Biology 2005

1. Biology 2005 AS 3.3: gene expression

2. Maintains the original chromosome number (2n) and creates new somatic cells Done for growth and repair One set of division Reduces the chromosome number (2n-n) Done to produce gametes Ensures that when two gametes fuse they can produce a diploid zygote Two sets of division Often results in ‘crossing over’, resulting in the combination of more alleles Mitosis and Meiosis

3. DNA and RNA DNA • Is combined with proteins to form chromosones, or chromatin • Certain sections of the DNA make up genes • Each base site (nucleotide) is made up of a base (adenine, cytosine, guanine, thymine), a sugar and phosphate. They are joined together to form polynucleotides • One DNA strand directs the synthesis of RNA and is the template strand, while the other is known as the coding strand CH2OH 5 Base O CH Sugar CH2OH 4 H2 1 1 1 3 2 CH CH OH OH Phosphate Ribose sugar RNA AA attachment site • Two forms; mRNA and tRNA Anticodon • mRNA, or messenger RNA, has the function of delivering the genetic code to the tRNA • tRNA, or transcription RNA, has the function of transcribing the genetic sequence into proteins

4. DNA Replication 5’ 3’ The entire process is known as semi-conservative replication, as each new DNA molecule consists of one old and one new strand 1. The DNA molecule is twisted at high speeds by helicase, and gyrase relieves the strain by cutting, winding and rejoining the strands in a gyrating motion Helicase gyrase Replication Fork RNA polymerase DNA polymerase RNA primers 3. Each of the two new double-helix molecules has one strand of the original DNA and one newly synthesised. These are rejoined by DNA ligase These are then super coiled to form chromatids for cell division 2. The formation of DNA is carried out by DNA polymerase. On the leading 3-5 end, free nucleotides are assembled continuously. On the other side, RNA primers (which are later replaced) are attached and synthesised by RNA polymerase in fragments known as Okazaki fragments NB: continuous DNA synthesis can only take place on the 3-5 end

5. R O C C NH2 OH H Amino Acids • Are basic unites from which proteins are made • Plants can manufacture them from molecules, but animals require the 10 essential amino acids from diet • These 10 construct the remaining amino acids • The order amino acids are linked in is controlled by genes and chromosomes Structure: • There are 150+ amino acids in cells, but only 20 commonly occur in proteins • They all have a common structure: • The R group is specialised in each amino acid, e.g: SH } This R group in cysteine NH2} this lysine R group CH2} forms disulphide bridges CH2} gives lysine alkali with other cysteine CH2} properties • Bonding: • A peptide bond is formed between the COOH group and NH2 group • H2O is lost as the C and N bond • Amino acids form long chains to make up proteins R R OH R + H2O C C R NH2 O C C NH2 O C C NH2 O H C C OH NH2 O OH H H H

6. Gene Code for Proteins • The genetic code is what determines the proteins created • Sets of triplets make amino acids, a gene makes a polypeptide chain, and a group of genes make a transcription unit • A three base codon specifies each amino acid (triplet code) • There is one start codon (AUG) for each protein, and three end codons (UAA, UAG, UGA) This is the start code to stop translating a polypeptide chain of AAs This is the start code to translate a polypeptide chain of AAs UAG AUG Protein from a Gene

7. AA AA AA AA AA AA AA AA AA Protein Synthesis Translation Transcription RNA Processing • A section of one strand of the DNA, the template strand, is used as a template to synthesise mRNA Translation is the linking of amino acids in the sequence specified by the mRNA base sequence, i.e. the gene. Each triplet/codon represents a certain amino acid. tRNA molecules act as adaptors to bring each amino acid to the specific codon. • Occurs in three steps: A specific nucleotide sequence on the 3-5 template strand called the promoter determines that the template strand is used. Once the RNA polymerase has recognised a bound to it, the RNA synthesises known as elongation. Finally, the polymerase reaches a series of basis on the DNA called the terminator sequence, at which pint the RNA polymerase stops transcription and the mRNA enters the cytoplasm for RNA processing. Cytoplasm Polypeptide chain tRNA Ribosome Helicase gyrase Introns sometimes remove themselves, known as ribozymes tRNA Replication Fork RNA polymerase AUG, start codon DNA polymerase The information in the RNA transcript is not yet ready to be translated because coding regions are separated by introns, which do not code for proteins and must be removed. In some cases introns will do this themselves. NB: a triplet is needed instead of a doublet, as there are 20 amino acids. The four bases in doublets, i.e. 4x4 (16) would not be enough, thus it must be 4x4x4 (64), a triplet

8. AA AA AA AA AA AA AA AA AA Structure and Function of Proteins Proteins can be: Enzymes: glucose Fructose • The precise folding of proteins to ensure their R groups are facing a specific way is essential • The way each R group faces gives the protein it’s chemical behaviour • Structural, e.g. keratin in nails • Enzymes (see over) • In membrane pores, e.g. semi-permeable membranes • Storage, e.g. egg whites • Transportation, e.g. haemoglobin • Muscle contraction • Protection, e.g. antibodies • Hormonal, e.g. insulin • Are catalysts in reaction • Operate on a lock and key hypothesis, sometimes with a cofactor • Require optimum heat, concentration and pH factors or else will go out of shape • Can either split or join molecules on an active site, e.g. glucose and fructose sugars to form sucrose • Are reusable Enzyme Sucrose • Tertiary Phase • Each protein has it’s secondary structure folded into a complex tertiary structure • This occurs due to attraction between various AAs, especially the disulphide bridges in cysteine • Primary Phase • A polypeptide chain is formed • The arrangement and repulsion of each AA determines all levels of organisation, and the protein’s role Protein Structure • Quaternary Phase • Some proteins such as enzymes function as tertiary structures • Some proteins, such as haemoglobin, are made up of several tertiary structures. Haemoglobin has 4 • Secondary Phase • Polypeptides are folded, normally producing an alpha helix or beta pleated sheet • These structures are maintained by H bonds between the NH2 and COOH between the AAs

9. Crossing Over • Is the mutual exchange of chromosome pieces, the swapping of whole groups of genes, between homologous chromosomes • Can only result in the first division of meiosis, as homologous chromosomes line up together • This upsets expected allele frequencies • The frequencies of crossing over can help provide a genetic map In the prophase of the first division of meiosis, chromosomes pair up to form bivalents. This process is known as synapsis, and allows the chromatids of the homologous chromosomes to come into very close contact The pairing of the homologues allows a chiasmata to form between the chromatids of the homologues. The chromatids become criss-crossed and the chromosomes exchange segments. The point at which the segments cross is called the chiasma New combinations of genes arise from crossing over, resulting in what is called recombination. When the homologues separate at anaphase of meiosis 1, each of the chromosomes will have new genetic material that will be passed into the gametes. This is an important source of genetic variation

10. Linkage and Recombination Linkage • Linkage refers to genes located on the same chromosome • They are therefore inherited together, and fewer genetic combinations are available • This reduces the variety of offspring possible • If all genes were located on separate chromosomes, there would be more combinations possible; linkage reduces this Recombination • Is the exchange of alleles between homologous chromosomes as the result of crossing over • The alleles of parental linkage groups separate, and new associations of alleles are formed as gametes • Offspring from these gametes show new combinations • The proportion of recombinance can be used to calculate the frequency of recombination, which in turn can determine positions of genes on a chromosome • In contrast to linkage, recombination increases genetic variation • It is shown through the number of recombinants in the offspring

11. Chromosome Mapping • Crossover frequencies can be used to map the relative positions of genes on a chromosome • The amount of crossing over between linked genes is a direct measure of the distance between the genes on the chromosome • This is because genes that are further apart on the same chromosome have more potential crossover points between them A B a b A b a b Step 1 Parents with known genotypes, e.g. AaBb and aabb, can only produce offspring of two genotypes; AaBb and aabb. However, if the children of these parents have four phenotypes, then crossing over must have occurred to produce these recombinants AaBb: 108 (parental genotype) Aabb: 33 (recombinant) aabb: 97 (parental genotype) aaBb: 42 (recombinant) Total: 280 Step 2 COV (%) = # of recombinant genes =33+42 x 100 Total number of offspring 280 =26.8% The frequency of recombination between the two genes provides an indication of the relative distance between those genes. Expressed as a crossover value, it can be calculated: Step 3 B A Using the crossover value determined above, a chromosome map can be created, with each percentage of crossover meaning one centimorgan. Known map distances for pairs of genes may be combined to produce a more complete map for genes. in this example there are three genes for which the crossover values are known. By trial and error, the genes can be laud out in different sequences to see if the genetic mapping distances fit. 26.8cM Known values: B-A = 22% A-C = 10% B-C = 12% |A| | | | | | | | | | | |C| | | | | | | |B| | | | |

12. Dominance of Alleles Codominance Incomplete Dominance • This refers to a situation where the action of one allele does not completely override the action of a recessive allele • The heterozygous phenotype, therefore, is intermediate • An example of this is the snapdragon, where red and white flowers will produce heterozygous offspring with an intermediate phenotype • This refers to inheritance patterns when both alleles in a heterozygous organism contribute equally to an organism’s phenotype • These alleles are independently expressed • Human blood groups are an example, where both A and B are dominant to O, of this, as are coat colours in cattle Mother Mother Mother Father Father Father CRCR CWCW AO BB RR rr B CR CR CW Cw A O B R R r r CRCW CRCW CRCW CRCW AB AB BO BO Rr Rr Rr Rr

13. Sex Linkage • Is the result of a certain gene being contained on an sex chromosome (almost always the X) • The result is that the characteristic will very rarely be seen in the homogametic, i.e. female, sex, but can be carried • This is because males, with only one X chromosome, will express whatever is on there, while females have two X chromosomes • A common example of this is haemophilia, but also cat coat colours • In some cases, a dominant allele will still be expressed, such as rickets, even if it is only carried on one X chromosome, by a female

14. Interactions Between Genes: Polygeny and Pleitropy Polygeny Pleitropy • A single gene may produce a product that can influence a number of traits in the phenotype of an organism • For example, the Hb gene codes for production of haemoglobin • However, it also affects other parts of the body, such as the kidney and heart, which can be seen when suffering from anaemia • Some genes may collectively express a trait • An example of this is melanin-coding genes affecting skin colour, resulting in a wide variety of continuous variation aabb Aabb aaBb AAbb AaBb aaBB AaBB AABb AABB

15. Interactions between Genes; Epistasis • Epistasis involves two genes masking the expression of one or another Complementary Genes Supplementary Genes • Some genes can only be expressed in the presence of other genes, they are known as complementary • Both genes have to have dominant alleles present for the phenotype to be expressed • There are usually two phenotypes produced • An example of this is the production of purple pigment in sweet peas, where a purple pigment will only be produced in the presence of two dominant alleles • This is pure epistasis, whereby genes mask the effect of others • There are usually three possible phenotypes • An example of this is coat colour in rodents • Melanin is controlled by one gene, while another decides whether it is black or brown • In albinism, a recessive allele in the second instane will result in albinism AAbb aaBB AaBb

16. Gene 1 Gene 2 Mutation Occurs Gene 3 Enzyme 1 Enzyme 2 Enzyme 3 Mutations How Mutations are Acquired: • A sudden, permanent change in the nucleotide sequence of DNA • A mutant gene will produce a mutant protein. Protein-coding mutations are mainly harmful • Sex produces new combinations of existing genetic information, so mutations are not usually hereditary • Will sometimes divide rapidly in unspecialised cells, producing tumours • Mistakes in DNA replication caused from mutagens, e.g. X-rays, UV light, radiation from cell phones, atomic bombs, cigarettes, high temperatures • A very low rate of mutation occurs continuously, as enzymes correct the majority of errors and DNA replication is high accurate • Mutations can be inherited, but only if they occur in gamete producing cells, e.g. testes Mutations affecting Enzymes: • Mutations in enzyme-coding genes will affect metabolic pathways, leading to disease If gene 2 mutates, the process cannot be carried out • An example of this disruption in Phenylketonuria (PKU) • This results in a build-up of phenylalanine, a harmful substance, in the liver, which PKU enzymes are required to destroy • Symptoms include mental retardation, body odour, light skin and muscular tension • PKU is tested from birth, and about 1 in 19,400 babies are born with it • Albinism is another example of a disrupted metabolic pathways

17. Gene Mutations • There are infinite ways in which a DNA sequence can change within genes and chromosomes. In all cases, if the amino acid coded for are affected significantly, there will be a change in the organism’s protein structure • Mutations can occur at three levels: Point (Gene) Mutations: • Only one nucleotide is involved • A nucleotide (or even short sequence) may be substituted, deleted, or inserted Substitution Mutations: Insertion and Deletion Mutations: C C T A G C T A C pro ser tyr • A base pair is replaced with another • This can be silent, a protein can be changed (mis-sense) or a ‘stop’ codon produced (non-sense) • A mis-sense mutation is where altered codons will still make sense, but will code for the wrong protein • A non-sense mutation will result in an amino acid being shortened, resulting in a shorter, usually non-functional protein Substitution Mutations Mis-sense: C-G change in AA sequence will result in different protein • Since mRNA codons are read in groups of three, a change of one nucleotide will affect the grouping significantly • It will result in a different amino acid sequence of all positions past it • If complementary insertions and deletions occur in rapid succession along the gene sequence, there may only be a partial frame shift C G T A G C T A C arg ser tyr No change: T-A change still codes for pro protein C C A A G C T A C pro ser tyr Non-sense: C-A change results in a ‘stop’ codon forming, shortening the chain C C T A G C T A A pro ser Stop Deletion: Deletion: C deleted at position 2, resulting in a frame shift changing the whole sequence C T A G C T A A leuala?? Insertion: A is inserted after position 1, resulting in a frame shit Insertion: C A C T A G C T A C hisStop tyr

18. Examples of Inherited Metabolic Disorders

19. Specific Examples Explained Sickle Cell Cystic Fibrosis CAC GTG GAC TGA GGA CAC CTC CCG TGG TAA TTT CTT TTA TAG TAG AAA CCA CCA Cystic Fibrosis is the result of an AAA triplet on the CFTR, or chloride regulation gene, being deleted, resulting in one less AA Sickle cell, or anaemia, is a result of a T base on the HBB, haemoglobin coding gene, for an A gene The haemoglobin produced is too soluble, and therefore cannot carry oxygen, deforming red blood cells The CFTR protein produced cannot regulate chloride effectively, and results in water leaking into cells meaning glands produce abnormally thick mucus This results in anaemia, chest pain, joint pain, jaundice, kidney failure, pneumonia, meningitis, blindness, swelling, gallstones, strokes Disruption of glands, infertility in both sexes

20. Block Mutations • Are the result of the rearrangement of blocks of genes within a chromosome, rather than a few nucleotides • Can be a genetic accident during crossover • Can be deletion, duplication, inversion or transfer mutations • Result in a new gene order in a chromosome • Genes on the borders of a block mutation may have their base sequence changed Different types of block mutations result in different degrees of change in the overall quantity of genetic material within a chromosome. Deletion mutations decrease chromosome size Duplication mutations increase chromosome size Inversion mutations rearrange genetic mutations, but don’t change the overall size of the chromosome Transfer mutations involve moving genetic material between or within chromosomes, hence there may be a chromosome size change

21. Aneuploidy • Euploidy in humans is the condition of having the correct haploid number of chromosomes, i.e. 2N = 46 • Aneuploidy is when the chromosome number is not an exact multiple of N, e.g. 2N+2 • Is the result of homologous chromosomes being unable to separate in meiosis, giving way to faulty gamete production • The two most common forms of aneuploidy are monosomy and trisomy

22. Aneuploidy in Sex Chromosomes Faulty Sperm Production Faulty Egg Production Mother Father Mother Father XY XX A mistake during meiosis results in gameteocytes with either two sex chromosomes or none at all XY XX XY O X X X Y XX O XY O X X X XY O X X Y Y O X XX XX O XO XXY XO XXY XXX XXY XO YO

23. Trisomy in Autosomes • Trisomy is a form of aneuploidy where one chromosome pair is represented by thee cells, resulting in a karyotype of 47 cells • About 50% of all spontaneous abortions result from trisomy • The three most common forms of this are Down Syndrome, Edward Syndrome and Patau Syndrome • They are usually the result of non-disjunction, but sometimes the result of transfer mutations

24. Polyploidy • The condition whereby an organism has more than two sets of chromosomes, e.g. triploidy (3N) or tetraploidy (4N) • More common in asexual organisms, e.g. vegetables • Can result in the rapid formation of a new species • Two types of polyploidy, which depend upon whether the extra set/s of chromosomes are from the same or different species • Is the result of non-disjunction of an entire set of chromosomes

25. Cabbage Radish 2N=18 RR CC R C CR Sterile hybrid, 2N=18 Organism carries out amphipolyploidy, which doubles its chromosomes CCRR Fertile hybrid, 2N=36 Autopolyploidy and Allopolyploidy Autopolyploidy Allopolyploidy SAME SPECIES DIFFERENT SPECIES • When both parents produce diploid gametes • Autotetraploids (4N) are fertile, but autotriploids (3N) are not as meiosis will not produce cells with balanced chromosome sets • Result of a cross between two different species, producing an organism derived from both • Is important in plant evolution • Relies on amphipolyploidy to produce homologous chromosomes required for meiosis • Homologous chromosomes are not present in hybrids, therefore amphipolyploidy is required Parent2 Parent2 Parent1 Parent1 AA AA AA AA AA AA A AA AAAA AAA Fertile hybrid Infertile hybrid

26. Control of Gene Expression • Although each somatic cell has an identical nucleus and genotype, each cell has a particular function and phenotype • To ensure only the correct genes in each cell are expressed, gene expression has to be controlled • Protein is only made when a gene is active • Two types of genes exist; structural genes, which make particular proteins, and regulatory genes, which are very short and control the level of activity in structural genes • The expression of genes is regulated through feedback mechanisms that rely on the binding of various molecules to particular parts of the DNA sequence • It is therefore controlled heavily at transcription level

27. RNA polymerase Transcription Regulatory Gene Promoter Operator Structural gene Operon RNA polymerase Repressor Transcription Inducer Regulatory Gene Promoter Operator Structural gene RNA polymerase Repressor Transcription Regulatory Gene Promoter Operator Structural gene Control of Gene Expression through Transcription in Prokaryotes • Prokaryotes regulate gene expression through the operon method • An operon consists of a group of closely linked genes that act together and code for enzymes and metabolic pathways • This contributes to the synthesis of amino acids • The structural genes contain the required information, which is transcribed as a transcription unit • These are controlled by a promoter, the site where RNA polymerase binds during transcription, and also an operator • A regulatory gene outside the operon will code for a repressor molecule, which will bind to the operator and block transcription of structural genes • The repressor will switch the structural genes on or off, thereby controlling the metabolic pathway • Gene induction is the reverse of gene repression, and occurs when repressor molecules are switched off by an inducer molecule Induction Regular transcription, whereby the RNA polymerase attaches to the promoter and synthesises the structural genes Some proteins are not required frequently. In this case, the genes coding for the protein are blocked by the repressor, coded for by the regulatory gene Repression When a protein, such as tryptophan, is produced in excess, it acts as an effector. This activates the repressor in the regulator gene, which binds to the operator gene When lactose is available, synthesis is required. Therefore, the lactose acts as an inducer, and binds to the repressor, forcing it out of shape meaning transcription can take place RNA polymerase Repressor Transcription Regulatory Gene Promoter Operator Structural gene tryptophan

28. Gene Control through Transcription in Eukaryotes • To be transcribed, a gene must first be unpacked from a condensed state • Once unpacked, it is reliant on transcription factors, with DNA sequences that control a specific gene • Initiation of transcription is the most important form of control in eukaryotic cells • Note: the operon model is not applicable to eukaryotes, as genes are not organised as operons Transcription factors • Eukaryotic cells are different from prokaryotic cells as they have large numbers of introns and regulating genes • However, they have still have a promoter region at the upstream end of the gene where the RNA polymerase binds • RNA polymerase is stimulated by transcription factors on regulating genes to begin binding • This occurs when a hairpin loop in the DNA, just upstream from the promoter, brings the transcription factors attached to the enhancer sequence into contact with the transcription factors of the polymerase at the promoter • Only when this is complete does transcription continue • This is deactivated when a terminator sequence is encountered • There is a large range of transcription factors and enhancer sequences in the human genome RNA Polymerase Transcription factor Enhancer regulatory gene Promoter RNA Polymerase Transcription factor Promoter

29. Control of Gene Expression through Enzymes • Enzymes, as a form of protein, are formed as a result of genetic nucleotide sequences • Enzymes control metabolic reactions, which oversee digestion to form chemical pathways • Restriction of enzyme levels in particular organisms can regulate gene expression • The presence of small amounts of a substrate may activate an enzyme, whilst large amounts of a substrate may deactivate it

30. Control of Gene Expression through Metabolic Pathways • Metabolism is the chemical activities of life • An example of a metabolic pathway is that of phenylalanine Faulty enzyme results in cretinism, causing dwarfism, mental retardation, retarded development Faulty enzyme causes phenylketonuria, resulting in retardation and eczma Faulty enzyme causes alkaptonuria, resulting in dark urine, poor muscle tone and arthritis Thyroxine Carbon dioxide And water Tyrosine Hydroxyphenyl- Pyruvic acid Homogentistic acid Aleyacetoacetic acid Protein Phenylalanine Melanin Faulty enzyme causes tyrosinosis, results in liver failure and kidney disease Faulty enzyme causes albinism

31. Control of Defective Genes • Under certain circumstances, cells are programmed to die • Cells that become damaged beyond repair will undergo this process, known as apoptosis • Cancer cells evade this control by becoming immortal, and continue to divide as a result of factors known as carcinogens • Chronic exposure to these carcinogens result in cancer • Defective genes may also induce cancer • Cancer results from changes in the genes controlling mitosis • The resulting cells become immortal, and do not carry out their roles • There are two genes that control this cycle; proto-oncogene, which start cell division, and tumour-suppressor genes, which switch off cell division • In their normal form, both kinds of genes work together, enabling the cell to carry out mitosis • Mutations in these genes disrupt this balance, and give rise to genes which carry out uncontrollable cell division • Mutations to tumour suppressor genes initiate cancers, as they prevent control of cell division • Cancerous cells no longer carry out their functions, and instead take nutrients from the body • There is no resting phase between cell division If this is combined with A tumour-suppressor Mutation, the gene will Replicate out of control If a gene becomes damaged, Tumour-suppressors self-destruct the cell A proto-oncogene Mutation means the Cell will divide uncontrollably

32. Biology 2005 3.4 plant responses and animal behaviour

33. Simple Orientation Responses in Animals • An orientation response is one where the animal positions itself or carries out specific behaviours when an environmental factor changes direction, duration or intensity • These responses help organisms to avoid adverse conditions • Simple orientation responses include taxes and kineses Kineses Taxes • Are responses towards or away from a directional stimulus • Animals can determine the direction a stimulus. One method is by comparing the input from receptors on each side of the animal at the same time; differences between them shwo the direction of the stimulus • A kinesis is a random movement response where the activity rate is determined by the intensity, not the direction, of stimulus • If the stimulus intesnity determines the organism’s speed or movement, then it is labelled an orthokinesis, and if it lnfluences turining it is called a klinokinesis Negative phototaxis Positive phototaxis Thermo-klinokinesis

34. Complex Orientation Response in Animals Homing Migration • Generally refers to the ability of animals to return home • Examples of this include newborns who must home back to their parents feeding site • Are regular, generally annual moements of large groups of animals from a breeding site to a feeding site, and back • Migration is risky in terns of energy use, so the advantages have to be worth the cost i.e. better food supplies • Examples of migrations in New Zealand are seals, whales, eels and shearwater, curlews • Is under genetic control and cued by daylength Navigation • Navigation involves an animal finding its way over unknown territory to a known destination • During the journey, the animal must know where it is in relation to its destination • It does this using sunlight, smell, stars, landmarks or the magnetic field • Experiments using migratory birds such as European starlings have shown that they have a sense of distance and direction. This was found by moving birds to a different location before they mograted. The travelled in the same direction as normal, so ended up in the wrong place • Distance may be determined by travle time. Direction seems to be the combination of several cues, such as the sun and stars • The plane of the polarisation

35. Biology 2005 AS 3.5 – patterns of evolution

36. The Basis of Evolution • Darwin said that naturally selection can be summarised as: • Present day species having evolved from ancestral form • Organisms produce more offspring than survive. The offspring compete for food and other essentials in a struggle for survival • Offspring produced by sexual reproduction will show variation; some will have characteristics that are more suited to their environment • Those individuals or species with favourable characteristics will survive longer and produce more offspring and so pass their favourable characteristics on. This is called ‘survival of the fittest’ • Successive generations will become modified over time, particularly if their environment is changing. Gradually the species will change sufficiently to be recognised as a new species • Since then, evolutionary principles have changed only slightly. The changes include • The use of the term ‘gene pool’ to define the collection of genes of all members of a population • Darwin believed variations in parents were blended in offspring, however this would actually reduce variation in a population. We now know this does not happen, as genes to not blend in organisms • We now know that variation is caused by • Meiosis and sexual reproduction, which reshuffle chromosomes into new genes • Crossing over, which results in new combinations of alleles at different loci • Mutations, which alter actual genes to produce evolutionary novelties • An adaptation is any inherited variation, structural, physiological or behavioural, that improves an organisms change of survival and passing on its genes • Genetic adaptations are differently from physiological adaptations, as physiological adaptations are made in response to the environment in the lifetime of an organism

37. Scientific Evidence for Evolution • Fossils: • Provide a record of ancient organisms, and their study shows evidence of lines of descent and intermediate species • Structural Similarities: • Living things are similar in their basic structures and processes • Studies of comparative anatomies, such as the pent dactyl limb, show strong similarities • Chemical Similarities: • Comparative studies of DNA sequences have shown that even extremely different species such as yeast and humans share some basic genes • This indicates that all species on earth had a common ancestor • Breeding: • The domestication of animals and plants has changed them dramatically from their ancestors • For example, artificial selection by humans in dogs has created the breeds seen today • If evolution can take place through artificial selection, it can also take place through natural selection • Antibiotic Resistance: • The development of antibiotic resistance in bacteria is an extremely fast example of evolution occurring • The strains of susceptible bacteria are carrying out thousands of mutations, giving them antibiotic resistance • Geographic Distribution: • The distribution of related species, even on islands such as the Galapagos, shows evidence of how new species have evolved e.g. Darwin’s finches

38. Causes of Evolution • A change in the frequencies of certain alleles in a gene pool over a few generations is known as microevolution • Large, irreversible changes, such as the formation of new species, are known as macroevolution • These are the result of evolutionary agents such as non-random mating, mutation, genetic drift, gene flow and natural selection

39. Evolutionary Agents • Non-random mating: • Involves desirable traits and organisms selecting certain phenotypes • For example, if all humans heavily favoured blondes, the frequency of brown haired women would decrease • Mutation: • Increases the variety of alleles present in a gene pool • Will only be passed on if they occur in sex cells of organisms • Natural selection eliminates harmful mutations, but slightly harmful mutations may linger in a population and gradually become favoured • Gene Flow: • Is caused by the movement of individuals between populations • Immigration of individuals will increase genetic variation, whilst emigration may decrease it

40. Genetic Drift • Occurs when random events change allele frequencies • Is most common in small populations • Two ways in which genetic drift take place are the bottleneck and founder effect Bottleneck Effect Founder Effect • The founder effect takes place when a small group of organisms colonise a new area • The new population will have different allele frequencies, not representative of the former population • This was the case with Darwin’s finches • The bottleneck effect occurs as a result of a natural event such as an eruption, or a sudden drastic loss of species numbers • The surviving population will be too few to carry the entire allele frequency of the former population

41. Normal variation in a population Natural Selection • This acts on the phenotype, rather than the genotype of organisms • Some allele combinations will produce organisms that fitter, i.e. have traits better adapted to their environments • Natural selection can be stabilising, directional or disruptive The range of phenotypes associated with a character in a population tends to be distributed normally, producing a ‘bell shaped’ curve when the frequency of a characteristic is plotted against the range of phenotype variation Stabilising Selection A stable environment selects individuals with ‘average’ phenotypes, selecting against individuals at the extremes of variation. This makes the population more uniform Directional Selection A stable environment selects individuals with ‘average’ phenotypes, selecting against individuals at the extremes of variation. This makes the population more uniform Stabilising selection Disruptive Selection Is where both extremes of phenotypes are favoured, meaning the average phenotype is selected against. May result in the formation of two different species Directional selection Disruptive selection

42. Time Evolutionary change Rate of Evolutionary Change • There are two main models for the rate of evolutionary change; gradualism, and punctuated equilibrium • There is evidence that supports both models, and it is possible that both models take place and different intervals on the evolutionary tree • According to the traditional model of gradualism, evolution proceed slowly and continuously • Eventually the accumulated changes result in the formation of new species • According to the newer punctuated equilibrium model, there are long periods of stasis, or little change, interrupted by short bursts of speciation • These rapid changed can be triggered by the environment in the form of genetic drift Time Evolutionary change Gradualism Punctuated Equilibrium

43. The Species Concept • It is hard to define a species, as all definitions have limitations • The biological species concept states that a species consists of groups of similar individuals who can interbreed with each other to produce fertile offspring but do not naturally interbreed with one another • Species usually exist in distinct populations, that may be separated geographically (known as demes) • Because organisms can only select a mate from within their deme rather than from other demes, demes often develop specific allele frequencies • A group of demes that have characteristics that change progressively across their range, but interbreed at the boundaries, is known as a cline • Often the groups at the end cannot interbreed, however this is not a separate species as there are common demes they can interbreed with • A ring species has a special kind of cline where the demes are arranged in a circle, where the extreme demes meet • Sometimes the extreme demes are given species or subspecies status • Demes can be an intermediate stage on the path to the evolution of a new species; however, for this to happen gene flow must be eliminated

44. Barrier Types of Speciation Sympatric Speciation Allopatric Speciation Instantaneous Speciation • Speciation is the process by which one or more new species are formed from an existing • Has to do with the multiplication of species rather than the modification of a species over time • It is possible for a new species to arise without geographical separation • Sympatric speciation occurs through ecological isolating mechanisms • This arises from a niche or lifestyle, where mating can be only between those who have adopted a new lifestyle (e.g. a new plant host) • This restricts mating within the population, and existing genetic differences between the ‘new lifestyle’ deme and the old deme become even more pronounced, so that the new population becomes even more different • Once populations are prevented from interbreeding, allele frequency differences build up and the species become increasingly different • Refers to the sudden appearance of a new species • This occurs frequently in plants due to polyploidy, where non-disjunction results in a new set of chromosomes • The plant is therefore reproductively isolated from the parent plant population, and reproduces through self fertilisation • For example, a tetraploid that produces diploid gametes cannot produce offspring with a diploid organism with haploid gametes • Therefore, the tetraploid will self propagate to breed • Occurs after populations have been separated by a geographic barrier • Occurs consequently as a result of gene flow between demes • Different conditions in the different demes result in different evolution • Eventually the differences will become so pronounced, that even if the demes, now species, come into contact, they will be unable to breed • An example of this is the New Zealand and Chatham Robins New lifestyle

45. Reproductive Isolating Mechanisms • Reproductive isolating mechanisms prevent populations of related species in the same area interbreeding • They can be prezygotic or postzygotic Prezygotic Mechanisms Postzygotic Mechanisms • Although a sperm an egg may fuse, there may be other problems on the path to development • Hybrid inviability: even if the sperm fertilises with the egg or the pollen joins with the ovule, the two different chromosome sets may not divide properly or some other problem may occur • Hybrid sterility: the offspring may reach maturity, but will then be sterile. A common example is the mule, a horse/donkey hybrid • Hybrid disadvantage: even if the hybrids can have offspring, they may be less fertile than normal or be less likely to survive, possibly due to natural selection • Can be temporal, behavioural, structural or gamete incompatible • Temporal: two related species may breed at different times, e.g. one species of duck breed in summer while another breed in the winter. This means they do not interbreed • Behavioural: the mating or courting behaviour differences between two species may prevent mating so individuals who don’t share the same courtship rituals will not mate • Structural: the reproductive structures of two related species may be incompatible, especially in insects where structures can be very species-specific. Structures in plants are genetically controlled and may be specific to particular animal pollinators • Gamete Incompatibility: the gametes of the two related species may not function successfully together; they may have incompatible surface chemicals or sex duct conditions may not be conducive to sperm

46. Competitive Exclusion Principleand Character Displacement • Also known as niche differentiation • States that when a new species has evolved, it will still be very similar to its ancestor, and they will therefore compete • Due to Gause’s principle, one species has to change or move • When the ranges of two species overlap, the difference between the species become far more pronounced, e.g. different plumage patterns in birds • This is called character displacement, and a selective advantage of this is more easy recognition of mates • When allopatric speciation takes place, niche differentiation and character displacement do not occur

47. The Importance of Extinction • Extinction is part of the ‘species life cycle’, just as the death of an individual is part of a normal life cycle • It is a consequence of natural selection • When a species becomes extinct its niche becomes available, clearing the way for other species • Extinctions are happening continually and always have. Of all the species that ever lived, only 0.01% exist today • There is no standard time for a species to survive • The rate of species loss has increased due to human activities, and it is suggested the world is in the middle of the ‘sixth mass extinction’ due to this

48. Patterns of Evolution Divergent Evolution Convergent Evolution • Evolution may cause related species to become different (diverge), or unrelated species to become similar (converge) • Most evolution is divergenal, i.e. it an ancestral ancestor species evolves into two or more species that become specialised to occupy different ecological niches • This may be due to the ancestral species spreading out to occupy new niches, and speiciation may take place • When an ancestral species diverges into a large number of species , this is known as adaptive radiation • An example of this is the Hebe plant • Adaptive radiation, especially in new Zealand, involves the founder effect, which provides the opportunity for a diversity of new niches • The most famous example of adaptive radiation as a result of adaptive radiation is Darwin’s finches, which adapted into 14 different species as a result of allopatric speciation from the founder effect • Species that have similar ways of life evolve similar features even though they have completely different evolutionary histories • For example, sharks (fish), penguins (birds) and dolphins (mammals) have all evolved to have a streamlined body and a large flipper • A New Zealand example is the wide-spreading branches of many shrubs, possibly as a result of the moa. These shrubs belong to 20 different families, ranging from violets to citrus Parallel Evolution • Similar features may evolve into related species whose common ancestral species did not have these features • This occurs through similar selection processes • Some biologists argue that it is a form of convergent evolution

49. Biology 2005 AS 3.6 biotechnological techniques

50. ‘Sticky’ end ‘blunt end’ Restriction Enzymes • Are used to make DNA molecules smaller by cutting them up • They cut DNA at specific sequences known as recognition sites, with each possessing a different sequence • Are taken from bacteria who use them as a defence against bacteriophage • Will cut DNA at either a ‘sticky’ or ‘blunt’ end • Are used to isolate strands from unneeded sequences