Genetics Exam 2 Study Guide
Genetics Exam 2 Study Guide 85033 - GEN 3000 - 002
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85033 - GEN 3000 - 002
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This 24 page Study Guide was uploaded by Toni Franken on Saturday February 13, 2016. The Study Guide belongs to 85033 - GEN 3000 - 002 at Clemson University taught by Kate Leanne Willingha Tsai in Summer 2015. Since its upload, it has received 313 views. For similar materials see Fundamental Genetics in Biomedical Sciences at Clemson University.
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GEN 3000 – Exam 2 2016 Study Guide Dr. Tsai, Clemson University Exam 2: Chapters 5 Modeled around Dr. Tsai’s recommended subjects to study – organized by chapter Chapter 5: Sex Chromsomes 1. Sex Determination Systems: Chromosomal Sex-determining system: o Homogametic Sex: Sex of a species that produces all the same gametes. (XX or ZZ as an example – produce all X or all Z gametes.) o Heterogametic Sex: Sex of a species that produces two different gametes (XY or XO as an example – produce X or Y or X or O). o In humans (and many mammalian species) we use chromosomal sex determination because we can see a difference in sex chromosomes . However, it is specific genes located on these chromosomes that determine if an individual develops into a male or female. o XX – XY system is found in some plants, insects, retiles, and all mammals – males have XY, females XX. XX – XO means the females have two XX chromosomes, and the males have only 1 chromosome (O is just a placeholder). This system has females that will have all gametes containing an X – the homogametic sex.) Whereas the male is the heterogametic sex – the sex that produces different gametes. o In the ZZ – ZW system, the male is homogametic (ZZ) and the female is heterogametic (ZW). Found in birds, moths, some amphibians, and some fish. o Note: The Drosophila have the same homogametic/heterogametic system as humans do, but sex is determined slightly differently. Instead of the simple presence of two X’s, or an X and a Y, the ratio of X’s to Y’s is what determines sex. There is more information about this in following sections. Genetic Sex-determining system: o Some organisms have a different type of chromosomal determination – based on ploidy, or the entire set of chromosomes. o In some species of bees and ants (Hymenoptera), there are no sex chromosomes. Males develop from unfertilized eggs. Males are haploid (have a single set of chromosomes) and undergo mitotic division only. Females result from fertilized gametes, and have two sets of chromosomes, or diploid. o There is no obvious differences in chromosomes (i.e., no sex chromosome) – genes determine the sex of an individual – similar to chromosomal sex-determining. This method is found in some protozoa and plants. Environmental Sex-determining system. o Temperature, presence of other individuals of the species, or other environmental factors influence the sex of the organism. o Alligators: temperature dependent. Cool temperatures produce females, and warm temperatures produce males. The genes that determine sex react differently to different temperatures. o Slipper limpet have the ability to become male or female. While in the larval stage, they will float around until they rest on a rock or surface. If no other limpets are around, it will develop into a female. It will send out signals that a female is present to attract other larva. These new larva will become male in the presence of the original female. If the female dies, or cannot produce the proper amount of signals, the males can switch to become female to keep the species going. Based on the environmental cues. o Some species can switch back and forth between sexes, while others switch indefinitely to one or the other. The limpet, once it switches to female it cannot switch back to male. The genes in the organism are the thing that says what repro structures are going to result. The environmental cues will say to use which gene at what time. There is overlap between of all of these – some species may have a combination of sex-determination systems. 2. Important people: Henking (1891): He noticed that there were differences in gametes between males and females. He noticed that male insects had a strange “body” in nuclei - X body = chromosome. McClung: Determined that the X body was a chromosome – female grasshopper cells had 1 more chromosome than males. Stevens and Wilson: Clarified this in 1905, saying female grasshoppers have two X chromosomes. Also, X in male cells was coupled with a smaller chromosome (called “Y”). X and Y separate into different sperm cells, while egg cells all get a single X. X would go into 50%, and the Y would go into 50% from male insects. In the system where males lack the Y chromosome, they would see that the X would go into half, while half of the gametes would be missing a chromosome. Barr (1949) observed a darkly staining body in the nuclei of cat cells – this was called the Barr body. Lyon (1961) proposed that the Barr body was inactive X chromosome, leading to the Lyon Hypothesis. 3. Nondisjunction: Nondisjunction, or the improper separation of chromosomes in anaphase, can happen in autosomes or in sex chromosomes. We can use fruit flies as models to examine nondisjunction, as well as some mammals. The Drosophila have three autosomes and a single set of sex chromosomes. In the process of disjunction, the chromosomes will separate. Morgan was looking at a group of flies (had about 1200 flies), and he noticed that 3 of this large group had white eyes. He knew from his cross that all should have had red eyes, and none of the parents carried the mutation. He attributed it to a random mutation. His student, Bridges, thought that this was too high of a number to be a random mutation. He hypothesized that X chromosome fails to separate in Anaphase I of meiosis (nondisjunction). Both X chromosomes went the same direction, did not do what they should have. Some gametes ended up with two copies of the X, while the other gametes did not get an X at all. Can happen in any anaphase of Mitosis or Meiosis. If we look at what we expect of a white eyed female crossed (X X ) - - + with a red-eyed ma-e+without the mutation (X Y). All females should have red eyes (X X ), all males should have white eyes since the female passed on her mutant X. o If nondisjunction were to occur in the female, we end up with two copies of the X in one gamete, and no X chromosomes in the other gamete. This could mean that the offspring of this female will have an extra X. If an individual gets three copies of the X, (X X X ) they have red eyes, but get a metafemale that dies soon after development (not very healthy). If an individual gets two copies of the X, and one Y (X X - - Y), it results in a white-eyed female where both copies of the white mutation are taken, and they also get the Y from the father. Flies that only get X from dad, and therefore have (X O) + develop into red-eyed males. Just getting the Y chromosome is lethal. An individual must have an X. You can have a Y chromosome and still be female. You cannot have the Y chromosome and have a male. It is not the Y chromosome that determines sex, but instead the ratios. o X:Autosome Ratios of Drosophila: 1.0 = female. .5 = Male. 1.5 = metafemale. .67 = Intersex. .33 = Metamale. 1.3 = Metafemale. The Y chromosome is not causing flies to be male – plays a part. o In humans, the actual presence of the Y chromosome will determine male characteristics. There are exceptions to this. 4. Syndromes related to sex chromosome abnormalities: Turner Syndrome: In humans if the autosomes are all the same, but we only get a single X chromosome, we get turner syndrome. All offspring with this syndrome are female, and they do not undergo puberty, have immature female secondary sex characters, a low hairline, and often have folds of skin on their neck. May have cognitive impairment or sterility. XO (O is representing the lack of a Y). o Note: There are no known cases of no X at all – suggest an embryonic requirement – no X = death) 1/2000 female births result in turner syndrome. o Karyotype = 45, X. – 45 normal chromosomes with only 1 copy of the X. If you do not get a copy of the X, it is lethal. Genes on X chromosome are essential. Klinefelter Syndrome: Two copies of all autosomes with three copies of a sex chromosome. Classic Klinefelters (XXY) often goes unnoticed due to low severity symptoms. However, fertility issues often reveal the disorder. 1/500 male births result in Klinefleter, making it more common than Turners. All individuals are male, and they have small testes, breast enlargement, and reduced facial/pubic hair. There can be one or more Y chromosomes, Multiple X chromosomes (can be XXXY, XXXXY, or XXYY). Symptoms become more severe with increased number of Xs. Individuals are often sterile. May have mild cognitive impairment. o Karyotype: 47, XXY. TriploX Syndrome: Female individuals with two X’s, and 1 or more additional X’s. They’re usually tall, thin, sometimes have normal fertility, and have normal intelligence: 1/1000 female births. Genes may be XXXX, XXXXX. Have normal female anatomy, but may have cognitive impairment – severity increases with the great number of X chromosomes. Again, X contains genetic information vital to both sexes – must have an X to survive. In humans, no matter how many Xs you have, if you get a Y, it triggers male development. The absence of Y yields female. Genes required for fertility are on X and Y – females need at least two Xs to be fertile (that’s why triploX syndrome individuals are often still fertile). Additional X chromosomes are detrimental. 5. SRY gene: A few XX males have been identified – how does this happen? All humans start undifferentiated without reproductive structures. Something triggers the development of testes in males to develop testosterone that cause other pathways for male development. If testosterone is never detected in the system, then it is always female (default). o The SRY (Sex determining region Y) was discovered in 1990. Found in all XX males, absent in many XY females. If the SRY is added to mice with XX chromosomes, it will cause them to be male. This suggests that this region sends the first trigger to develop testes, which will then cause male development via testosterone. Notice that the SRY is on the p arm of the Y chromosome. o During Meiosis, the X and Y line up, but do not have the level of homology that the autosomes do. They have regions at each tip called the Pseudoautosomal regions where they match, allowing their synapses to take place so they can be split evenly between the gametes. Can call them PARS. They are called pseudoautosomal because the genes in those regions look like they’re inherited from autosomes, not sex chromosomes. Very close to this pseudoautosomal region is the SRY region – crossing over is suppressed in sex chromosomes, but may happen, and remove the SRY from the Y chromosome, and transfer to the X chromosome. This is how you can end up with an XX male because it triggers testes development. Lack of SRY = female. o Androgeninsensitivity syndrome: Other genes besides the SRY can influence sexual development. The SRY is the first trigger, but if anything changes in the pathway after that, it can interrupt that switch. All of the individuals with androgeninsensitivity syndrome have female sexual characters, but lack a uterus, oviducts, or ovaries. Testes are found in the abdominal cavity (due to SRY being sent, but then lost). If SRY is blocked anywhere, it will result in female. Female athletes that get called out for being too masculine. All females have X and Y, and all have functioning SRY, and depending on where the process changes, they might produce testosterone, some might not produce testosterone, and some receptors will not respond, others will respond slightly, others will respond more. 6. Pseudoautosomal regions: Regions on each end of the X and Y sex chromosomes that match and allow them to line up. May allow for crossing over, and due to the proximity of the SRY gene, may take the SRY gene from the Y chromosome to the X chromosome. Results in androgen- insensititvity. 7. Dosage compensation: Because females have 2 copies of the X chromosome, you would expect that they produce twice the products that males do. However, dosage compensation, or genetic alteration to equalize gene activity, keeps this from happening. o In the fruit fly, dosage compensation will double the activity of genes on the X in males. o In worms, the activity of genes on both X chromosomes is halved o In placental mammals, one of the X chromosomes is inactivated. Barr (1949) observed a darkly staining body in the nuclei of cat cells – this was called the Barr body. Lyon (1961) proposed that the Barr body was inactive X chromosome, leading to the Lyon Hypothesis. This suggests that there is X inactivation – females heterozygous at the X loci will express one allele or the other in a given cell – females are mosaic for expression of Xlinked genes – piece together individually from each chromosome. Note: The number of Barr bodies a female individual has will be equal to the number of X chromosomes they have, minus 1. Mosaicism: o Calico/Tortoiseshell cats – Mosaicism makes an appearance in the color of cats. There is a coat color gene located on the X chromosome. In male cats, + you will see either black or orange, but not both, because they can only get X (black) or X (orange). In females, if you get X X , both colors will be displayed in different areas because in each area of fur, only 1 allele for color will be expressed, but it will vary throughout the animal’s body. Through mitotic divisions in embryonic development, 1 X allele or the other will be turned off, and that will stay throughout the mitotic division of the entire line of cells. X inactivation takes place early in development – inactive X remains inactive (as do all somatic descendent cells) throughout their life. X inactivespecific transcript (XIST) gene is located on the X chromosome, and CANNOT be turned off. Only the copy of XIST on the inactivated X is expressed, and it is expressed during activation. Does not encode a protein, but RNA it produces may bind to inactivated chromosome, prevent transcription. Other genes escape inactivation completely because they need to be used at some point. It is very important to have the right level of all of your protein products. GEN 3000 – Exam 2 2016 Study Guide Dr. Tsai, Clemson University Exam 2: Chapter 6 Modeled around Dr. Tsai’s recommended subjects to study – organized by chapter Chapter 6: The Nature of Chromosomes 1. Karyotype: The complete set of visible metaphase chromosomes – allows us to see autosomes and sex chromosomes (if present) in an organism. Chromosomes, in general, are named by size (Chromosomes 1 is the largest, then smaller and smaller) Karyotype can be changed by chromosomal mutations, chromosomal rearrangements, an alteration to the number of chromosomes (aneuploidy – addition or deletion of individual chromosomes), or a complete copy of every single chromosome (polyploidy). 2. Duplications: replication of a gene sequence somewhere along the chromosome. Types: o Tandem Duplication: Where there is a duplication of gene sequence is right next to each other. o Displaced duplication: Where the replicated info is completely in a different place on the chromosome. Consequences: When you look at cells during meiosis, and there is a duplication present, you can visualize a replication due to the presence of a loop due to the matching up of genes correctly, but the uncertainty of what to do with the replicated material. o Often times, though not always, a duplication will change the phenotype. This is most likely due to the action of gene dosage, or the inactivation of a certain number of genes to balance the amount of activity produced. If there is more activity than normal, the body isn’t sure how much to inactivate. Fly Eye Example: Normally look large and circular. There is a region called a bar region that controls the eye shape. The eye shape shrinks if there is a duplication of this region. The more duplications present, the smaller the eye will be. o A duplication may happen due to unequal crossing over, where the chromosomes don’t line up quite correctly, causing information to be swapped in the incorrect place. Once a duplication happens once, it is more likely to happen in subsequent divisions due to higher probability of misalignment. In a type of fish, genes A, B, and C work together to produce a striped fish. If you have a duplication of the B gene, twice as much of the product of B is made, and all four of the genes (ABC, and Bdup) attempt to interact. Another possibility is that the genes will not use the extra product from the duplicated B gene, but that extra product then goes off and does something completely different than it should. 3. Deletions: A complete removal of a gene sequence from a chromosome. Types: o Homozygous deletions: Both sets of genes on the chromosome are deleted. o Heterozygous deletions: Only one set of alleles gets removed from the chromosome. Consequences (heterozygous deletion): o During Meiosis, there will be a loop in one of the chromosomes (similar to a replication) due to some missing genes. o Balance: The amount of product that the allele set produces will be imbalanced if a heterozygous deletion has occurred. o Pseudodomiance: Heterozygous deletions allow recessive alleles on undeleted chromosomes to be expressed. Recessivity is where two copies of the allele are necessary to produce the phenotype. If we have a recessive phenotype, and the dominant allele gets deleted, now we will see the recessive without two copies. o Haploinsufficiency: Some genes have to be present in two copies to produce enough gene product. Therefore, they are haploinsufficient (if they only have 1 copy of the diploid set, they will not work properly). If you have a wild type copy, and a deletion caused the loss of the second wild type copy, you will have a completely different phenotype. The wild type requires both copies to make the normal phenotype. An example is in wing shape of Drosophila – if you have a deletion of a wild type copy, you end up with a notch phenotype – notches taken out of a wing. Both alleles are required to get a normal, smooth wing shape. 4. Inversions: The movement of genetic sequences without actually adding or deleting genes. Types: o Paracentric Inversion: An inversion that does not include the centromere. o Pericentric Inversions: An inversion that includes the centromere. o Inversions – gene order is changed, can break a gene in two – regulation of genes is sometimes context dependent. A gene must be continuous for it to actually work and produce its product. Consequences (e.g. position effect): o Position effect: There is information on this chromosome that may not actually make the gene product, but is essential to make sure the product of other genes is used at the right time. Often times, these controls are near the genes they control. If inversion happens, they may no longer be near each other, and therefore correct control over the gene is missing. o During meiosis, an inversion loop will be formed. Basically, both chromosomes end up looping to try to match up their inverted gene order. The result is a tangled mess of genetic material, and if crossing over takes place, a dicentric bridge may form between the two chromosomes, keeping them linked. Dicentric bridge has two centromeres. During Anaphase 2, the two chromosomes separate and the bridge is pulled and pulled until it snaps so a fragment is left over, and then lost. This genetic material loss may be lethal to the organism. o Organism lethality: Inversion can cause serious problems when replication occurs. There may be a loss of genetic material due to improper crossing over (dicentric bridge), and as such, the important genetic material is required for life. 5. Translocations: Movement of genetic material between NONHOMOLOGOUS chromosomes. (chromosomes that would not line up during meiosis). Types: o Nonreciprocal: Where there is a passing of genetic material from only one chromosome to the other, and the second chromosome does not give any genetic information back to the first. o Reciprocal: Where there is an exchange of genetic material between two chromosomes – both chromosomes get new genetic sequences. o Robertsonian Translocation: A translocation plus a deletion. Often a cause of Down Syndrome. May happen due to a weak point on two different chromosomes near their centromere. Those spots snap, and the two longer segments of each chromosome combine, while the two shorter segments combine. This very small segment can be easily lost. Consequences: o Altered Gene Expression: Position effect Burkitt lymphoma is one example of such an effect. Genes cannot be expressed properly due to their improper location. o Break in Gene: A break in the genetic sequence may result from translocation, causing a loss in genetic material, which could lead to death. 6. Aneuploids: A change in the number of individual chromosomes. How: Aneuploidy can result in a number of ways. o Loss of chromosome which has lost its centromere: If a chromosome has lost its centromere, it is much more likely to get lost to the body throughout the process of division. The centromere is what keeps chromosomes aligned, and allows the spindle fibers to attach. Without it, they cannot do so. o Robertsonian translocation: The translocation plus a deletion, resulting in the loss of a portion of the genetic material. o Nondisjunction: Improper separation of chromosomes during anaphase. May result in more than one of the same chromosome in a gamete or mitotically divided cell. Can occur in Meiosis I or II, as well as Mitosis. Types: o Nullisomy: The loss of both members of homologous pairs. The entire gene sequence for the chromosome is no longer in the individual. Often lethal due to necessity of a complete gene set. Can be shown with the formula 2n2 (n = haploid number of chromosomes). Example: Humans 2n=46. 46 – 2 = 44, a form of nullisomy. This would be lethal. o Monosomy: The loss of a single chromosome from the genome. Can be expressed as 2n1. Example: Humans 46 – 1 = 45. o Trisomy: The gain of a single chromosome which can be expressed as 2n+1. Example: Humans 46+1 = 47. o Tetrasomy: The gain of two homologous chromosomes which can be expressed as 2n+2. Example: Humans 46 +2 = 48. Note: an organism with an extra copy of two different chromosomes is not tetrasomy. This would instead be considered double trisomy. Examples: o Human Sex Chromosome Aneuploidy: The sex chromosome versions of aneuploidy are the most survived due to dosage compensation – there are already mechanisms in place to take care of too much or too little gene activity. XYY has very little impact, due to lack of genetic info on Y Turner/Klinefelter (XO/XXY) are common examples of sex chromosome aneuploidy in humans. o Human Autosomal Aneuploidy: There are very few autosomal aneuploidy conditions that are survivable, but those that are typically involve chromosomes that are very small, and therefore contain fewer genes. Trisomy 21: Also known as Down syndrome, which takes place when there is an extra copy of chromosome 21. This can occur through nondisjunction, or through a Robertsonian translocation. 75% of cases of Down Syndrome results from nondisjunction in maternal cells. The occurrence of Downs also increases with maternal age. This is probably due to the prolonged suspension of Meiosis from fetal development to ovulation for the oocytes. Therefore, oocytes may be quite old when ovulated. Familial Down Sydrome: This is the inherited form of Down syndrome that occurs due to parental gametes undergoing a Robertsonian translocation. This most often happens between chromosomes 14 and 21. There are 6 different gamete possibilities from this translocation, and if crossed with a normal second parent, will result in only 1/2 probability of embryo survival. Of the six possible genotypes, 3/6 will be aborted in utero. 2/3 of live progeny will be normal, and 1/3 of live progeny will have Down Syndrome. There are benefits and downfalls to Down syndrome. Individuals with trisomy 21 have higher chance of developing leukemia, but lower probability of developing solid tumors. Trisomy 18: Edward Syndrome, severe problems. Most die by age 1. Trisomy 13: Patau syndrome. 50% of affected individualsdie within 1 month; 95% die by age 3 Trisomy 8: Mosaic individuals can have normal life expectancy. 7. UPD: Uniparental Disomy Occurs when both chromosomes of a homologous pair are inherited from one parent. It can result from trisomy that is resolved by loss of a chromosome during embryogenesis. Can occur if dad’s gamete has no chromosomes, and mom’s has two copies. Can have trisomic zygote rescue: A gamete that underwent nondisjunction (copy of mom’s is doubled) leads to trisomy. If one of those chromsomes is lost during a later mitotic division, we could end up with two copies of mom’s, or if one copy of mom’s is kicked out, could result in normal number of chromosomes – makes trisomy survivable but doesn’t mean you’re free of a phenotype. 8. Mosaicism: The presence of two or more populations of cells with different genotypes in one individual who has developed from a single fertilized egg. Extreme example. If you have a very early mitotic error, you could result in a half male/half female. Started with two X chromosomes, and a very early mitotic nondisjunction resulted in the loss of a chromosome, a part of the animal will be female, a part will be male. Creates a split right down the middle from the error occurring along the spine. Very obvious in butterflies. The later the nondisjunction happens, the less the change will show. This does not happen in mammals (due to fatality of the loss of an X chromosome). Most likely not reproductively viable. o Gynandromorph: An individual that is both sexes XX and XO (best example is in the Drosophila. 9. Polyploid: A complete replication of the entire chromosome set. How: o Errors in meiosis, events at fertilization, or errors in mitosis following fertilization can cause this doubling. o Dispermy is one that occurs at fertilization – simultaneous fertilization of egg with two sperm. Genome from the egg plus sperm 1 genome plus sperm 2 genome. 3 copies total of genome, seen in humans. Thought to be one of the main mechanisms that polyploidy occurs triploidy is the most common (found in 15 – 18% of spontaneous abortions) – 75% have two sets of paternal chromsomes – dispermy. 1% of all conceptions are triploid – 99% die before birth (1 in 10,000 live births – fatal shortly after birth.) Types: o Triploidy: Three complete sets of chromsomes – often results from dispermy. A form of autoploidy o Autopolyploidy: All chromosome sets are from same species. Can occur through mitosis – for whatever reason, the process gets stuck, preventing chromatids from being pulled to opposite poles and creating two new cells. Results in a 4n cell. Can also happen during meiosis – nondisjunction prevents gametes from splitting. An even number of chromosomes means gametes are more likely to be balanced. Still have 4 chromosomes trying to line up. Triploid = 3 different chromosomes – creates lots of different outcomes, but the likelihood of a balanced gamete is incredibly unlikely. Triploids are usually sterile – used to create seedless fruits (which are often larger fruits as well). Wild type bananas have seeds. o Allopolyploidy: The chromosome sets are from two different species as a result of hybridization. Hybridization is then followed by chromosome doubling. These two chromosomes have to be somewhat similar in genetic makeup for this to be possible (think of the mule – cross between donkey and horse). The resulting hybrid is still considered diploid because they have two copies of all of their genes, even if they’re in different places. However, the genes will not line up properly between homologous chromosomes. Generally don’t get viable gametes due to imbalance. However, if a nondisjunction event occurs, you can end up with a hybrid becoming an allotetraploid that has 4 copies of the genes (2 copies of each individual gene). When this tries to form gametes, they can line up, and they can get balanced gametes. Modern wheat is the result of an allopolyploid. This process happened naturally, and took hundreds of years. Cross of einkorn wheat and wild grass = hybrid, and then created emmer wheat (a tetraploid), which then crossed to a wild grass species, which then underwent nondisjunction, creating a completely different species. Consequences: o Sterility: Odd numbers of chromosomes in alloploidy will most likely result in sterility. The chromosomes do not have homologous numbers to line up to. o Lethality: In mammalian species more than plant species, polyploidy is most likely going to be lethal. The genetic makeup simply isn’t suited for survival. 10. Fragile Chromosomes: Regions on chromosomes that are prone to breaking. Common in some tumor cells. Trinucleotide repeat expansion: Fragile X syndrome – 1 in 2000 males, 1 in 4000 females. Noticed that there was a certain region of the chromosome that was prone to breaking. In this location, there is a trinucleotide repeat. Trinucleotide means there are 3 bases, and they are repeated over and over and over again. CGGG repeat in every human being. Can have an expansion of these repeats, which forces the cell to start put epigenetic type marks on the chromosome to prevent this occurrence. This changes the chromosomal background for nearby genes – the gene nearby gets turned off – changes how a gene works. Anticipation: Once you get repeats (all humans have repeats, but different numbers), there is a higher likelihood and occurrence of repeats in subsequent generations, causing an earlier or more severe clinical representation. Also seen with Huntington’s disease. 11. Rearrangements in Evolution (importance): Rearrangements may not all be bad. They could be beneficial evolutionarily. Humans and chimps share over 95% of the same genome. If we look at the rearrangements, there is a pericentric (including a centromere) inversion found on chromosome 4 of chimps and humans. This allows the genes to be used very differently. The biggest difference when comparing human to nonhuman primates – there are 46 chromosomes in humans versus 48 in nonhuman primates – possibly due to a Robertsonian translocation. There have been multiple rearrangements between the human and gorilla genomes, also. Duplications: There are genes that are very good to have an extra copy of. This is how new genes are made due to copies that change through time. If something happens to one copy, you have a backup. It’s good to have a lot of copies of some genes – this is gene amplification. The gene has been duplicated multiple times, and therefore there are many copies throughout the genome. There is a region of 14 that has an area of its genome that is copied time and time again. If that portion is lost, there is not a phenotypic consequence. o If you have a duplication, the second copy of the gene could start changing. It could either become a null allele (a pseudogene – compare it, it looks like a gene/has characteristics of a gene, but is no longer functional), or could have gene families – copied genes start changing in parallel in a beneficial way. All of these duplicated genes are involved in the same pathway, but with time, the first gene might specialize in one part of the process, and the other genes focus on other parts of the process. They’re all involved in the same pathway that the gene was originally involved in, but they are more efficient. Many genes in the immune system have arisen due to duplication. GEN 3000 – Exam 2 2016 Study Guide Dr. Tsai, Clemson University Exam 2: Chapter 7 Modeled around Dr. Tsai’s recommended subjects to study – organized by chapter Chapter 7: Linkage, Recombination, and Gene Mapping 1. Review of Concepts: Principle of segregation: Each diploid individual possesses two alleles that separate in meiosis, one allele to each gamete. Chromosome theory of heredity: Developed by Sutton genes are found on chromosomes. 2. Linked genes: Not every gene can undergo independent assortment because they’re located on the same chromosome, and are therefore linked. The closer two genes are, the less likely they are to be recombined. When genes are on the same chromosome, they also have a much lower chance of being recombined due to their proximity. Mendel got very lucky with his choice of genetic traits. 3. Morgan and Sturtevant: Alfred Henry Sturtevant – student of T.H. Morgan – suggested that genes on the same chromosome segregated together – closely linked were rarely subject to recombination. In 1911 he generated the first map of chromosome based on recombination frequency. Morgan: located genes located on sex chromosomes – started identifying many different types of genes. Now, he knew that there was a whole subset of genes that were located on the same chromosome (X). When they did crosses, they got different results for their breakdown of recombinant, and nonrecombinant. In one cross, got 99.5% parental, and only .5% recombinant. In another cross, he found 65.5% parental, and 35.5% recombinant. o Sturtevant – went home and generated the very first chromosomal map. Postulated that frequency of recombination could be used to determine the physical distance separating two genes on a chromosome. The further apart genes are, the more often you see recombination. A closer the genes are, the less likely you are to see recombination. o Sturtevant used Morgan’s crosses to estimate distance. The first cross suggested that genes are closer together, while the genes in the second cross were further apart from each other. Used as an estimation of distance. It wasn’t until 1930’s that Creighton and McClintock were able to show evidence of how crossing over worked. Were able to follow chromosomes that looked slightly different from their homologue, and were able to see that the characteristics were separated by meiosis, and were now on completely new individuals. How do we determine the recombination frequency? 4. Recombinant vs. Nonrecombinant: Recombinant Genotype: The recombinant genotype is a genotype that varies from the gamete combination of the parents. If there are two heterozygous parents crossed (AaBb x AaBb), then and are recombinant gametes would be genotypes would include AAbb, aabb, and more. Nonrecombinant: A genotype that is the same as the gametic combination of the parents individuals. If there are two heterozygousparents crossed (AaBb), the parental genotype would be AaBb. 5. Consequences of linkage in next generation: Linkage results in an overrepresentation of parental gametes – in other words, the closer two genes are to one another on the parent chromosome, they are less likely to separate during meiosis. Linkage will also prevent certain phenotypes from appearing often, or very close to ever. Very easily missed in experimentation. 6. Recombination frequency: Complete Linkage: Completely linked genes – located on the same chromosome, and without crossing over, there will be a 1:1 ratio of parental (same genotype as parents) offspring – all offspring will have parental characteristics of one parent or the other. Whereas if genes assort independently, the alleles have the same opportunity to end up with each other. Gives us the 50/50 split of parental/recombinant. There aren’t any genes that are truly completely linked. However, they’re so close together that recombination is so very rare, it’s almost impossible to see the recombination. It’s such a small probability, we can easily miss it. Get almost entirely parental genotypes. If genes are not completely linked, but partially, there will still be chromatids that were not involved in crossing over. Single crossover leads to half recombinant, half nonrecombinant. In the F1 generation o What does this mean for the next generation? We see an overrepresentation of nonrecombinant/parental genotypes. With linked genes, and some crossing over, nonrecombinant progeny are predominating. Genes on different chromosomes: we have independent assortment, combine randomly. Interchromosomal recombination: Recombination between genes on different chromsomes – arise from independent assortment in anaphase I of meiosis. Intrachromosomal recombination: Recombination between genes on same chromosome – crossing over in prophase I of meiosis. 7. Cis vs. trans: 8. Determining gene distances: Recombination frequency cannot be greater than 50% for two genes. If any genes are farther than 50 centimorgans apart, we expect independent assortment (50% recombinate, 50% parental). Once past 50%, can no longer distinguish how far apart the chromosomes are. o If a recombination frequency is within 50%, but still relatively large (45% ex.), we must take into account that we can miss crossover events due to the large amount of distance between them. Sometimes we have double crossovers that create recombinant chromosomes, but it appears that crossing over never happened. This makes us underestimate how far apart genes are due to missing recombination events. If we see greater than 50% recombinance, we have to assume genes are on separate chromosomes. o Note: Gene Maps aren’t restricted to 50 centimorgans – we can create linkage groups. As you gather more data, you can extend the overall linkage group beyond 50 map units (centimorgans) due to the combination of multiple frequencies. Threepoint crosses are more efficient than twopoint crosses. If looking at 3 genes, doing a 3 point cross will let us see the relationship of all of the genes, not just two at a time. Recombination frequency: Number of recombination progeny/total progeny x 100%. o Percentage of recombinations – only start by looking at two chromosomes – have to take into account both the single and double crossovers. Have to account for double crossovers twice. Can be used check your answer. 9. Maps: Genetic Maps: Gene mapping can be done with recombinant frequencies. A genetic map is an estimation – can determine approximate distances. It is not absolute. Originally developed by Sturtevant. o Can translate into map units – 1% recombination frequency = 1 map unit. These map units were named as centimorgans (shoutout to Sturtevant’s advisor/mentor). o We can start trying to order these genes on the chromosome. In the example in the powepoint, there are many possible combinations of placements of those genes relative to have you arrange them on a chromosome. However, if we have genotypes of offspring, appropriate order may be established. Physical map: A form of genetic mapping that is considered absolute – measured by base pairs. Based on physical distances. Genetic maps came long before these techniques, which can be used today. 10. Linkage groups: Linkage groups can allow us to build an entire gene map based on all of the interactions between individual genes. This is more easily seen and understood when observing the steps to developing a genetic map seen below. 11. Testcrosses: Cross a hybrid individual for three genes with a homozygous recessive parent for all three traits. We will only look at the genetics of the heterozygous parent to determine the crosses of the offspring. The homozygous recessive traits just allow us to observe the crosses that might occur. 12. 3point mapping: First step of 3 point test: Identify your parent group. Second Step: Identify your double crossovers. Third Step: Identify the middle gene. o Comparing double crossovers to parentals, what’s different? The gene that varies between the other genes when compared with a parental cross is the gene that is found in the middle of the others. Whichever is the hybrid parent, that is the parent you pay attention to determine gene map. Crossing over on a homozygous individual we cannot see due to same genes. Recombination frequency = number of recomb progeny/totalprogeny x 100%. Percentage of recombinations – only start by looking at two chromosomes – have to take into account both the single and double crossovers. Have to account for double crossovers twice. Can be used check your answer. Remember, when you look at the 3pt cross, you still have to consider cis and trans coupling – ALWAYS USE YOUR NUMBERS TO MAKE SURE YOUR PARENTAL CHOICES MAKE SENSE. Overrepresentation of parentals. 13. Interference: The actual frequency of crossovers can be hindered by the fact that crossovers can cause interference with each other. You see fewer double crossovers because one crossover interferes and keeps other crossovers occurring in their immediate vicinity. You see fewer double crossovers than you expect. Coefficient of coincidence, how many did I expect? Saw 8 out of expected 13.4 – only saw 60% of expected. Interference is 1COC, so 1 .6 = .4. Means that 40% of our double crossovers will not be observed due to interference. If intereference equals 1, that means 100% interference, so no double crossovers will be observed. Interference gernerally ranges from 0 – 1. 0 means no interference. 1 is complete interference, no double crossovers that are expected are seen. You can have a negative interference, where you see more double crossovers than expected. The genetic map, map based on recombination, you are restricted to the recombinants you can see. There might be areas of more or less crossing over than expected. Have a restriction of 50 centimorgans. Far apart genes within the 50 centimorgans might be underrepresented for crossing over. 14. Molecular markers: We’re not limited to mapping physical traits – we can use molecular markers – still based on segregation of two or more markers. Molecular markers are regions that are found throughout the genome – main point of this sections is that YOU ARE NOT RESTRICTED TO PHENOTYPES TO MAP. Can use molecular markers that do not have a phenotypic effect to map. RFLP – Restriction fragment length polymorphism. changes in DNA sequence that modify restriction enzyme recognition sites. VNTR – variable number of tandem repeats – differences in copy number – SSLP, Minisatellite, microsatellite. SNP – single nucleotide polymorphism – a single base change. Microsatellite markers – di, tri, tetra nucleotide repeats – we all have some of these repeats, but different people have different numbers of copies. No phenotypic consequence, but now we can detect recombination events and use them to map. o We can distinguish between different alleles with markers – we can now track through meiosis, and track from one generation to the next, and can identify where crossover has taken place. Fragile X are microsatellite markers. Snips – single base change. GEN 3000 – Exam 2 2016 Study Guide Dr. Tsai, Clemson University Exam 2: Chapter 8 Modeled around Dr. Tsai’s recommended subjects to study – organized by chapter Chapter 8: Bacterial and Viral Genetics 1. Advantages of bacteria/viruses: Rapid reproduction – can have multiple generational turnover to observe inheritance in within the course of a day or two. Many progeny produced – thousands of progeny can be produced from a few colonies in a day or two, allowing for easy observation of inheritance. Have one single haploid genome – allows all mutations to be expressed directly. Asexual reproduction simplifies the isolation of genetically pure strains – should get exact replicas of each cell. o Can have many many daughter cells and the genome should be identical. Medically important – many human diseases and genetic disorders can be studied by using prokaryote genetics. Small genome to work with, easier to follow genetic abnormalities and inheritance. We look at E. coli a lot as a model bacterial organism – a lot is known about them. Contains one circular chromosome, about 4.5 million bases, 4000 genes. However, some have multiple chromosomes, and a few have linear genomes. Even though it is a “small genome,” the DNA makes up the majority of the cell. 2. Prototroph vs. Auxotroph: Prototroph: Wildtype (normal) bacteria that can synthesize all their compounds needed from growth from simple ingredients. They can survive on the bare minimum of nutrients needed. Can be grown on minimal media. Gives them their necessary carbon source and nitrogen source, etc. Auxotroph: Bacteria that have lost the ability to make some of those components. They are mutant, and have lost the ability to synthesize necessary nutrients. Will die on minimal media. Will grow on supplemented media (complete media). Can remember that auxotroph are mutants by thinking of this: Auxotroph has an X. Xmen – mutants – memory tool. o Can have selective media – selects out certain types of cells. Start with complete media. They can survive. Can we take away something, do they survive? If they die, they cannot make that substance you’ve taken away. They are mutant. o Can take a membrane in replica plating to move from one type of media to the next. Makes an exact copy of the colony distribution. Can look at each individual colony on different media types, and see which one is missing. o Experimenters noticed that mixing two Auxotrophs together produced wild type progeny. This is due to horizontal gene transfer. Sexual reproduction is vertical gene transfer. Horizontal gene transfer is two already present, living cells can exchange genetic information, and their genome is changed. This is how a lot of antibiotic resistance gets passed around. 3. Bacterial characteristics: Has a cell wall and a plasma membrane, contains ribosomes and DNA. Tend to be small and less complex. Contain no membranebound nucleus or organelles. It includes the classifications of eubacterium and the archaebacterium. Archaebacterium contain characteristics of bacteria and eukaryotes. Eubacteria = true bacteria. Generally reproduce asexually through binary fission. Reproduction: Contains a single, circular chromosome attached to the plasma membrane. The chromosome begins to replicate, and the plasma membrane grows, causing two chromosomes to separate, followed by separation of organism into two individual cells. Each cell is identical 4. Lederberg and Tatum experiment: Lederberg and Tatum – 1946 – figured out conjugation – a form of horizontal gene transfer, and determined that necessity of direct contact between bacteria for exchange of DNA to happen. (reminder: + = wild type; prototroph; = mutant auxotroph.) MM = minimal media. o Mix two different auxotrophs, which die if plated individually on MM, and they actually develop colonies due to horizontal gene transfer. Lederberg and Tatum were attempting to discover how. Utube experiment – Put the bacteria into two sides of a U shaped tube, separated by a filter, so the bacteria could not replicate. The media could pass between both sides. With the filter, no growth was observed whatsoever. This showed that there was a physical contact necessary for horizontal gene transfer, and the media wasn’t allowing it to happen. 5. Types of Gene transfer: Vertical Gene Transfer: o Sexual reproduction/Asexual reproduction – genes are transferred from one generation to the next in a vertically linear manner. Horizontal Gene Transfer: Genes are transferred between two individuals in the same generation and time frame. Really only seen in prokaryotes. o Conjugation: Direct transfer of DNA from one bacterium to another. (donor to recipient only) – physical contact. o Transformation: DNA free floating in the environment gets taken up from the medium and added to the cell. o Transduction: Viruses act as transductors to Plasmids are transfer genetic material from one cell to another. o DNA exchange and reproduction are not coupled in bacteria. The cell remains haploid. They switch out their copy of the gene for the new copy of the gene. 6. Conjugation: Conjugation can take place because of a small circular piece of DNA called a plasmid. o This plasmid makes a pilus, or a tubelike structure, which shares?
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