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Genetics 3000 Exam 2 Study Guide

by: Lisa Blackburn

Genetics 3000 Exam 2 Study Guide 85033 - GEN 3000 - 002

Lisa Blackburn

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This study guide is based off the suggested materials given to us by Dr. Tsai. This has chapter 5-8.
Fundamental Genetics
Kate Leanne Willingha Tsai
Study Guide
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This 11 page Study Guide was uploaded by Lisa Blackburn on Sunday February 14, 2016. The Study Guide belongs to 85033 - GEN 3000 - 002 at Clemson University taught by Kate Leanne Willingha Tsai in Fall 2015. Since its upload, it has received 179 views. For similar materials see Fundamental Genetics in Biomedical Sciences at Clemson University.

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Date Created: 02/14/16
Terms Important People Diseases Key Topics Examples Study Guide: Exam II (Chapters 5-8) Chapter 5  Terms: o Nondisjunction: Chromosomes fail to separate during anaphase in mitosis or during anaphase in meiosis (I or II). o Dosage Compensation: How the body deals with extra X chromosomes.  Example: Females have two copies of the X chromosome; therefore, they would produce twice as much gene product than males who only have one X chromosome. The body compensates for X chromosomes by creating a Barr Body. o Monecious: organism has both male and female reproductive systems. Meaning that both reproductive systems are within a single individual. o Dioecious: an organism has either a male or female reproductive system. Meaning that only a single reproductive system is within a single individual. o Pseudoautosomal Region: A region on the sex chromosomes. Any gene that is found in this region appears to not be related to the sex chromosomes and appear to be from an autosomal chromosome; therefore, it is a “fake autosomal” gene.  Important People: o Henking: discovered that male insects have a “body” in the nuclei and he named it the “X body” o McClung: determined that the “X body” is a chromosome o Stevens and Wilson: discovered that female grasshoppers have two “X bodies” or in other words, two X chromosomes. o Morgan: looked at a ton of flies that he had crossed, in the 1 generation. All but three flies had red eyes. These three flies were males with white eyes (should have red eyes based on cross). Marked this occurrence as a random mutation. o Bridges: Student of Morgan. Decided that the male flies with white eyes occurred it too high of a number to be considered a random mutation. Came up with the theory of nondisjunction. o Barr: discovered a dark stained body in the nucleus of cats. Named this body the Barr Body. He noticed this body during interphase of female cat cells only. o Lyon: Came up with the Lyon Hypothesis to explain what the Barr Boy is. Determined that the body is an inactive X chromosome due to dosage compensation.  Key Topics: o Mechanisms for sex determination (ways to determine a sex of an individual/organism)  Chromosomal sex-determining system: determining the sex of an organism through the structure of the sex chromosomes.  A gene located on a chromosome will trigger the development of sex of an individual. Therefore, sex is determined on if this chromosome is absent or present.  What was discovered through insects: Males have one X chromosome while female have two X chromosomes. The males also have a second chromosome that is smaller and is called the Y chromosome. o During meiosis for males: The XY chromosomes split up and each gamete is given an X or a Y chromosome, this is a 50/50 split o During meiosis for females: the XX chromosomes split up, but since they are two of the same chromosomes, the female gametes all end up with the same chromosome (X).  The sex chromosomes used to determine sex do not have to be the same: o XX-XY: Females are XX. Males are XY o XX-XO: Females are XX. Males are XO  “O” is a placeholder, meaning that there is no second sex chromosome in the males. o ZZ-ZW: Females are ZW. Males are ZZ. Z and W are not new sex chromosomes, they are used so it is able to be distinguished that the males are the ones that are homogametic and the females are heterogametic. (Opposite from humans).  Haplodiploidy and the Social Insects: some types of bees have no sex chromosomes, meaning that males are developed from an unfertilized egg. o Males are haploid: have only one set of chromosomes o Females are diploid: have two sets of chromosomes o How it works: a female will undergo meiosis and develop haploid gametes. If a gamete is fertilized by the haploid gamete of a male, then the zygote that is developed will become a female (it will be diploid). If a gamete is not fertilized, it will develop into a male (it will be haploid).  Genetic Sex Determination System: this determines the sex of an individual based on the genes of the individual in question.  There is no difference in the sex chromosomes, so the genes can be used to determine the sex of an individual.  This is similar to chromosomal sex determination because genes are located on the chromosomes and are what control the determination of sex. Certain genes will exist throughout the individual that will trigger the sex of the individual based on which genes are present.  This system can be found in protozoans and plants.  Environmental Sex Determination System: the environment will play a factor in determining the sex of an individual.  The environment will output a signal or cue that will effect certain genes to be activated, which will determine the sex of individual.  Temperature Dependent: the temperature will trigger which genes will be in affect and this will decide the sex of the individual. Warm temperatures could mean that the individual will develop as a male.  Common Slipper Limpet: Undergoes sequential hermaphroditism. The sac will float until it hits a rock. If there are no other ones present, it will become a female and send out a signal. Another will come and land on the rock, when it detects the signal it will become a male. This occurs and many males will attach to the rock. If something happens to the female, the male that is next up will change to a female. o Mosaic: This results from dosage compensation and X inactivation.  X inactivation is caused to compensate for having more than one X chromosome. One X chromosome is “turned off” and a Barr Body is created. This can result in a mosaic pattern of color for heterozygous females.  Consider: a female cat is heterozygous for fur color and the gene is located on the X chromosome. X results in black color while X results in orange color. If a female is heterozygous for fur color than she would be X X .  Due to dosage compensation, one of the X chromosomes will be turned off in each cell. Depending on which chromosome is turned off, it will determine what color that cell will produce. If the Barr Body is the X chromosome, than the cell will produce orange color since it only has an active orange allele and vice versa. Due to multiple cells producing different colors, the individual would have patches of certain colors.  NOTE: If cell “A” turns off X then all cells it produces from mitotic division will have this X chromosome turned off as well. This is what helps with the pig patches of color on the individual. o SRY Gene: Sex determining region Y  Where/when is it found?  This is found in all males that are genetically XX. Absent in all females that are genetically XY. o This means that if an individual is XX, but has the SRY gene, then the individual will be male even though no Y chromosome is present. If an individual is XY, but does not have the SRY gene, then the individual will be female though a Y chromosome is present.  Caused genetically XX mice to become males when the SRY gene is engineered into their genome.  What does this mean?  This gene is what determines if an individual is male or female and is located on the Y chromosome. It is the first trigger to create a male.  Diseases: o Turner’s Syndrome: effects females, results in having a single X chromosome.  Symptoms: do not undergo puberty, immature female sex characters, low hairline, folds of neck skin are pronounced, cognitive impairment, sterility.  Sex Chromosomes: XO  “O” is used as a place holder, there is no second X chromosome  Probability: 1/2000 female effected, pretty common.  Distinguished: 45, X o Klinefelter Syndrome: effects males, males have multiple X chromosomes and a single Y chromosome  Symptoms: small testes, enlarged breasts, reduced facial and/or pubic hair, some cognitive impairment, often sterile. Symptoms are not severe enough to notice something is wrong.  Sex Chromosomes: XXY, XXXY, or XXYY  The more X chromosomes the individual has, the more noticeable the symptoms, but does not increase severity of condition.  Probability: 1/500 males affected, males often not diagnosed  Distinguished: 47, XXY  NOTE: can be 48, XXXY or 48, XXYY depending on the disorder for the individual in question. o Androgen-insensitivity Syndrome: XY females (Refer to SRY Gene above)  SRY or other genes can have effect on the development of sex of an individual.  Symptoms: female characteristics on the outside. No uterus, oviducts, or ovaries. Testes can be found in abdominal cavity.  The females have XY chromosomes and all have the SRY gene. The SRY gene starts the process of developing a male by the development of testes. The testes secrete testosterone, but the women affected do not have the receptor for the testosterone. This means that further development of male characteristics do not take place, creating a female on the outside. Chapter 6:  Terms: o Karyotype: display of a completed set of chromosomes, usually chromosomes in the metaphase stage due to being the most condensed at this phase. 1st chromosome is the largest and the 21 /22 chromosomes are the smallest. o Duplications: region of DNA that is repeated  Tandem: duplication is adjacent to the copied region  Displaced: duplication region is located some distance away from the copied region or even on a different strand of DNA o Deletion: a region of DNA is taken out of the sequence  Heterozygous Deletion: If an individual is heterozygous for a gene (Aa) and a deletion occurs for the “A” allele o Inversions: the gene order of a certain segment of a DNA sequence is flipped.  Paracentric Inversion: when an inversion takes place that does not include the centromere.  Pericentric Inversions: when an inversion takes place that does include the centromere. o Translocations: movement of a gene region from one chromosome to another nonhomologous chromosome. This is not crossing over.  Nonreciprocal Translocation: there is movement of one gene sequence from Chromosome A to Chromosome B (nonhomologous chromosomes), but there is no movement from Chromosome B to Chromosome A. It is a one way flow of genes.  Reciprocal Translocation: There is movement of one gene sequence from Chromosome A to Chromosome B (nonhomologous chromosomes) and there is movement from Chromosome B to Chromosome A. It is a two way flow of genes.  Robertsonian Translocation: translocation takes place as well as a deletion. Causes some forms of Downs Syndrome. o Aneuploidy: a change in the number of individual chromosomes, can lose or gain an entire chromosome.  Nullisomy: loss of both members of a homologous pair (from mom and dad). In humans: it is lethal. Expressed: 2n-2  Monosomy: loss of a single chromosome. In humans: results in Turner’s Syndrome if loss of the X chromosome takes place, or can be lethal otherwise. Expressed: 2n-1  Trisomy: gain of a single chromosome. Expressed: 2n+1.  Double Trisomy: an extra copy of two nonhomologous chromosomes.  Tetrasomy: gain of two homologous chromosomes. Expressed: 2n+1 o Uniparental Disomy: both chromosomes are inherited from a single parent. o Polypoids: one or more complete sets of chromosomes that are added  Autopolyploidy: all chromosome sets are from a single species  Allopolypoidy: chromosome sets are from different species  Key Topics: o Duplications and consequences: duplications occur when part of a chromosome is repeated.  Results in:  During meiosis, a loop will form to properly align the chromosomes, the duplication will be pushed back in a loop  Chromosomes want to maintain a certain level of gene product, if it has a duplication and both genes (original and duplication) are active, then the gene product will be doubled. This can alter phenotype. o Deletions and consequences: deletions are loss of a part of chromosome  Results in:  Loss of essential genes, which can be lethal or the proportions being off  Deletion of a portion where the centromere is located will lead to the loss of the chromosome entirely  Heterozygous deletions: o The products of the gene will become imbalanced o Some recessive alleles that are not deleted will be shown in the phenotype which will result in pseudodminance  If the deletion of the dominant (wild type) allele, then the recessive will show/be expressed. This can be lethal or alter the phenotype o Some genes require two copies to be present to produce enough gene produce so it can result in being haploinsufficient  Can have the wild type allele but not express the phenotype because it does not have enough gene product being created. This will result in a phenotype being in between the dominant and the recessive phenotypes.  During meiosis, a loop will for to line up the homologous chromosomes properly. o Inversions and consequences: an inversion is when a chromosome segment order is flipped 180 degrees.  This can change the order of a chromosome or can break. If a chromosome breaks in the middle of a gene, it will no longer be functional.  Position effect: a gene A may need to be in front of gene B to make sure that gene B is active (or inactive). If the order is switched and gene B is in front of gene A, then gene B will not be active (or inactive). This results in the loss of control over a gene.  Crossing over taking place: if crossing over takes place when a gene forms a loop, to make sure homologous chromosomes line up properly, then it may cause an issue for when the chromosomes split during meiosis. Will create nonviable gametes. o Translocations and consequences: movement of a gene sequence/region from one chromosome to another nonhomologous chromosome. Can result in the same outcomes as inversions. o Aneuploidy: change in the number of individual chromosomes. Can gain or lose a chromosome. Results from nondisjunction.  Human Aneuploidy:  Sex Chromosome aneuploidy: chromosomes have mechanisms for canceling out extra chromosomes or to compensate for a loss of chromosomes (dosage compensations)  XYY: has very little impact on the individual due to the lack of genetic information located on the Y chromosome. This is the most known aneuploidy overall  Turner/Klinefelter: another form of aneuploidy  Autosomal Aneuploidy: the smaller the chromosome is, the more tolerated the aneuploidy is  Down Syndrome (21): most common autosomal aneuploidy (a type of trisomy aneuploidy). Chromosome 21 is a small chromosome with not a lot of genetic material on it compared to other chromosomes. It is easier for this chromosome to balance out the extra genes.  Trisomy 18: Edward Syndrome, severe, die by age 1  Trisomy 13: Patau syndrome, 50% die within 1 month, 95% die by age 3  Trisomy 8: mosaic individuals and can live normal life expectancy  Down Syndrome:  75% results from a nondisjunction in the mother. 2 of the 3 chromosomes 21 comes from the mom while the third comes from the dad.  Primary down syndrome increases with maternal age  Familial Down Syndrome: occurs when translocation of part of chromosome 21 occurs. This runs in families (parents have undergone Robertsonian translocation) o Fragile Chromosomes: a chromosome that is prone to breaking  Most common form of mental impairment that is inherited.  Results from an increase in the number of trinucleotide repeats.  Breakage is not a cause of disease  Trinucleotide expansion and permutation: will lead to blockage of transcription, fragility is related to the length of repetition  Genetic Anticipation: number of repeats in future generations which will result in worsening of symptoms  Fragile X Syndrome: occurs in 1/2000 males and 1/4000 females o Rearrangements in Evolution:  Duplications: if you have two “A” genes, one can be used normally while the other can be changed. If it changes too much, the gene can become no longer functional. Or, both genes can change  Through time, the genes can specialize to do certain parts of their job. Each duplicated gene will be involved in the same pathway, but different specialized parts of the pathway to make up the whole. Will become better at the individual pathways then when it was in charge of the overall pathway.  Gene amplifications: duplication multiple times, can be used as backups if something happens to the original gene Chapter 7:  Key Terms: o Linked Genes: genes on a chromosome that are close together and stay together during meiosis, meaning that they separate dependently o Recombinant: new combination of alleles for a gamete o Nonrecombinant: the allele combination is the same as the parental gametes. o Coupling (Cis): when the wild type alleles are on one chromosome and the mutant alleles are on the other chromosome o Repulsion (Trans): when each chromosome has one wild type allele and one mutant allele o Interference: occurs when the number of predicted DCO is different from what is observed. Crossovers may influence where another one takes place, which will alter how many DCO actually take place  Important People: o Morgan: genes on same chromosome segregated together, those closely linked together were not usually subject to recombination o Sturtevant: a student of Morgan. Generated the first map of chromosomes by using recombinant frequencies.  Key Topics: o Consequences of linkage in Next Generation:  When there is no linkage of genes and independent assortment occurs, the F2generation will have a ratio of 9:3:3:1. When there is a linkage of genes, there is an overrepresentation of parental progeny o Recombination Frequency: (# of recombinant progeny/total # of progeny)*100%  Can be used to predicting the number of recombinant progeny o Determining Gene Distances: 1% recombinant frequency=1 cM. This can be used as an approximate distance between genes.  NOTE:  The recombinant frequency cannot be greater than 50% for two genes.  Recombinant frequency greater than or equal to 50% means you cannot determine if the genes are linked or on separate chromosomes  Genes that are far enough apart can undergo double crossovers and will look like no crossing over took place o Maps:  Genetic Maps: uses recombination frequencies to make a map of the chromosomes and genes. It is an approximate map.  Physical Maps: a map of chromosomes and genes that uses physical distances and is absolute.  Puzzle like in structure, have to be able to figure out the order based on distances. Can have different orders as long as the distances are the met. o Linkage Groups: the more gene/markers the more information that can be gathered. If we calculate that gene A and F are 50% recombination, then we assume that they are on different chromosomes. However, if we know that gene A and B are at 30% recombination and that gene B and F are 20% recombination, then we know that the order is ABF on the same chromosome.  Intermediate markers: allow for a linkage group to be at a span greater than 50 cM to be connected together (like in the example of ABF above) o Two-Point Test Cross: Test cross between two genes  Example: looking at genes a, b, c, d  Cross gene a and b: 50% recombination frequency (assume genes located on different chromosome)  Cross gene a and c: 50% recombination frequency (assume genes located on different chromosome)  Cross gene a and d: 50% recombination frequency (assume genes located on different chromosome)  Cross gene b and c: 20% recombination frequency (on same chromosome)  Cross gene b and d: 10% recombination frequency (on same chromosome)  Cross gene c and d: 28% recombination frequency (on same chromosome)  What do we know? Know that gene a is on chromosome 1. Genes b, c, d, are on chromosome 2. But in what order? o Each gene must be apart the distance that is given from the recombination frequency. So, the order can be dbc or cbd. o Gene d is 10 cM from b and c is 10 cM from b. When adding this together, we get that gene d is 30 cM from gene c. However, when using the recombination frequency from above, it states that gene c is 28 cM from gene d. So why is this different? o The distance is different due to double crossing over taking place, this causes us to get 28 cM when it is really 30 cM. o Three-point Test Cross: more efficient than two-point test cross  The order of genes can be established after a single cross  Double crossovers can be detected and will provide more information  Double crossovers: yields a recombinant chromosome that has an altered middle gene. If a change in a single gene occurs while the other two genes remain the same, then the changed gene is the gene that is located in the middle of the sequence.  Steps of a 3 Point Test Cross:  Identify the parent groups: which group has the most?  Identify the double crossing over: which group has the least?  What is the difference: compare the parental to the DCO. Which gene is different/switched? This gene is the gene located in the middle of the sequence. o Molecular Markers: can be used to make a genetic map  Restriction fragment length polymorphism (RFLP): changes in DNA sequence will modify restriction enzyme recognition sites.  Variable number of tandem repeats (VNTR): differences in copy number  Microsatellite markers: number of repeats in different in everyone, producing different phenotypes  Single nucleotide polymorphism (SNP): a single base change Key Terms Important People Key Ideas Exam 2 Study Guide: Chapter 8  Key Terms: o Prototroph: Wild type bacteria, can synthesize all compounds needed for the growth of the bacteria from simple ingredients o Auxotroph: mutant strain bacteria that will lack one or more enzymes that are required when metabolizing nutrients, this strain will grow on supplemental media o Merozygote: bacteria that is partial diploid. Formed when the F factor and several adjacent genes are excised from the chromosome of an Hfr cell and transferred to an F cell. o Conjugation: Can transfer the F factor. The plasmid will go across a bridge formed, at the end of the process, both will have a copy of the F plasmid. o Fertility Factor (F): Cells that contain this are F and cells that do not have it are F . This contains the origin of replication, the gene involved in conjugation. o F Cell: Present as a separate circular DNA. Donor in role of conjugation - o F Cell: Is absent. Recipient in the role of conjugation o Hfr: present and integrated into bacterial chromosome. High frequency donor in role of conjugation. o F Cell: Present as a separate circular DNA, carries some bacterial genes. Donor in the role of conjugation. o Transformation: DNA is taken up from the surrounding and is incorporated into the genome of the cell. This can occur naturally.  Competent: Cells that will take part in transformation (not every cell is willing to take up unknown DNA) o Transduction: use of viruses to carry genomic information to cells. The genome has to be a small segment to be able to fit into the head of the virus to be injected into a cell and take over the cell. o Lytic Cycle: The virus infects a cell, replicates within cell, kill cell.  Virulent Phage: is reproduced only in the lytic cycle o Lysogenic Cycle: The virus will infect the cell, integrate into the DNA and stay. All daughter cells of this infected cell will have the virus. The virus will remain in the DNA until a trigger, then will follow lytic cycle.  Temperate Phage: uses either the lytic or the lysogenic cycle. o Recombinant Frequency: works the same as for eukaryotes. (Recombinant plaques/total plaques)  Important People: o Francois Jacob and Elie Wollman: Did gene mapping by interrupting conjugation. If the gene is close to the F factor, then the gene will make it across the bridge. They interrupted the conjugation to determine what makes it across and what does not, this gives them a distance (based on time) to determine the gene order. They would place it on different mediums to determine what made it through. o Lederberg and Zinder: Generalized transduction. Noticed that some cells did not follow the auxotroph to prototroph concept through the filter. Determined that a phage could fit through a filter (the virus) and were lysogenic for some cells and would later become lytic.  Key Ideas: o Advantages of Bacteria/Viruses:  Reproduction is rapid  Produces a lot of progeny  The haploid genome will allow for all mutations to be directly expressed  Asexual reproduction simplifies isolation of genetically pure strain.  Growth in the lab is easy and does not need a lot of space  Genomes are small in size  Techniques are available for isolating and manipulating their genes  Medical importance  Can be genetically engineered to produce commercial valued substances o Characteristics of Bacteria:  Single circular chromosome, most only have one but some have multiple. A few have linear genomes. o Conjugation Mapping: if a gene is close to the F factor, then the probability of it making through the bridge during conjugation is high. When the conjugation gets manually interrupted after x amount of time, scientists can take the bacteria and place it in a media to determine what genes are present and have made it through the bridge. They continue this process while lengthening the time the conjugation takes place. This will help to determine the order and distance of genes. The distance is based on a unit of time (minutes). o Transformation Mapping: A competent cell will pick up only a portion of DNA to protect itself from possible harmful DNA strands. After picking up the strand, it will look for homologous regions. It will then incorporate the DNA strand into its chromosome, forming a heteroduplex (this is when it only takes a portion of a single strand). During division, one cell will be the original and will live while the other will have the foreign DNA strand and be transformed. Depending on if the strand is good or bad, the cell will live or die.  Since the cell will only pick up a portion of the DNA, this means that if it has a high rate of cotransformation (transformation of multiple genes at a single time) then those genes will have most likely been close together. o Characteristics of Viruses: all organisms are infected by viruses. It is a nucleic acid coated in proteins. Can have different types of DNA segments in the head but only a small portion, linear to circular genome.  Plaques: different viruses leave behind different plaques. A way to determine the phenotypes of viruses. o Mixed-Infection Experiment: two viruses infect the same cell. Using plaques, they can determine the phenotypes and what is recombinant or Nonrecombinant.


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