HSC Module 5 & 6 Summary PDF

lOMoARcPSD|48455185 HSC Module 5 & 6 - Summary Biology HSC (Ryde Secondary College) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Amy Bui ([email protected]) ...

lOMoARcPSD|48455185 HSC Module 5 & 6 - Summary Biology HSC (Ryde Secondary College) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Contents Module 5: Heredity...........................................................................................................................2 1. Reproduction......................................................................................................................2 1.1 The Mechanisms of Reproduction that ensure the Continuity of a Species, by analysing sexual and asexual methods of reproduction in a variety of organisms, including:................2 1.2 Features of fertilisation, implantation and hormonal control of pregnancy and birth in mammals......................................................................................................................................8 1.3 The impact of scientific knowledge on the manipulation of plant and animal reproduction in agriculture /....................................................................................................11 2. Cell Replication................................................................................................................16 2.1 Model the processes involved in cell replication, including:.............................................16 2.2. Assess the effect of the cell replication processes on the continuity of species..............22 3 DNA and Polypeptide Synthesis....................................................................................23 3.1 Construct appropriate representations to model and compare the forms in which DNA exists in eukaryotes and prokaryotes.......................................................................................23 3.2 Model the process of polypeptide synthesis, including:....................................................25 3.3 The structure and function of proteins in living things.....................................................32 4 Genetic Variation.............................................................................................................34 4.1 Predict variations in the Genotype of Offspring by modelling meiosis, including the crossing over of homologous chromosomes, fertilisation and mutations..............................34 4.2 The formation of new combinations of genotypes produced during meiosis, including 40 4.3 Represent frequencies of characteristics in a population, to identify trends, patterns, relationships and limitations in data, for example:.................................................................48 5. Inheritance Patterns in a Population...............................................................................54 5.1 Use of technologies to determine inheritance patterns in a population using, for example:.....................................................................................................................................54 5.2 Use of data analysis from a large-scale collaborative project to identify trends, patterns and relationships, for example:.................................................................................................57 Module 6: Gene琀椀c Change..............................................................................................................61 1. Mutation................................................................................................................................61 1.1 Explain how a range of mutagens operate, including:............................................................61 1.2 Compare the causes, processes and effects of different types of mutation, including:...........61 1.3 Distinguish between somatic mutations and germ-line mutations and their effect on an organism......................................................................................................................................61 1.4 Assess the significance of ‘coding’ and ‘non-coding’ DNA segments in the process of mutation.......................................................................................................................................61 1.5 Causes of genetic variation relating to the processes of fertilisation, meiosis and mutation..61 Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 1.6 Evaluate the effect of mutation, gene flow and genetic drift on the gene pool of populations.....................................................................................................................................................61 2. Biotechnology.......................................................................................................................62 2.1 Investigate the uses and applications of biotechnology (past, present and future), including:62 3. Genetic Technologies..........................................................................................................62 3.1 The uses and advantages of current genetic technologies that induce genetic change............62 3.2 Compare the processes and outcomes of reproductive technologies, including.....................62 h琀琀ps://www.conquerhsc.com/hsc-biology-syllabus-notes Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Module 5: Heredity 1. Reproduction Inquiry ques琀椀on: How does reproduc琀椀on ensure the con琀椀nuity of a species? 1.1 The Mechanisms of Reproduction that ensure the Continuity of a Species, by analysing sexual and asexual methods of reproduction in a variety of organisms, including: Reproduction is the process of creating a new individual or offspring from their parent(s) 1.1.1 Animals: advantages of external and internal fertilisation External Fertilisation- The union of male and female gametes (sperm and ova) occurs outside the body. Tends to occur between aquatic animals Advantages:  Greater quantity of gametes are produced. Leads to a greater overall amount of offspring’s produced. Supports the continuity of species more than internal fertilisation.  External fertilisation can give rise to more mating partner options than internal fertilisation. This can lead to greater genetic variation in species population as the mating process is less selective than internal fertilisation. Disadvantages:  Upon fertilisation, the zygote is exposed to the environment rather than protected inside the mother’s body. Due to the limited defence capabilities of the zygote (e.g. against predators), it is more susceptible to death. Gametes more likely attacked by predators or fail to be fertilised. The zygote therefore has a lower chance of survival  Is restricted to aquatic environments. The flagellum component of the sperm cell allows it to move through water that otherwise would not be possible on land. If performed on land, the egg will dry out.  Lower fertilisation success rate than internal fertilisation. This is because the sperm and egg cells are subjected to greater amount of factors in external fertilisation. For example, the more environmental factors such as predators (Sea life) and harsh aquatic environment conditions (e.g. harsh currents). Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Internal Fertilisation- union of male and female gametes occur inside the body. Tends to occur between terrestrial animals Advantages:  Occurs inside the female’s body so the zygote is protected from the external environment of the parent. Less environmental factors that affect the zygote which increases the survival.  Internal fertilisation is NOT restricted to terrestrial environments unlike external fertilisation which is restricted to aquatic environments only.  Internal fertilisation has higher fertilisation success rate on a per gamete basis compared to external fertilisation. This is because the sperm does not need to travel by chance to fertilise an egg. Internal fertilisation provides the sperm a direct route towards to egg cell inside the female’s body. During such journey, the sperm cell is subjected to less variable and/or violet environment factors such as strong current or predators. Disadvantages:  Less mating partner options than external fertilisation. This can lead to a lower genetic variation in species population as the mating process is more selective  More energy in search for a mating partner and perform the mating process which are unnecessary in external fertilisation.  Less gametes are produced compared to external fertilisation. This leads to a lower overall amount of offspring produced. Lower chance of the continuity of a species 1.1.2 Plants: asexual and sexual reproduction Asexual Reproduction -is the process of forming an offspring (usually a cell) from just ONE parent through cell division. Many cell division process. In humans and many other mammals, this cell division process is called mitosis. Thus, the offspring has genetic materials that is IDENTICAL to that of its single parent – offspring is a CLONE of the parent. Distinguishing factor between sexual and asexual reproduction is whether or not the fusion of gametes occurred. For sexual reproduction, there must be a fusion of gametes whereas, in asexual reproduction, there is no fusion of gametes. Vegetative Propagation Type of asexual reproduction that occurs in plants. It results in the parent producing a plant that is genetically identical. Runners, bulbs, fragmentation are some examples of vegetative propagation. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Tubers - are swollen underground stems that store food and new plants can grow from the tuber. For example, a potato is a tuber and the ‘eye’ of the potato are buds which can each grow into a new potato plant Stolons- are many plants, especially the grasses that have long stems called stolon or ‘runners’ that grow along the surface producing new roots and leaves at nodes, e.g. spinifex grass. Rhizomes -are underground stems that give rise to new shoots and roots at the node. Suckers- are new shoots that arise from roots or underground stems, often after fires. Several Australian plants reproduce by suckers. Fragmentation- is when the original organism separates a small part of itself. This occurs in starfish where a part of its body can be separated from its parent and the separated section can develop into a new starfish that is genetically identical to parent starfish via cell division. Runners- Strawberry plants can develop runners which are stems extending from the plant and along the soil. At certain points along the runners, nodes can develop which extends to the soil, resulting in the formation of new plant roots at another area of the soil whereby a new strawberry plant can grow. The runner joins the new (and genetically identical) strawberry plant to the parent plant. Bulbs - are bud cells that are found underground. These buds can develop into new plants such as onions. New plant forms, the underground bulb provide nutrients to the plant for its survival. Sexual Reproduction The process of forming a new organism from the fusion of the offspring’s parents’ (male + female) gametes. Gametes are sex cells such as sperm and egg cells for humans. The offspring that is formed from sexual reproduction has the genetic material from its parents. Offspring’s genetic material is NOT IDENTICAL to their parents (it’s mixed). In humans and many other mammals this process of producing gametes is called meiosis.  Self pollination involves one plant (parent) and is a type of sexual reproduction. This is because the plant can produce both pollen and ovules (male and female plant gametes). These gametes can combine to produce either a genetically identical offspring or genetically different offspring. Whether the offspring is genetically identical or different, it will depend of whether the single parent plant is homozygous or heterozygous for those genes. Continuity of species Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 During reproduction, the parents’ genetic information (DNA) is copied and passed onto the offspring. The offspring’s genetic material is stored in their cells’ nucleus. There are two types of cells: somatic and non-somatic (sex) cells. Humans and many other mammals offsprings are produced from non-somatic cells. Only the parents’ genetic material in non-somatic cells’ (or sex cells’) genetic material is passed onto the offspring. Genetic information is passed onto the next generation ensures the continuity of the species. Importance of creating variation in offspring’s genetic information (new allele combinations, increasing variation in the alleles which gametes can inherit as well as variation in the gametes that are fertilised during fertilisation). The increased variation in the offspring’s genotype will enhance the chances of survival of a species’ population and thus supporting the continuity of the species. Reproduction increases the number of offsprings in a population, effectively increasing population size. 1.1.3 Fungi: budding, spores Budding in fungi such as yeast involves the parent cell developing a bud cell, a daughter nucleus. This usually occur when the environmental conditions are favourable for the fungi. Over time, this bud undergoes cell division while still being attached to the parent which may result in a chain of bud cells due to cell division. During cell division, but prior to separation of the protruding bud from the parent yeast (fungi), the parent’s nucleus’ DNA replicates and nucleus divides equally, but, the cytoplasm divides unequally (hence bud is smaller than parent). One copy of the DNA moves into the bud cell which results in the successful transfer of the parent’s DNA into the daughter (bud) cell. The bud separates from its parent fungus when it grows to a sufficient size to be able support itself independently. This now-separated bud undergoes further cell division to produce more bud cells. The result is yeast that is genetically identical to parent. Budding is also found in another type of organism called Hydras and the budding process is similar to that of fungi. Asexual spore production in Fungi Spores are microscopic reproductive units (cells) that can be formed as a result of mitosis or meiosis. Spores different to gametes as they do NOT need to combine or be fertilised by another spore to form an offspring. Mycelium is part of a fungi that branches out into a network structure of fine ‘threads’ called hyphae (plural for hypha). Each hypha have ends of that are capable Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 of producing spores called sporangia (plural for sporangium). These sporangia (and thus spores) are produced when environment conditions are favourable for the fungi’s survival. Mushroom is a type of fungi where the mushroom cap is above the hyphae spread along the stem and to the mushroom cap. The mushroom cap therefore has basida, which are examples of sporangia, that produces spores. These asexual spores are usually produced when ambient environment conditions are favourable via mitosis. These spores are usually carried by the wind as they are light-weight. These spores then germinates to form genetically identical fungus when environmental conditions are favourable. This typically involves the spores absorbing moisture and decaying organic matter from its environment, allowing the cytoplasm to expand and the fungus developing into a mycelium whereas new spores can be produced. Sexual spore production in Fungi Sexual spores are developed when opposite gender hyphae are combined together to develop a sporing-producing structure known as zygospore. The zygospore is diploid as each of the hypha are haploid. Under favourable conditions, the diploid zygospore undergoes meiosis to produce haploid sexual spores which are dispersed into the environment. These spores that are genetically different from their parents. Under favourable conditions, these spores will germinate and a genetically different fungus to its parents will be formed. These fungi are haploid as most fungi spend their lives as haploid organisms until time of sexual reproduction where hyphae combine to form a diploid zygospore to produce haploid sexual spores. In some fungus, the mycelium contains hyphae of two genders (male and female). This means that these fungus can produce spores via meiosis and disperse them into the environment. The term ‘plasmogamy’ refers event where the nucleus of the one hyphae enters the cytoplasm of another hyphae. The term ‘karyogamy’ refers to the event where the two nucleus are combined into one. 1.1.4 Bacteria: binary fission Commonly performed by unicellular organisms such as bacteria, though some multiceullar organisms can reproduce asexually via binary fission too. The process starts with the copying the genetic material (in the form of bacterial chromosomes) of the parent cell. Each chromosome moves to each side of the cell. This is followed by the elongation of the cell and cytokinesis which is the splitting of the cell membrane and cytoplasm of the cell into two daughter cells. As there is no cell nucleus in bacteria, there will not be the splitting of cell nucleus. It is important to note that the parent cell won’t exist at the end because it is now part of the two daughter cells. The two daughter cells are genetically identical to each other as well as identical to the parent which they obtained their genetic information came from. There are some multicellular organism that reproduce asexually via binary fission. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 1.1.5 Protists: binary fission, budding Binary fission The mechanism of binary fission in protist is similar to that of bacteria’s binary fission process. DNA is stored in the nucleus (no nucleus in bacteria), the chromosome will move to each side of the nucleus before the splitting of the nucleus and eventually splitting of the cell membrane and cytoplasm into two daughter cells. The splitting of the parent cell into two daughter cells is called cytokinesis. Binary fission in protist vs bacteria and budding in protist vs fungi are similar. For example:  Protists are mostly unicellular whereas fungi are mostly multicellular. 1. Fungi also have hypha. 2. Protists are microscopic whereas fungi are macroscopic. 3. Protists are eukaryotes whereas bacteria are prokaryotes. Budding Starts off by the parent protozoan producing a bud which is a daughter nucleus that is created based on the replicate of nucleus DNA, followed by equal nucleus division but unequal separation of the parent protozoan’s cytoplasm. This means that the bud is smaller than the parent. Over time, this daughter nucleus undergoes further cell division via mitosis to grow and mature, resulting in a protists that is genetically ideal to parent. 1.2 Features of fertilisation, implantation and hormonal control of pregnancy and birth in mammals Fertilisation Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185  Requires gametes (sperm and egg) meet and combine to form a zygote  Gametogenesis is the name of the gamete formation process.  Gametogenesis can be divided into spermatogenesis (producing sperm) and oogenesis (formation of matured egg cells)  The hormone testosterone is produced in cells’ in the testes organ of male as part of spermatogenesis as it plays a role in producing sperm cells.  The hormone oestrogen in males help with the maturing of the sperm cells in males.  The fertilisation process and fusion of gametes occurs in the fallopian tube of female’s body  The zygote will develop into a living organism that has mixed genetic information from the parents.  Zygote is the continuity of a species  Fertilisation involved multiple stages that MUST be fulfilled for successful fertilisation and zygote formation to produce new offspring.  Three necessary stages for successful fertilisation are: 1. Formation and maturation of gametes 2. Spermatozoa must journey into the oviduct 3. Spermatozoa must make contact and fuse with the egg cells.  The gametes fuse with one purpose – to form a zygote, single cell with 46 chromosomes  During fusion, the head of the sperm cell detaches from its tail (flagellum) and the sperm-egg species journeys down the female’s uterus. - Sperm cell activates the egg cell resulting in cell division of the egg cell growth/development. The resulting product is called a blastocyst.  Once the sperm fused with the egg, other sperms will no longer be able to fuse with the same egg  The gametes must be from the same species in other for successful fertilisation. Implantation  Implantation is the process of adhering the fertilised egg to stick to the walls of the reproductive tract, providing the most suitable environment for zygote development.  Crucial phase for successful pregnancy. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185  The blastocyst is implanted on the walls of the reproductive tract (uterine wall).  This implantation process onto the walls establishes blastocyst’s access to nutrients to develop into an embryo (blood vessels surrounding the blastocyst carries blood which has dissolved nutrients)  Embyro develops into a fetus (approx 5-11 weeks)  Embryro becomes a new organism upon release from female’s body. At ovulation stage, the matured egg cell is released from the follicle and travels up and along the fallopian tube (the C-shaped tube) that connects the ovary to the uterus. It at the uterus where the embryo is implanted on the uterus wall (endometrium) during implantation phase. Successful implantation of the embryo means successful pregnancy. When the sperm enters the vagina, up to the uterus, along and down the fallopian tube where it can combine and fertilise the mature egg. This means that the mature egg and sperm encounter each other head-on as the egg is moving in the direction from ovary to uterus and sperm is moving in the direction of uterus to ovary. This means that they are likely to meet at the fallopian tube, which is where fertilisation of the mature egg cell most commonly takes place in reality. In the diagram below, we see that the zygote (fertilised egg) is formed in the fallopian tube where the sperm meets and fertilises the egg. Hormonal Control of pregnancy and birth in mammals Other roles of progesterone during pregnancy Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185  Encourage the growth of blood vessels, allowing greater volumes of blood and thus nutrients surrounding the embryo.  Help develop and maintain the lining of the placenta.  Strengthening muscles of pelvic floor which support the delivery of offspring via the uterus then cervix and then through the vagina. During birth:  Oxytocin hormones are released stimulate uterine muscles to increase the strength and frequency of dilation and contraction of the cervix. This allows the parent to deliver the offspring by pushing out placenta. The hypothalamus produces oxytocin and stores it in the pituitary gland, situated below the hypothalamus. Upon stimulation of hypothalamus’s neurone cells, the pituitary gland will secrete oxytocin into the bloodstream.  Endorphin hormones are released to increase concentration and relief pain to focus on the delivery of offspring. The levels of endorphin peaks as the strength and frequency of cervix dilations and contractions increase to combat pain.  Adrenaline hormones are released during giving birth. This is due to the body’s response to fear and pain. Adrenaline provides energy for the parent to continue delivering the offspring by producing stronger dilation and contractions of the cervix. However, adrenaline may also cause the opposite response which is decreasing cervix contractions due to fear. 1.3 The impact of scientific knowledge on the manipulation of plant and animal reproduction in agriculture / Advancement in scientific knowledge provided humanity the knowledge that genes play an important role in the process of protein-synthesis. The protein that is formed during protein-synthesis will determine an organism’s characteristics. Not just structural characteristics (phenotype) but also physiological and behavioural characteristics! With this knowledge, scientists uses various technologies and methodologies to alter an organism’s gene sequence. As a result, the modified organism’s offspring would have the favourable traits that was manipulated by the scientists. The following methodologies are used to manipulate the reproduction processes of plants and animals in the agriculture industry: Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185  Artificial insemination  Artificial pollination  Cloning  In-vitro Fertilisation All four above are types of artificial reproduction. Earlier in this week’s notes, we talked about natural reproduction. Artificial Insemination It involves a male sperm cell being inserted into a female’s reproductive tract. The fusion of the sperm and egg cell results in fertilisation of the egg cell, producing of zygote. Hence, artificial insemination is a form of sexual reproduction (involves gametes). Artificial insemination is primarily used to produce offsprings with favourable characteristics, mix of both male and female parents. Artificial insemination is a form of selective breeding because it allows the sperm cell of a selected male to fertilise the egg cell of a selected female. Usually, both the male and female parents have favourable characteristics that an offspring would combine. Other benefits of artificial insemination involves minimising the costs of transporting animals from one country to another in order to be crossed over. This is because the sperm cell of a selected male can be frozen and transported to another country, ready to be fused with a selected female’s egg cell. Mass artificial insemination will reduce genetic variation. This is because one selected male’s sperm cells can be used to inseminate many female egg cells. OR A selected female’s egg cell fusing with a selected male’s sperm cell. Imagine producing offsprings from the same selected male and female over and over again. The majority of the population’s would be genetically identical – having same mixed genes of the selected male and female parent. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Thus, mass artificial insemination reduces the number of offsprings produced by random breeding (speaking from a total population’s genetic variation perspective). Artificial Pollination Artificial Pollination involves the manual transfer of pollens into stigma of another plant to combine with the egg cell (ovule) of the plant. This type of reproductive technology was used by the well-known scientist and monk, Gregor Mendel in his pea plants experiments – which helped create modern laws of genetic inheritance. We will talk more about Gregor Mendel in later weeks. Anyways, successful transfer results in pollination and fertilisation of the egg cell, producing a seed. Each of these seeds will develop into an offspring, a new plant. Artificial pollination is used to produce offsprings with favourable characteristics, that are the mix of the two plants. Since these two parent plants were selected and made to breed with each other, artificial pollination is therefore a form of selective breeding. Example: Producing plant offsprings that have both purple and red flower colours – combined characteristics of the two plants Artificial pollination is cost effective way of producing new plant variations with relative ease. This is because artificial pollination can be performed manually. No fancy technology required. Artificial pollination is a form of sexual reproduction. Mass artificial pollination would reduce genetic diversity. This is because if artificial pollination is used to produce a million plants, the majority of the plant population will be genetically identical. Similar concept to artificial insemination. Cloning Cloning is a type of asexual reproduction used to create offsprings that are genetically identical to the parent. Some farmers may want their crops to be genetically identical because they have the favourable traits. Example: Maybe a flower with a really pretty yellow colour. Many genetically identical flowers can be produced via cloning. Remember earlier, genes determine phenotype (physical traits e.g. colour) Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 For plant cloning, it involves cutting a section of the mother plant’s which contains at least one stem cell. The cutting is then planted in the same environment as the mother plant to allow the cutting to develop the same characteristics as the mother plant, producing the same yield with the same harvest time. Since clones are genetically identical, mass cloning activities would make the entire cloned population susceptible to an entire wipeout. Example: a deadly virus (environmental agent) that the cloned population has no resistance to. Please note that, although artificial insemination and artificial pollination are forms of sexual reproduction, if the majority of offsprings are genetically identical, they are equally susceptible for a major wipeout. Hence, all forms of mass selective breeding is equally risky if consequences are not evaluated. The cloning of plants have been used for tens of centuries but the cloning animals is more complex and less understood. Dolly the Sheep (cute sheep clone example) In 1988, Dolly the Sheep is an offspring that was a clone offspring. Dolly was successfully cloned using a sheep’s (sheep A) mammary gland (a group of somatic/body cells). The scientists then removed the nucleus (therefore DNA) of another sheep’s (sheep B) egg cell and inserted the nucleus of the somatic cell from the mother sheep into the egg cell. The egg cell undergoes cell growth and development inside a foster mother sheep (sheep C) to produce Dolly the Sheep. Dolly the Sheep has the same genetic information as Sheep A (inherited Sheep A’s genetic information) and thus is a clone of Sheep A. However, Dolly the Sheep died earlier than scientists’ expectation. :'( This led to questions relating to health and ethical problems of cloning. In Vitro Fertilisation In vitro fertilisation (IVF) is a reproductive technique used for increasing the likelihood of developing offspring when couples have fertility problems but wishes to have their children. As females are born with a lifetime limited supply of oocytes, their age may be a cause of infertility. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 For males, abnormalities in their sperm cells’ ability to fertilise mature eggs may be their cause in infertility. Some males not be able to produce sufficient quantities of sperm cells required to fertilise egg cells which means the rate of fertilisation (and thus zygote formation) is low. Firstly, IVF processes involves a stage known as a ovulation hyperstimulation where multiple matured egg cells or oocytes are produced. If you recall from the natural female menstrual cycle, only one mature oocyte is produced. Hyperstimulation is possible when the female takes the supplied fertility drugs such as those containing FSH (Follicle-stimulating hormone) or GnRH hormones as mentioned in the hormonal cycle. Following ovaulation hyperovulation, IVF involves removing good quality, mature these oocytes from the female’s ovaries. These egg cells are then placed in a petri dish to be fertilised with sperm cells. The petri dish is then placed inside a incubator for cultivation where conditions are optimised for the enhance the probability of the zygote developing into an embryo and eventually blastocyst. About three days later, those zygote that successfully developed into a blastocyst are transferred into the women’s uterus (womb). The female is later tested for successfully pregnancy which depends on the number of embryo that is transferred to the woman’s uterus (womb). Of course, there is a limit. Left out good quality embryos can be frozen and stored. The female’s age is also another factor in determining the success rate of successful pregnancy. Notice that by using IVF, more egg cells are fertilised with sperm cells than without IVF. This will increase the chance of couples with fertility problems in producing their children. IVF can bypass the fertility issues of many couples rendering them having a low probability in producing an offspring. There are many ethical issues surrounding in vitro fertilisation. The mother of the offspring can be of an old age (over the age of 70) when her children is born. In these cases, the mother may not be able to support their children and their children may lose their mother before they hit their teenage years. For such reasons, many governments have banned the use of in vitro fertilisation techniques for women over a certain age. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 2. Cell Replication Inquiry ques琀椀on: How important is it for gene琀椀c material to be replicated exactly? 2.1 Model the processes involved in cell replication, including: 2.1.1 Mitosis and Meiosis Mitosis There are two terms that you need to know before we get start understanding the diagram! These terms are:  Chromatid: A single-stranded chromosome  Chromosome: A molecule that is made up of DNA and protein Some terms you already know from Preliminary HSC Biology:  Nuclear membrane (depicted as the purple circle in diagram)  Cell membrane (depicted as the black circle in diagram) Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Now that we know learnt some new terminologies, let’s explore what is exactly occurring in each of the stages of the mitosis illustrated in the diagram above! Random Somatic Cell: Mitosis starts off with a somatic (body) cell, i.e. a cell that is not involved in the production of gametes (Gametes can be sperm or egg cells). The somatic cell is a diploid cell. A diploid cell means that it has two sets of each chromosome. For example, in humans, we have 23 sets of chromosomes. Each set of chromosome contains 2 chromosomes that are homologous to each other. We call them homologous pairs. We will explore what homologous pairs actually mean later as we get into the steps of mitosis. A haploid cell only contains one set of each chromosome, i.e. contain only half the amount of total chromosomes compared to diploid cells. There is only one chromosome per ‘set’. At the end mitosis, the number of chromosomes is retained. This means that, at the conclusion of mitosis, each of the two daughter cells that are produced from the parent somatic cell are also diploid cells. Interphase (Step 1): DNA replication occurs here. Each chromatid (single stranded chromosome) has its DNA duplicated, forming another chromatid that is genetically identical. These two genetically identical chromatids are called sister chromatids. Remember a chromatid is a single-stranded chromosome and as stated earlier in the definitions. Also note that a chromosome is made up of DNA and protein. I have coloured the chromatids in the above diagram to outline that there are two sets of chromosomes (orange and green sets), i.e. two homologous pairs. In reality, humans have 23 sets or homologous pairs but only two pairs are depicted for the purpose of simple illustration. It is important to note after DNA replication, the number of chromosomes have not changed! There are still two sets of pairs illustrated in the somatic cell after interphase! The chromosomes have just changed from being single stranded (chromatids) to double stranded (sister chromatids). So, after DNA replication, there are still 23 sets of chromosomes in humans like there is 2 sets of chromosomes illustrated in the diagram. Apart from the DNA being duplicated, the centrosomes (illustrated as the two pink ‘rectangles’ at right angles) have also been duplicated during interphase. Each of the rectangles represents a centriole in the centrosome if you are curious. Centrosomes play an important role in the later stages of mitosis. Prophase: During prophase, the chromosomes coil up. You can now see chromosomes in their classic “X” shape under a compound or light microscope. During prophase, the nuclear membrane dissolves in the cytoplasm. Also, the centrosomes begins to move and align up at opposite ends of the cell’s equator Metaphase: During metaphase, the chromosomes line up above each other along the poles the cell. The microtubules (fibres structures illustrated as blue lines), which Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 attached to the centrosomes, will now have access and attach to the chromosomes’ centromeres (the point of which the sister chromatids in each chromosomes are attached, illustrated by the pink dot). The microtubules randomly attaches to the chromosomes’ centromeres. So, microtubules effectively join centrosomes and chromosomes together. Anaphase: During Anaphase, the chromatids that are attached to centrosomes via microtubules are being pulled towards opposite sides of the somatic cell. The cell membrane is also starting to alter its shape for cell division. Telophase: During Telophase, single-stranded coiled chromosomes start to uncoil. Cytokinesis occurs and the nuclear membrane starts to form again. The somatic cell divides into two. Each daughter cell have identical and equal amounts of genetic material as the original parent somatic cell. Each daughter cell is capable of entering interphase to undergo mitosis when given instruction to do so. No genetic variation created. Having explored the mechanisms of the asexual reproduction process, Mitosis, we will now move on to explore meiosis, a sexual reproduction process. There are two stages of Meiosis because there are two sets of cell division. In mitosis, one cell split into two. In meiosis, one cell splits into two and each of the two cells further splits into two. So, at the end of meiosis, there are four cells (gametes) produced. Meiosis Meiosis I – Cell Replication Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Unlike Mitosis, Meiosis starts off with a germ cell rather than a somatic cell. A germ cell is found in the reproductive organ of an organism can undergo meiosis to produce gametes such as sperm and egg cells, depending on the gender of the organism. Like a somatic cell, a germ cell is also a diploid cell. However, unlike mitosis, meiosis does not maintain the overall number of chromosome number throughout the process. Therefore, the gametes cells that are produced at the end of meiosis are NOT diploid but haploid cells. Interphase I: DNA replication occurs here. Each chromatid has its DNA duplicated, forming another genetically identical (sister) chromatid. I have coloured the chromatids here. The yellow chromatids are from the father and the green chromatids are from the mother. Similar to Mitosis’s interphase stage, the number of chromosomes have not changed before and after interphase. Apart from the chromatids, the centrosomes have also been duplicated. Prophase I: During prophase, the chromosomes coil up. The nuclear membrane dissolves in the cytoplasm. The centrosomes begin to move and align up at opposite ends of the cell’s equator. You can now see chromosomes under the microscope in their classic “X” shape. Unlike in mitosis, homologous chromosomes in propose of meiosis will line up side-by-side (not on top of each other) across the equator of the cell for crossing over. During crossing over in Prophase I, the double-stranded homologous chromosome pairs (one from father and one from mother) exchange their genetic material. This will mean that the (non-sister) chromatids involved in the crossing over would create new allele combinations. This means that the resulting gametes can inherit new allele combinations that are different from their parents. Notice that PRIOR to crossing over:  The allele combinations in each of the two double chromatids were (BHC and BHC).  The allele combinations in each of the two pink chromatids were (bhc and bhc). Notice that AFTER crossing over:  As seen in the above diagram, the allele combinations for the chromatids (from left to right): BHC, bHC, Bhc and bhc.  Two new allele combinations are created. These are bHC and Bhc which did NOT exist before crossing over or if crossing over did not happen. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Metaphase I: As the nuclear membrane dissolves, the microtubules attached to the centrosome can bind with the chromosome at their centromeres. This binding process of microtubules to chromosomes is random. This random binding process results in what is called the independent assortment of non-homologous chromosomes. Independent assortment is the process where the alleles specifying for different genes (in non-homologous chromosomes) assort themselves independently. This would therefore mean the independent alignment of the chromosomes between non- homologous pairs on the equator of the cell. This process of independent assortment will affect the genetic material of the two haploid cells that will be produced in the later steps. We will explain how independent assortment increases genetic variation very shortly after explaining Meiosis I and Meiosis II. Anaphase I: The microtubules move the chromosomes in each homologous pair move to different sides of the cell membrane. As the microtubules do no selectively bind to a chromosome (as mentioned in Metaphase I), the side of the cell to which the chromosomes will be pulled towards will depend on how they are connected to a centrosome via microtubules. Telophase I: The coiled chromatids of each chromosome starts to uncoil. The microtubules begin to break down and a new nuclear membrane is created to enclose the chromosomes. Since each chromosome of the homologous pair are now in different cells, there is no longer homologous pairs in each of the haploid cell. This is all due to independent assortment in Metaphase I. Meiosis II- Sexual Reproduction Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Prophase II: Centrosome duplicates for each haploid cell. Chromosomes coils up. The nuclear membrane formed during the Telophase I dissolves. Metaphase II: The two centrosomes in each of the haploid cells move opposite poles of the cell. The chromosomes line up side-by-side along the equator of the cell. Microtubules attaches the chromosomes to centrosomes. Anaphase II: Random segregation occurs here. The process of random segregation refers to the random separation of chromatids to different poles in a haploid cell and, ultimately, affects the chromatids that end up in each of four gametes.  Note that each chromatid may contain different alleles for a particular gene which end up in different gametes. During Anaphase II, the microtubules separate the sister chromatids of each chromosome, pulling one chromatid to a different pole in each haploid cell. The result is that on each pole for each haploid cell, there are two chromatids. This segregation process is random, i.e. you cannot determine which chromatid will end up at which of the four gametes during Cytokinesis II which occurs in the next step (Telophase II). Unlike independent assortment, we are dealing with individual chromatids here instead of homologous chromosome pairs. Segregation increases the genetic variation of the gametes and thus offspring (derived from gametes). We will clarify as to why segregation increases genetic variation shortly. Telophase II: The coiled chromatids starts to uncoiled. Cytokinesis II occurs during Telophase II, forming four haploid gamete from the splitting of each of the two haploid cells. Each of the gamete inherits one allele of every gene. This is because each of the double-stranded chromosomes that contains two alleles for different genes have separated during Anaphase II. During Telophase II, the microtubules begin to break down and a new nuclear membrane is created to enclose the two chromatids in each of the four daughter cells (gametes). One centrosome to each daughter cell. Depending on the germ cell and, hence gender of the organism, the four gamete is either sperm or egg cells. The gamete can fuse with its opposite kind (e.g. sperm cell with egg cell or vice versa) to form a diploid cell, a zygote so that the zygote will have two alleles for a given gene. 2.1.2 DNA replication using the Watson and Crick DNA model, including nucleotide composition, pairing and bonding Step 1: DNA replication starts with a double-stranded DNA helix molecule. Step 2: The enzyme, helicase, attaches to and unwinds the double-stranded DNA helix. Helicase also facilitates the breaking of hydrogen bonds between the nitrogenous bases (Adenine, Thymine, Guanine and Cytosine). This would lead to the separation of the two DNA strands. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Step 3: Each of the two now separated DNA single strands act as templates for free (available) nucleotides from the nucleoplasm (inside nuclear membrane) to join via complementary base pairing, i.e. Adenine bonds with Thymine and Guanine bonds with Cytosine. The enzyme, DNA polymerase, moves along the DNA strands during this process to catalyse the reaction, allowing complementary base pairing to occur. Step 4: The enzyme, DNA ligase, secures each of the new DNA strands formed with free nucleotides (monomers) with complementary base pairing. Step 5: Each DNA double strands return to their chemical stable state by winding up spontaneously to form a two double-stranded DNA helix. 2.2. Assess the effect of the cell replication processes on the continuity of species If an organism has favourable characteristics that allow it to tolerate the selective pressures of its ambient environment, cell replication is critical in allowing such favourable characteristics to be passed onto o昀昀springs. With the o昀昀spring inheriting favourable adaptations, they would have a higher chance of survival in its environment than without. This is why mitosis is important. Mitosis basically produces clones, thus ensuring that favourable characteristics are inherited by o昀昀springs throughout the population. This is seen in plants’ runners leading to new plants that are clones (genetically identical) of their parents. In humans, our muscle cells, hair cells and so many other cells reproduce via mitosis. Mitosis is important for cell development and growth! Compared to meiosis, there is no crossing over in mitosis. Crossing over occurs during Prophase I of meiosis where non-sister chromatids in homologous pairs exchange genetic materials, creating new allele combinations. As crossing over increases the genetic variation in the resulting o昀昀spring and, thus the species population, it reduces the probability that a sudden change in environment will lead to an extinction event. This will therefore ‘ensure’ the continuity of a species through meiosis. In addition to crossing over in meiosis, the processes of independent assortment and random segregation during meiosis also help increase variation in the resulting o昀昀spring. In general, the both lead to increased genetic variation of the resulting gametes. We have already touched on this during the meiosis steps but let’s review and tie it to the learning objective! Similar to crossing over, we have already talked about independent assortment and random segregation already in terms of increasing genetic variation in the gametes and, thus, o昀昀spring when the gamete is fertilised. Therefore, all of these processes (including random fertilisation) Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 serves to increase the genetic variation in o昀昀spring. By increasing genetic variation, the o昀昀spring of the next generation would have di昀昀erent characteristics which would increase the probability of the species’ population surviving the event of a sudden change in the ambient environment. This is because the survival of the species population of the next generation will not be dependent on a 昀椀xed characteristic or characteristics as variation increases. Also, the unique allele combination in each of the four gametes (per germ cell’s meiosis) increases the genetic variation of the zygote that is formed. This is because any gamete have equal chance (25%) in combining with its counterpart gamete (e.g. sperm with egg or vice versa) to form a zygote. This would therefore increase the genetic variation in the o昀昀spring and thus ‘ensures’ the continuity of a species. 3 DNA and Polypeptide Synthesis Inquiry ques琀椀on: Why is polypep琀椀de synthesis important? 3.1 Construct appropriate representations to model and compare the forms in which DNA exists in eukaryotes and prokaryotes  There are two types of DNA namely Chromosomal DNA and Extrachromosomal DNA.  The di昀昀erence between these two are that the former is located inside a cell’s nucleus whereas the latter is located outside a cell’s nucleus. Remember that there are many cells in the body  Plasmids are circular DNA molecules that are found outside the nucleus in prokaryotes’ cells. Hence, they are a type of extrachromosomal DNA.  Mitochondrial DNA and chloroplast DNA are also classi昀椀ed as extrachromosomal DNA as they are not found within the nucleus of a cell. These two types of circular DNA are found in eukaryotes.  Chromosomes are classi昀椀ed as linear chromosomal DNA as they contain linear DNA and are located within the nucleus of a cell. Chromosomes are found in eukaryotes’ cells. The table below highlights more di昀昀erences between the DNA found in the cells of prokaryotes and eukaryotes. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Prokaryotes Prokaryotes have circular DNA as shown in the diagram. In the case of bacteria, it has circular bacterial DNA.  Notice that bacterial DNA is double stranded but it is circular in shape. Prokaryotes also contain plasmids which are circular DNA molecules Eukaryotes How DNA is involved in the protein synthesis process where proteins produced determine the traits (physical, physiological and behaviour traits) of living organisms. We will first be focusing on protein synthesis in eukaryotes which consists of two separate stages. i.e. transcription and translation. Then after that, we will look into protein synthesis in prokaryotes. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 3.2 Model the process of polypeptide synthesis, including: 3.2.1 Transcription and translation Transcription *Typo in diagram: Ribonucleotide Triphosphate should read Ribonucleoside triphosphate. These are RNA nucleotides. RNA nucleotides are different to DNA nucleotides as they do not contain thymine nitrogenous base. They have Uracil (U) nitrogenous base instead. Furthermore, they different in their sugar molecule. More specifically,  A RNA nucleotide can have – C, G, A or U nitrogenous bases. Each nucleotide has a ribose sugar and phosphate group.  A DNA nucleotide can have – G, C, A or T nitrogenous base. Each nucleotide has a deoxyribose sugar and phosphate group In eukaryotes, transcription is the first stage of the two-stage protein synthesis process. Transcription (‘transcribing’) is the process whereby the genetic information of a gene, situated in DNA strand, is copied to mRNA molecule that is synthesised during the process. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Step 1: RNA polymerase (enzyme) attaches itself to the DNA at the promoter sequence region, breaking the hydrogen bonds that is bonded the nitrogenous bases. This results in the unwinding of a section of the DNA double helix. This process is known as initiation.  Note that RNA polymerase does not unwind the entire DNA molecule, only a section consisting of a gene that is required to code for a particular polypeptide chain. Step 2: The section of DNA is unwound to allow free ribonucleoside triphosphate molecules to perform complementary base pairing with the template strand of the DNA. That is, Adenine will pair with Uracil and Cytosine will pair with Guanine.  Note that there is NO thymine base in ribonucleoside triphosphate molecules, they are replaced with Uracil. This is because the mRNA molecule consists of Uracil, Adenine, Cytosine and Guanine whereas the DNA strand consists of Thymine, Adenine, Cytosine and Guanine.  NOTE: Only one strand (the template strand) of DNA gets transcribed.  Fun point about enzymes: Most enzymes have their names ending with ‘ase’. For example, DNA polymerase, RNA polymerase and helicase. Step 3: RNA polymerase moves downstream of the DNA (from 3′ to 5′ as shown in diagram) as more nitrogenous bases on the template strand are being paired with ribonucleoside triphosphate. These free RNA nucleotides are found in the nuclear sap, this is the same place where the free nucleotides are found during DNA replication. This process is known as elongation or sometimes also referred to as propagation because more RNA nucleotides are being paired with the nitrogenous bases on the template strand. As RNA polymerase moves downstream of the DNA, the enzyme rewinds the DNA behind it to reform the double helix. Step 4: The propagation stage of transcription stops when the RNA polymerase arrives at a termination sequence. Here, the enzyme releases the chain of ribonucleoside triphosphate from the complex, creating an mRNA strand that has identical genetic information as the coding strand of the DNA (only difference is that uracil is present rather than thymine) as it is formed via complementary base pairing using the template DNA strand. Translation Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Translation is the process whereby mRNA information is used to create polypeptide chain and specifying its amino acid sequence. A polypeptide chain is consist of a chain of amino acids. There are proteins that are only made up of one polypeptide chain but there are also proteins that are made up of more than one polypeptide chain. Step 1: The mRNA migrates out of the cell nucleus and into the cell’s cytoplasm via the nuclear membrane pore. Step 2: A small ribosomal unit attaches to the mRNA Step 3: Following the small ribosomal unit, the large ribosomal unit attaches to the mRNA  With the mRNA enclosed by the ribosome, it means that translation occurs within ribosomes. The rough endoplasmic reticulum (organelle) contains many ribosomes on its surface. This was from the Year 11 Preliminary HSC Biology Syllabus. Step 4: There are tRNA molecules found in the cytoplasm that have an anticodon. One anticodon is made up of three RNA nucleotides, each RNA nucleotide has a nitrogenous base – A, U, C or G. Each of these tRNA molecules can bind with a specific type of amino acid that is specific to its anticodon. This binding process requires the assistance of an enzyme (enzyme name not necessary for HSC Biology). Step 5: The mRNA codon specifies the tRNA, carrying an amino acid, with the complementary anticodon to bind with itself. The ribosome reads the mRNA codons so that the tRNA molecules with the correct anticodon bind with the correct mRNA codon.  Note: Each codon (a sequence of three RNA nucleotide) on the mRNA strand will specify the tRNA anticodon for successful binding. For example, an mRNA with the codon AUC will specify and only allow an tRNA molecule with the UAG anticodon to bind with it.  In effect, each mRNA codon specifies a tRNA molecule (based on complementary anticodon) and, thus, specifies the amino acid. Hence, the amino acid is specific to the mRNA codon (as well as specific to tRNA anticodon, of course). Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185  In the HSC Exam: You will be expected to know that each mRNA codon specifies an amino acid. This is why the translation table shows the mRNA codon that corresponds to an amino acid. Step 6: As the next mRNA codon speci昀椀es the another tRNA to bind with it, the prior tRNA molecule will detach from the mRNA and ‘transfer’ its amino acid to the new tRNA molecule that entered the ribosome complex. The amino acids undergo a condensation chemical reaction to bond with each other via a peptide bond. As this elongation process of building the amino acid chain progresses, the ribosome unit moves along the mRNA to continue reading subsequent mRNA codons. Step 7: The elongation process of building the amino acid chain stops when the ribosome complex reads the mRNA stop codon (a sequence of three RNA nucleotides). At this stage, a release factor comes into ribosome and binds with stop codon. This release factor causes the amino acid chain to separate from the tRNA molecule, resulting a polypeptide chain. Step 8: The ribosome complex separates into its small and large ribosomal subunits and mRNA separates into its individual nucleotides, i.e. ribonucleoside triphosphate. Step 9: The polypeptide chain coils up as the amino acids forms hydrogen bonding with each other. This single polypeptide can be a protein. (In diagram, I added extra amino acids, solely to depict coiling of polypeptide). Whether or not this polypeptide is a protein will depend on the type of protein that the original organism’s gene was expressing at the start of protein-synthesis. However, if the expressed protein has only required one polypeptide chain then it will be called a protein. If the protein to be expressed requires more than one polypeptide, then the polypeptide chain form will interact and bond with other polypeptides which together will fold or coil to form the protein. Protein Synthesis in Prokaryotes What we have just explored is protein-synthesis in eukaryotes. But how does the process of protein-synthesis differ in prokaryotes? Let’s find out In eukaryotes’ protein-synthesis there are regions called introns and exons. Exons are areas responsible gene expression and introns are non-coding regions of DNA that does not specify for an amino acid. Both of these DNA sequences get copied to the mRNA strand. Before translation, splicing occurs where introns DNA segments are removed from the mRNA strand. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 For prokaryotes, they have minimal introns and thus splicing is rarely occurs. In prokaryotes, transcription and translation occur simultaneously rather as separate steps because prokaryotes’ DNA are not separated from the cytoplasm via nuclear membrane. Lastly, each mRNA in prokaryotes contains genetic information from multiple genes. Comparatively, each mRNA in eukaryotes contain genetic information for only a single gene. So, in general, this means one mRNA in a prokaryote can code for more than one polypeptide compared to one mRNA in an eukaryote. 3.2.2 Assessing the importance of mRNA and tRNA in transcription and translation mRNA Part of the transcription involves the creation of a mRNA molecule that contains nitrogenous bases that are complementary to those nitrogenous bases found in the template strand or identical to nitrogenous base to those bases found in the DNA coding strand (except that uracil is present rather than thymine). From this, we can see that mRNA is important in ensuring that the organisms’ genes code for the correct mRNA codons. This allows the correct tRNA molecule with matching anticodons that correct the amino acid that corresponds to the mRNA codon to form the correct amino acid sequence for the polypeptide chain. Thus, the polypeptide chain(s) can fold correctly resulting in a correct protein structure and function. I know the word ‘correct’ was used many times there but that was for you to understand how the amino acid attached to the mRNA is SPECIFIC to the mRNA codon! The correct gene will allow the correct mRNA, formed from complementary base pair, to specify the correct tRNA carrying a specific amino acid to bind with the matching mRNA codon. This ensures that the right amino acids sequence of the resulting polypeptide chain and, hence, the correct protein to be created. tRNA The tRNA’s role is important in ensuring that it’s anticodon specifies and binds to the correct amino acid. This will ensure that the resulting polypeptide chain will have the right amino acid sequence that allow the protein-folding process to occur correctly. If not, the protein will not have the correct shape (primary structure)! The shape of the protein is critical in determining its function! Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 This can be seen in the example of enzymes, a type of protein. Without enzymes, many metabolic processes such as cellular respiration simply will not occur as the reactants will not form chemical bonds with each other to create the products. The enzymes involved in catalysing mammals’ metabolic processes are proteins. Enzymes allows reactions to occur with lower energy at faster rates. Enzymes work by binding reactants together at the enzymes’ active site to weaken their chemical bonds and create products. The enzyme’s active site is critical in ensuring that the enzyme is able to attach the specific reactants by their specific shape. The enzyme’s active site and the specific reactants’ shape matches specifically! So, if the enzymes’ (protein) shape is not correct due to incorrect amino acid sequence in protein synthesis, the enzymes’ (protein) cannot correctly perform its function in catalysing the required metabolic process such as cellular respiration. Without cellular respiration, the cells of the organism will not be able to able ATP (Energy). Without specific energy, the organism cannot perform daily activities such as hunting for food, cell growth, cell repair, cell division, maintain its core temperature, or even walk. This means that the organism will die. Apart from enzymes being made up of proteins, it is important to note that proteins also specify an organism’s characteristics (structural/physical, physiological and behavioural traits). A structural (or physical) characteristic may be hair colour. The details of how this works is beyond the HSC Biology Syllabus.  In the final learning objective of this week’s notes, we will explore more examples of proteins, apart from enzymes which we just talked about, in terms of how their structure is related to their functions. So, to wrap up, we should now realise that proteins are important. Protein shape is important to their function. Therefore, the right amino acid sequence is important as well as the right mRNA codon sequence and, hence, DNA is important. Previously, we have touched on the importance of DNA in terms of how genetic variation (allele combinations) are important in specifying the right characteristics of an organism for tolerating against ambient environment’s selective pressures. Now, we have touched on how DNA is important coding for the right protein which specifics for physical traits as well as catalysing necessary metabolic processes. 3.2.3 Analysing the function and importance of polypeptide synthesis Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 This learning objective would be related to the purpose and importance in creating polypeptide chains and therefore proteins. This has already been discussed towards the end of the the previous learning objective. So, scroll up a little to refresh your mind (if you are returning to this set of notes for exam revision). However, to add on to what has already been said, here are some more pointers that is specific to this learning objective. As already mentioned, gene expression refers to process whereby polypeptides are produced by the coding of genes. Hence, gene expression is part of the polypeptide synthesis and, thus, protein synthesis process. Polypeptide synthesis is a highly regulated process. For example, our white blood cells only produce proteins known as antibodies to immobilise and defend against foreign matter such as bacteria when necessary. After a successful defence, our white blood cells will stop producing antibodies. That is, gene expression will stop (we will learn more about regulatory DNA sequences that control gene expression in Module 6). While antibodies are only produced when the first and second line of defence has failed to defend against foreign matter such as bacteria. Haemoglobin is a protein molecule that is inside our red blood cells are continuously produced in the bone marrow. Haemoglobin is a protein that is made up of four polypeptide chain and helps increase the amount of oxygen that our red blood cells can carry to our cells for cellular respiration. 3.2.3 Assessing how genes and environment affect phenotypic expression The relationship between genes and phenotypic expression This has already been discussed. The flow chart below summarises the process of how genes are responsible for an organism’s traits via protein synthesis. Gene —> mRNA —> tRNA attached to amino acid —> Polypeptide chain — > Protein —> Codes for a characteristic which can be structural, physiological or behavioural.  For example, a structural or physical trait can be eye colour.  In reality, most traits are specified by more than one gene. The relationship between environment and phenotypic expression Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 So far, we have touched on how gene expression in protein synthesis is responsible for an organism’s phenotype. However, what studies have found is that there are in fact many environmental factors that will affect an organism’s gene expression and thus phenotype Some examples are outlined below. The organism’s diet or availability of food/water: Pea plants that have limited availability of water would be shorter than pea plants that have access to abundant volumes of water, provided their pea plants are genetically identical. pH of soil: Hydrangeas exhibit pink and blue colours depending on the pH of the soil. If the soil pH is less than 6, the hydrangeas will be blue. If the pH is greater than 7, they are pink. Hydrangeas colour are dependent on the concentration of aluminium ions in the soil where ion availability is affected by pH. Temperature of ambient environment: Himalayan rabbits are found to have different fur colour based on temperature affecting their gene expression in producing fur pigments. Above thirty five degrees celsius, they have white fur (better at reflecting heat). Below thirty degrees celsius, they have black fur (better at absorbing and trapping heat). You will learn about mutation in future modules. However, just to touch on it a little bit, mutations can also affect an organism’s phenotype by altering an organism’s DNA sequence. For example, UV radiation will modify the DNA sequence of a gene. If the mutation affects a gene that is a oncogene which controls cell growth, then the mutation may lead to uncontrolled growth of unspecialised cells (cancer cells). These unspecialised cells take the nutrients from surrounding specialised (useful) cells, leading to the death of specialised cells and increasing numbers of unspecialised cells (cancer cells). Such abnormal cell growth may appear as ‘bumps’ on an organism’s phenotype. In short, you can think that Genotype + Environmental Factors = Phenotype. 3.3 The structure and function of proteins in living things We have already briefly touched on the relationship between protein structure and function in living organisms. Recall that in learning objective #4, we used the example of enzymes (example of a type of protein) and their unique active site’s shape (protein structure) in catalysing specific chemical reactions by binding to specific reactants (protein function as catalyst for metabolic processes). To add what we have already explored in learning objective #4, for this learning objective, we will explore couple of more examples of how proteins can Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 perform various functions and how their structure help support the protein’s success in performing such activities. Keratin is a protein that has the function in providing the structure for an organism. Specifically, keratin provides the flexibility of an organism’s skin (protein’s function). The highly-coiled, rope-like protein structure of keratin allows the protein to stretch by without snapping (i.e. chemical bonds does not break), thus, allows the skin to withstand stretching forces. Another example is involves protein that adopt the function as part of an organism’s immune response. In short, when a foreign substance such as a bacteria enters the organism’s blood stream, plasma B cells gets activated leading to the release of proteins called antibodies. These antibodies are produced (via gene expression) have the same shape as the antigen (proteins) on the bacteria. This allowed antibody to bind with the antigen and neutralise the bacteria, preventing the bacteria to produce any toxic chemicals. Note that this is an investigation task. So, if you wish you can do further research other types of proteins that exist in living organisms. During your research, you can then document how the protein’s structure is related to their specific function in supporting the survival of the living organism. More on protein structure specifically In terms of protein structure specifically, there can be four levels of structure for a protein: Primary structure, secondary structure, tertiary structure and quaternary structure. Primary structure – is related to the amino acid sequence of the polypeptide chain(s). The way amino acids are ordered will determine how chemical bonds can and cannot be formed between amino acids. The primary structure is critical in determining how the secondary, tertiary and quaternary structures (shape) would be like! Remember, protein shape is related to its function. Secondary structure – is related to the way that each polypeptide chain will coil up into helixes by forming more hydrogen bonds between carboxyl and amine groups. Secondary structure is critical in providing chemical stability to polypeptide chains. Tertiary structure – is related to the way that the now-coiled-up polypeptide chains further coils up to form an irregular three-dimensional structure. This is critical in providing the shape of the eventual protein which is critical for the protein’s function. Up until this point, the main forms of chemical bonds are hydrogen bonding. However, to create this tertiary structure, there are other forms of bonds including ionic bonds. These new bonds increases the protein’s ability to tolerate variations in pH and temperature. However, at the end of the day, the range Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 of temperatures and pH in which proteins can operate efficiently are generally quite narrow. Quaternary structure – is related to the way different polypeptides interact with each other via hydrogen bonding, forming a functional protein such as an enzyme that is able to catalyse a chemical reaction. If you zoom into any section of the quaternary structure of the protein using an electron microscope, you will be able to see first see the tertiary structure then secondary structure and eventually the primary structure (amino acid sequence) of the protein. 4 Genetic Variation Inquiry ques琀椀on: How can the gene琀椀c similari琀椀es and di昀昀erences within and between species be compared? 4.1 Predict variations in the Genotype of Offspring by modelling meiosis, including the crossing over of homologous chromosomes, fertilisation and mutations Genetic Variation created by crossing over Crossing over- process involving the exchange of corresponding gene segments of non-sister chromatids between homologous chromosome pairs (double-stranded chromosome pairs for the most organisms). This effectively creates creates new allele combinations, known as recombination. It is important to stress that stating ‘new allele combinations being created as a result of crossing over’ is critical in HSC Biology as it is what appears on the marking criteria. Below is a diagram illustrating the crossing over process between one pair of homologous chromosomes. Notice that the crossing over occurs between non-sister chromatids, one from each double-stranded chromosome of the homologous pair. Each parent of the organism contribute one double-stranded chromosome.  For example, perhaps the blue one can be from the father (paternal chromosome) and the pink one can be from the mother (maternal chromosome). Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Chiasma is the point where crossing over occur. Plural is chiasmata. There can be multiple chiasmata, usually the longer chromosome, the more points of crossing over. The chiasma the visible component of the homologous chromosomes during crossing over in Prophase I in meiosis I. Recall from Week 2’s notes that crossing over does not occur in mitosis because the homologous chromosomes are NOT aligned side-by-side along the equator of the cell to allow overlapping segments of non-sister chromatids along the equator in the nuclear membrane.  Fun Fact: Crossing over can in fact occur between sister chromatids in one double-stranded chromosome (with requiring another double-stranded chromosome). However, it is ONLY crossing over between non-sister chromatids in a homologous pair where where new allele combinations are created.  You may be wondering why? Well, if you recall that sister chromatids are exact copies of each other, this means that the alleles on sister chromatids (coding for the any of the genes) are identical! Take a look at the diagram above. Each red dashed line highlights a locus on each chromatid. Prior to crossing over, each locus (position) on each sister chromatid has the same allele. For example, take the blue double-stranded chromosome, both of the sister chromatids have the ‘B’ allele that codes for black hair colour. Now, look at the other double-stranded chromosome (pink) in the homologous pair. At the locus of both sister chromatids that carries the gene that codes for eye colour, they both have the ‘b’ allele that codes for blue eye colour. NOTE: In this example, ‘B’ is an allele means that it codes for black eye colour and ‘b’ is an allele codes for blue eye colour. The letters (or alleles to be exact) can code for different colours or genes depending on the question given to you on the day. For instance, in the exam, the question will tell you that what gene each letter codes for AND what the capital and lowercase of each letter would mean in terms of alleles.  By convention, capital letter represents a dominant allele and lowercase represents a recessive allele. We will talk about dominant and recessive alleles soon in this week’s notes. Just to enhance your prior knowledge from Week 2: As you can see from the diagram shown above, the blue and red double-stranded chromosomes are called homologous pairs because, at the each locus (each locus shown by a red dashed line) of the chromosomes in the homologous pairs there are alleles that code for the same gene. Fun Fact: The longer the distance genes are separated along each of the chromosome (chromatid to be precise), the greater the chance of crossing over. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Generally, this will depend on the length of the chromosome. The greater the length, the more chance of crossing over and more chiasmata will exist during crossing over. In the previous diagram, I have drew light green arrows on the homologous chromosomes after crossing over to indicate the alleles that belong to each of the four chromatids. If I were to separate the four chromatids in the previous diagram on its own, the resulting allele combinations for the four chromatids would be as follows: There are two NEW allele combinations that has been created as a result of crossing over. These new allele combinations are bHC and BhC which did not exist prior to crossing over. Significance of crossing over The process of crossing over creates new allele combinations adds diversity of the gene pool of the population as the four gametes formed in meiosis will not be identical but rather can have different an allele for each gene. Also, upon fertilisation, two random gametes with some variation in their alleles for certain genes will combine and produce an offspring with an unique allele combination to their parents. This therefore increases genetic variation in a population and can introduce new phenotypes that potentially* could be expressed. Genetic variation in a population provides a pathway for evolution to occur. Without genetic variation, there will be no mechanisms for evolution. Genetic variation can be introduced into a population’s gene pool via:  Sexual reproduction (crossing over, independent assortment, random segregation and fertilisation) or  Mutation *The word ‘potentially’ is used because whether or not the allele will be expressed will depend on whether or not it is recessive and dominant which also depends on the complementary allele for the same gene. Dominant and Recessive Alleles Alleles are alternative (or different) versions of a gene that differ by their DNA sequence but codes for a protein that responsible for a same trait (e.g. hairy or hairless). An allele can be classified as dominant or recessive. Dominant alleles are always expressed over recessive alleles if they are both present in the genotype for a gene of the organism. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185  By convention, dominant alleles are denoted with capital letters.  Recessive alleles are denoted with lower-case letters.  If the the alleles are coding for the same trait, the same letter is used. If not, different letters are used. For example, in the diagrams shown previously, for the gene that codes for hair colour, there are two types of alleles, B and b. The ‘B’ allele would be the dominant allele for hair colour and b would be the recessive allele for hair colour. In HSC Biology, the question will tell you what the hair colour for dominant allele as well as for the recessive allele for hair colour. Some question requires you to determine what trait each allele expresses and whether or not they are dominant or recessive, in that case, the question will give you sufficient information to allow you to work it out. In that case, you will need to use Punnett Squares which we will learn this week. There will be these questions in this week’s homework set to allow you to practice. Give it a go. Solutions will be uploaded soon. Anyhow, below are some rules of thumb about dominant and recessive allele combinations:  If the organism (parent and/or offspring) has two dominant allele for a particular gene, the dominant allele will be expressed.  If the organism (parent and/or offspring) has two alleles for a particular gene, one dominant and the other is recessive, the dominant allele will be expressed.  If the organism (parent and/or offspring) has two recessive alleles for a particular gene, the recessive allele will be expressed. Fertilisation As illustrated in previous diagram, ‘Four different combinations of alleles after crossing over’, each chromatid begin segregating in Anaphase II and be completely segregated into a different gamete after Telophase II.  This occurs for all 23 pairs of homologous chromosome (one pair being sex chromosomes, XX or XY). In the previous diagrams , we only drew two chromosomes (a homologous pair) that are crossing over just to satisfy the purpose of a simplistic illustration of the crossing over of chromosomes in a homologous pair. As you may know now, when the gametes fuse together (egg and sperm except for fauna), a zygote is formed which has a diploid number of chromosomes. That is, the zygote has 46 chromosomes (23 homologous pairs). Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 So, in meiosis, the process of crossing over effectively creates the genetic variation in the gametes due to their difference in alleles for various genes (as we have mentioned earlier). Also, the random process of fertilisation between gametes (egg and sperm) also give rise to the genetic variation in the zygote whereby the two gamete have different alleles such that the zygote will have different allele combinations than its parents.  Due to meiosis, each gamete will have one allele that codes for a particular gene. Upon fertilisation where the female and male gametes fuse together to form a zygote, the zygote will then two alleles that code for each gene (e.g. gene for eye colour).  Therefore, the process of fertilisation creates new genotypes for the offspring that are, for the most part, different from each individual parent. Note that if both parents the homozygous dominant for the same gene. Homozygous dominant just means that the individual has two same alleles (homozygous) and the alleles are dominant (capital letter). So, if both parents have homozygous dominant alleles for a trait, then the offspring will have genotype that is exactly the same as the parent (homozygous dominant too) though ONLY for that particular gene. It is unlikely that both parents will have EXACTLY the same genotype (allele combinations) for EVERY GENE. In that case, they be twins. LOL.  We will further explore and talk about homozygous dominant later when we look at Punnett Squares later in this week’s notes.  Also note, in reality, most traits (e.g. height) are governed by more than one gene. Recall that independent assortment and random segregation both facilitate in increasing the genetic variation in offsprings of the new generations. Although they do not create new allele combinations, they do introduce variations in the way which alleles that specifies different genes on non-homologous chromosomes are assorted independently relative to each other (independent assortment) and eventually different chromatids that carries different alleles for certain genes can be segregated into different gametes (random segregation).  This means that these two independent assortment and random segregation introduce (genetic) variation into the alleles that each gamete inherit after Cytokinesis II in Telophase II. The specifics in how independent assortment and random segregation increases the genetic variation in the offspring was discussed in Week 2’s note. If required, please revisit that section to refresh memory. Mutation Recall that crossing over introduces new combinations of alleles that already exist in the chromatids by exchanging corresponding gene segments between non-sister chromatids. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Mutation, however, alters the allele’s identity because the DNA sequence is altered. This new DNA sequence can lead to an alternative expression of the gene (e.g. blue eye colour instead of black eye colour), hence new allele (different DNA sequence for same gene) is created. In most cases, mutation only involves the modification of a DNA nucleotide, changing its nitrogenous base (point mutation). In some more extreme cases, it can modify the DNA sequence of a portion of chromosome that involves one or more genes (chromosomal mutation). We will explore point mutation and chromosomal mutation in Module 6 – Inquiry Question 1. Anyhow, after learning about protein-synthesis in last week’s notes, where the creation of mRNA uses the DNA sequence of a gene as a template, it is clear that altering the nucleotide sequence of a gene will result in the specification of a different protein OR may modify the structure and function of the protein such that it will no longer functions as efficiently or completely not functional at all. Suppose, you have an allele that codes for blue eye colour. This allele can be exchanged with another non-sister chromatid during crossing over. However, mutation completely alters the identity of this allele originally coded for blue eye colour. This means that it may code for something slightly or completely different instead. Perhaps maybe, green eye colour. Since alleles are altered, this would mean that through mechanisms of sexual reproduction and fertilisation, mutated allele will be inherited by gamete and possible give rise to offspring when fertilised. This would mean that a new allele will be introduced into the population. This would mean that there would be an increase in genetic variation in the population as allele frequency will increase. Note that mutation on genes in autosomes and sex chromosomes will be passed onto offspring if ONLY the mutation occurs in the parents’ germ cell. The gametes derived from the parent germ cell then becomes an offspring when gamete is fertilised where the offspring can inherits the mutation. Most mutations passed onto offspring may not expressed as they could be recessive so offspring needs to inherit one mutated allele from each parent in order to express the mutated characteristic. Whether or not the zygote will express the new allele due to mutation will depend on the zygote’s genotype (dominant or recessive for that gene) which we will explore very shortly when we deal with Punnett Squares. If the mutated allele is expressed, it is important to consider whether or not the expressed trait that it codes for will become an improvement or hinderance to the organism’s daily activities. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185  Mutations are permanent changes to an organism’s DNA sequence.  Mutation and its implications will be discussed in greater detail in Module 6. Mutation is considered the principal and original source in creating genetic variation in a population. This is because they provide the creation of new alleles by altering DNA sequence. The parent can be copy such mutated DNA via meiosis I which gametes and, when fertilised, the offspring can inherit such mutated DNA.  Not all of the four gametes must inherit such mutated DNA though. Anyways, similar to crossing over, independent assortment, random segregation, we should now know that mutation also creates genetic variation in a population which provides a pathway for evolution to occur. Without genetic variation, there will be no mechanisms for evolution. This ties nicely to support your responses when asking questions regarding ‘ensuring’ the continuity of species as per inquiry question one. As genetic variability in a population increases, the species’ population ability to adapt to its environment over time also increases. It is through such adaptability of species in a population overtime whereby we witness evolution due to shifts in dominant or new characteristics in the species’ population. 4.2 The formation of new combinations of genotypes produced during meiosis, including 4.2.1 Interpreting examples of autosomal, sex-linkage, co-dominance, incomplete dominance and multiple alleles An autosome is a chromosome in an organism that is not a sex chromosome. In humans, we have 22 pairs of autosomes and one pair of sex chromosomes. Genes are present in both autosomes and sex chromosomes. The process of transferring genes (DNA) present in the parents’ autosomes to offspring is called autosomal inheritance. The process of transferring genes (DNA) present in the parents’ sex chromosomes to offspring is called sex-linked inheritance or X-linked inheritance. The genes that is present in autosomes and sex chromosomes, when passed to offsprings, exhibit different inheritance patterns or combinations of genotypes in terms of phenotype. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185  More specifically, the likelihood of an offspring exhibiting a recessive trait that is passed on autosomal inheritance is equal for both males and females. However, the likelihood of offspring exhibiting a recessive trait that is passed on via sex chromosomes inheritance is greater for males than in females. Autosomal inheritance Recall that in humans, there are two alleles for a given gene where the alleles help determine the trait of organism (both the parents and offspring). For illustration purposes, let’s use the gene that codes for eye colour. The gene that codes for eye colour will be present in both the female and male.  Just to get a clearer picture and as a recap, do recall that a gene is basically a segment of a DNA or a sequence of DNA nucleotides. Chromosomes are made up of DNA (wrapped around proteins called histones) for eukaryotes. Approximately 40% of a chromosome is made up of DNA and the other 60% is made up of proteins. Now, let’s return to our example. So, each parent will have two alleles for its eye colour gene. Suppose that:  The mother has an allele that codes for blue eye colour and an allele that codes for black eye colour.  The father have both alleles that code for black eye colour.  Let’s also suppose that the allele that codes for black eye colour is denoted by ‘B’ and the blue eye colour is denoted by ‘b’.  As mentioned earlier, the dominant gene is denoted by a capital case of the letter and the recessive gene is denoted by the lower case version of the same letter. Therefore, in our case, black eye colour is a dominant gene whereas blue eye colour is a recessive gene.* * In the exam you could either be told which is allele is dominant or recessive through the use of capital and lower case letters. If not, you will be told by words e.g. “Black eye colour is a dominant gene whereas blue eye colour is a recessive gene.” In that case, since no letter is given to you, you will need to chose a (same) letter to denote both alleles where the lower case letter represents the recessive allele and capital letter for the dominant allele.  Make sure you write down in words that letter you chose to use represent for that particular gene as well as what lower case and capital letter means in terms of recessive/dominant alleles and what characteristics they represent (e.g. black/blue eye colour). Let’s have a look at how the alleles coding for eye colour can be passed on via the crossing over of the mother and father gametes. To do this, one method is to construct a Punnett Square. Downloaded by Amy Bui ([email protected])  lOMoARcPSD|48455185 Therefore, in our example, the mother will have the genotype, Bb, which is crossed over with the father with genotype, BB.  It does not matter which side (top or left of the square) you write the genotype for the male or female.  The order of the alleles also does not matter, e.g. (Bb or bB for the mother). Each letter represents the allele for that particular gene (in this case gene for eye colour) that the parent inherited. Since each gamete only inherits one allele for each gene from each parent, you could think that each letter is essentially a gamete if you wish. Recall that each parent has two alleles for the eye colour and it can pass on one of the two alleles to its offspring (B or b).  In the above example, the mother has B and b alleles for eye colour. So, she can pass on either the B or b allele to each of its gametes (egg cells) during meiosis. This is shown on the left of the Punnett Square.  For the father, he only two B alleles. So, he can only pass on B alleles to its gametes (sperm cells). This is shown on top of Punnett Square.  Don’t forget that each parent can produce many, many of gametes during his or her or its lifetime. So, the Punnett Square therefore considers all the possible alleles which the parent have and could potentially pass onto its gamete and crosses these alleles together to depict the different allele combination for a particular gene which the offspring can inherit from both parents. The Punnett Square allows us to get four genotype combinations (allele combinations for a gene) as shown in the four boxes in the Punnett Square above. Some of the genotype combinations can be identical to each other as shown in the diagram. When the mother and father crosses over, the resulting offspring will inherit one allele from each parent. There are four different possible genotype combination for the offspring’s eye colour. These are BB, Bb, BB and Bb. This means there are 50% chance that the offspring will have the genotype – BB. Also, there is 50% chance that the offspring will have genotype Bb. Recall that the B allele is dominant over b allele (hence the capital letter). This means that although the offspring can inherit one of the two different genotype combinations, the resulting offspring only has one phenotype combination! That is, the offspring will have a 100% probability to have a black eye colour regardless of which genotype combination (BB or Bb) that its inherits from the parents. t is important to know that when both alleles for a gene of a parent are identical, the parent is called homozygous for that particular trait or gene. If the parent’s alleles for a gene are different, the parent are called heterozygous for that gene or trait. The same concept applies to offsprings. Downloaded by Amy Bui