Genetics Exam 2 Study Guide Chapter 7: Sex Determination and Sex Chromosomes Concepts & Terms to Know: ∙ Primary sexual differentiation ∙ Secondary sexual differentiation ∙ Homogametic sex ∙ Heterogametic sex ∙ Diseases associated with X and Y chromosomes ∙ The Lyon Hypothesis ∙ Barr Bodies ∙ Dosage Compensation ∙ Inactivation mechanism ∙ SexIf you want to learn more check out the cultivation of plants for subsistence through nonintensive use of land and labor
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determination and genotypes in fruit flies ∙ Bilateral gynandromorphy Practice Questions: 1. In humans, which sex (male or female) is the homogametic sex? Which is the heterogametic sex? How do you know? 2. What chromosome designates males in humans Name three genes on that chromosome and explain what they do. 3. What is dosage compensation? How do Barr Bodies relate to dosage compensation? 4. What does the Lyon hypothesis say? 5. Explain X inactivation. Include the two inactivation components listed in class. 6. True or false: Y chromosomes in fruit flies do not play a role in sex determination. 7. What occurs in bilateral gynandromorphy? 8. How is sex determination different in reptiles than it is in humans? Chapter 8: Chromosome Mutations: Variation in Number & Arrangement Concepts & Terms to Know: ∙ Chromosome mutation ∙ Aneuploidy o Monosomy o Disomy o Trisomy ∙ Euploidy o Diploidy o Polyploidy ∙ Nondisjunction ∙ Haploinsufficiency∙ Autopolyploidy o Autotriploids o Autotetraploids ∙ Allopolyploidy o Allotetraploid ∙ Endopolyploidy ∙ Deletion o Terminal o Intercalary ∙ Duplication o Gene redundancy o Gene amplification o Copy number variants o ∙ Inversion o Paracentric o Pericentric ∙ Translocations o Reciprocal o Alternate segregation o Adjacent segregation Practice Questions: 1. What is a chromosome mutation? 2. How do aneuploidy and euploidy differ from each other? 3. How does nondisjunction result in mutation? Which 2 specific mutations can nondisjunction result in? 4. True or false: Monosomy of autosomal chromosomes is usually okay in humans. 5. What is the biggest issue with monosomy? (besides the fact that one chromosome is missing from the pair) 6. What does the idea of haploinsufficiency say? 7. True or false: Trisomy is tolerated in humans. 8. Give a common example of trisomy in humans. Which chromosome(s) does it affect? 9. What is the most common origin of the extra chromosome/ 10. Which parent is responsible for the majority of trisomy 21 cases? 11. Is polyploidy more common in plants or animals/humans? 12. How does autopolyploidy differ from allopolyploidy? 13. What role does colchicine play in the creation of autotetraploids? 14. What causes structural changes in DNA? 15. What is a deletion? 16. What must occur or form if a chromosome with an intercalary deletion is to pair with its normal homolog? Why?17. What happens to the portion of the mutated chromosome that contains the centromere? What about the portion that does not contain the centromere? 18. What is a duplication? 19. How do duplications generally arise? 20. If an essential gene is duplicated, will mutational changes occur and be tolerated? Why or why not? 21. Why can’t unique genes acquire certain mutations through duplication? 22. How does duplication produce phenotypic variation? 23. What is an inversion? 24. What is required for an inversion to take place? 25. How does a paracentric inversion differ from a pericentric inversion? 26. What is an inversion heterozygote? 27. What is required for an inversion heterozygote to pair? What kind of gametes result if crossing over does not occur? What kind of gametes result if crossing over does occur? 28. When crossing over occurs in a paracentric inversion, what 2 recombinants are formed? 29. What is a translocation? 30. How are translocations and inversions different from duplications and deletions? 31. What common condition do Robertsonian translocations often result in? Explain the mechanism. 32. What is a fragile site? What is fragile X syndrome? Chapter 9: Extranuclear Inheritance Concepts & Terms to Know: ∙ Uniparental inheritance ∙ Endosymbiotic theory ∙ Heteroplasmy ∙ Maternal Effect Practice Questions: 1. What organelles have a part in heredity? 2. What does the endosymbiotic theory state about these organelles and their role in heredity? 3. True or False: Mitochondrial DNA (mDNA) is not able to be mutated. Explain why this is or is not true. 4. Name 2 disorders arising from mDNA. 5. Explain the concept of 3-parent babies and how mDNA plays a role. 6. What 2 ideas were realized when looking into mitochondrial-based disorders? 7. Explain how phenotypic traits are controlled in maternal effect.Chapter 10: DNA Structure and Analysis Concepts & Terms to Know: ∙ Tetranucleotide hypothesis ∙ Transformation Principle ∙ Griffith’s Experiment ∙ Avery, McLead & McCarly experiment ∙ Hershey-Chase Experiment ∙ Denaturation ∙ Renaturation ∙ Watson-Crick Model ∙ Molecular Hybridization ∙ Fluorescent in situ hybridization (FISH) ∙ Reassociation Kinetics Practice Questions: 1. Name the 4 characteristics genetic material must exhibit. 2. Why did people think protein was the genetic material at first? What are proteins made of? 3. Explain the tetranucleotide hypothesis and why it is incorrect. 4. What was Griffith’s Experiment? 5. What three scientists confirmed Griffith’s theory? What was this theory? 6. What did the Hershey-Chase Experiment find? 7. Name and explain the two forms of indirect evidence that supports that DNA is the genetic material. 8. True or false: RNA is never genetic material. 9. What are the three components of DNA structure? 10. What end of the sugar is the phosphate group of DNA attached to? 11. What nucleotides are purines? What nucleotides are pyrimidines? 12. What type of bond forms the sugar-phosphate backbone of a DNA strand? 13. What type of bond connects two strands of DNA? 14. What are the 2 complementary base pairs? 15. True or false: There is a hydrogen triple bond between A&T and C&G. 16. Name and describe 2 alternative forms of DNA. 17. How does the structure of DNA differ from the structure of RNA? 18. What is molecular hybridization? 19. What can fluorescent in situ hybridization (FISH) do for the analyzation of DNA? 20. How is “complexity” of DNA defined? How does complexity effect the reassociation of DNA?21. What does gel electrophoresis do? Chapter 11: DNA Replication and Recombination Concepts & Terms to Know: ∙ Semi-conservative ∙ Conservative ∙ Meselson-Stahl Experiment ∙ Helicase ∙ Replication Origin ∙ Replication Forks. ∙ DNA polymerase ∙ RNA primase ∙ Continuous & Discontinuous Synthesis ∙ Proofreading ∙ Mismatch repair ∙ T-loop Practice Questions: 1. How do semi-conservative and conservative replication differ? Which one is DNA replication? 2. What does helicase do in the DNA replication process? 3. What is the difference between the replication origin and the replication forks? 4. What is the purpose of DNA polymerase? What is the purpose of RNA primase? 5. How many polymerases are there in eukaryotes? (the ones that carry out the bulk of synthesis) 6. Synthesis always goes in what “direction”? 7. How do continuous and discontinuous synthesis differ? 8. Which process (proofreading or mismatch repair) can correct a mistake only right after the mistake is made? Which one can repair the mistake after replication is over? 9. What is the purpose of telomerase? Chapter 12: DNA Organization of Chromosomes Concepts & Terms to Know: ∙ Supercoiling ∙ Topoisomerases ∙ Histones ∙ Heterochromatin ∙ Octomer ∙ Chromosome Banding ∙ Repetitive DNA∙ Repetitive Transposed sequences Practice Questions: 1. Which is simpler: viral/bacterial DNA or eukaryotic DNA? 2. What happens if helical turns in DNA get unwound? 3. What is the equation for supercoiling/linking number? 4. In living things, is most DNA negatively or positively supercoiled? 5. What is the purpose of topoisomerases? 6. What are histones? What do they do and where are they located? 7. What is heterochromatin and where is it located? How is it different from euchromatin? 8. What is the octomer? 9. What are the two types of repetitive DNA? Give examples of each type and say where they are located. 10. What are the two types of repetitive transposed sequences? 11. True or false: the majority of DNA does not encode functional genes. 12. What is “junk DNA” important for? Chapter 15: Gene Mutation, DNA Repair and Translocation Concepts & Terms to Know: ∙ Mutation o Spontaneous o Induced ∙ Luria-Delbrunk Test ∙ Replication Errors ∙ Base Modification ∙ Replication slippage ∙ Tautomeric Shifts ∙ Deamination ∙ Oxidative damage ∙ Alkylating agents ∙ Acridine dyes ∙ Ultraviolet light ∙ Ionizing radiation ∙ Breakage Bridge Cycle ∙ Photoreactivation repair ∙ Base & Nucleotide excision repair ∙ NER ∙ BER ∙ Xeroderma pigmentosum (XP) ∙ TransposonsPractice Questions: 1. What is a mutation? 2. How do spontaneous and induced mutations differ? 3. What did the Luria-Delbrunk Test find? 4. What are the four classifications of mutations based on location? 5. What are the seven classifications of mutations based on phenotypic expressions? 6. What are the three classifications of mutations based on type of molecular change? 7. Where/What do spontaneous mutations arise from? 8. True or false: DNA replication errors are common and mutate entire sequences. 9. What is replication slippage and where is it common? 10. What are tautomeric shifts and what causes them? How common are they? 11. True or false: DNA mutation and damage are the same. 12. What is an AP site? 13. What is deamination? 14. What is oxidative damage? 15. Where do induced mutations arise from? 16. Explain how the following change or damage DNA: a. Base Analogs b. Alkylating agents c. Acridine dyes d. Ultraviolet light e. Ionizing radiation 17. True or false: Human diseases caused by trinucleotide repeats can only be passed on from one parent. 18. What are the two types of proofreading that only occur in bacteria? 19. Explain how BER and NER repair DNA. 20. What is a transposon? 21. What is XP? 22. Explain how the breakage bridge cycle works. 23. How much of the human genome is made up of transposable elements? 24. List and explain the two different methods transposons use to move.Genetics Exam 2 Study Guide Answer Key Chapter 7 1. The female is the homogametic sex. Females have 2 X chromosomes so their chromosomes do not determine the sex of the progeny. The males are the heterogametic sex because they have the “unlike” 2. The Y chromosome designates maleness in humans. Three genes on the Y chromosome are the SRY gene, the PAR gene or region, and the MSY region. The SRY gene allows for a Y chromosome. It is the sex determining region of the chromosome. The PAR or pseudoautosomal region is where the X and Y pair in meiosis. The MSY region is the male specific region of the chromosome. It makes up the majority of the Y chromosome. 3. Dosage compensation is the process that equalizes the expression of the X and Y chromosomes. It prevents over expression of X. Barr bodies are inactivated X chromosomes that are inactivated as a part of dosage compensation. They are only associated with females. 4. The Lyon hypothesis explains X inactivation. It says that when X inactivation occurs, the chromosome that is to become inactive is chosen at random, but once it is inactivated, it stay inactive all through division. 5. In X inactivation, the X chromosomes pair briefly at the XIC locus. The XIC locus is the inactivation center. It includes several genes such as the XIST gene. The XIST gene is the specific transcript for X inactivation. After the X chromosomes align at the XIC locus, the XIST gene is deleted and the chromosome shuts down. 6. True. 7. In bilateral gynandromorphy, one chromosome is lost after division. 8. In some reptiles, sex is determined by temperature variation because certain male or female hormones work better at certain temperatures. Chapter 8 1. A chromosome mutation is a modification of genetic material at the chromosome level. It can include a change in total chromosome number, deletion or duplication of a gene or rearrangement of genetic material. 2. Aneuploidy is when an organism gains or loses one of more chromosomes, but not a complete set. Euploidy is when complete haploid sets are gained. 3. Nondisjunction is when paired homologs fail to disjoin during segregation. This can result in abnormal gametes carrying two members of the affected chromosome or none at all. This ends in trisomy (gain of one chromosome) or monosomy (loss of a single chromosome from a diploid set). 4. False5. Monosomy masks lethality so if one gene on a chromosome is represented by a lethal allele, the unpaired chromosome condition will result in death of the organism. 6. The idea of haploinsufficiency says that a single copy of a recessive gene may be insufficient to provide adequate function for sustaining the organism. 7. True. 8. A common example of trisomy is Down Syndrome. It involves translocation of chromosome 21 and results in 12-14 unique characteristics. 9. The extra chromosome most commonly originates from nondisjunction in meiosis I. 10. The mother is responsible for 95% of trisomy 21 cases. 11. Polyploidy is more common in plants. 12. Autopolyploidy is the addition of 1 or more extra sets of chromosomes, identical to the normal haploid complement of the same species. Allopolyploidy is the combination of chromosome sets from different species occurring as a consequence of hybridization. 13. Colchine interferes with spindle formation. This prevents replicated chromosomes from separating and causes 4n chromosomes. 14. Structural changes in DNA are due to one or more breaks along the axis of the chromosome followed by the loss or rearrangement of genetic material. 15. A deletion is when a region of the chromosome is removed. It can be near one end of the chromosome (terminal) or within the interior of the chromosome (intercalary). 16. A deletion loop must form for the chromosome with the deletion to pair with the normal chromosome because the two chromosomes need to line up correctly in order to properly pair. 17. The portion that contains the centromere is maintained through cell division. The portion that does not contain the centromere is lost and not passed on to progeny. 18. A duplication is a repeated segment of a chromosome. 19. Duplications usually arise as the result of unequal crossing over between synapsed chromosomes. 20. Yes, mutational changes will occur and be tolerated in the extra copy of future generations because the original gene provides all the functional information needed. 21. Unique genes that are duplicated cant acquire mutations that will alter their functions because their unique function will be lost. 22. Duplication produces phenotypic variation through copy number variants which play a crucial role in the expression of traits. 23. Inversion is a type of mutation where a segment of a chromosome is turned around 180 degrees within the chromosome. 24. For an inversion to take place, there needs to be breaks at 2 points in the chromosome and a reinsertion of the inverted segment.25. A paracentric inversion is an inversion that involves the centromere. A pericentric inversion is an inversion that does include the centromere. 26. An inversion heterozygote is an organism with one inverted chromosome and one non-inverted homolog. 27. An inversion loop is required for inversion heterozygotes to pair. If crossing over doesn’t occur , the homologs will segregate , resulting in 2 normal and 2 inverted chromatids. If crossing over does occur, all abnormal chromatics are produced. 28. One recombinant dicentric (2 centromeres) and one recombinant acentric (no centromeres). 29. A translocation is a mutation that alters the location of chromosomal segments in the genome. A reciprocal translocation is the exchange of chromosomal segments between 2 non-homologus chromosomes. 30. Translocations and inversions do not involve loss or gain of genetic material like deletions and duplications. 31. Robertsonian translocations often result in Down Syndrome. One parent has a G group chromosome 21 attached to the end of the D group chromosome 14 and this parent is phenotypically normal. When that parent produces a gamete, the gamete has 2 copies of chromosome 21, so when the gamete is fertilized, there are 3 copies total of chromosome 21. 32. A fragile site is a chromosomal region that is susceptible to breaks or gaps. Fragile X syndrome is when a single gene on the long arm of the X chromosome shuts down and fails to produce a protein FMRP, which is vital for brain development. Fragile X syndrome is the most common form of mental retardation. Chapter 9 1. Chloroplast and mitochondria 2. The endosymbiotic theory states that mitochondria and chloroplasts arose independently 2 billion years ago from free living bacteria. These bacteria were engulfed by larger eukaryotic cells and a beneficial symbiotic relationship developed. 3. False. 4. Lebers heredity optic neuropathy and Kearns-Sayre Syndrome. 5. A baby is made using the nuclear DNA from mom and dad, but mitochondrial DNA is taken from a third female donor because the mother’s mitochondrial DNA is damaged in some way. 6. When looking into mitochondrial-based disorders the importance of organelles during normal development and the relationship between mitochondrial function and neurological disorders were realized. 7. In maternal effect, an offspring’s phenotype is under the control of nuclear gene products present in the egg. The nuclear genes of the female gamete are transcribed and the genetic products accumulate in the egg cytoplasm. Chapter 10 1. Genetic material must exhibit replication, storage of information, expression of information and variation by mutation. 2. People thought protein was the genetic material because it is more complex. Proteins are made up of amino acids. 3. The tetranucleotide hypothesis was the idea that DNA is a linear, single-stranded polynucleotide with the same 4 repeating bases. This is incorrect because base-composition studies showed that the ratio of each complementary pair (A:T and G:C) is equal. DNA is also a double stranded helix with multiple bases in different orders. 4. Griffith’s experiment involved injecting mice with virulent or avirulent cell colonies and observed whether the mice lived or died. When Griffith realized that injecting each type alone did not result in death of the mice, he expected that injecting mice with both virulent and avirulent colonies would not result in death of the mice either, but the mice died 5 days later. He found that bacteria converted avirulent cells into virulent cells. The concluded that there might have been part of the polysaccharide capsule or a compound required for capsule synthesis, but the capsule itself did not cause pneumonia so protein could not be the genetic material. This became called the transformation principle. 5. Avery, McLead and McCarly confirmed Griffith’s lead that DNA was the genetic material. 6. The Hershey-Chase experiment found that if you infect a form of bacteria (E. Coli) with a bacteriophage, the phages reproduce and are released from the bacteria. They added the phage to 2 different mediums to determine whether DNA or protein was the genetic material for the phage and found that DNA was entering the bacteria, while protein was not. They concluded that DNA was the genetic material. 7. Two forms of indirect evidence are distribution of DNA (DNA was found where it was needed, in the nucleus, and protein was found everywhere) and mutagenesis (nucleic acid had highest absorption rate at the same UV wavelength where mutation frequency was highest). 8. False, RNA serves as genetic material for some viruses. 9. Phosphate, sugar and base. 10. The phosphate is attached to the 5’ end of the sugar. 11. Cytosine, uracil and thymine are pyrimidines and adenine and guanine are purines. 12. Phosphodiester bond. 13. Hydrogen bond.14. In DNA, adenine pairs with thymine and cytosine pairs with guanine. In RNA, thymine is replace with uracil. 15. False, there is a triple bond between cytosine and guanine, but there is a double bond between adenine and thymine. 16. The two alternative forms of DNA are A-form (high in salt and has a crunched structure) and Z-form (is a left helix and appears in-vitro). 17. RNA is made of ribonucleotides and DNA is made of deoxyribonucleotides. Uracil replaces thymine in RNA. RNA is usually single stranded and DNA is double stranded. 18. Molecular hybridization is the process of 2 complementary strands coming together. 19. FISH can be useful to locate genes on chromosomes. 20. Complexity of DNA is defined by the length of unique DNA. DNA with lots of repetitiveness will reassociate faster than unique DNA. 21. Gel electrophoresis separates different forms of DNA based on their size. Chapter 11 1. Semi-conservative replication uses 2 strand with 1 old and 1 new strand. Conservative replication uses 2 newly synthesized strands. 2. Helicase unwinds the DNA helix for replication. 3. The replication origin is where DNA is unwound and the replication fork is where actual replication begins. 4. DNA polymerase adds nucleotides to the 3’ end of the primer strand. RNA primase starts the synthesis for polymerase. 5. There are three polymerases in eukaryotes that are responsible for the bulk of synthesis (alpha, delta and episilon). 6. Synthesis always goes 5’ to 3’. 7. Continuous synthesis is done on the leading strand or the newly synthesized strand. Discontinuous synthesis takes place on the lagging strand, the strand opposite of the DNA template. It is made of okazaki fragments. 8. Proofreading can only correct a mistake right after the mistake is made and mismatch repair can notice the mistake and correct it after replication is over. 9. Telomerase adds several repeats of a single-stranded tail to the 3’ end of the strand. The addition of the repeats lengthens the telomeres and protects the chromosome. Chapter 12 1. Viral/bacterial DNA 2. If helical DNA gets unwound, the DNA molecule gets unstable and supercoils. 3. L (linking number)=T (turns of helix)+W(supercoils) 4. Most DNA is negatively supercoiled (underwound). 5. Topoisomerases control the linking number and supercoiling.6. Histones are small basic proteins . They function in coiling DNA to form nucleosomes and are located in the nucleus. 7. Heterochromatin are chromosomal regions where nucleosomes are really tightly packed. They are located near centromeres and telomeres. Euchromatin are chromosomal regions that contain most of the structural genes and nucleosomes are relatively uncoiled. 8. The octomer makes up the core of the nucleosome with 2 sets of histones H2A, H2B, H3 and H4. 9. Highly repetitive DNA and middle repetitive DNA. An example of highly repetitive DNA is satellite DNA, which is a short sequence repeated over and over located near the centromere. Examples of middle repetitive DNA are minisatellites and microsatellites. They are scattered throughout the genome. 10. SINES (short interspersed elements) and LINES (long interspersed elements). They comprise more than 20% of the genome. 11. True 12. Junk DNA was found to be important for coding and transcription and translation. Chapter 15 1. A mutation is a change in the DNA sequence. 2. Spontaneous mutations are mutations that occur as a natural consequence and induced mutations occur when someone does something that brings on the mutation. 3. The Luria-Delbrunk test found that mutations are random, not adaptive. 4. Somatic, germline, autosomal and x-linked. 5. Loss of function, gain of function, morphological, nutritional, behavioral, lethal and conditional. 6. Substitution, deletion and insertion. 7. Spontaneous mutations arise from replication errors and base modifications. 8. False, DNA replication errors are rare and are a source of point mutation. 9. Replication slippage occurs at repetitive sequences when the new strand mispairs with the template strand. They are likely the sources of insertions or deletions and are more likely to occur in repetitive sequences 10. Tautomeric shifts are spontaneous isomerizations of a base to a different hydrogen-pairing base. They change the bonding structure of the molecule, allowing hydrogen bonding to occur between non complementary bases.They are caused by a specific chemical phenomenon. 11. False. 12. An AP site is a site lacking a base.13. Deamination is the loss of an amine group and causes the identity of the base to change. 14. Oxidative damage is when metabolic byproducts cause damage to DNA. 15. Induced mutations arise from DNA damage. 16. Explain how the following change or damage DNA: a. Base Analogs cause mutations in DNA by changing its chemical form and is chemically related to a DNA nitrogenous base. b. Alkylating agents are agents that donate an alkyl group. They can cause a transition mutation. They can also change helical chemistry and induce strand breakage. c. Acridine dyes are a type of intercalating agent that promote strand slippage, insertions and deletions. d. Ultraviolet light can form a thymine dimer in DNA and can induce mutations that can lead to cancer. e. Ionizing radiation can induce the formation of reactive molecules (free radicals). They can alter purines and pyrimidines, break phosphodiester bonds and produce deletions, translocations and chromosomal fragementation. 17. True 18. SOS response and photoreactivation repair. 19. BER corrects DNA that contains a damaged base. It recognizes lesions and nicks the DNA strand and fills the gap with DNA polymerase and ligase. NER pathways repair bulky lesions in DNA that alter or double the helix. 20. A transposon is a DNA segment that moves sites in the genome. 21. XP, or xeroderma pigmentosum, is a disease where NER is unable to work. The individual with XP becomes pre-exposed to severe skin abnormalities and skin cancers. 22. The breakage bridge repair is when DNA gets broken and a telomere is lost. After the chromatid is duplicated, the sister chromatids are fused together. Because of the fusing, anaphase cannot take place and the chromatids cannot separate and an anaphase bridge is formed. 23. More than 50%. 24. Replicative method is when DNA synthesis makes a copy of a transposon and the copy moves. The non-replicative method does not involve replication and the transposon itself moves from its original site to a new site.