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    • Biology – Cellular Control, Biotechnology, Environments,Responding to the EnvironmentModule 1 – Cellular Control/Genetics 1) HOW DNA CODES FOR PROTEINSA gene is a length of DNA that codes for one or more polypeptides. In the humangenome, there are about 25,000 genes. Each gene occupies a locus on thechromosome.The sequence of nucleotide bases on a gene provides a genetic code, instructionsfor the construction of a polypeptide. It has a number of characteristics: - It is a triplet code, i.e. a sequence of three nucleotide bases codes for an amino acid. The number of different triplet sequences is 64. - It is a degenerate code, i.e. all amino acids except methionine have more than one code. - Some codes do not code for an amino acid, but indicate “stop” – the end of the polypeptide chain. - It is widespread but not universal. All triplet codes may not code for the same amino acids in all organisms.TranscriptionA messenger RNA molecule is made. For this, one strand of the length of DNA isused as a template. There are free DNA nucleotides in the nucleoplasm and freeRNA nucleotides in the nucleolus. - A gene to be transcribed unwinds and unzips. To do this, the length of DNA that makes up the gene dips into the nucleolus. Hydrogen bonds between the complementary base pairs break. - Activated RNA nucleotides bind, through hydrogen bonding, to their exposed complementary bases. This is catalysed by the enzyme RNA polymerase. - The two extra phosphoryl groups are released. This releases energy for bonding adjacent nucleotides. - The mRNA produces in complementary to the nucleotide base sequence on the template strand of the DNA and is therefore a copy of the base sequence on the coding strand of the length of DNA. - The mRNA is released from the DNA and passes out of the nucleus, through a nuclear pore in the nuclear envelope, to a ribosome.
    • 2) TRANSLATIONTranslation is the second stage of protein synthesis, when the amino acids areassembled into a polypeptide. The sequence of amino acids is dictated by thesequence of codons on the mRNA.Transfer RNAAnother form of RNA, transfer RNA, is made in the nucleus. They are lengths ofRNA that fold into hairpin shapes and have three exposed bases at one end where aparticular amino acid can bind. At the other end of the molecule are three unpairednucleotide bases, known as an anticodon. Each anticodon can bind temporarily withits complementary codon.Assembly 1) A molecule of mRNA binds to a ribosome. Two codons are attached to a small subunit of the ribosome. The first exposed mRNA codon is always AUG. Using ATP energy and an enzyme, a tRNA with methionine and the anticodon UAC forms hydrogen bonds with this codon. 2) A second tRNA, bearing a different amino acid, binds to the second exposed codon with its complementary anticodon. 3) A peptide bond forms between the two adjacent amino acids. An enzyme, present in the small ribosomal unit, catalyses the reaction. 4) The ribosome now moves along the mRNA, reading the next codon. A third tRNA brings another amino acid, and a peptide bond forms between it and the dipeptide. The first tRNA leaves and is able to collect and bring another of its amino acids. 5) The polypeptide chain grows until a stop codon is reached. There are no corresponding tRNAs for these three codons (UAA, UAC and UGA), so the polypeptide chain is now complete. 3) MUTATIONS – 1A mutation is a change in the amount of, or arrangement of, the genetic material in acell. It is a random change to the genetic material, due to a change in the DNA (basedeletion, addition or substitution; inversion or repeat of a triplet), or by chromosomemutation, involving a change to the structure of a chromosome (deletion, inversion ortranslocation). Mutations can also occur during semi-conservative replication ofDNA. Certain substances, like tar from tobacco, UV light, X-rays and gamma rays,can cause mutations.
    • There are two main classes of DNA mutations: - Point mutations, where one base replaces another. These are also known as substitution mutations. - Insertion/Deletion mutations, where one or more nucleotide pairs are inserted or deleted from a length of DNA. This causes a frameshift.Many genetic diseases are the result of DNA mutations: - In 70% of cystic fibrosis cases, the mutation is the deletion of a triplet of base pairs, deleting an amino acid from the sequence of 1480 amino acids in the normal polypeptide. - Sickle-cell anaemia is the result of a point mutation on codon 6 of the gene for the beta-polypeptide chain of haemoglobin. It causes the amino acid valine to be inserted at this position of the polypeptide chain in place of glutamic acid. - Growth-promoting genes are called proto-oncogenes, which, by a point mutation, can be turned into oncogenes. While proto-oncogenes can be switched off, oncogenes cannot be, so oncogenes result in unregulated cell division, leading to a tumour. - Huntington disease results from an expanded triple nucleotide repeat – a stutter. The normal gene for Huntington protein has repeating CAG sequences. If they expand above a threshold number, the protein is altered sufficiently enough to cause Huntington disease. 4) MUTATIONS – 2If a gene is altered by a change to its base sequence, it becomes another version ofthe same gene. It is an allele of the gene. It may produce no change to theorganism’s phenotype if: - The mutation is in a non-coding region of the DNA. - It is a silent mutation: although the base sequence has changed, it still codes for the same amino acid, so the protein is unchanged.Mutations that have neutral effects are mutations that change the genotype andphenotype of the organism, but the changed characteristic gives no particularadvantage or disadvantage to the organism. 5) THE LAC OPERONThe bacterium E. coli can synthesise about 3000 different polypeptides. However,there is great variation in the numbers of different polypeptides within the cell. Theremay be 10,000 molecules of ribosomal polypeptides in each cell and just 10molecules of some of the regulatory proteins.Enzymes involved in basic cellular functions are synthesised at a fairly constant rate.Inducible enzymes are synthesised at varying rates, according to the cell’s
    • circumstances. Bacteria adapt to their environments by producing enzymes tometabolise certain nutrients only when those nutrients are present. For example, E.coli metabolises glucose, but it can also use lactose as a respiratory substrate.The lac operon is a section of DNA within the bacterium’s DNA. It consists of anumber of parts:Structural genes: One gene codes for the enzyme beta-galactosidase but anothergene codes for the enzyme lactose permease.The operator region: A length of DNA next to the structural genes. It can switch thestructural genes on and off.The promoter region: A length of DNA to which the enzyme RNA polymerase bindsto begin the transcription of the structural genes.How the lac operon works when lactose is absent: 1) The regulator gene is expressed and the repressor protein is synthesised. The repressor protein can bind to both lactose and the operator region. 2) The repressor protein binds to the operator region, which also means it covers some of the promoter region. Because of this, RNA polymerase cannot attach as it normally does. 3) The structural genes cannot be transcribed into mRNA. 4) Without mRNA these genes cannot be translated and the enzymes cannot be synthesised.How the lac operon works when lactose is present: 1) Lactose (inducer) molecules bind to the other site on the repressor protein. This causes molecules of the repressor protein to change shape so that its other binding site cannot now bind to the operator region. 2) This leaves the promoter region unblocked, so RNA polymerase can bind to it and initiate the transcription of mRNA for the genes that code for beta- galactosidase and lactose permease. 3) The operator-repressor-inducer system acts as a molecular switch. It allows transcription and subsequent translation of the structural genes into the lac enzymes.
    • 6) GENES AND BODY PLANSDrosophila DevelopmentWhen the eggs are laid a series of mitotic divisions is triggered, at a rate of oneevery 6-10 minutes. - At first, no new cell membranes form, and a multinucleate syncytium is formed. - After the 8th division, the 256 nuclei migrate to the outer part and by the 11 th division the nuclei form an outer layer around a central, yolk-filled core. - The division rate slows, and the nuclear genes switch from replicating to transcribing. - The plasma membrane invaginates around the 6000 nuclei, and the resulting cells form a single outer layer. - After another 2-3 hours, the embryo divides into a series of segments. These correspond to the organism’s organisation or body plan. - Three segments merge to form the head, three to form the thorax and 8 to form the abdomen.Genetic Control - Some genes determine the embryo’s polarity. Polarity refers to which end is anterior and which end is posterior. - Other genes, called segmentation genes, specify the polarity of each segment. - Homeotic selector genes specify the identity of each segment and direct the development of individual body segments. These are the master genes in the control network of regulatory genes. There are two gene families:- - The complex that regulates development of thorax and abdomen sections. - The complex that regulates development of head and thorax sections.Homeobox genes control the development of the body plan of an organism,including the polarity and positioning of organs. There are homeobox genes in thegenomes of segmented animals from segmented worms to vertebrates. Thehomeobox genes each contain a sequence of around 180 base pairs, producingpolypeptides of about 60 amino acids. Some of these polypeptides are transcriptionfactors and bind to DNA upstream to prevent or allow the expression of other genes.Homeobox genes are arranged in clusters known as Hox clusters: - Nematodes have one Hox cluster. - Drosphila has two Hox clusters. - Vertebrates have four clusters, of 9 – 11 genes, located on separate chromosomes.
    • 7) APOPTOSISApoptosis is programmed cell death that occurs in multicellular organisms. Cellsshould undergo around 50 mitotic divisions (the Hayflick constant) and then undergoa series of biochemical events that leads to orderly cell death. This is contrasting tocell necrosis, a damaging cell death that occurs after trauma and releases hydrolyticenzymes. - Enzymes break down the cell cytoskeleton. - The cytoplasm becomes dense, with organelles tightly packed. - The cell surface membrane changes and small bits called blebs form. - Chromatin condenses and the nuclear envelope breaks. DNA breaks into fragments. - The cell breaks into vesicles that are taken up by phagocytosis. The cellular debris is disposed of and does not damage any other cells or tissues.The process is controlled by a diverse range of cell signals, some of which comefrom inside the cells and some from outside. The signals include cytokines made bycells of the immune system, hormones, growth factors and nitric oxide. Nitric oxidecan induce apoptosis by making the inner mitochondrial membrane more permeableto hydrogen ions and dissipating the proton gradient. Proteins are released into thecytosol. These proteins bind to apoptosis inhibitor proteins and allow the process totake place.One signal that can cause a cell to undergo apoptosis is a cytokine called TNF. Itbinds to a receptor on the plasma membrane which has a “death domain” on thecytoplasmic side. When TNF is bound, the death domain can bind to the deathdomain of a different protein called FADD, which has a “death effector domain.”When FADD binds to the death domain of the receptor, it activates an enzyme calledcaspase that initiates the process of apoptosis.Apoptosis and DevelopmentApoptosis is an integral part of tissue development. There is extensive division andexpansion of a particular cell type followed by pruning through programmed celldeath. The excess cells shrink, fragment and are phagocytosed so that thecomponents are reused and no harmful hydrolytic enzymes are released into thesurrounding tissue.Apoptosis is tightly regulated during development, and different tissues use differentsignals for inducing it. It weeds out ineffective or harmful T-lymphocytes during thedevelopment of the immune system. During limb development, apoptosis causes thedigits (fingers and toes) to separate from each other.
    • If the rates of apoptosis and mitosis are not balanced: - Not enough apoptosis leads to the formation of tumours. - Too much leads to cell loss and degeneration. 8) MEIOSISIt is important to remember the significance of having homologous pairs ofchromosomes in the nucleus of a cell.All living organisms can reproduce. In eukaryotes, asexual reproduction can beachieved by mitosis, and in prokaryotes, binary fission. The offspring producedthrough asexual reproduction are produced to be genetically identical; however,variation occurs through random mutation.In sexual reproduction, the offspring are genetically different from each other andfrom the parents. Each parent produces special reproductive cells, known asgametes. Gametes (one from each parent; in the case of humans a sperm cell andan egg cell) fuse together at fertilisation to produce a zygote.When two gametes fuse together to make one cell, the cell produced must have adiploid number of chromosomes in its nucleus. Therefore, the gametes must have ahaploid number of chromosomes; this ensures that, after fertilisation, the originalchromosome number is restored. Because of this, meiosis is the type of nucleardivision where the chromosome number is halved.Meiosis consists of two divisions, meiosis I and meiosis II, and each division has 4stages: prophase, anaphase, metaphase and telophase. Before meiosis I,interphase occurs, and the DNA replicates.Meiosis IProphase I - The chromatin condenses and undergoes supercoiling so that the chromosomes shorten and thicken. - The chromosomes come together in their homologous pairs to form a bivalent. Each member of the pair has the same genes at the same loci, and consists of one maternal and one paternal chromosome. - The non-sister chromatids wrap around each other and attach at points called chiasmata. - They may swap sections of chromatids with one another in a process called crossing over. - The nucleolus disappears and the nuclear envelope disintegrates. - A spindle made of microtubules forms.
    • - Prophase I can last for days, months or even years, depending on the species and on the type of gamete (male or female) being formed.Metaphase I - Bivalents line up across the equator of the spindle, attached to spindle fibres at the centromeres. The chiasmata are still present. - The bivalents are arranged randomly (random assortment) with each member of a homologous pair facing opposite poles. - This allows the chromosomes to independently segregate when they are pulled apart in anaphase I.Anaphase I - The homologous chromosomes in each bivalent are pulled by the spindle fibres to opposite poles. - The centromeres do not divide. - The chiasmata separate and lengths of chromatid that have been crossed over remain with the chromatid to which they have become newly attached.Telophase I - In most animal cells two new nuclear envelopes form – one around each set of chromosomes at each pole – and the cell divides by cytokinesis. There is a brief interphase and the chromosomes uncoil. - In most plants, the cell goes straight from anaphase I into meiosis II.Meiosis IIProphase II - If the nuclear envelope has reformed, then it breaks down again. - The nucleolus disappears and the chromosomes condense, and the spindles form again.Metaphase II - The chromosomes arrange themselves on the equator of the spindle, and they are attached the spindle fibres at the centromere. - The chromatids of each chromosome are randomly assorted (arranged).Anaphase II - The centromeres divide and the chromatids are pulled to opposite poles by the spindle fibres. The chromatids randomly segregate.
    • Telophase II - Nuclear envelopes reform around the haploid daughter nuclei. - In animals, the two cells now divide to give four haploid cells. - In plants, a tetrad of four haploid cells is formed. 9) GENETIC CROSSESTwo alleles: G – white skin g – green skinParent phenotype: green greenParent genotype: gg ggGametes: (g)(g) (g)(g)Offspring genotype: ggOffspring phenotype: greenHomozygous individuals are said to be “true breeding” or “pure breeding” becausethey can only pass on one particular allele for a particular gene. The same would betrue if the individuals were homozygous dominant rather than homozygousrecessive.If an individual’s phenotype is white skinned, we do not know whether their genotypeis homozygous (GG) or heterozygous (Gg). To found out, we would have to carry outtest crosses. 10) CODOMINANCECodominance occurs when both alleles for a particular gene contribute to thephenotype. Neither allele is dominant over the other and the overall phenotype isdue to a mixed effect of two alleles.The alleles are defined by superscript letters in the gene, i.e. red colour is C^R andwhite colour is C^W.Parent phenotype: red flowers white flowersParent genotype: C^RC^R C^WC^WGametes: (C^R)(C^R) (C^W)(C^W)Offspring genotype: C^RC^WOffspring phenotype: pink flowers
    • 11) THE CHI-SQUARED TESTThe chi-squared test tests the null hypothesis through statistical analysis. The nullhypothesis is a useful starting point in examining the results of a scientificinvestigation. It is based on the assumption that “there is no (statistically) significantdifferent between the observed and expected numbers, and any difference is due tochance.”The formula for calculating a value of :ExampleThe numbers of resulting offspring for each observed phenotype of Drosophila werecounted:Straight wing, grey body – 113Straight wing, ebony body – 30Curled wing, grey body – 29Curled wing, ebony body – 115Phenotype Straight/grey Straight/ebony Curled/grey Curled/EbonyO 113 30 29 115E ratio 1 1 1 1E 71.75 71.75 71.75 71.75O-E 41.25 -41.75 -42.75 43.25(O-E)^2 1701.5625 1743.0625 1827.5625 1870.5625(O-E)^2/E 23.71515679 24.29355401 25.471255436 26.07055749 = 99.55 (to 2 s.f.)A degrees of freedom of 3 should be used, as there are four classes.By looking up the critical value in a table, we know that it is 7.82.Since the chi-squared value is greater than 7.82, we know that there is a very lowprobability that the difference in the observed results compared to the expectedresults occurred by chance. This means that independent assortment of these geneloci is unlikely to have occurred.
    • 12) SEX LINKAGEParent’s sex: Female MalesParent’s chromosomes: XX XYGametes: (X)(X) (X)(Y)Offspring chromosomes: XX XYOffspring sex: Female MaleThe sex chromosomes X and Y also carry genes. However, the X and Ychromosomes are not a true pair because part of the Y chromosome is missing. Thismeans that some alleles present on the X chromosome are not present on the Ychromosome. Therefore, males sometimes only possess one allele for a particulargene locus.Such alleles are sex linked:The “yellow” gene has only one allele in males, as it is only present on the Xchromosome and not the Y. The “red” gene, however, will act in the same way asany other gene, with the dominant allele being expressed over the recessive.The allele that causes red-green colour blindness is sex linked. The genotype of thismale with red-green colour blindness is r-. This is often written as X^rY, indicating asex-linked condition.Exampler = red-green colour blindness R = normal visionParent genotype: X^rY X^RY X^rX^r X^RX^R X^rX^RGametes: (X^r)(Y) (X^R)(Y) (X^r)(X^r) (X^R)(X^R) (X^r)(X^R)Offspring genotype: X^rY X^RY X^RX^r X^RX^ROffspring phenotype: colour blind normal normal normalOffspring sex: male male female femaleThe offspring with colour-blindness must be male.
    • 13) DIHYBRID CROSSESA dihybrid cross involves studying the inheritance of two genes (2 loci) at the sametime.Genotype: TtGg Genotype: HhFFGametes: (TG)(Tg)(tG)(tg) Gametes: (HF)(HF)(hF)(hF) 14) EPISTASISEpistasis is the interaction between two genes where one locus (epistatic gene)masks or suppresses the expression of the gene at the other locus (hypostaticgene).The epistatic gene and hypostatic gene may work in a complementary fashion (workwith each other) or may work in an antagonistic fashion (work against each other).Complementary FashionTwo genes that code for enzymes in a sequential metabolic reaction are examples ofcomplementary alleles, e.g. melanin is a brown pigment made indirectly from anamino acid phenylalanine via another amino acid called tyrosine.Phenylalanine E1 Tyrosine E2 MelaninProduction of melanin required the consequential action of enzymes E1 and E2coded for by genes A and B respectively. The dominant alleles are needed toexpress active enzymes. Without either active enzyme, the phenotype is ALBINO(WHITE) rather than brown.AABB – not albino aABB – not albino AAbB – not albino aaBB – albinoaabB – albino aabb – albinoAntagonistic FashionGenes may work against each other in two ways, dominant epistasis andrecessive epistasis.Dominant epistasis is where the expression of a dominant allele at one locusmasks the expression of alleles at a different locus. H - hairy E – masks H E – does not mask H h - hairlessHHEE – hairless HhEE – hairless HHEe – hairless HhEe – hairlesshhEE – hairless HHee – hairy Hhee – hairy hhee – hairless hhEe – hairless
    • Recessive epistasis is where the expression of a dominant allele at the epistaticlocus is needed for the expression of alleles at the hypostatic locus. Therefore, ahomozygous recessive individual for the epistatic gene results in no expression ofthe hypostatic gene. P - purple A – white ifrecessive a p - pinkAABB – purple AABb – purple AAbb – pink AaBB – purple AaBb – purpleAabb – pink aaBB – white aaBb – white aabb – white 15) VARIATIONVariation in biology is the presence of differences between individuals. It results indifferent phenotypes for the individuals. Variation occurs between members of thesame species as well as between members of different species. Even identical twinscan show slight phenotypic variation from one another.Discontinuous Variation – there are discrete categories for the phenotype. Theseare qualitative phenotypes. It may be caused by the inheritance of different alleles ofone gene only (monogenic). For example, cystic fibrosis is caused by the inheritanceof a mutated allele of a single gene. Discontinuous variation may also be caused byinheritance of a few genes which interact with each other in an epistatic manner.In discontinuous variation, different alleles for the same gene will have large effectson a phenotype. Different loci will have quite different effects on the phenotype.Dominant, recessive and codominant patterns of inheritance are examples ofdiscontinuous variation.Continuous Variation – there are a range of phenotypes with a minimum andmaximum value and many intermediate values in between. These are quantitativephenotypes. Continuous variation is caused by the inheritance of two or more genes.Each gene has a small additive effect on the overall phenotype of the organism.Different alleles at the same locus have a small effect on the phenotype. A largenumber of genes may affect the phenotype (POLYGENIC).Variation is also caused by environmental influence, e.g. nutrition, UV, radiation, etc.
    • 16) POPULATION GENETICSPopulation genetics involves determining the frequency of alleles in wholepopulations rather than in individuals. A whole population is likely to possess moredifferent alleles than an individual. Population geneticists study the genetic structureof whole populations.The set of genetic information carried by a whole population is referred to as thegene pool. Population geneticists measure the frequency of different alleles in thegene pool.When alleles show codominance, this is quite easy to do as the number ofheterozygous phenotypes is the same as the number of heterozygous genotypes.In a population of snapdragons, 30 are red, 49 are pink and 10 are white. Thefrequency of each allele is easy to measure in this population of plants:Red alleles – 109White alleles – 69However, the situation is more complicated with dominant and recessive alleles andthe Hardy-Weinberg principle must be used:The frequency of the dominant allele is assigned letter “P” and the frequency of therecessive allele “Q.”In a cross between two heterozygotes the offspring are produced in the followingratio and the frequency of each genotype is described using P and Q as follows:1 homozygous dominant (p^2)2 heterozygous (2pq)1 homozygous recessive (q^2)The frequency of genotypes adds to one: p^2 + 2pq + q^2The frequency of alleles also adds to one: p + q = 1If the frequency of the homozygous recessive genotype is known, then thefrequencies of p and q can be calculated.e.g. phenylkatenuria is caused by a recessive allele. It occurs in 1 in 10,000 livebirths:q^2 = 0.0001q = 0.01p = 0.99p^2 + 2pq + q^2 = 12pq = 0.0198
    • 17) GENES AND ENVIRONMET – EVOLUTIONA selection pressure is an environmental factor that confers greater chances ofsurvival to reproductive age on some members of the population. If a selectionpressure maintains a phenotype, it is known as stabilising selection. If theenvironment changes and the phenotype begins to become more/less prevalent, thisis known as directional selection and acts as an evolutionary force leading toevolutionary change.Any change to the frequency of alleles in a population is referred to as genetic drift.Genetic drift is more likely to happen in smaller populations of organisms.Populations can become smaller by a variety of isolating mechanisms: - Geographical (ecological), where subpopulations are separated by barriers such as rivers, seas, mountain ranges, etc. This can lead to alopatric speciation. - Seasonal (temporal), where barriers such as climate change throughout the year separate populations. - Reproductive barriers, where individuals can no longer physically mate due to incompatible genitals, breeding seasons or courtship behaviours.In each different subpopulation, different alleles may increase or decrease, maybeeventually leading to a new species, i.e. that can no longer breed at all. This processis called speciation.Genetic drift is more likely to occur in smaller populations because allele frequenciescan change in a more dramatic fashion. However, in a large population, only smallchanges in allele frequency would be expected. However, this may not be the case ifevolutionary forces caused directional selection.In extreme cases, genetic drift can cause elimination of an allele from a population.This will remove variation and could reduce the chances of survival in a newenvironment. It could therefore contribute to the extinction of a species. Genetic driftcan also lead to the formation of a new species. 18) WHAT IS A SPECIES?Biological Species Concept – “a group of similar organisms that can interbreed toproduce fertile offspring and is reproductively isolated from other such groups.” Thisis used for classification but presents problems for organisms that do not reproducesexually, i.e. binary fission in bacteria.Phylogenetic Species Concept – “organisms that have similar morphology(anatomy), physiology, embryology (stages of development) and behaviour; and alsooccupy the same ecological niche.” The phylogentic approach us based uponanalysis of differences or similarities between the DNA of different organisms.A particular base sequence of an organism is called its haplotype, which can becompared between organisms.
    • A divergence can be calculated as:The least divergent organisms are put into a group called a clade, and a cladogramshows evolutionary relationships between groups, i.e. phylogeny.The cladistic approach uses: - Evolutionary relationships rather than structural similarity - Quantitative analyses requiring computer programs. - Relies on DNA (and RNA) sequencing.If often confirms Linnaean classification, but sometimes leads to organisms beingreclassified, as was the case for the 3-domain system of classification.