Module 5: Heredity (COMPLETE) Reproduction Inquiry question: H ow does reproduction ensure the continuity of a species? Syllabus Dot-point Content Explain the mechanisms of reproduction that ensure the continuity of a species, by analysing sexual and asexual methods of reproduction in a variety of organisms: Reproduction ● Fundamental evolutionary process that ensures the continuity of a species and the gene pool by producing offspring ● Reproductive success determined by an organism’s ability to produce offspring that survive to reproductive maturity. This can is measured by biological fitness - relative likelihood that alleles (variants of a gene) will be represented in future generations ● The k ey to successful fertilisation is that the single haploid gametes must meet and not dehydrate in the process Sexual Involves the combination of gametes which carry genetic information from both parents. G enetic diversity a nd variation are the primary a dvantages as the offspring contains a mix of parental genes and are not genetically identical to parents or other offspring. This can also possess variations that become well-suited to a changing environment, allowing them to outcomplete parents and gain a selective advantage. However, d isadvantages include that the process demands greater expenditure of energy: gamete production, finding a mate, mating etc. Asexual Involves reproduction of identical offspring (clones) from one parent through the process of mitosis, where each daughter cell receives a copy of every chromosome of the parent cell. There is no production or fusion of gametes and no mixing of genetic information to introduce variation. These are common in unicellular organisms due to lack of cell specialisation (no reproductive organs or germ cells to produce gametes) Advantages ● Allows individual organisms to reproduce in isolation when selective pressures (shortage of resources) are present ● Favourable, enabling rapid population expansion when environmental conditions are ideal as there is no disadvantage in reproducing offspring with the same inherited traits as the parent. They will be well-suited to a stable and uniform environment Disadvantages ● Lack of genetic variation limits adaptability and evolutionary potential in long term and leads to overcrowding ● When environmental conditions are variable and subject to change - organism are not adaptable to new conditions Hermaphroditism i s when an organism possesses both male and female reproductive organs. The process is advantageous for species with low population density or low-motility. Animals: advantages and disadvantages of external and internal fertilisation Internal fertilisation Process where the female gamete is fertilised by the male gamete inside the female reproductive tract External fertilisation Process where fertilisation occurs externally to the female ● ● ● Most common in m ammals, birds and reptiles (multicellular land and terrestrial organisms) During intercourse, a large number of male gametes are released, however only a small number of female gametes are available. This results in the production of a small number of zygotes. ○ Eutherian ( placentals) embryonic development occurs in uterus where the p lacenta organ develops and supplies the young with nutrients and oxygen Advantages ● Internal protection from immediate predation and dehydration of gametes leads to a higher success rate ● Reptile oviparous eggs develop a shell are laid in the external environment to complete its development Disadvantages ● Seasonal and less frequent due to the need for greater expenditure of energy and higher success rate ● Male and female organisms do not have to be in contact for fertilisation to occur. This results in the production large numbers of zygotes that develop outside the male and female parents. Most common form of reproduction in a quatic and moist environments ○ Staghorn coral: c olony of invertebrate marine polyps that shed gametes and pheromones i nto the sea which results in coordinated spawning Advantages ● Rapid form of reproduction with higher breeding frequency due to lower success rate ● Aquatic environments prevent gamete dehydration Disadvantages ● Lack of protection means not all zygotes survive ● Limited parental investment ● Vulnerable to environmental elements: temperature, predation, infection Relative successes of fertilisation Natural selection eliminates certain inherited characteristics if they fail to confer adaptations to suit their changing environment Plants: asexual and sexual reproduction Diagram of sexual Sexual reproduction ● Angiosperms: vascular flowering plants where seeds are enclosed in an ovary (fruit) ● Gymnosperms: vascular plants with unenclosed seeds often configured as cones reproduction 1. Pollination 2. Fertilisation 3. Seed dispersal 4. Germination: produces radicle (root to absorb water and nutrients) and plumule (develops green leaves for food production) Self-pollination Requires less energy as there is no requirement to produce structures to attract pollinators (petals, nectar). Favourable for plants that live in isolation. Cross-pollination Rely on external pollinating abiotic (wind, water) and biotic (insects, birds) agents to carry out fertilisation and transfer male gametes from the anther to the stigma. This results in greater variation of offspring. Asexual reproduction Vegetative propagation The production of vegetative organs from which new plants can arise ● Perennating organs: underground roots or stems that contain sufficient amounts of stored food to sustain plant in dormant state. They develop into buds that begin to grow during adverse conditions. ○ Runners → modified stems that grow on surface of soil and produce new leaves and roots at each n ode ○ Rhizomes → modified stems that can propagate new shoots at each node ○ Suckers → modified roots where shoots can grow and develop into new plants ○ Apomixis → generative tissues that give rise to plantlets that produce seeds asexually Artificial propagation of plants Used in agriculture to produce perennial plants in commercial quantities. Favourable when seeds are unavailable or difficult to germinate or when farmers want to perpetuate features of a desirable plant. The technique also used in research and recovery programs for endangered plant species (round-leaved sundew, Wollemi pine). Fungi: budding, spores Eukaryotes that secrete enzymes over the surface of their food and absorb the breakdown products directly Budding: adult organism gives rise to a small bud which develops as an outgrowth on the parent cell. The bud is smaller but genetically identical to the parent. Repeated budding forms a chain of connected but independent cells. Most y easts reproduce asexually by asymmetric budding Process 1. Parent cell forms small outgrowth that grows larger and forms bud 2. Nucleus splits into a smaller nuclei which migrates to daughter cells 3. Bud pinches inward at the base to detach from parent cell. Although in some organisms, it may remain in contact Spore formation (typical): spores are tiny haploid unicellular reproductive cells capable of developing into an adult without fusion with a second cell. Daughter cells are genetically identical to parent fungus and often arise from structures called s porangia, which produce spores in large numbers. Spores are encased in a protective coating, which turns black as it ripens, and its light mass enables widespread air dispersal. If a spore lands in a favourable environment, it germinates, forming a new fungus. ● ● Bacteria: binary fission Asexual → spores are called m itospores and are produced by mitosis Sexual → spores are called meiospores and are produced by meiosis Binary fission is the main method of asexual reproduction in unicellular organisms where a newly divided cell replicates its genetic material and splits into two genetically identical cells. Process 1. A dividing bacterium copies its DNA (single circular chromosomes with no nucleus) in the o rigin of replication located on chromosome by r eplication enzymes. The bacterial chromosome is found in the nucleoid. 2. Two split origins move towards opposite ends of the cell, pulling the rest of the chromosome along with them. 3. The cell elongates and a septum forms down the middle of the cell (division of the cytoplasm) 4. The cell pinches in two to form two identical bacteria cells Differences to mitosis ● No mitotic spindle (strings that keep chromosomes organised) forms in the bacteria during cell division ● DNA replication and separation occurs in tandem ○ Unlike in mitosis, DNA is copied during the S phase, prior to its separation in the M phase Protists: binary fission, budding Asexual binary fission: typical mode of reproduction Process differs to bacteria due to the need to replicate a membrane-bound nucleus. The parent cell no longer exists but neither has it died. Rather, it has redistributed itself to genetically identical daughter cells. The length of time needed for fission varies between organisms and with environmental conditions. Binary fission can be along a l ongitudinal axis (splits along its longest axis) or along a transverse (shortest axis) - Paramecium → p rotist of ciliate group Multiple fission can occur in parasitic protists where the nucleus in parent cell divides repeatedly and at a rapid rate to produce large numbers of daughter nuclei for the formation of multiple progeny Plasmodium falciparum → causes malaria in humans Budding: o ccurs on outside of a cell from which it detaches to live independently or in contact to form a colony. Unlike fission, the cytoplasm is unequal to parent cell as it is smaller in size. Analyse the features of fertilisation, implantation and hormonal control of pregnancy and birth in Mammals have several reproductive mechanisms to maximise reproductive success: Hormonal control Hormones: chemical substances that act as messengers in the body. Coordinates bodily processes so that actions within the body are synchronised. ● Sex hormones: specifically affects the growth and functioning of reproductive organs. Part of endocrine system mammals and are produced in special tissues in the ovaries, testes, and pituitary gland. ○ Pituitary gland (located at base of brain) secretes hormones that stimulate/inhibit other endocrine glands and regulates the release of their hormones for growth, metabolism and reproduction. ○ In humans, reproductive organs (gonads) mature and begin their function when stimulated by hormones during puberty Reproductive processes that hormones regulate ● Breeding seasons: regulate sexual behaviour by limiting ability of some mammals to reproduce at certain periods ○ Seasonal breeders are “in oestrus” during periods of female fertility ● Gametogenesis: production of male and female gametes in respective gonads ● Male and female reproductive cycles ○ In females, the pituitary gland secretes gonadotropic hormones (FSH and LH) for the maturation of follicles in ovaries as well as a l actogenic hormone called prolactin f or the preparation of breast tissue for milk production. Types of hormones involved in mammalian reproduction 1. Androgens: male hormones that regulate male sex organs and secondary sex characteristics (deepening voice, increase in growth etc.) Cells in testes secrete a ndrogen testosterone during spermatogenesis. While present in both sexes, levels are higher in males. They are also precursors of oestrogens. 2. Oestrogens: female hormones (with the converse of male characteristics). M ain functions are ovarian functioning and fertility in females 3. Progestogens: second main group of female hormones responsible for the regulation of pregnancy, secretion of milk in mammary glands (lactation) and menstruation. Fertilisation Occurs when the haploid nucleus of an egg fuses with that of a sperm, forming a diploid zygote. ● Sperm are attracted to the egg by r heotaxis (movement through a fluid) where they are held in storage in the oviduct. The presence of p rogesterone and a lkaline pH allow sperm to mature so they can penetrate the 3 layers of the egg: f irst membrane which contains fragments of follicle cells, z ona pellucida, and plasma membrane. Surface proteins allow only one sperm to penetrate the final barrier, which triggers enzymes that destroy the glycoproteins in the second layer and prevent other sperm from entering. ● Fertilised egg travels along oviduct and begins embryonic development Implantation Implantation of embryo into the uterine wall for internal development ● Oestrogen and p rogesterone, produced by the ovaries, prepares the uterus for the implantation of a fertilised egg each menstrual cycle. If fertilisation does not take place, the levels of both hormones decrease and the lining of the uterus tears away. ● Once implantation has occurred, the main role of progesterone is suppressing uterine activity, thus supporting foetal development and reducing risk of foetus being disturbed by uterine contractions Evaluate the impact of scientific knowledge on the manipulation of plant and animal reproduction in agriculture Pregnancy Pregnancy begins when fertilised egg implants on uterine wall ● Corpus luteum in ovary secretes hormones for first three months of pregnancy. Once it begins to degenerate, the placenta d evelops and takes over the role of producing hormones to maintain pregnancy for the latter six months ● Levels of oestrogen and progesterone are optimised during ovulation to create ideal conditions for implantation ○ Oestrogen → promotes growth of endometrium ○ Progesterone → stimulates secretion of mucus by cells lining endometrium and growth of blood vessels. Also reduces mother’s immune response to foetal antigens. A dequate progesterone production by corpus luteum is essential in maintaining pregnancy until placenta takes over at 7-9 gestational weeks. ○ Placenta → connected to foetus by umbilical cord where blood vessels pass to and fro to transport oxygen and nutrients and remove wastes ○ Other hormones prevent foetal overgrowth and regulate nutrients that cross placenta Birth Prostaglandins s ecreted by the wall of the uterus initiates labour, softening the tissue of the cervix to allow the passage of the baby. Secretion of o xytocin promotes coordinated contraction of the smooth muscle of the uterus, and secretions continue after the birth to expel the placenta and limit blood flow to the uterus. P rolactin promotes the enlargement of mammary glands for milk production. Reproductive technologies applies to the use of any technology to assist and improve reproduction. Agriculture - breeding and cultivation of animals, plants, fungi for food, biofuels and other products used to enhance human life Human intervention in necessary to improve the quality and yield of production (info already written in notes) Cell Replication Inquiry question: How important is it for genetic material to be replicated exactly? Model the processes involved in cell replication: - Mitosis and meiosis - DNA replication using the Watson and Crick DNA model, including Mitosis Meiosis Form of nuclear division that ensures daughter cells receive exact copies of chromosomes ‘Reduction’ cell division that takes place in reproductive organs and results in the formation of gametes with haploid number of chromosomes. nucleotide composition, pairing and bonding Role and importance Growth of multicellular organisms - mitotic division followed by c ell assimilation, enlargement and differentiation Repair of damaged tissue and replacement of worn-out cells Asexual reproduction - cloning, budding Genetic stability - ensures equal distribution of chromosomes Process: SPMAT + Cytokinesis - - - Diploid zygote arises from the fusion of haploid gametes that were formed respectively by maternal and paternal chromosomes Ensures chromosome number of species is maintained Genetic variation is introduced Process: DNA replication occurs before division 1. Meiosis I - d iploid cell divides into two haploid cells 2. Meiosis II - t wo cells divide again to form four haploid daughter cells (tetrad) Telomeres - DNA-protein regions on the ends of chromosome that shortens with age, preventing further division and leading to c ell senescence/death DNA Replication ( info already written in notes) Relatively recent discovery of its structure (60 years) XRD- X-ray Diffraction - DNA is the SAME in every cell (different sections are turned on and some are turned off) - Each of 46 chromosomes has one large DNA molecule Assess the effect of the cell replication processes on the continuity of species (info already written in notes) DNA and Polypeptide Synthesis Inquiry question: W hy is polypeptide synthesis important? Construct appropriate representations to model and compare the forms in which DNA exists in eukaryotes and prokaryotes The genetic code is u niversal → the same nucleotide base-pairing code is used in all living organisms for protein synthesis. Prokaryotes Circular chromosomal DNA is contained in one chromosome that holds two circles of single-stranded DNA twisted around each other. The chromosome is found in the nucleoid and measures about Eukaryotes DNA is linear and not circular. DNA molecules are organised into chromosomes and are located in nucleus. Model the process of polypeptide synthesis, including: - Transcription and translation - Assessing the importance of mRNA and tRNA in transcription and translation - Analysing the function and importance of polypeptide synthesis - Assessing how genes and environment affect phenotypic expression 1300µm. In most eukaryotic cells, a large proportion of DNA is non-coding DNA, and are not used directly to make proteins or RNA. Only 3% of DNA is coding DNA. May have one or more small rings of non-chromosomal DNA (plasmids), which replicate independently of chromosome. These plasmids do not necessarily code for the essential features required for survival, but provides bacteria with a selective advantage (resistance to antibiotics). Non-nuclear DNA is found in the mitochondria and chloroplasts of cells. These replicate and are inherited independently of nuclear DNA. Mitochondrial DNA is linked to maternal inheritance: used to study evolutionary relatedness and trace a direct genetic line, as mtDNA are only passed down from the mother. DNA supercoils around a central protein (scaffold) to form nucleoid. DNA winds around proteins (histones) to form n ucleosomes. There are 5 main histones which are responsible for the packaging of DNA. Polypeptides are chains consisting of amino acids held together by peptide bonds and fold in 3D conformations to form proteins. The sequence and arrangement of amino acids determines the configuration of a protein. Therefore, any change in the sequence may change the shape of the protein and hinder its ability to carry out its function. Polypeptide synthesis Transcription: a section of DNA is transcribed by mRNA 1. RNA polymerase enzyme binds to a part of the DNA ‘ sense/non-coding’ strand (promoter). The DNA helix unwinds and unzips. The sense strand acts as a template for RNA nucleotides to attach to its complementary base pair on the DNA strand (HOWEVER, A b inds with U [uracil]). a. In eukaryotes, ‘editing’ or splicing of pre-mRNA may take place: RNA processing - Eukaryotic cells mRNA transcribed from DNA is termed pre-mRNA a s it requires further editing before it acts as a template for translation. pre-mRNa contains coding sequences of nucleotides (exons) with sequences of noncoding nucleotides (introns) Introns code for their own removal, forming mature-mRNA. Splicing and rearrangement of blocks of mRNA is important for gene regulation in complex organisms as it can give rise to different versions of the same protein (isoproteins) - can produce antibodies specific to a pathogen/invader 2. The mRNA molecule exits the nucleus via the nuclear pores and enters the cytoplasm, where it will attach to a ribosome. (Usually, the mRNA template is read by many ribosomes so that the same polypeptide product is produced in larger quantities) Translation: mRNA binds with tRNA on the ribosome to synthesise a polypeptide chain 1. Ribosomes move along the mRNA strand. tRNA molecules bind with amino acids in the cytoplasm and subsequently attaches to mRNA by temporarily pairing the bases of the tRNA anticodon to its complementary codon on mRNA. The ‘start’ codon initiates the synthesis of the polypeptide. 2. A chain of amino acids form, held together by an enzyme 3. After the amino acid on a tRNA molecule binds with the growing polypeptide chain, tRNA moves away from the mRNA and back into the cytoplasm to attach another amino acid 4. Polypeptide chain is processed in the cell where it folds to form protein in a 3D configuration 5. Once the ‘stop’ codon is reached, the mRNA breaks down into its individual nucleotides, which can be reused Assessing the importance of mRNA and tRNA in transcription and translation mRNA (messenger) Single stranded and are a few thousand bases long, shorter than DNA. Functions as the intermediate molecule that carries info from DNA to ribosomes in cytoplasm. tRNA (transfer) Each molecule is 75 nucleotides long and twisted in the shape of a clover-leaf. At one end are three unpaired bases (anticodon) which attach to its complementary bases (codon) on mRNA. Formed from DNA Other end holds a site of attachment for amino acids. The sequence of the three bases determines the amino acid carried. Importance ● mRNA allows for the genetic code in DNA to be translated into proteins. This is because DNA is held in the nucleus of a eukaryotic cell and is too large of a molecule to penetrate the nuclear membrane. The single-stranded mRNA is able to pass Importance ● tRNA is an important molecule in transcription that attaches to mRNA and gives rise to a specific sequence of amino acids that synthesise into a protein ● Important for the attachment of amino acids to form a growing polypeptide chain. It maintains the sequential synthesis of the protein after it detaches from the mRNA to bind with another amino acid that will contribute to the rRNA (ribosomal) Made in the nucleolus and act as enzymes that aid in protein synthesis and forms a structural component of ribosomes. through and thus translate the genetic instructions to the protein. Role ● Responsible for the carrying of genetic information contained in DNA to the ribosomes in the cytoplasm. making of the protein. Role ● The main function of tRNA is to transport amino acids to the ribosome. The other end of a tRNa molecule contains the anticodon triplet that will bind to its complementary codon on mRNA. Analysing the function and importance of polypeptide synthesis Importance ● DNA unzipping is essential for the formation of mRNA. A section of DNA containing the gene required for the synthesis of a specific protein unwinds and unzips where RNA nucleotides can attach to the exposed “sense” strand and form an mRNA molecule that carries transcribed genetic information from the DNA. This section provides the c ode for the production of a protein. ● The processes of transcription and translation are carried out in tandem in cells for the creation of proteins. Proteins are essential biological molecules that cells and tissues require for their specific function. ● It is crucial that the genetic information being translated via RNA contains full and accurate instructions for the correct functioning of a cell. If any errors occur in the creation of mRNA or the pairing of nucleotides, the end-products of synthesis may change and hinder the survival of an organism, especially if the required protein is not being produced. ● Gene expression is regulated by proteins, hence, it is important that these proteins undergo accurate synthesis according to DNA instructions to produce an overall phenotype for an organism Assessing how genes and environment affect phenotypic expression Genotype → all the alleles present on a chromosome for a particular trait Phenotype → physical expression of an organism, based on its dominant genotype ➔ Some variations can be genetically-determined or influenced by environment ➔ Genes that ARE expressed dictate the types of proteins in cells and thus, the overall phenotype of organism Genes ● Dependent on the accurate synthesis of Environment The environment does not chemically modify the genome (sequence of bases), but proteins that are coded for by specific sections of genes on DNA influences the phenotype via chemical markers or tags being added to DNA. ● Temperature can cause organisms to express the phenotype of mutant alleles through colour of fur etc. ● Hydrangeas → the pH of soil influences the phenotype and causes a change in the colour of the flower Regulation of genes ● Modifying DNA for transcription: methylation represses gene expression. It increases the density of binding between DNA and histones, restricting access by RNA polymerase. ● Post-transcription (modifying and processing RNA): includes splicing (removal of introns) and regulation of the length of time for which mRNA remains active and stable. ○ MOST COMMON REGULATION IN EUKARYOTES ● Post-translational regulation: activation of protein by adding or removing a chemical group Investigate the structure and function of proteins in living things Chemical structure ● Contains carbon, hydrogen, oxygen and nitrogen (sometimes sulfur). Proteins are composed of chains of amino acids bonded together by peptide bonds. Folds into a particular shape that is crucial to its functioning. ○ Protein → single chain of 40-50+ amino acids folded in a specific manner ○ Polypeptide → chain shorter than 40-50 amino acids and combines with other chains to fold into functional protein Physical structure Primary → polymers containing an amino acid sequence arranged in linear chains called polypeptides. This structure determines the secondary and tertiary structures, and any incorrect amino acid may hinder the shape of the protein and therefore, its function. Secondary → three-dimensional arrangement of polypeptides by twisting + hydrogen bonds. Can fold into a lpha helices or p leated sheets. F ibrous proteins have a secondary physical structure. Tertiary → further folding into complex 3D conformations caused by interactions between polypeptide and immediate environment. Typical of globular proteins. Quaternary → proteins made up of more than one polypeptide chain Types of protein groups Fibrous Forms structural components of cells and tissues. Are long and insoluble in water. E.g. keratin, collagen, elastin Globular More complex proteins with tertiary structure and are spherical in shape. Compact and soluble. E.g. transport proteins, enzymes, immunoglobulin, hormones Functions of main group proteins Structural Promotes structural support and movement of cells (Tubulin i n microtubules are responsible for forming the cytoplasm, Actin a llows for the contraction of the cytoplasm during cytokinesis and promotes the crawling movement of protists) Enzymes Is involved in all biochemical aspects of cell metabolism - anabolic and catabolic reactions. The shape of the active site determines its binding specificity. Important molecule in gene functioning, replicating, repairing and protein synthesis. Cell communication, signalling and biological recognition Proteins embedded in membranes regulate the movement of ions and molecules between internal and external environments. These include transport a nd storage p roteins. Sensory Responds to stimuli (changes in environment) by changing its shape or biochemical activity Hormones a nd neurotransmitters a ct as chemical messengers between cells - biological recognition between chemical messengers and their target cell is essential. Receptor proteins i n cell membranes are responsible for receiving these messages and must have a shape that is reciprocal t o the molecule with which it binds. Genetic Variation Inquiry question: H ow can the genetic similarities and differences within and between species be compared? Conduct practical investigations to predict variations in the genotype of offspring by modelling meiosis, including the crossing over of homologous chromosomes, fertilisation and mutations (Info on meiosis in above dot point) How is genetic variation introduced? Mendel’s laws of genetics ● Random segregation (1st law) → pair of alleles segregate and each gamete receives one allele for a gene ● Independent assortment (2nd law) → a lleles for each different trait separate independently of other alleles ● ● Model the formation of new combinations of ○ There are 2 23 possible combinations of chromosomes in the formation of gamete from independent assortment alone Fertilisation → random fusion of two gametes ensures further mixing of genetic material, producing variations in phenotype that may be acted upon through natural selection in process of evolution ○ Offspring arising from gametes of u nisexual animals will produce greater genetic variability than those from hermaphroditic animals ○ Offspring arising from cross-fertilisation between plants will have greater genetic variability than those from s elf-fertilisation Mutation → occurs during DNA replication prior to cell division Mendel’s model of inheritance: Autosomal recessive inheritance ● Alleles pass from one generation to the next according to s et ratios genotypes produced during meiosis: - Interpreting examples of autosomal, sex-linkage, codominance, incomplete dominance and multiple alleles - Constructing and interpreting information and data from pedigrees and Punnett squares ● ● ● The alleles in an individual: ○ Are the same in homozygous/pure-breeding offspring ○ Differ in h eterozygous/hybrid offspring ■ In heterozygous individuals, the trait that is expressed is the d ominant allele and the one that is hidden is the recessive allele. For a recessive allele to be expressed, both alleles need to be recessive. ■ These alleles are located on one of the non-sex chromosomes (autosomes). Humans have 22 pairs. The one sex chromosome determines gender. Diploid individuals inherit two alleles of the same gene (one from each parent) and haploid cells have only one allele of each gene However, despite there being multiple alleles of a gene in a population, an individual can only carry two alleles of one gene. These are dependent on the alleles passed down from parental chromosomes. ___ Techniques Phenotype does not necessarily tell us what the genotype of an organism is. A testcross c an be used to determine whether an organism is homozygous or heterozygous → the tested organism is crossbred with an organism that is homozygous for the recessive gene. (INCLUDE PUNNETT SQUARES) Pedigree charts are used to identify inheritance patterns of a particular trait in a family lineage and make predictions about the expected phenotypes and genotypes of future offspring. (INCLUDE TABLE) Sex-linkage ● In humans, genes on sex chromosomes code for the production of sexual reproductive organs and the development of secondary sexual characteristics that define whether an individual is phenotypically male or female ○ Y carries testis-determining gene Sex linkage occurs when genes on sex chromosomes code for characteristics other than gender. ● Genes on X = females have two alleles for that gene and males will have only one = recessive disorders appear frequently in males ○ Haemophilia is a bleeding disorder and X-linked. Males who inherit this mutant allele on X chromosome will suffer from the disorder as they have no equivalent allele to mask the gene on the Y chromosome. ○ If a female inherits one copy of the allele from haemophilia, she will not suffer from disorder if her other allele is dominant. She is termed a carrier → disorder may be passed on to her sons (affected) or daughters (carriers or affected) ○ If a daughter inherits pair of defective alleles, the condition is lethal Rest of info written in notes Collect, record and present data to represent frequencies of Population genetics → study of how the gene pool of a population changes over time, leading to a species evolving. Combines Mendelian genetics and Darwinian evolution to explain how changes in allele frequencies arise and how these can result in micro or macroevolution. Scientists conduct frequency studies to predict the potential of populations to adapt, as well as future resilience, stability and survival. characteristics in a population, in order to identify trends, patterns, relationships and limitations in data, for example: - Examining frequency data - Analysing single nucleotide polymorphism ● ● Gene pool is the sum total of all genes and their alleles present in a population Genetic diversity is the total of all genetic characteristics in the genetic makeup of a species and is dependent on genetic variability (tendency of individual traits to vary). Species that have a greater degree of variability is more likely to adapt and survive. Allele frequency → measure of how common an allele is in a population F requency of allele A = N umber of copies of allele A in population T otal number of copies of the gene (A+a) in population Factors affecting allele frequency: selective environmental pressures, natural selection, other external (gene flow, genetic drift) ● ● To conduct a scientifically valid study, pop. geneticists use a model based on the allele frequencies derived from a stable population with Mendelian inheritance (population in equilibrium) and compare this to populations exposed to selective pressures. They study mathematical changes in frequencies to develop quantitative ways of exploring evolutionary hypotheses. Single nucleotide polymorphism ● SNPs are mutations where one nucleotide has been incorrectly inserted during DNA replication, creating an error in the base sequence at a particular location on a chromosome (loci on chromosomes where alleles differ at a single base). They are often termed ‘genetic markers’ because they are used to compare genetic similarities and differences between individuals without sequencing the genome. ○ Genetic markers → identified sequence of DNA at a known site on a chromosome ● The rarer allele must have a frequency of 1% in a certain population to be termed a SNP. ● SNPs usually occur in non-coding regions (introns) of DNA GWAS (genome-wide association studies) ● Bioinformatics technology (DNA manipulation techniques) is used to scan the genomes of people and find genetic variations associated with a particular disease or phenotypic trait. SNPs are studied to identify disease susceptibility and evolutionary relatedness. ● SNPs that occur in higher frequencies in people with a particular disease are said to be associated with such disease ● Computer technology allow hundreds or thousands of SNPs to be analysed at the same time → genotyping (identifying genetic variations in individuals) is faster and cheaper than sequencing whole genomes. ● GWAS are based on the presence of a g roup o f SNP markers (haplotype) associated with a trait, rather than individual SNPs Limitations: ● Data from GWAS is reliable as long as the regions selected are evenly distributed throughout the genome.Genetic markers that are more closer together give more accurate data → for haplotype studies, SNPs inherited from one parent are studied, thus, crossing over during meiosis mean the SNPs on a chromosome might not all be inherited together. Inheritance Patterns in a Population Inquiry question: C an population genetic patterns be predicted with any accuracy? Investigate the use of technologies to determine inheritance patterns in a population using: - DNA sequencing and profiling DNA sequencing → exact nucleotide sequence (order of bases) of a gene on a chromosome is determined ● Sanger chain method (dideoxy DNA sequencing - d dDNA) ○ DNA is isolated from cells and replicated by the polymerase chain reaction (PCR) ■ SEQUENCING REACTIONS: ○ Double-stranded DNA is separated into single chains by heating ○ A small piece of DNA called a p rimer binds to the start of template DNA strands and acts as a template to build the complementary strand using free nucleotides ○ After a chain-terminating nucleotide (dideoxy nucleotide triphosphate) h as attached to their complementary base on template strand, they prevent other nucleotides from attaching (ddATP, ddTT P, ddGT P, ddCT P) Each of these are labelled with fluorochromes (fluorescent dye). ○ Chain termination occurs at different positions leading to varying fragment lengths of DNA ○ Process continues until every position on template strand has been identified with a ddNTP ○ DNA fragments are placed into a tiny capillary tube containing a gel where an electric current is used to pull the strands through. When strands emerge, they pass through a laser beam which causes them to glow at a particular wavelength specific to the base defined by the ddNTP at the end of the fragment. ○ Computer analyses colours and displays chromatogram of base sequence in original DNA sample (order of complementary bases on different lengths of dye-stranded DNA allows sequence to be determined). ● ● Maxim-Gilbert method → sequencing of DNA by modifying the chemical conditions suited to a specific base, allowing them to be removed from the ribose sugar it is attached to and creating fragments of different lengths where the DNA has been cleaved. Fragments undergo gel electrophoresis and all patterns derived from each base are compared to determine final sequence. ○ DNA is radioactively labelled on one end by adding phosphorus atom to the phosphate molecule prior to modification of conditions ○ Chemical reactions are specific to two groups of bases: pyrimidines (C and T) and purines (A and G) Nanopore sequencing → propelling a DNA molecule with a motor protein through a protein nanopore. Pore in a membrane separates two compartments both containing a buffered KCl solution. Differences in current when passing through is dependent on the identity of the DNA sequence. DNA profiling ( DNA fingerprint analysis) → organism’s unique DNA profile is determined and represented as a distinct series of bands ● Whilst 99.9% of DNA is common to all humans, STRs ( Short tandem repeats) are unique. These are sections of non-coding DNA following a repetitive sequence (e.g. TATATATA) ○ Number of repeats in non-coding regions of DNA varies between individuals and gives rise to different profiles ○ Process: DNA is isolated and the PCR is used to increase the amount of DNA under study. Strand undergos gel electrophoresis and fragments will migrate different lengths in the gel depending on the amount of repeats. Investigate the use of data analysis from a Population genetics: ● Genetic differences between species can be analysed to determine the evolutionary history of populations - those with similar gene large-scale collaborative project to identify trends, patterns and relationships: - The use of population genetics data in conservation management - Population genetics studies used to determine the inheritance of a disease or disorder - Population genetics relating to human evolution pools are most closely related Conservation management ● Aims to avoid extinction of a species by employing conservation methods that ensure biodiversity is maintained. Involves gathering genetic data that will aid in identifying conservation strategies to increase the chance of saving and protecting endangered populations. ● Methods: ○ Field observation by sampling and statistical analysis - distribution and abundance of a species ○ DNA analysis (SNPs, GWAS, haplotypes) → determines kinship lineages, improved scientific understanding of microevolution by selection and mutation ■ Enabled scientists to identify sections of the genome that are essential for adaptation to the environment and to identify deleterious alleles and any mutations that can enhance biological functions ● Scientists study past extinction events to develop models that can assist in modern-day conservation of endangered species Wooly mammoth extinction → mammoths in isolation on Wrangel Island suffered a ‘genomic meltdown’ with various detrimental mutations that hindered the potential for the species to survive. ● Mutations primarily affected olfactory processes and reduced number of urinary proteins which reduced their ability to mark and recognise territory, hunt and mate. ● Others include a mutation for fur (cream coloured, satiny coat) which reduced its insulating properties which were essential in ice age climates. Resultant inbreeding and loss of genetic diversity (precursor to disease susceptibility) led to their extinction. Modern koala populations → two biogeographic barriers that have emerged in the last ice age (20 000 years ago) led to a split in the koala population. Further habitat fragmentation and other selective pressures including those instigated by human activity (fur trade, habitat clearing, disease) have reduced the distribution of koalas over time. Current research is being implemented on local scales to collect DNA samples and analyse genetic variation in koala populations. Disease New-generation gene-sequencing technologies have allowed scientists to identify genes associated with genetic diseases and disorders and individualise diagnosis of specific diseases and predict the possibility of offspring inheriting conditions quickly and accurately. Large-scale screening and DNA analysis provide opportunities for early detection and improved treatment options. SNPs unique to a particular disease can be detected in newborns → NSW newborn screening program provides free genetic tests for SNPs associated with various congenital diseases (cystic fibrosis, phenylketonuria etc.) Human Gene Mutation Database stores info on germline mutations associated with human-inherited diseases Human evolution Anthropological genetics aims to explain the causes of human diversity over time. Scientists study the human genome to gain a greater breadth of understanding of human evolution. Human migration theories ● Multiregional hypothesis (MRE) → relies mainly on fossil evidence and suggests all human populations can be traced back to when Homo erectus f irst left Africa about 2 million years ago. ○ Suggests gene flow (change in allele frequency from individuals leaving and entering) between neighbouring populations ● Replacement hypothesis (Out of Africa) → suggests archaic Homo sapiens left Africa and proposes a second migration happened about 100 000 years ago. Modern humans of African origin conquered archaic groups and replaced them by interbreeding and out-competing them. ○ Modern genetic studies have shown that if MRE were correct, modern populations would contain ancient alleles scattered in different regions of the world. Mitochondrial DNA was used due to a relatively uninterrupted lineage. ■ Humans were grouped according to mutations in mtDNA: members that share the same mutations must be descendents of a common ancestor (haplogroups). Phylogenetic trees were produced from mtDNA haplogroups. ○ However, genetic evidence favours the Replacement hypothesis as it was discovered that most of the variation in mtDNA sequences were shown only in African populations. The mtDNA of other ethnic groups represent just a subset of total human mtDNA diversity (M and N haplogroups). ■ 2 surviving haplogroups (M and N) that colonised other continents are most closely related to the African L3 haplogroup ○ Evidence for the Out of Africa hypothesis suggests that two other species of humans (Neanderthal and Denisovans) had also migrated out of Africa, interbreeding with our human ancestors in Eurasia. A small amount of Neanderthal DNA was introduced into the human genome and persists today → most Europeans and Asians have 2% Neanderthal DNA. Notes for later modules: - Occasionally, n ondisjunction of chromosomes may occur during meiosis, where sister chromatids do not separate. This results in an incorrect number of chromosomes in the offspring.
