromosome. The positions of the lines, and the distances between them, are determined by analysis of linkage data such as that described above.
Testcrosses and Backcrosses

Two more techniques used in genetics experiments are testcrosses and backcrosses. In a testcross, an individual who is homozygous recessive (say tt) is crossed (mated) with an individual with the dominant phenotype to determine that individual's genotype. (The dominant phenotype means that the genotype could be Tt or TT.) The phenotypes and ratios of the offspring of such a testcross reveal the unknown genotype. (Do the possible Punnett squares to satisfy yourself of the outcomes.) In a backcross, an F1 generation organism is mated back to one of its parents. If the F1 has the dominant phenotype and it is mated back to a parent with the recessive phenotype, then this is the same as a testcross. In this case the backcross may be used to gain genetic information about the other parent if this is not known. This type of mating can also be carried out to deliberately increase the inbreeding in the population. This can be useful in breeding plants or animals with desirable characteristics for farming.
Gender Determination

In humans, the gender of an individual is determined by the particular combination of one of the pairs of chromosomes that individual possesses. Because these chromosomes are so important, they are often called the sex chromosomes. They are given names, X and Y, in humans but other letters in some other species. Like the autosomes, the sex chromosomes are randomly assorted during gamete formation. Possession of two X chromosomes in humans gives the genotype XX and the phenotype female. The genotype XY gives the phenotype male. It is clear that in mammals it is the sex chromosome of the sperm which determines the gender of the offspring. Sperm can carry either an X or a Y sex chromosome. But all ova carry X chromosomes. So the sperm, either X- or Y-carrying, which is used to fertilise the ovum determines the gender of the offspringfemale XX or male XY respectively. In the interest of your complete biological education, you should know that gender determination in birds is significantly different from that of humans and other mammals. Birds' sex chromosomes are named W and Z. The female has the genotype ZW and the male has the genotype ZZ. So in birds, it is the particular ovum which determines offspring gender, as ova can contain either Z or W sex chromosomes. Bird sperm all contain the Z sex chromosome. (You'll notice that even in birds, I have called the 13 VCE Unit 4 Chapter Summaries
p.

female gametes ova. This is the correct biological term. However, in common language the term egg is used for a bird ovumtry to be biological and use the correct term in answering exam questions.)

p. 14

VCE Unit 4 Chapter Summaries

Many insects, including the honey bee, have an even more complex system of gender determination. There is only one sex chromosome, called X, but how many an individual has, and the environment, are the factors that determine not only gender but the role in the bee society that the individual plays:
Type of bee
DRONE (male) WORKER (female)

Chromosome compliment Haploid; sex chromosomes X0 (0 means absent)


Diploid; sex chromosomes XX

QUEEN (female)

Diploid; sex chromosomes XX

COMMENT Drones develop from unfertilised ova of the Queen bee. Drones can produce haploid sperm by mitosis Sterile workers develop from fertilised Queen bee ova. The larvae are raised in the absence of royal jelly. The workers do not produce gametes Queen bees develop from fertilised ova. Larva is fed royal jelly which is rich in protein. Queen bees produce gametes by meiosis. The haploid gametes (ova) may be fertilised to create females, or unfertilised to create drones

X-linked genes

Whilst it is true that the sex chromosomes have important information for the determination of gender, that is not all the genetic information that they carry. However, the X and Y chromosomes, unlike all of the autosomes, are not a completely "matched pair". In fact the Y chromosome is less than half the length of the X chromosome. Apart from the alleles determining "maleness", which are dominant to the corresponding alleles on the X chromosome, there does not appear to be much genetic information at all on the Y chromosome. The X chromosome, however, does carry some important genetic information and without at least one X chromosome life is impossible. In fact, there are over 150 traits mapped on the X chromosome. In a female, with XX genotype, normal dominant/recessive rules apply to the phenotype for these X-linked traits. But in the male, with only one X chromosome, the allele on that X chromosome will always be expressed in the phenotype as there is no corresponding allele on the Y chromosome to affect it. In working through problems concerning sex-linked, or more properly X-linked, genes, you need to keep track of both the X and Y chromosomes as well as the different alleles which an X chromosome may carry. An example will illustrate this. Red-green colour blindness, in which the green-sensitive cones in the retina are defective, is due to an X-linked recessive allele. The symbols needed to follow this allele through a Punnett square are
XC = X chromosome carrying the normal (dominant) allele Xc = X chromosome carrying the defective (recessive) allele Y = Y chromosome, with no allele for this gene on it

Suppose a woman with a colour-blind father, and a mother with no history of colour blindness in her family, marries a man with normal colour vision. What are the likely genotypes and phenotypes of any children they have? Woman's genotype must be XCXc (Since she has inherited XC from her normal mother and Xc from her colour blind father.) Man's genotype must be XCY (Since he has inherited XC from his mother which has given him normal colour vision, and he has Y from his father to make him male.) Punnett squares of possible gametes and resulting offspring gives us:
XC X
C

Y
C

X X

XCY XcY

Xc

XCXc

Children's phenotypes: 50% females:50% males (we knew that anyway!). Of the females, all normal vision, but 50% carriers of the affected allele. Male children expected to be 50% with normal colour vision, 50% colour blind. This is another area of the VCE biology syllabus where you would benefit from doing LOTS of practice problems.
Pedigree Diagrams

These are a convenient graphical way to follow the passage of a trait (just one trait per diagram) through many generations. They are used by animal and plant breeders, as well as people interested in human traits, to keep track of, and sometimes predict, the occurrence of the phenotype of interest. From the relationships within the pedigree, the genotypes of certain individuals may (but cannot always) be deduced. Some textbooks try to offer "rules" for interpretation of pedigree diagrams. Beware of these! They are complex to learn and they often don't work! There are, however, a few conventions which you do need to remember before you can work out the genetics of a family's pedigree: 15 VCE Unit 4 Chapter Summaries
p.

Generations in a pedigree diagram are numbered, by convention, using Roman numerals, starting with the parental generation, at the top of the diagram as generation I. The first filial generation, which we have called F1 earlier, would be generation II in a pedigree diagram. For convenience, the members of each generation are numbered across the line, from left to right, using normal numerals. Below are three pedigree diagrams. They represent the three most common forms of inheritance seen in genetics, autosomal dominant, autosomal recessive and X-linked recessive respectively.

p. 16

VCE Unit 4 Chapter Summaries

Pedigree 1: Inheritance of an autosomal dominant trait. Assign symbols D and d for the trait and determine the genotypes of the numbered individuals in the diagram. I II III
1 2 3 4 5 1 1 2 2 3

Pedigree 2: Inheritance of an autosomal recessive trait. Assign symbols R and r for the trait and deter-

mine the genotypes of the numbered individuals in the diagram. Since the trait is recessive, individuals who do not show it in their phenotype may be RR or Rr. If you cannot determine the second allele from the information given, the notation R? is acceptable.

I II III IV
1 2 3 1 1 2

Note that in this pedigree, individuals III1 and III2 are first cousins. The mating between them is shown with a double line as it is termed a consanguineous mating (= a mating between closely related individuals). Matings such as this increase the chances of a recessive gene in a family being expressed phenotypically.
Pedigree 3: Inheritance of an X-linked recessive trait. Assign symbols XR and Xr for the trait and determine

the genotypes of the numbered individuals in the diagram. Don't forget that males have a Y in their genotype! I II III IV 1 2 1 1 2

This is yet another area of the VCE biology syllabus where you would benefit from doing LOTS of practice problems.
Human Intervention in Genetics

Humans have been manipulating the phenotypes of useful species for thousands of years. Recently, understanding of the molecular biology of genes and their action has opened up new areas for humans to exploit. Whilst it is not appropriate to give lengthy descriptions here of all the ways DNA and genes are manipulated, you should read widely on this topic. It is not until you understand the many applications of our knowledge of the molecular biology of the gene that you will appreciate the potential that this area of biology has for the future.
Plant and Animal Breeding

By selecting plants (such as food crops) and animals for their desirable phenotypes and using them to produce the next generation, humans have been manipulating many species for hundreds of generations. The results are usually seen as desirable to the breeders and farmers who become more productive using the species produced by these selective breeding techniques. Occasionally, unwelcome outcomes develop from these breeding processessusceptibility to disease in crops such as wheat, skeletal problems in some 'breeds' of the domestic dog.
Recombinant DNA Technology

17 VCE Unit 4 Chapter Summaries

p.

It has recently (in the last 30 years) become possible for geneticists to use restriction enzymes to cut pieces of DNA from chromosomes. Once this is done, selected pieces of DNA may be inserted into the DNA from a different species, often a bacterium because these are so easy to grow quickly in large numbers. The altered transgenic organism might then express the information on the added DNA, producing the gene product, a polypeptide, often in large amounts. It is a simple matter, then, to "harvest" the desired protein, purify it, and use it for whatever purpose it is needed. This is the method now used to produce the hormone insulin for use by diabetics. In other cases, the transgenic organism, perhaps a plant such as a strawberry, will have acquired a gene which confers a specially desirable property on it. Strawberries have been altered to be resistant to frost and are therefore able to be grown in previously impossible locations. The possibilities for transgenic organisms are just unfolding. Used with care, these techniques may improve the quality of life for all humans. Cloning (NB the information below was current in 1997lots has happened since) Once an organism with desirable characteristics has been developed, either by selective breeding or by genetic engineering techniques, the special set of genes it possesses may be maintained if all future reproduction is by mitosis. Remember that mitosis accurately transfers genetic information from generation to generation of cells with little opportunity for alteration of that information. On the other hand, meiosis, and sexual reproduction, mixes up the genes both within the gametes and during the process of fertilization. By carefully controlling the conditions in which a sample of tissue is suspended, molecular biologists can establish many generations of identical cells. This is known as cloning. A clone is a large population of genetically identical cells, derived from one original cell. At the level of the whole organism, a clone is a number of genetically identical organisms, produced from one original parent organism. This is relatively easy to achieve in plants, where cuttings, tissue culture and grafting are all methods of reproduction by mitosis to give new plants or parts of plants. In bacteria, this is the normal mode of reproduction, although some strains of bacteria do, under some circumstances, exchange genetic material in a form of sexual reproduction. In mammals cloning is much more difficult to do. Earlier this year, Scottish geneticists reported cloning a sheep, Dolly, using the nucleus of a somatic cell and implanting that into an enucleated ovum from a different sheep. The ovum was then implanted in a receptive ewe's uterus and developed into a lamb which was named Dolly. No-one knows yet exactly how Dolly will develop, and whether or not it will be normal in all respects. Very recently, American scientists have reported the cloning of a cow. Not surprisingly, they named their clone Gene! This interesting new technology will provide more news in the futurekeep listening for the latest!
Medical Applications

The increased understanding of chromosomes, genes and genetic engineering has led to many improvements in the way doctors treat their patients. Genetic counseling can identify the risks of members of families inheriting unpleasant genetic disorders. Genetic engineering techniques can produce high quality products for use in treatment of a variety diseases and disorders. It can also be used to examine, at the molecular level, the chromosomes of people at risk of inherited disorders. Gene therapy is just beginning to be used to replace defective genes in people with life threatening diseases. There are many ethical issues related to the practices being developed in applied biotechnology.

Area of Study 2
Variation within Populations
Causes of variation between individuals in a population

The variations we see in the phenotypes of individuals of any single species can be quite spectacular. Look around a group of Homo sapiens and variation is evident immediately. Since we know that phenotype = genotype + environment we can conclude that the genotype, that is the DNA, of the individuals must be responsible for at least some of the variation we see. In fact, if a number of individuals of a species have identical genotypes, usually as a result of their propagation by means of asexual reproduction, we observe that they also have identical phenotypes. Such organisms are often called clones. However, if a number of clones, for example 20 identical azalea plants sold to 20 different people in a nursery, are subjected to different environments, the 20 different gardens to which they are taken home, they will surely display a variety of phenotypes in a number of years. Some of the plants will be growing vigorously and flowering brilliantly, some will be struggling, some will be covered with insect pests and some will be dead ... all from the same genotype! The environment has a profound influence on the variability of the phenotypes of genetically identical individuals! Such simple observations as these demonstrate the biological basis of variation and lead us into the consequences of that variationNatural Selection and Evolution.
Genetic Effects

If variations in organisms' phenotypes are to be explained in terms of variation in DNA composition, we need to consider how such variation between individuals could arise.
p. 18 VCE Unit 4 Chapter Summaries

Mutations

A mutation is a change in the DNA of an organism which may or may not have an effect on the genotype and phenotype. Normally, mutations are rare and random events, but under certain environmental conditions, this may not be true. Since DNA is a complex molecule, there is a number of ways it can be altered. This has been described in more detail under "New Proteins, Cells and Individuals". Basepair substitutions occur when one nucleotide and its partner from the other DNA strand are replaced with another pair. Since these substitutions only occur at one site on the DNA strand they are sometimes called point mutations. Point mutations often cause no effect at all (not all DNA codes for protein synthesis), but minor changes to proteins may occur (if one amino acid is altered but not in a way that changes the protein's function too much), and occasionally such mutations may be lethal (protein product absent or non-functional). Mutations which involve insertion or deletion of segments of DNA into a chromosome are also known. If these involve lengths of DNA which are not a multiple of 3 bases, the triplet code of whole exons can be changedthese are then called frame shift mutations. Because long segments of DNA can be changed in this process, these are more likely to result in changes to protein products. Such changes are mostly for the worse, but at times an improvement to structure/function is the result. It is often said that mutations provide the raw material on which Natural Selection will act. If this is true, the altered chromosomes need to be passed on to offspring of the individual in which the original mutation arose. In sexually reproducing organisms, this means that: Only mutations which occur during gametogenesis can be passed on to offspring; Somatic (body cell) mutations die with the body in which they arose.
Sexual Reproduction

In order to understand why sexually reproducing species show much greater variation than asexually reproducing species, you need to review the details of sexual reproduction. Focus your attention on where the homologous chromosomes can go, and how not all the gametes from one parent are identical. Meiosis is the process by which gametes are formed. Gametes are haploid, but somatic cells are diploid. During meiosis, chromosomes replicate and become entwined. During this period, breaks in homologous chromosome pairs occur quite frequently. This is known as crossing over and when enzymes repair the breaks, recombination of the strands of DNA occurs, but not necessarily in the original form. In this way alleles can "swap" from one chromosome to another, sometimes with marked consequences to the offspring which inherits the new combination. Even if crossing over and recombination did not occur, the fact that the homologous pairs of chromosomes (with their individual allele compositions) are randomly assorted into the gametes makes many different sets of genes possible in the gametes. (An organism with a haploid number of 3 can be shown to produce 8 different combinations of gametes, the relationship is n = 2n , where n = no. of different gametes, N = haploid no. of the organism. For humans, with a haploid no. of 23, this means that there are 8 388 608 ways those chromosomes may be combined in a gamete!) (No, you do not have to remember this.) The final way that chromosomes and their alleles become dispersed through a generation is in the process of fertilisation, the union of two haploid gametes, from different parents, to form a new diploid individual. (In the above example, the organism with haploid no. of 3 could produce 8 x 8 different combinations of offspring from one pair of parents. For humans, the number is (8 388 608)2 or approximately 7.03 x 1013! (You don't have to remember this either). And we still haven't factored in crossing over or mutations! Once the gametes have united in fertilisation, the diploid zygote begins the long process of repeated mitotic divisions, each one resulting in diploid cells of identical chromosome composition. Eventually differentiation of the growing mass of cells occurs and tissues, organs and functioning systems develop. These are the somatic cells, all diploid, all containing the full compliment of genetic information, but differing in which particular genes are "switched on" in each cell type. A mutation in one of these cells may affect the functioning of that cell, and all those which form by mitosis from it. But unless the cell is a gamete producer, such effects cannot be passed on to future generations.
Gene flow

Gene flow is the exchange of genes between populations of a species. For example, the various populations of magpies found in different locations around Australia do not usually interbreed, and they have observably different phenotypes in different areas. However, if some magpies migrate between locations, and interbreed with the magpies in the new location, their genes have 'flowed' out of the original population and into the second population. This introduction of new genes into a population is often beneficial as it may supply the so called hybrid vigour which increases the survival potential of the next generation of individuals. Can you think of another animal species where interbreeding between previously isolated populations is allowing gene flow between groups? (Keep reading this page, you'll find the answer later.)
Environmental Effects

We already know that the environment can play a significant role in the phenotype of individuals. Nutritional requirements must be met, disease can alter phenotype and physical damage is always a 19 VCE Unit 4 Chapter Summaries p.

threat to individuals. Other environmental factors can be shown to play a part in altering DNA, or in selecting for certain individuals.
Variation in Habitat

The earlier example of a clone of azalea plants taken to 20 different habitats provided a somewhat artificial example of the effect of habitat ( = living place) on organisms. In nature, this can be seen to be true in populations of organisms, perhaps living close to each other, but in an area where there is a gradual change in some feature of the environment. Some of these features which may affect the growth and survival of plant or animal species include: * Water availability * Nutrient (food) availability * Temperature range * Altitude * Shelter from wind As the population's exposure to the environment changes, some individuals will be better able to survive there than others of the same species. The reason for the difference in the ability to survive is in the genes of the individuals. But it is not until some factor in the environment reveals the survival advantage some individuals possess, that such a genetic difference becomes important. This is the basis of Natural Selection, about which there is more below.
Clines

Gradually varying phenotypes and genotypes of a species over a range of geographic locations are called clines. A species that varies with geographic location in this way is said to show clinal variation. One of the most obvious examples of clinal variation is in the population of the species Homo sapiens. If we consider the many groups of humans in the world that we call 'races' this idea of clinal variation is well illustrated. Although we all belong to the same species, different environmental pressures have, over time, selected for different phenotypes (and different genotypes) in different geographical locations. With the ease of world travel these days, many H. sapiens are moving away from their traditional geographic locations. Gene flow is occurring between the groups and some interesting, and often very beautiful, offspring are produced.

p. 20

VCE Unit 4 Chapter Summaries

Mutagens

Mutations were described at the molecular level earlier on this page and in the section called New Proteins, Cells and Individuals. A number of physical and chemical agents in the environment, known collectively as mutagens, can interact with DNA to increase the frequency of mutation. Some mutations have been shown to be temperature sensitive, that is, the altered protein functions normally at a certain range of temperatures, but not outside this range. If this type of mutation extends the range of tolerance of an organism, it could be of great benefit. In practice, such mutations generally reduce the tolerance limits of the protein and so are disadvantageous. With the current trend towards global warming due to the greenhouse effect, such temperature sensitive mutations may become important in the survival (or not) of some species. Radiation, such as in X-rays and ultraviolet rays, may be increased in the environment due to human activity, but a constant natural source of such radiation is the sun, and this is undoubtedly the reason for some of the spontaneous mutations which occur with measurable frequencies. Mutagenic chemicals can be the product of bacterial metabolism, viral activity inside cells, digestive processes or nonspecific defence to foreign organisms. In recent times, human activity has added many new chemicals to this list. As stated before, mutagens and the mutations they cause can produce somatic changes in eukaryotes, or they can affect developing gametes. The outcomes for evolution are vastly different!

Natural Selection
Introduction

Long before Charles Darwin published The Origin of Species people had tried to explain the diversity of living things they observed around them. Theologians had a nice, convenient story of creation, and for many hundreds of years that belief satisfied almost everyone. (If it's still good for you, that's fine, but please keep on reading, because you will not get marks for exam questions with a creationist answer.) But, as always, there were the sceptics who needed scientific 'proof' and set about forming and testing their own hypotheses. One of the popular explanations for species diversity around Darwin's time came from Jean-Baptiste Lamarck. Lamarcks theory of acquired characteristics was so popular that it is today often known as 'Lamarckism', but scientists can find no evidence to support this theory any more. (You should read a little about Lamarckism from a biology text, just to know how NOT to answer exam questions.) Whilst reading of The Origin of Species is probably not high on your priority list at present, I'd recommend that if you're seriously interested in understanding where the planet's species, including our own, came from, it is a fascinating piece of writing and scientific deduction. In brief, Darwin, during his journey around the world on HMS Beagle made detailed observations of the animals and to a lesser extent the plants he found. On his return to England, he pondered these observations for many years, trying to make sense of them and explaining the patterns he had observed. It was many years before he published the book which still underpins what scientists now believe about species, their evolution and their relationships. Here is an outline of Darwin's observations (O) and deductions (D): (As you read this list think about a few species other than humanswe tend not to obey Darwin's "rules", with consequences which may prove to be fatal!) * All species produce far more offspring than are needed to replace the parents. (O) * Although populations fluctuate in numbers, they do so about a mean (average number) which usually does not change much. (O) * Therefore most offspring must die without reproducing. (D) * Within a population individuals vary. No two are exactly alike. (O) (Yes we all know about identical twins, but how common are they in the animal kingdom?) * Therefore some individuals, the "fittest", have a better chance of surviving to reproduce. (D) * Since most variation has at least some genetic basis, the second generation (the offspring of the fittest in the previous generation) will resemble their parents more than those that did not survive. (D) * If the survivors are not the 'average' for the population, then over many generations, the population will slowly change. (D) Add to Darwin's theory another 100+ years of scientific investigation, especially the advances in molecular biology techniques of the recent past, and we have a story that's difficult to dismiss:
The Genetic basis for Natural Selection

The origins of variation within a population are mutation and random assortment of chromosomes during meiosis. These mechanisms, then, can be considered as the genetic basis for natural selection. Without variation within a population, there could be no natural selectionthe population would either survive or die as minor environmental changes were encountered, since all members of the population would be genetically identical and all would be equally well or badly equipped to deal with the changes. Natural selection can be described as the varying success in reproduction of different phenotypes resulting from their interaction with the environment. Therefore, unless there are different phenotypes in 21 VCE Unit 4 Chapter Summaries
p.

a population, there can be no natural selection. There are three common ways that natural selection can act: Stabilising selection removes the extreme variants from a population, reducing the trend towards phenotypic variation and maintaining the status quo. This is most likely to be the case where an environment is itself stable. Directional selection shifts the overall make-up of the population by favouring one extreme phenotype. This is likely to occur when the environment undergoes a marked change. The case study of the Biston betularia (peppered moth) illustrates this. (Look this up in your textbook, it's almost certain to be there.) Diversifying selection favours the extremes over intermediates. If the environment of the species contains two different features (eg. in background colourlight/shade) two different phenotypes have a selective advantage, depending on location. Another form of natural selection occurs in species where the males and females are very different in appearances or behaviour, apart from the physiological differences due to gender. This is called sexual dimorphism, an example of which is plumage (feather colour) differences in male/female birds. This can itself, be an agent of natural selection, with the best plumed male birds gaining the largest number of matings within their population. This ensures that the genes for the "desirable" traits are passed on to the next generation and that genes from the "less desirable" males are reduced or eliminated.
The Gene Pool

The gene pool can be defined as the total aggregate of genes, and all of their alleles, in a population at any one time. For a diploid individual, each gene locus is represented twice in the genome, and the two alleles may be the same (homozygous) or different (heterozygous). There may, however, be more than two alleles for a gene within a population's gene pool (e.g. the ABO blood groups in humans), although each individual can only have two of those alleles. If a population of a species is stable and non-evolving, the composition of that population's gene pool is constant, since it is in equilibrium. This is known as the Hardy-Weinberg Equilibrium and it can be demonstrated mathematically to be true. It is stated as follows: No matter how many generations' alleles are segregated by meiosis and combined by fertilisation, the frequencies of the alleles in the gene pool will remain constant unless acted on by other agents. For this to be true, five conditions must be met: 1. The population must be very large. 2. The population must be isolated. There must be no migration of individuals into or out of the population. 3. There are no net changes to alleles due to mutations. 4. Mating is random. 5. All genotypes are equal in reproductive success. Whilst these conditions can be approached in nature, they are never achieved for very long.
Population Genetics

Population genetics is the scientific study of gene pools and the genetic variation within populations. Because the five conditions for Hardy-Weinberg equilibrium are seldom maintained for many generations, gene frequencies in gene pools do change. If a population is small, genetic drift may occur. Chance events in matings may cause the allele frequencies to drift randomly from generation to generation. (e.g. toss a coin 10 times, you will not necessarily get 5 heads and 5 tails.) Only luck would result in these random changes improving adaptations. Sometimes non-representative sub-groups of a larger population become isolated. This can lead to the founder effect, where a new, different allele frequency exists in the founding population and is maintained in subsequent generations. This can be seen in some small isolated populations of humans where the frequency of inherited diseases is high and can be traced back to an original founder of the settlement. The bottle-neck effect is similar to the founder effect. It can be seen when a population is reduced to a very small number, such as by natural disaster or recently by unnatural activity imposed by humans (e.g. hunting of gorillas to near extinction). The allele frequencies in the surviving population may not reflect the original larger population so phenotypic variation may be reduced. A phenotype with an environmentally poor survival outcome is less likely to be maintained in a population, and the frequencies of the alleles which code for this phenotype would be expected to decrease in the population's gene pool. Since most populations are not entirely reproductively isolated, the population may gain or lose alleles by gene flow, the migration of fertile individuals or the transfer of gametes, between populations. A new mutation that is transmitted to gametes must immediately change the gene pool by substituting one allele for another. This is true whether or not the mutated allele is "new" to the gene pool, although the effects of a mutation are likely to be more pronounced if it gives rise to a new phenotype better or worse. Non-random matings are more common that one might first expect. In many populations, family groups stay within loose geographical boundaries within the larger group. This can lead to localised inbreeding and pockets of very different allele frequencies within the larger group. Similarly, if individup. 22 VCE Unit 4 Chapter Summaries

als with a particular phenotype are perceived as more desirable mates (e.g. Elle MacPherson compared with Elle MacFeast or James Hird compared with John Howard!), the "desirables" (assuming that they are willing to mate with multiple partners!) are more likely to pass on more of their alleles to the next generation. This is termed assortative mating. Similarly, a genotype which leads to a phenotype with a positive survival advantage in the face of a changing environment would be expected to increase in a population's gene pool over many generations. This is the basis of natural selection.
The struggle for survival

All species have such great potential fertility that their population size would increase exponentially if all individuals born would eventually reproduce, at their full potential. The fact is that populations are generally relatively stable in size, except for seasonal variation. What keeps populations constant? Why do some survive? Why do many die? The answers to these questions all help explain the struggle for survival which occurs constantly in all populations of all species, including our own.
Selection Pressures

Selection pressures are those biotic and abiotic factors of the environment that can influence the survival and reproduction of individuals, and ultimately of populations and species. Selection pressures include: * Competition for food, water, shelter, mates. The competition may be within the species or between species. The result is that not all individuals obtain equal shares of the resources, some survive, some do not. * Migration. If populations outgrow or exhaust their resources, one solution for all or part of the group may be migration to a new location. This in itself may lead to many deaths during the journey, and may have a significant effect on population gene pools, as previously discussed. * Geographical features. If natural events such as floods or earthquakes split a population, with or without killing many, the remaining population sub-groups may never recombine. This is a form of reproductive isolation. Over time, changes in the gene pools of each sub-group will occur, as described earlier. This can eventually lead to the evolution of new species. Adaptation NOTE: The correct spelling is 'adaptation' (not 'adaption') please try to remember this. Individuals with structural (anatomical), functional (biochemical) or behavioural adaptations which give them a better chance of survival to adulthood and/or give them a reproductive advantage are more likely to pass their genes on to the next generation of the population. Adaptations are acquired by an individual as a set of genetic informationthe chance combination of alleles obtained at fertilisation. N.B. avoid the notion that "individuals can adapt"this is Lamarckism and is not able to be supported scientifically. (Read about Lamarck to understand this fully). Individuals can only express in their phenotype the characteristics for which their genotype codes. This can include many variants of phenotype, within the one individual. For example a weight lifter changes his body shape over time with a great deal of training, but his children will not be born as mini-Schwarzeneggers because he did so! What the weight lifter has done is manipulate his own environment to realise all his genetic potential in his phenotype.
"Fitness"

The phrases "struggle for survival" and "survival of the fittest" can be misleading if taken literally. They are not meant to mean that only the strongest, physiologically fittest individuals will survive and reproduce. Rather they mean that, over many generations, species will accumulate favourable characteristics (become "fitter") which enable viable populations of that species to survive. Relative fitness is the contribution of a genotype to the next generation compared to the contribution of alternative genotypes at the same locus. From this it can be seen that the phenotype corresponding to a high frequency genotype is probably advantageous in the environment of the species at the timeor at least it is not disadvantageous.
Natural Selection

Natural selection is the differential success in reproduction of different phenotypes resulting from interaction of organisms with their environment. With time, natural selection causes changes in relative frequencies of alleles in the gene pool.
Speciation SPECIES: A particular kind of organism; members of a species possess similar anatomical characteristics and have the ability to interbreed, producing vigorous (= healthy), virile (= able to reproduce sexually) offspring.

When a population of a species splits, usually due to selective pressures (as previously described), the populations may become reproductively isolated. As described earlier, this will almost certainly, over many generations, lead to changes in the gene pool of each sub-group. As these changes progress, random chance makes it highly likely that significant differences in phenotypes will develop in each group. For a while, breeding between groups will remain theoretically possible, if individuals were to meet and mate. Eventually, however, the accumulated changes in each group's gene pool would lead to a significant lack of homology at a number of gene loci. Viable offspring between the groups would now be impossiblethe groups are no longer members of the same species. Speciation has occurred. (Whether there is one new species and the original species in the other group, or whether there are 23 VCE Unit 4 Chapter Summaries p.

two new species, both different from the original, could only be determined by observations of outcomes of mating experiments. Can you work out how a biologist might investigate this?) Speciation has been, and still is occurring constantly since life began on Earth. We can see evidence of it in nature. For example, Australian magpies, species Gymnorhina tibicen, show phenotypic variation in different populations on the east coast, from Tasmania to Cape York. In some of these sub-groups (sometimes termed races), interbreeding is still possible, especially if their home ranges overlap. Where the populations are geographically separated by large distances or high mountains, the populations may no longer be able to successfully interbreed. Deciding exactly where one species stops and another starts can be very difficult in cases such as this. Human activity has recently hastened this process by manipulating selection criteria in many species. Many cultivated plants, bred originally from natural "wild" species bear little resemblance to the originals and are now infertile, being reproduced asexually (e.g. by cuttings) for commercial purposes.
Extinction

Sometimes environments change relatively rapidly. If the species which live in those changing environments are not lucky enough to already possess genes which enable the species to survive in the face of such change, or if random mutations do not accumulate sufficiently quickly, all members of the unlucky species may die. This is extinction. Extinction may be localised to one species in an ecosystem, often due to destruction of that species habitat, or it may widespread. The fossil record indicates that there have been at least twelve periods during the history of life on Earth where mass extinctions occurred. The two most extreme of these occurred about 250 million years ago (m.y.a.) (>90% of marine species died) and 65 m.y.a. (>50% of marine species, and many terrestrial species, including the dinosaurs, died). Palaeobiologists are still divided as to the explanations for theseasteroid collisions and global climate changes are currently the two leaders in the explanation stakes.

EvolutionThe Evidence
Introduction EVOLUTION: "All the changes that have transformed life on Earth from its earliest beginnings to the diversity that exists today."

The currently accepted theories of evolution have been developed and refined by biologists as evidence has become available to support and extend the mechanisms first proposed by Alfred Wallace and Charles Darwin. Earlier explanations, especially those of Lamarck are not well supported by the current evidence and are generally not accepted by current scientists. The evidence upon which the current theories of evolution are based is varied in its origins, and it is this multi-faceted approach which, taken together, provides the strength of the theory. If your personal views on evolution are very different from the current scientific beliefs you are, of course, perfectly entitled to hold such views! You are, however, urged to adopt a pragmatic approach to your study of this part of the VCE course and to try to understand the current scientific explanations that is what you need to gain marks on GA 3 questions!
The Fossil Record FOSSIL: "A relic or impression of an organism from the past, usually preserved in rock."

Fossils can take many forms: * Hard parts of animals (teeth and bones) are often fossilised * Thin tissues such as leaves may be preserved as films * Entire organisms may be preserved e.g. frozen or in amber * Plant tissue is sometimes found "petrified" * Imprints, such as footprints of dinosaurs, occur, but rarely. Fossils are most often found in sedimentary rocks such as sandstone, mudstone, shale and limestone. The layers of silt or other debris which accumulate over time exert pressure on plant and animal remains, or settle into the imprints left by passing animals, minerals are exchanged, and fossils are formed.
Stratification STRATIGRAPHY: "The science of study of rock strata (layers). Often associated with estimations of the ages of the rocks by the ages of the fossils found within them. Similarly, succession of rock composition, and events associated with deposition of each stratum, can be inferred from the rocks and the presence or absence of fossils within them."

Over thousands and millions of years sedimentary rocks form in strata, or layers. As a consequence of this, the layers reflect the order in which the fossils were deposited; the oldest fossils are in the lowest layers, with progressively "younger" fossils in each higher layer. This stratification of the sedimentary rock enables palaeobiologists to assign relative ages to fossils. Where similar fossils are discovered at different, separated locations, these index fossils can be used to correlate evolutionary events at the different locations, by comparing and contrasting the fossils in the strata above and below them. Analysis of fossils in strata does not give dates in terms of years, but only in terms such as before or after and earlier or later. This is known as relative dating. However, if the fossils or the rocks in which they are found, can be dated using radio-isotopic methods, then absolute dates may be obtained. Because of the constant, slow movement of the Earth's crustal plates (plate tectonics), the strata in some locations have been buckled and broken. This causes some difficulty in the interpretation of the fossil
p. 24 VCE Unit 4 Chapter Summaries

record in these places but a combination of geology and biology can be used to infer what has happened.
Radio-isotopic dating of fossils. RADIO-ISOTOPES: An isotope is one of several forms of a particular element. Isotopes differ from each other in atomic arrangement, but they all behave identically in terms of chemical reactions.

Some naturally-occurring isotopes are radioactivethey release energy in a measurable, constant, characteristic way. Radioactive isotopes gradually decay to form other, non-radioactive elements. This method relies on the properties of naturally occurring radioactive isotopes to determine the age in years of rocks and the fossils within them. These isotopes are present in constant amounts in living organisms, but decrease in concentration after death at a rate determined by the rate at which the radio-isotope decays. Since radioactive isotopes have known half-lives (the time taken for the radioactivity to decay to half its initial value), measurement of the radioactivity in a sample can easily be calculated as a function of number of years since death occurred. Carbon-14 dating is most useful for relatively recent fossils, that is fossils up to about 50 000 years old. Isotopes of other elements, such as potassium-40 are used to date rocks which are hundreds of millions of years old and so infer the age of fossils embedded in them. Other elements also have isotopes that are useful in fossil dating. The experts in such matters choose the best isotope for the predicted age of the fossil they are dating. Radioactive dating has an error of approximately 10%.
Biogeography BIOGEOGRAPHY: "The study of past and present distribution of species."

By studying and comparing similarities and differences in present species environments and their global distribution, inferences can be made about the likely environments of extinct similar species which are now only known from the fossil record. Study of the biogeography of islands is also instructive in the study of evolution as initially barren locations (such as the island remaining after the eruption of Krakatoa) have given valuable information about succession in such environments. The events during the much longer time span of evolution of life and ecosystems on planet Earth become a logical extension of such an investigation.
Comparative Anatomy ANATOMY: "The structure of organisms."

By comparing the anatomy of species, gradual progressions in structural characteristics can be observed. For example, comparison of skulls of gorillas, chimpanzees, orang utans, humans and many now extinct anthropoids has made it possible to suggest pathways of evolutionary progression from a common primate ancestor to the existing species. When combined with radioactive dating of the fossils, the timing of this evolution can also be estimated.
Homologous and Analogous Structures

When comparisons are made of the anatomy of structures which seem to have evolved very different functions, it can be seen that the process of natural selection has led to these differences. Homologous structures such as the forelimbs of a variety of mammals (e.g. human, cat, whale and bat) can be shown to possess the same skeletal elements, suggesting that a common ancestral forelimb has been modified for many different functions. Homologous structures such as those described above should not be confused with analogous structures (e.g. bat wing and insect wing), where evolution has given rise to anatomically very different structures which have similar function (aid in flying) where this function provides a survival advantage in a particular environment.
Embryology EMBRYOLOGY: "The study of the developing embryo (stage from fertilisation to hatching or birth in animals) in animals or plants."

Closely related organisms go through similar stages in their embryonic development. In fact, the similarities between early embryos of fish, frogs, snakes, birds, cats and humans are much more evident than are the subtle differences. By following the progression of development of embryos, and studying the paths of differentiation of tissues in different species, many similarities between species which are difficult to detect in adults become increasingly clear.
Biochemistry BIOCHEMISTRY: "The study of the chemistry of living organisms."

With recent technological advances in the analysis of the molecular composition of biological molecules, some of the most compelling evidence for evolution has been discovered. Since the hereditary information of an individual is located in its genes, we would expect that closely related individuals (e.g. siblings) would have a large amount of very similar DNA and proteins. This is found to be true. For the same reason, we would expect that members of the same species would also possess much common DNA and many common amino acid sequences in their proteins. This is also found to be true. Examination of nucleotide sequences in DNA and amino acid sequences in similar proteins from a large number of species has shown conclusively that closely related species have much in common biochemically, whilst evolutionary distance (and time for accumulation of mutations) leads to wider and wider differences between phenotypes, genotypes, proteins and DNA.
Paths of Evolution EVOLUTION: "Evolution is the accumulation of inheritable changes within populations over time."

The agents of evolution include: * natural selection 25 VCE Unit 4 Chapter Summaries
p.

* mutation * genetic drift * migration * non-random mating. Of these, only natural selection leads to adaptations in populations within their changing environments. The others merely produce new opportunities for natural selection to work. However, without mutations to provide the raw material on which natural selection can work, the variability in populations would be strictly limited. With this in mind, it is possible to trace the evolutionary pathways taken from ancient ancestral species to the present day species. Whilst the biochemical thread of evidence is only possible to trace in current species, the combined information of the ancient fossil evidence and our understanding of relationships between present species together provides powerful support for the modern theory of evolution.
Divergent Evolution DIVERGENT EVOLUTION: "One ancestral stock evolves into two or more species, which continue to evolve and become less and less alike over time."

e.g. an ancestral mammal probably existed about 190 million years ago. It was around at the time of the dinosaurs, but with the extinction of the dinosaurs, the mammals were able to undergo extensive adaptive radiation to fill a wide range of ecological niches, giving rise to giraffes, cows, cheetahs and anteaters, for instance.
Parallel Evolution "In parallel evolution two related species arise from a common ancestor. The two species then evolve in much the same way over time, probably in response to similar environmental selection pressures."

For example, both the woolly mammoth, which occupied parts of North America, and the elephant, still found in Asia and Africa are presumed to have evolved from a common ancestor. Their geographical isolation and environmental selection pressures caused further evolution of the species, but each, in its own location, occupied a similar niche.
Convergent Evolution "Convergent evolution occurs when two or more quite unrelated come to resemble each other more and more as time passes. This is usually the result of occupation of similar habitats and the adoption of similar environmental roles."

e.g. from ancestral birds, insects and mammals, we now have modern flying birds, insects and bats, and there used to be flying reptiles.
Diagrams of Evolutionary Relationships

You will see several types of diagrams in evolution chapters of text books. You may even be asked to interpret such a diagram as part of an exam question. It helps to recognise the three main types of diagrams and understand what each is representing.
Gradualism
vr dr ey ak ee dr e v n ak r pet d r r t y ak dre ak r c m o a c so o mn n e t r lig t r he v r lig t ey h e e lig t r v n he q it lig t ue h

This type of diagram illustrates one view of the rate of evolution. It shows a branching of an evolutionary path, from a common ancestor, and the gradual emergence of one or more new, different species. The gradual slope of the branches indicates that many intermediate forms of the organism are believed to have existed although evidence of them (usually by fossils) is absent or incomplete. These diagrams may or may not be accompanied by time scales. The time scales may or may not be linear.

p. 26

VCE Unit 4 Chapter Summaries

Punctuated equilibrium

m c lig t r u h he

lo s lig t r t he

ee dr e v n ak r

lig t r he

dr e ak r c m o a c so o mn n e t r

This type of diagram reflects the theory that evolution has not occurred at a constant rate, rather it has occurred in short bursts with long periods of stability between. This theory explains the absence of the infinite range of intermediate fossils in branches of evolution such as the vertebrates. Again, these diagrams may or may not be accompanied by time scales. The time scales may or may not be linear.
Cladogram

This type of diagram reflects the evolution relationships of organisms based on the distance from common ancestors. Again, they may or may not give an indication of time. Cladograms are often constructed on the basis of biochemical evidence; these days DNA homology is the most useful. If there is very little difference in the DNA of two species, they are said to show evolutionary 'closeness', since there has not been sufficient time for many mutations to accumulate in their DNA. Similarly, the more different the DNA (the less homology shown), the further the evolutionary distance between the species and the longer the time since they shared a common ancestor. Cladograms take one of two forms, but each shows essentially the same information. If you look closely you can see that they are sometimes similar to pedigree diagrams in construction. However the branches of a cladogram represents the development of a new species, not just a new generation.
brown bear sun bear spectacled bear giant panda lesser panda raccoon dog 100 75 50 25 0

millions of years ago (mya)

This complex cladogram shows that brown bears and sun bears are more closely related than either are to the raccoon or the dog. It shows not only the relationships between bears, panda and dogs, but it gives an idea of time since these animals shared common ancestors. A word about time scales: Time scales are often included on evolution diagrams. Take care with the interpretation of these. Carefully find the point on the scale that represents 'the present'. This might be at the top or bottom of a vertical time scale, or it might be at the far right of a horizontal time scale. Next look at the scale's label. Is it m.y.a. or perhaps m.y.b.p. (millions of years before the present) or something else? You need to know this before you can sensibly use the time scale to determine the age of fossils or events represented on it. Last, get the information that you want from the time scale, remembering that the scale usually appears to go 'backwards', so interpolation between markers should be thought about carefully. A word about getting information from a diagram: If you're asked to do this in an exam you are very silly if you don't rule straight pencil construction lines on your exam paper to guide your reading of an evolution diagram. There are hundreds of students who, in the past, have used a rough estimate in such cases, been too far off the correct answer and lost the chance of a mark!
Summary of the process of evolution

DNA mutations changes in genotype changes in phenotype variability in populations (adaptation) fittest individuals pass on their genes (under selection pressures) changes in allele frequencies in the gene pool many generations of selection pressure EITHER EXTINCTION (inability to cope with environmental pressures) OR EVOLUTION (continued success in the environment).

Human Evolution
Introduction

The mechanisms that led to the evolution of the huge diversity of species living today are believed to be identical to those that led to the evolution of our own species. Whilst true in general, there are details of the evolution of humans which are still the subject of much research and sometimes much con27 VCE Unit 4 Chapter Summaries
p.

troversy. It is generally accepted that humans share a common ancestor with the other primates, and many lines of evidence support this. Most textbooks will have a diagram showing the most likely relationships between primates. Some of the animals on such diagrams survive today; others have long been extinct.
Features of Primates

Look at other primate pictures in your textbook, visit the Primate Gallery Web site, or best of all, take a trip to the Zoo and look at the primates there. You will see that all of these animals (including our own species), share many common structural, functional and behavioural characteristics, that is, there are many similarities in our phenotypes, including: * rounded faces with reduced snouts; eyes protected by bony ridges. * relatively large brains, with a small area for smell, a larger area for vision. * large eyes point forward, giving binocular 3-D vision; colour vision present. * variation in tooth size and shape; a varied, omnivorous, diet is possible. * collarbones present, enabling brachiation (swinging by arms). * mobile limb joints, giving a wide range of limb movement. * five digits on hands and feet; nails, not claws; opposable thumbs enable grasping. * many quadrupedal, but most sit upright; some bipedal, freeing hands for other activity. * internal fertilisation, long gestation; long period of parental care. * social groups usually well developed; hierarchies common; communication evident. This seems too much of a coincidence to blame on convergent evolution. When the biochemical evidence, based on similarity of DNA sequence for selected, common genes, is examined, it is clear that all of these animals are closely related. Does this similarity between ourselves and our primate relatives mean that we came from "monkeys", or that "monkeys" evolved from humans? Certainly not! This is merely another example of divergent evolution from a common ancestor. Somewhere back in evolutionary history the first primate ancestor appeared. Then, over time, mutations occurred in some populations of that animal, natural selection acted to favour the best adapted individuals for the particular environments, and slowly new species evolved. This evolution continued and the 'branches' of the primate tree sprouted. Some branches flourished, some died, but what we are left with is a variety of similar but significantly different species. All are primates, all came from that common ancestor, but they are each the products of the environments that shaped their present forms.
We started in Africa

At least 4 million years ago the first hominid ancestor appears in the fossil record in Africa. Family Hominidae are humans and their (now extinct) close relatives. As the hominids evolved, many phenotypic changes were observed: * Body size varied, with a tendency to an increase over time. * Some species had thick, robust skeletons, others were gracile, or fine boned. * Skull capacity, and presumably, brain volume increased. * Skull bones and teeth had proportions more like apes than like modern humans. * But pelvis and thigh bones indicated that they walked on two feet (bipedal gait). * With increasing brain size it seems that the ability to make and use tools slowly developed. Eventually one species of hominid remained. Perhaps Homo sapiens was better adapted to survive a major environmental change. Perhaps 'he' was merely smarter and he directly or indirectly caused the extinction of other Homo species which were already beginning to migrate out of Africa.
Migration

The evidence does seem strong that the origin of our species is somewhere in Africa, but the details will probably never be known for sure. However, there is a great deal of evidence to show that many groups of early Homo sapiens migrated out of Africa about 200 000 years ago. The pressures of selection and adaptation that have been described for other species have acted on these population founding groups over the succeeding years and produced the sub-groups of the human species that we know as races. Since interbreeding between members of different human races can and does occur, these groups must still be classified, according to the rules of taxonomy, as members of the same species.
Cultural Evolution

Early hominids developed a unique phenotype. The combination of structural features and enlarged brain enabled hominids to manipulate their environment in a way no other animal has been able to do. Over hundreds of thousands of years, hominids, and later members of the Genus Homo, gradually learned how to live and survive in a variety of environments. Major milestones in this journey from hominid to modern man (Homo sapiens) have included: * 2.01.5 m.y.a.: Homo habilis, in E. Africa has permanent dwelling places, makes stone tools. * 1.7 m.y.a.200 000 BP: H. erectus, in Africa, Asia and Europe, migrates out of Africa, uses fire. * 90 00030 000 BP: H. sapiens neanderthalensis, in Europe, Africa and W. Asia, practise ceremonial burial. * 30 000 BP to present: H. sapiens sapiens, world wide, use bone needles, produce art forms, perhaps begin their own decline by irreversible habitat destruction...? NB BP means before present.
Human Intervention in the Process of Selection p. 28 VCE Unit 4 Chapter Summaries

For many years, humans have been manipulating the process of evolution to suit their own ends. By choosing organisms with desired phenotypes as breeding stock, humans are practicing artificial selection. There is value in this practice when desirable characteristics such as disease resistance in crop plants is achieved. But sometimes undesirable results are obtained, such is the case with the development of antibiotic resistance in some pathogenic organisms. As a result of human activity, rapid environmental changes have occurred in some locations. These, in turn, have changed ecosystems and habitats. As we have discussed earlier, mutations occur very slowly and are not necessarily favourable. It is, therefore, not surprising that many species are now endangered and many others have recently become extinct. Recent advances in medical technology have reduced the incidence of death from human genetic disease, with affected individuals now remaining in the population long enough to reproduce. The implications for the frequency of the "disease" alleles in population gene pools should be obviousthey would be expected to increase. This may not seem to be a problem if the affected individuals can be treated, but the cost of such treatment may eventually place economic burdens on families and communities. Such issues will need to be addressed.

29 VCE Unit 4 Chapter Summaries

p.