Molecular Biology and Genetics Block 2 Learning Objectives PDF

**[Molecular Biology and Genetics Block 2 Learning Objectives]** Chromosome Perspective ***LO 1. Explain the following terms and their relationship to both genotype and phenotype: chromosome, homologous chromosome, sister chromatid, autosome, bivalent, independent assortment, segregation, linkage,...

**[Molecular Biology and Genetics Block 2 Learning Objectives]** Chromosome Perspective ***LO 1. Explain the following terms and their relationship to both genotype and phenotype: chromosome, homologous chromosome, sister chromatid, autosome, bivalent, independent assortment, segregation, linkage, cis vs trans, and recombination*** 1. **Chromosome:** DNA with associated proteins a. Consists of linear sequences of genes b. Contain genetic information (genotype) that specifies physical expression of a phenotypic trait c. 46 chromosomes in human diploid cells i. 44 autosomes and 2 sex chromosomes d. Inherited in haploid sets with one set from maternal lineage and one from paternal 2. **Homologous Chromosome:** pairs of chromosomes (one maternal, one paternal) that contain the same sequence of genes, but the genes' expression is not identical (alleles) e. **Allele:** two or more versions of a gene at a specific location f. Different alleles of the same gene segregate at meiosis I g. Alleles of different genes sort independently in gametes h. Sequences of genes is not equivalent to sequence of bases 3. **Sister Chromatid:** duplicated versions of chromosomes connected at centromere i. **Centromere:** constriction point j. After replication, cell has four sister chromatids, making two homologous chromosomes 4. **Autosome:** any chromosome that is not a sex chromosome k. Have 44 in human diploid cells 5. **Bivalent:** two homologs when synapsed 6. **Independent Assortment:** unlinked genetic material aligns and assorts independent of one another 7. **Segregation:** separation of homologous chromosomes 8. **Linkage:** genes present on the same chromosome and that are inherited together l. Violates Mendel's assortment law 9. **Cis:** mutant alleles of both genes are on same chromosome m. Can either be both dominant or both recessive 10. **Trans:** mutant alleles are on different homologues of same chromosome n. Dominant and recessive together 11. **Recombination:** linked genes located on the same chromosome that have homologous crossing over o. Recombination changes allelic arrangement on homologous chromosomes p. Recombination between linked genes occurs at same frequency whether alleles are in cis or trans configuration q. Recombination frequency is specific for a particular pair of genes r. Recombination increases with increasing distance between genes s. Maximum frequency of recombination between any two genes is **50%** t. **Cold spot:** recombination is not advantageous u. **Hot Spot:** recombination is advantageous ***LO 2. Describe the process of chromosome separation during meiosis by stage and explain how crossing over contributes to chromosome behavior and repulsion during prophase I*** 1. *Summarize the steps of meiosis with emphasis on chromosome behavior and content* a. **Prophase I:** nuclear envelope disintegrates while chromosomes condense a. Genetic material is having conversation that enables recombination and proper separation following recombination events b. Homologous chromosome pairing leads to crossing over leads to repulsion leads to chiasmata c. In other words, material is organized, lined up, and exchanged b. **Metaphase I:** bivalents positioned with centromeres of two homologs on opposite sides of metaphase plate d. As each bivalent moves into metaphase plate, its centromeres are oriented randomly with respect to eh poles of the spindle e. Genes on different chromosomes undergo independent assortment because nonhomologous chromosomes align at random at metaphase I i. Exceptions occur by regions of homology f. Nondisjunction occurs when chromosomes stay together ii. One cell gets too much genetic info and the other not enough c. **Anaphase I:** separation of homologs d. **Telophase I:** when the chromosomes arrive at the poles g. Chromosomes decondense e. **Interkinesis:** time between conclusion of meiosis I and beginning of meiosis II where chromosomes decondense because we need to access the genes to do the next part f. **Prophase II:** spindle reforms (with new spindles), chromosomes recondense, nuclear membrane breaks down g. **Metaphase II:** chromosome alignment is driven by microtubules h. **Anaphase II:** separation of sister chromatids to opposite poles i. **Telophase II:** chromosomes arrive at the poles h. Chromosomes decondense, spindle breaks down, cell membrane forms i. Reducing genetic material j. Chromosome Complements: haploid form of cell (23 chromosomes) iii. Diploid means two chromosomes complement (46) j. **Cytokinesis:** separation of cytoplasm into to new daughter cells via contractile ring 1. *List the sequential subphases of prophase I of meiosis and describe the major events of each subphase* a. **Leptotene:** first phase of prophase I when chromosomes become visible under light microscope i. Nucleus remains intact and process appears like prophase of mitosis ii. Condensation of the chromosomes continue b. **Zygotene:** continued chromosome condensation and homolog pairing iii. Homologs will synapse initiating crossing over iv. **Synapse:** tight association between the sister chromatids of each homolog that allows for correct alignment while chromosomes twist, bend, and turn 1. Forms bivalent 2. Different numbers of chromosomes involved in synapse are given different names a. **Univalent:** solo chromosome b. **Trivalent:** three chromosomes c. **Pachytene:** continued chromosome condensation and chiasmata present but difficult to visualize v. Physically associated but have not exchanged yet d. **Diplotene:** begins homolog repulsion (twins push each other away) vi. Forces to drive exchange and separation begin vii. Chiasmata are clearer as chromosomes have condensed further 3. Homologous Recombination: each chiasma is formed by a breakage and rejoining event between non-sister chromatids viii. Synaptonemal complex breaks down and the arms of bivalent separate 4. Now, they are only connected at chiasmata e. **Diakinesis:** chromosome condensation continues and maximum forces to drive chromosomes apart ix. Maximum contraction x. Concludes with breakdown of nuclear membrane and weaker association between homologs ***LO 3. Explain the concept of regions of homology and how they contribute to chromosome behavior during alignment, homologous recombination, and separation*** 1. Define regions of homology and describe how they are generated a. **Regions of Homology:** areas of architectural similarity in 3D architecture i. Homology can be induced by similarities in DNA sequence but, at the chromosomal level, are most strongly associated with linear gene sequence 2. Link regions of homology to the processes that enable two or more nonhomologous chromosomes to align b. The similarity in architecture (regions of homology) induces alignment and enables crossing over ***LO 4. Evaluate the processes involved in generating genetic variation in offspring and explain how changes in the seps and stages associated with meiosis affect outcomes*** 1. *Describe the two factors associated with increasing variation of offspring* a. Crossing over or recombination i. **Crossing over** creates novel combinations of alleles on chromosomes ii. Many chromosomes will undergo multiple **recombination** events dramatically increasing genetic variation in the daughter cells b. Alignment and segregation iii. Each homolog pair is independent iv. Random segregation can produce unique combinations of human chromosomes v. Premature separation of chromosomes is a major mechanism of aneuploidy 2. *Explain the process of recombination and the corresponding consequences of different forms of crossing over* c. Homologous recombination repair utilizes many of the mechanisms we associate with traditional homologous recombination vi. Regions of homology enabling strand crossover and exchange is very similar to homology search and strand invasion vii. Recombination when done correctly as intended should not produce error 3. *Explain how alignment and segregation relate to independent assortment* d. **Independent Assortment:** unlinked genetic material aligns and assorts independent of one another 4. *List the potential consequences of alignment and segregation for multiple chromosomes* e. Inappropriate alignment can result in duplications and deletions like our strand slippage during replication viii. Repetitive regions do not always align perfectly ix. If crossing over occurs after inappropriate alignment, one copy will have too much information (duplications) and one will have too little (deletion) x. Chromosome deletions are among the most common genetic abnormality observed clinically 1. Almost always correlate with phenotype 2. Catastrophic to lose genetic information ***LO 5. Assess the consequences for genotype and phenotype with parental and recombinant chromosomes with consideration of cis and trans arrangements*** 1. **Recombinant chromosomes:** new chromosomes that will undergo/underwent recombination 2. **Non-recombinant chromosomes:** match parent 3. The meiotic outcome would be different depending on cis or trans configuration Chromosome Structure and Function ***LO 1. Define the following terms:*** 1. **Chromatin:** lesser condensed form of DNA with associated proteins (histones) a. Makes up chromosomes b. Form of genetic material most of the time 2. **Chromosome:** DNA molecule with associated proteins in more condensed form c. Contains key structures in fully condensed chromosome (centromere and telomere) d. Can be any full condensed form even after anaphase (not just classic duplicated form) e. Linear chromosomes consist of linear sequence of genes that convey genetic information which specifies the physical expression of a phenotypic trait f. Regardless of centromere position, they will always have two sides i. Petite arms (upper) ii. Q arms (lower) g. There is consistent segregation when p and q are balanced 3. **Chromatid:** longitudinal subunit produced by chromosome replication h. Duplicated and fully condensed 4. **Chromatin Remodeling Complex:** protein aggregates that reorganize nucleosomes of chromatin 5. **Satellite DNA:** highly repeated non-coding DNA sequences i. Strongly correlated with formation of higher order structures of chromosomes j. Collective name for tandem repeat clusters k. Ex: alpha satellite DNA forms structural basis for making centromere 6. **Chromosome Territories:** groups of chromatin fibers in nucleus of nondividing cell l. Correlated with gene disparities m. Territories that are relatively gene rich tend to be located toward the interior of the nucleus because it places them closer to machinery for transcription 7. **Histone:** major class of small proteins (octamer) that forms nucleosome n. Highly conserved across organisms 8. **Nucleosome:** basic structural unit of chromatin o. Generates chromatin and enables DNA to associate into ordered complex with proteins whose orientation is based on histones p. Cannot form higher order structure without it 9. **Centromere:** attachment site for two sister chromatids and landing pad of kinetochore q. Main section we retain for function of chromosome segregation 1. **Kinetochore:** protein complex essential for proper chromosome segregation during mitosis a. Massive complex requires several proteins 10. **Neocentromere:** an inappropriate or unexpected incorporation of centromeric histones to regions of DNA not intended to serve as a centromere 11. **Telomere:** repeat DNA sequences on ends that act as sacrificial buffer 12. **Karyogram:** pictorial representation of chromosomes by size and other differentiating markers r. Metaphase spread analysis 13. **Karyotype:** summary information from a karyogram that describes numbers and appearances under a light microscope 14. **Autosome:** any chromosome that's not a sex chromosome 15. **Repetitive DNA:** clustered repeated sequences in one or a few locations s. Generally heterochromatic t. Approx. 10-15% of genome u. Arrays of tandem repeats 16. **Pseudo-autosomal Regions:** regions of homology for sex chromosomes that look the same on 3D architecture v. Sex chromosomes (X and Y) are not identical by share some genes w. Males are genetically haploid for most genes on X chromosome which results in unique pattern of X-linked inheritance iii. Because they are haploid, need to balance chromosome content in female 17. **Banding/Banding Pattern:** chromosomal patterns of dark and light bands 18. **Euchromatin:** less condensed chromosome regions high in gene content 19. **Heterochromatin:** compact, heavily staining chromosome regions rich in satellite DNA and low in gene content (difficult to activate transcription) x. Around important regions so telomeres and centromeres can function 20. **Locus (Loci):** specific position on a linear chromosome for a particular gene or sequence 21. **Allele:** two or more versions of a gene at a specific location y. Homologous chromosomes contain the same sequence of genes which may vary in alleles and/or expression ***LO 2. Explain the relationship between types of DNA sequences and the structures formed in chromosomes and identify the expected chromosome structure formed from a sequence of DNA or histone variant incorporated at a given chromosome position*** 1. Two types of DNA a. **Unique Sequence:** most common and represented once in haploid set of chromosomes i. Genes that encode for proteins ii. **Genes:** any DNA sequence that encodes for a product (doesn't have to be protein) b. **Repetitive DNA:** interspersed repeated DNA iii. Can be highly repetitive (\>105) and middle repetitive (102-104 copies) iv. Strongly correlated with non-coding regions 2. As a diploid species, we have two chromosome complements in each cell c. **Ploidy:** number of chromosome complements 3. **Interspersed Repetitive DNA:** mixed in with other elements throughout genome and can be divided into two categories d. **Short/Sine:** Alu Family approx. 300 bp in length that are related by not identical in sequence v. Approx. 10% of human DNA vi. Enriched in regions of GC content (G-light bands) e. **Long/Line:** mostly L1 sequences and are up to 6 kb in length vii. Approx. 20% of genome viii. Enriched in regions rich in AT content (G-dark bands) ***LO 3. Summarize the processes of chromosome condensation with particular emphasis on the components involved in the generation of fully condensed chromosomes and assess the consequences for changes in protein availability or incorporation in terms of chromosome structure or condensation level*** 1. **High Order Structures for DNA:** when DNA and proteins come together to increase complexity and organization a. DNA is a polymer of nucleotides that has high order structures involved in folding in 3D space and association with proteins (do primary, secondary, tertiary, and quaternary folding) 2. Nucleosomes are composed of three things b. **Histone Octamer:** core particle that has 2 H2A, 2 H2B, 2 H3, and 2H4 with approx. 145 bp of DNA i. Arrangement of histones is critical to generation of chromosomes ii. Organization around histone can be adjusted based on chromatin remodeling complex activity iii. **CENP-A:** histone H3 variant found exclusively at functional centromeres 1. Helps form structures necessary for formation of kinetochore c. **Linker DNA:** links adjacent core particles (approx. 55 bp) d. **H1:** binds to core particle and to linker DNA iv. Associate nucleosome with DNA and ensures core particle binds appropriately 3. **Process of chromosome condensation:** e. Begin with a strand of nucleotides f. DNA forms double helix g. DNA wraps around nucleosome forming beads-on-a-string h. Nucleosomes coil to form higher order DNA structure which is 30nm fiber v. **30nm Fiber:** left-handed superhelix or solenoidal supercoil that has 6 nucleosomes per turn i. 30 nm fiber coils into coiled coils/fibers j. Condensin coils coiled coils into organized, fully condensed, chromosome vi. Tightest configuration vii. **Condensin:** forms coils by wrapping them into flower shape with condensing at the core and the genetic material as the flower around it 2. If absent, DNA cannot fully condense, then it cannot segregate in mitosis/meiosis, and cannot do cell division 3. Made of SMC2 and SMC4 k. **Cohesin:** holds two sister chromatids together in duplicated metaphase chromosomes viii. Not a direct part of condensation ix. Made of SMC1 and SMC3 ***LO 4. Summarize the function, location, gene content, and importance of the following*** 2. **Centromere:** attachment site for two sister chromatids and landing pad of kinetochore b. Main section we retain for function of chromosome segregation c. Region of highly specialized chromatin that is largely heterochromatic and contains lots of alpha satellite DNA d. Centromere Proteins: more than 20 now known e. Have combination of repetitive DNA and key histone variants 3. **Kinetochore:** protein complex essential for proper chromosome segregation during mitosis f. Massive complex requires several proteins g. Highly conserved structure 4. **Telomere:** repetitive sequences of DNA at the ends of chromosomes that assist with protecting the chromosome from genetic loss (along with other critical functions) h. TTAGG i. Needs to be certain length to curl in on itself and cap j. Acts as sacrificial buffer for protection of genetic material k. **Telomerase:** enzyme that maintains and restores telomeres l. **End Replication Problem:** ends of linear chromosomes cannot be fully replicated leading to progressive loss of information i. Can lead to cancer because of limitations in replication potential m. **Critical Telomere Length:** when capping cannot occur, and chromosome looks broken n. Telomere length correlates with age 5. **Nuclear Organizer Regions (NORs**): site of ribosomal RNA genes and production of rRNA (ribosomes) o. Located on satellite stalks of acrocentric chromosomes ii. Acrocentric chromosomes are redundant because p arm is NOR p. Redundancy is good here q. Located on nucleoli formation in interphase r. Highly prone to rearrangement because short and redundant s. Have regions that are differentially methylated ***LO 5. Explain the role of the centromere and kinetochore in chromosome segregation with an emphasis on components required for function and the role of centromere positioning to chromosome segregation*** 1. Centromeres can be positioned in different regions of chromosome depending on type a. **Metacentric:** located in middle of chromosome b. **Submetacentric:** located closer to one end of chromosome (smaller p arm) c. **Acrocentric:** located near one end of chromosome (much shorter p arm) d. **Telocentric:** located at telomer i. Not normal and can result in loss of genetic material 2. Different degrees of problems can occur in segregation due to positioning effects of centromere e. Kinetochore builds off location of centromere ii. Harder to build kinetochore off integrity of genetic material when very little on one side f. Can have only one or too many centromeres that leads to improper segregation iii. **Dicentric:** two centromeres; if not attached to kinetochores properly, can have breakage iv. **Acentric:** cannot control segregation and will end up in daughter cells randomly ***LO 6. Connect the kinetochore, the processes of chromosome condensation, and centromere positioning with cellular regulation, kinase activity, and the Anaphase Promoting Complex from Block 1*** 1. In the structure made by the kinetochore landing on the centromere, more than 100 proteins are now known to participate in this complex structure a. Components of anaphase promoting complex are physically here 2. Heart of kinetochore is specialized nucleosome containing CENP-A 3. Part of kinetochore structure holds microtubule while other components are regulatory 4. Kinases and phosphatases play a role in regulating process regarding microtubule attachment b. **Aurora B kinase and CDK 1:** detach and reattach to correct spindles c. **Ndc80, Ska, and Knl1 complex:** holds onto microtubule 5. Erroneous cell division results in errors of segregation d. Erroneous attachments are eliminated by poorly understood mechanism that relates to tension on kinetochore and activity of Aurora B kinase and chromosome oscillation 6. Inappropriate attachment of kinetochores is different from separation checkpoint ***LO 7. Assess the consequences for the chromosome or cell particularly in terms of chromosome integrity of DNA repair induction following changes in length, availability, or activity of telomere/telomerase associated proteins, activity, or function of telomerase*** 1. **Cap:** forms when telomeres with their associated proteins loop in on themselves to protect the ends of chromosomes 2. **Capping:** G strand overhang folds back and invades dsDNA forming T and D loops a. **G strand overhang:** 3' overhang that has enough reactivity to loop back around b. Two main associated proteins i. **TRF 1:** telomere repeat binding factor 1; functions in length regulation ii. **TRF 2:** telomere repeat binding factor 2; functions in protective end cap 3. If there is a loss of capping, there is reduced chromosome integrity c. Loss of buffer leads to loss of genes leads to change in regions of heterochromatin d. **Senescence at G1:** triggered by critically short telomere and DNA repair 4. **Telomerase:** enzyme that maintains telomere length e. It's only one enzyme that is so critical to the integrity of DNA that, if lost, would result in many disorders f. Activated in more than 90% of cancers ***LO 8. Evaluate the process of telomerase-mediated elongation of telomeres and explain the role of telomere associated proteins in telomere maintenance and/or telomerase activity*** 1. **Telomerase:** enzyme that maintains telomere length a. Increases cell lifespan by making telomeres longer in cell population that needs to be maintained long term b. Combats end of replication problem c. Has two main components i. **Reverse Transcriptase Protein Subunit (hTERT):** RNA base that makes DNA ii. **RNA component (hTR/hTERC**): human telomerase template RNA d. Associates with approximately 39 proteins ***LO 9. Explain how chromosome abnormalities are named and identify the proper designation for a given change*** 1. *Be able to identify the specific change from a summary karyotype* a. **Nomenclature:** International standard for chromosome designations and conversations i. Map to say what happened, what's different, and how the arrangement has changed the phenotype b. **Telomere classification** ii. Metacentric 1. Large = 1 to 3 2. Short = 3 and 4 iii. Submetacentric 3. Large = 4 and 5 4. Medium = 6 to 12 and X 5. Short = 16 to 18 iv. Acrocentric 6. Medium = 13 to 15 7. Short = 21, 22, and Y c. Banding resolutions and patterns vary depending on method v. **First Number:** arms are divided into regions vi. **Second Number:** regions are divided into bands 8. **Bands:** \~ 5-10 Mb of DNA that show staining patterns 9. Gene content in bands is variable and represents functionality vii. Final reports must state the level of banding resolution and method due to variability in both 10. **Resolution:** how well we see bands d. Ex: 7q34 viii. Chromosome 7, arm q, has three regions and four bands e. **G-Banding:** traditional ix. **Giemsa:** stain that helps differentiate between heterochromatin and euchromatin x. How we stain gives us different information because each stain has a different technique f. In karyotyping, there are two main rules to remember xi. Sex chromosome abnormalities are listed before autosomal with X and Y xii. Then autosomal is listed in numerical order xiii. Any other rules are for increasing specificity g. Abbreviations we should know xiv. **Del:** deltetion or loss of chromosome material (terminal or interstitial) 11. Most likely clinically xv. **Dup:** duplication xvi. **Inv:** inversion (peri or pera) 12. Effect meiotic consequence xvii. **R:** ring chromosome 13. Lack end caps xviii. **Rec:** recombinant chromosome due to meiotic crossing over 14. Effect meiotic consequence xix. **T:** balanced translocation h. Short system rules are retained in the detailed system xx. Exception: an abbreviated description of band composition starting at pter and progresses to qter replaces breakpoints within the last parantheses 15. Bands are identified in order of occurrence within the derivative chromosome 16. Single colon = break 17. Double colon = breakage and reunion 18. Arrow indicates from, to i. Determining when to use short system rules is based on whether short is sufficient to visualize it j. Nomenclature is evolving and updating regularly 2. *Be able to write the summary karyotypes for a given specific change (or normal human karyotype) or identify the specific change (or normal expectation) from the karyotype summary provided* k. Will practice in class Mitosis, Errors in Chromosome Segregation, and Aneuploidies ***LO 1. Define the following terms*** 1. **Nondisjunction:** inappropriate chromosome segregation a. Can occur in meiosis and mitosis, but with different consequences for the organism i. Results in mitosis depend on tissue specificity (can be nearly all tissues if it occurs early enough in development) 1. Impacts the cell population after it ii. Results in meiosis depends on full organism/creation of errors in offspring unless corrections during embryogenesis mitoses 2. Impacts everything 2. **Aneuploidy:** inappropriate chromosome numbers b. **Aneuploid:** individual/cell with unbalanced chromosome content c. Mostly maternal d. Severity of autosomal aneuploid correlates with gene content of chromosome iii. The more significant the gene content, the more severe the phenotype iv. It's not about how much is lost; it's about what is lost e. The severity of the abnormality is directly connected to the probability that cell line will undergo cell death and be removed f. Aneuploidies for chromosome rich in genes (particularly structural genes) are less likely to survive (embryonic lethal or even prevented from implantation) g. As diploid species, we should have two copies of genes h. There is a direct correlation between the timing of an event and the fraction of cells exhibiting aneuploidy v. Early events mean aneuploidy will affect more tissues and have a broader impact phenotypically 3. **Euploidy:** chromosome content is abnormal, but balanced i. Everything that's supposed to be there is present 4. **Trisomy:** three copies of corresponding chromosome (one is extra) j. Trisomies for all autosomes have been reported in products of conception from spontaneous pregnancy losses k. Observed frequencies varies vi. **Trisomy 1:** spontaneous pregnancy losses though no fetal pole had developed vii. **Trisomy 16:** \~30% of all spontaneous pregnancy losses l. In live births, trisomies other than 13, 18, and 21 are rare and only mosaic 5. **Monosomy:** one copy of corresponding chromosome (one is missing) m. Rare in both spontaneous losses and live births, implying lethality before sufficient tissue is present for analysis n. **Turner Syndrome:** sex chromosome monosomy that is the sole exception for adult viability 6. **Chimerism/Chimera:** merging of two different cell types that are derived from two separate and external sources 7. **Mosaicism/Mosaic:** two or more complements in a cell with different genetic material that occurs because of failure to segregate properly 8. **Uniparental Disomy:** two copies of chromosome received from one parent 9. **Isodisomy:** both chromosomes from uniparental disomy are identical o. Both from grandma 10. **Heterodisomy:** both chromosomes from uniparental disomy are different p. One from grandma, one from grandpa ***LO 2. Summarize the mechanisms of maternal meiotic nondisjunction and mitotic nondisjunction*** 1. Mechanisms for Meiosis I Nondisjunction: a. **Both homologous chromosomes to one pole** i. Homologous chromosomes don't separate b. **Premature separation of one of the homologous chromosomes** ii. Separase is active and breaks down cohesin prematurely iii. More common 2. **Mechanisms of Mitotic Nondisjunction:** failure to split sister chromatids or failure to capture properly and have multiple outcomes c. Can result is too much or too little genetic content at the end of every division iv. Ratios of 3:1 or 4:0 d. Detection requires analysis of more than one tissue type e. First few mitoses are particularly vulnerable because they're fast and bypass the importance of elongated G1 phase v. Possible for more than one mitotic error and thus more than one unique aneuploidy cell line to develop (rare) vi. This does not always give us a bad outcome become because the good cells out-compete the bad ones f. In mitotic error, one cell has more material, and one has less vii. The one with more is more competitive while the one with less is less competitive ***LO 3. Compare and contrast consequences of mitotic and meiotic nondisjunction in terms of organismal structures, function, and mechanisms of action*** 1. Inappropriate chromosome numbers are most derived from inappropriate chromosome segregation 2. **Nondisjunction of maternal meiosis I:** a. **Exception:** chromosomes 7, 13, and 18 i. 13 shows equal number of maternal meiosis I and II errors 3. **Production Line Hypothesis:** maturation of oocytes occurs in the same order as original development in fetal life b. The first oocyte has been sitting there for a while and doesn't do what it should later c. All cells that will be oocytes are predetermined d. Not a good, full picture so next model was created 4. **Limited Oocyte Pool Model:** number of follicles in antral state degreases with increasing age e. Fewer number of follicles equals increase in probability that a lower quality one will be chosen f. The best oocytes are picked first, but the number to choose from decreases later, and you need to use the not-as-good ones g. Incomplete model because there are earlier risks (ex: environmental) 5. With the hypothesis and model, the main takeaway is that **with age, nondisjunction increases (increased errors)** ***LO 4. Explain the role of mosaicism in perpetuation of chromosomal abnormalities and aneuploidies and compare the different types of mosaicism (CPM and fetal with and without placental involvement)*** 1. **Mosaicism:** two or more complements in a cell with different genetic material that occurs because of failure to segregate properly a. Levels vary because bad cells outcompete the healthy cells since they can divide at different rates b. **Segmental Mosaicism:** when one portion of chromosome is affected, rather than the whole chromosome i. **Confined Placental Mosaicism:** chromosomal abnormality in the fetus, but not in the placenta ii. **Fetal Mosaicism (with and without normal placenta):** chromosomal abnormality in the fetus iii. Testing is done in early stages by chorionic villi sampling to analyze cells of placenta 2. Does not need to be orderly or organized 3. Structural rearrangement mosaicism is rare because it can involve two lines of opposite imbalance 4. Gonadal Mosaicism is common but not frequently evaluated c. There is evidence that all women may be gonadal mosaic for chromosome 21 aneuploidies 5. Change in development versus maturation results in tissue specific mosaicism 6. There can be different dermatological patterns based on how cells migrate ***LO 5. Explain the differences between chimerism and mosaicism*** 1. **Chimerism:** merging of two different cell types that are derived from two separate and external sources a. Includes individuals with cells from two separate fertilized eggs and post-zygote fusion of dizygotic twin zygotes b. A fusion or absorption event c. **Confined Chimerism:** only specific tissue possesses the two unique cell lines/populations d. Explains the presence of two cell lines in a single individual where no apparent error is observed i. Someone phenotypically different can appear normal e. Most likely underlying mechanism for hermaphroditism (46 X,Y/46,XX) and a 45,X/69,XXY fetus identified f. Explains diploid and triploid mosaics (though dispermy may also be a cause) 2. This is different from mosaicism because mosaicism is two different cell types from within the organism while chimerism is the merging of external sources ***LO 6. Explain how chromosome segregation can result in chromosome abnormalities during mitosis*** 1. Errors in meiosis (gametogenesis) a. Monosomies b. Trisomies c. Sex chromosome aneuploidies 2. Errors in mitosis leading to mosaicism d. Can include rescue of trisomic cell (with or without UPD) e. Chimerism 3. Errors in fertilization f. Triploidy g. All chromosomes from one parent h. Partial and complete moral pregnancies 4. Structural abnormalities and rearrangements ***LO 7. Explain how uniparental disomy can lead to phenotypic consequences and disease manifestation with emphasis on differentially methylated regions and compare whole chromosome UPD with segmental UPD in terms of these consequences*** 1. Each autosome is intended to be inherited with one copy from the maternal parent and one copy from the paternal parent 2. **Uniparental Disomy:** both copies are derived from a single parent a. Two copies of the chromosomes or region of chromosome from maternal source or paternal source exclusively b. Can result in homozygosity for autosomal recessive genes c. **Isodisomy:** both chromosomes from uniparental disomy are identical i. Both from grandma d. **Heterodisomy:** both chromosomes from uniparental disomy are different ii. One from grandma and one from grandpa 3. Most UPD appear without any phenotypic consequence but can have significant implications in differentially methylated regions 4. Most common clinical conditions of uniparental disomy are deletions e. One gene from the mother or father was deleted while the other one shut it off, so then there's zero copies 5. **Segmental UPD:** UPD of only parts of a chromosome instead of the entire chromosome f. Greatest consequences observed for chromosomes subject to imprinting g. Can impact specific tissues and exhibit mosaicism h. Mechanisms: iii. Postzygotic somatic recombination between maternal and paternal homologs iv. Meiotic nondisjunction producing a disomic gamete followed by a trisomic conception with crossing over between maternal and paternal homologs and chromosome loss v. Repair of double strand break via break-induced replication ***LO 8. List the main mechanisms of whole chromosome UPD and explain how UPD can develop*** 1. Each UPD mechanism requires two separate abnormal events a. Error (meiotic or mitotic) i. Almost always sporadic with no increased risk of recurrency in a family if parents are normal b. Attempt to correct error 2. Root cause is nondisjunction always 3. Four mechanisms that affect whole chromosomes c. Gametic Complementation: not well understood d. Monosomic Rescue e. Trisomic Rescue (most UPD) f. Mitotic Error and Rescue 4. Trisomic rescue and mitotic error and rescue are both cases where there were too many chromosomes, and one was given up g. If the wrong one is given up, the result is UPD ***LO 9. Compare and contrast trisomy 21, 18, 13, 16, Turner and Klinefelter syndromes in terms of causes, phenotypic consequences, and viability*** 1. **Trisomy 21:** three copies of chromosome 21 a. 47, XY, +21 or 47, XX, +21 b. Partial trisomies are also clinically relevant and fit the classification c. Most common trisomy in viable offspring d. Presents as flattened nose and face, upward slanting eyes, single palmar crease, short fifth finger that curves inward, widely separated first and second toes, and increased skin creases e. Most common single known cause of intellectual disability f. Increased ratio of males to females i. Preferential segregation of extra 21 with Y ii. Selection against female trisomy 21 fetuses in utero must also exist g. Associated with heart defects h. Critical region: 3 Mb at 21q22 i. Example genes: MX1 (morphological features) and RCAN1 (linked to heart) 2. **Trisomy 18/Edwards Syndrome:** three copies of chromosome 18 j. 47, XY +18 or 47, XX +18 k. More females than males l. Viability is variable with significant losses in utero or within the first days of life iii. Mosaicism is more viable option m. 90% exhibit congenital heart defects n. Presents as small mouth, short neck, shield chest, short and prominent sternum, wide set nipples, prominent back of skull, malformed ears, clenched hands with overlapping fingers, flexed big toe, and prominent heels 3. **Trisomy 13:** three copies of chromosome 13 o. 47, XY, +13 or 47, XX, +13 p. Slightly more common in females q. Acknowledged recurrence risk for future pregnancies of approx. 1% r. Variable consequences though 80% will not survive past the first month of life iv. More positive outcomes in mosaic form s. Presents as small head, absent eyebrows, cleft lip and palate, malformed ears, clenched hands, extra fingers, and abnormal testes 4. **Trisomy 16:** embryonically lethal (30% early pregnancy loss) t. Only survival forms of alterations are mosaicism, partial trisomy, UPD, and partial deletions u. If mosaic trisomy baby is born healthy, outlook for survival past newborn is better than if any health issues are observed v. Clinical features: 35.7 weeks of gestational age and smaller than average birth weight v. Other features can include cardiac malformations, hypospadias, and pulmonary hypoplasia 5. **Turner Syndrome:** missing all or part of the second X chromosome w. 45, X x. Most viable human monosomy y. In infant, presents as swollen hands and feet, and wide and webbed neck z. In older females, presents as absent or incomplete development at puberty, including sparks pubic hair and small breasts and short height a. Ways to get to Turner Syndrome: vi. Mosaicism modifies phenotypic features 1. 45,X/46,XY: ranges in physical appearance and associated Y is structurally abnormal 2. 45,X/47,XXX: more mildly affected in terms of clinical phenotype vii. Isochromosome X 3. Two copies of long arm, observed in mosaicism, and phenotypically distinguishable from pure 45,X karyotypes viii. Ring X 4. Mosaic with varying size 5. Lacks classic somatic features and can have several phenotypes 6. Severe phenotypes associated with lack of XIST and failures in activation 7. Have tissue limited expression 6. **Klinefelter Syndrome:** one or more additional copies of all or part of the X chromosome in male cells b. 47, XXY c. Extra genetic material on X negatively impacts development of male sexual characteristics (reduces testosterone) ix. Amount of additional X as it relates to gene content and types of genes correlate with severity of phenotype d. Delayed or reduced puberty due to loss of testosterone e. Some cognitive impairment ***LO 10. Explain why there is variable viability across autosomal and sex chromosome aneuploidies*** 1. Viability is listed within each disorder Chromosomal Structural Abnormalities and Rearrangements Introduction ***LO 1. Define the following terms:*** 1. **Acentric:** chromosomes without centromeres a. Rapidly lost and not really observed in karyotypes b. Unable to control how material is passed to daughter cell 2. **Dicentric:** presence of two centromeres c. Can form a structural rearrangement or form a process that results in structural rearrangement d. Major issue in chromosome segregation e. Closely packed centromeres can act as a single centromere and negate the effects (so close, they're functionally one single chromosome) 3. **Neocentromere:** centromeres generated via changes to nucleosome associated f. Sometimes function as actual centromeres and can generate kinetochores g. Can make broken material get a centromere 4. **Pseudodicentric:** two centromeres on chromosome where one is active, and one is inactive 5. **Chromosome Breakage/Straddling Limbo:** occurs when opposite poles attach and can lead to the exclusion of chromosomes from both cells 6. **Regions of Homology:** areas of architectural similarity in 3D architecture 7. **Interchromosomal Recombination:** recombination across homologous chromosome 8. **Intrachromosomal Recombination:** recombination within or between sister chromatids 9. **Nonallelic Recombination:** different loci that are not alleles, but have some similarity on homologous or nonhomologous chromosomes are exchanged h. Exchange occurs with two versions of the same gene ending up together 10. **Haploinsufficiency:** loss of one copy with the remaining copy not enough to maintain full function i. Ex: males are hemizygous (XY) so loss of one sex chromosome would be loss of both 11. **Pseudodominance:** appearance of recessive trait/phenotype in pedigree due to loss of dominant allele j. Showing recessive version because dominant is missing (possible due to structural rearrangement) so recessive is expressed k. Ex: 50% of pigment appears different than 100% of pigment ***LO 2. Explain how rearrangements are possible, what features contribute to rearrangements, and how the size of the rearrarrangment/amount of genetic content correlates with viability and phenotype*** 1. There are areas of chromosomes that are more prone to breakage and rearrangement due to underlying chromosome structure 2. Some rearrangements are benign while some are considered expected population variation 3. All structural rearrangements involve breakage to some extent a. The more complex the rearrangement, the more breaks that occur 4. Structural rearrangements can occur when exchanges between nonallelic chromosome regions take place b. Most are paternally derived although they can also inhibit sperm function i. Exception: maternally inherited rearrangement 5. Many recurring and some sporadic rearrangements occur secondary to nonallelic recombination due to regions of homology c. Majority of regions of homology involved low copy repeats (non-gene coding) d. High copy repeats (gene coding) can also be involved in rearrangements ii. Alu-mediated recombination (role of SINEs) iii. Alpha satellite recombination and centromeric fusions (short arms of acrocentric chromosomes) 6. Size and type of rearrangement correlate with: e. Location (one arm can be more prone to synapse than a part of it) f. Size (if small, it may not be able to synapse) g. Orientation (ABC vs CBA) h. Number of crossings over events between the low copy repeats 7. Other chromosome architecture that contributes to rearrangement: i. Sequences capable of forming a particular secondary DNA structure (Hairpin or cruciform-shaped) j. Areas susceptible to double strand breaks (DNA is already at risk) iv. AT rich palindromic sequences, topoisomerase II cleavage sites, DNase I sensitive sites, scaffold rearrangement portions, expanded trinucleotide repeat regions 8. Chromosomes exist in 3D space so they can take on complicated structures and orientations k. Expected/normal recombination occurs at same loci/alleles and can be interchromosomal and/or intrachromosomal 9. Some rearrangements can result in loss of genetic information l. Lose gene activity or transcription resulting in the loss of products that were supposed to be created by the absent genes m. Lose function or protein level activity if product doesn't work as it should 10. Some rearrangements can result in gain of genetic information n. Gain gene activity or transcription resulting in increased amount of product o. Gain function or protein level activity if product is always on ***LO 3. List the types of rearrangement that can occur and explain how they both occur and contribute to final chromosome architecture*** 1. Unexpected or abnormal recombination are nonallelic recombination events a. Abnormal exchanges occur between different loci i. In homologous chromosomes, it would occur from altered alignment so that loci/alleles are not exchanged evenly ii. In sister chromatids, it would occur within one single chromatid or across chromatids unevenly iii. In nonhomologous chromosomes, it would occur from inappropriate recombination (not supposed to exchange at all) 2. Five types of rearrangement from recombination b. **Direct Repeats and Homologues Recombine:** altered alignment so alleles are not exchanged evenly, resulting in short chromosomes and missing genes c. **Direct Repeats and Sister Chromatids Recombine:** results in exchanging within self incorrectly d. **Direct Repeats with Intrachromatid Recombination:** arm loops in on itself, generated acentric ring material e. **Inverted Repeats with Intrachromatid Recombination:** change order of material with no loss or gain in material f. **Direct Repeats and Nonhomologous Chromosomes Recombine:** creates derivative chromosomes from aligning when not supposed to 3. Five general categories of structural rearrangement g. Deletion (often paired with duplication so one is lost, and one is gained) h. Duplication (often paired with duplication so one is lost, and one is gained) i. Inversion j. Insertion (changes orientation) k. Translocation (combination of inversion and insertion) ***LO 4. Compare and contrast balanced and unbalanced rearrangements in terms of phenotypic consequences*** 1. **Balanced Rearrangements:** no net loss or gain of genetic information; can have phenotype but also might not a. Phenotypically normal with positional effects leading to any observable phenotype (downstream expression change) b. Have two of everything you're supposed to have two of 2. **Unbalanced Rearrangements:** additional and/or missing material that has a clinical effect (degree dependent on amount gained or lost) c. The more apparent the change, the more likely it is to be detected d. Most commonly deletions i. Deletions almost always change phenotype e. Molecular cytogenetic techniques are essential to diagnostic process ***LO 5. Compare and contrast de novo and familial rearrangement in terms of inheritance and phenotypic consequences*** 1. **De Novo Rearrangement:** can be parental derive or not but is observed newly in patient (no family member before them had it) 2. **Familial Rearrangement:** many generations affected by it a. If balanced, rearrangement can go generations without detection i. Associated with high incidence of infertility and multiple spontaneous pregnancy losses ii. Can have some family members with abnormal phenotypes b. Often unique/family specific (rare exceptions) 3. Risk for abnormal phenotype is higher for an individual with apparently balanced de novo rearrangements than for individual who has inherited a similar rearrangement from parent Deletions and Duplications ***LO 6. Define the following terms:*** 1. **Deletion:** the loss of genetic material (most common observed in viable offspring) a. Can be partial aneuploidies, segmental aneusomies, or contiguous gene disorders b. Losses or gains of material have the potential to affect adjacent material c. Small size deletions can follow Mendelian inheritance (larger dels deviate more) d. Most are de novo e. Have considerations for expressivity and penetrance (if a phenotype is present and to what degree) f. Gonadal mosaicism in parent is possible as is dynamic mosaicism from postzygotic mitoses i. **Dynamic Mosaicism:** healthy cell types outcompete unhealthy cell types 2. **Terminal Deletion:** deletion at the ends of chromosomes that results in loss of downstream material (no discernable material beyond site of breakage) except for telomere g. Telomere is retained (by telomere capture) or a new telomere is required (by telomerase) h. Only one break point 3. **Interstitial Deletion:** two break points (proximal and distal) after missing material followed by continuation of normal chromosome banding pattern 4. **Duplication:** presence of an extra copy of a genomic segment (also called a partial trisomy) i. Pure duplication means there are no other imbalances j. Can occur in combination with other rearrangements k. Gene content does not need to be in tandem to be duplicated, but it is the most common l. Phenotypes of duplications are less severe than deletions (losing material is worse than gaining it) 5. **Tandem Repeats:** continuous doubling of a segment m. **Direct Tandem Duplication:** have same orientation as original (most common) n. **Inverted Tandem Duplication:** have opposite orientation as original ***LO 7. Modified Aim 2: explain the unique features of dels and dups, how dels/dups can be generated and how size of the del or dup correlates with presence of a phenotype and/or the severity of the phenotype*** 1. Deletions and duplications are often grouped together because the loss of genetic material must be gained by something else (except when lost to repair error) ***LO 8. Explain how deletions and duplications can be paired rearrangements and how they can both be found in the same individual*** 1. Postzygotic mitoses can generate del/dup paired mosaics a. If the rearrangement occurs in the initial division, all cells will be dels or dups that are complementary (50/50) b. If the rearrangement occurs later in the division, there is potential for normal cell lines to be present (fewer places are impacted) c. Cell lines of lesser viability (less competitive) may be lost i. Potential for dynamic mosaicism and growth restriction (cell division is impacted so growth in terms of increase in cell size or number is impacted) 2. Duplications have the potential to have the opposite phenotype of their deletion counterparts d. Absence of genetic material from deletion results in excess duplication of that material from its counterpart ***LO 9. Explain the meiotic consequences of deletions and duplications*** 1. In subsequent meioses in individuals with deletions and duplications, loops form to maximize alignment a. Looping is done to prevent further rearrangement, unless rearrangement itself becomes rearranged i. Then one will continue to elongate and the other will continue to lose material ***LO 10. Identify the genes involved in the following deletion syndromes and link the syndrome to the expected phenotypic outcomes:*** 1. **Williams Syndrome:** microdeletion (small deletion at chromosome level) a. \~1.5 Mb deletion within the proximal long arm of chromosome 7 i. Impacts \~30 known and predicted genes 1. Includes ELN (elastic gene implicated in cardiovascular abnormalities) and LIMK1 (impacts cognitive features) b. Low copy repeats sequences contribute to chromosome breakage like unequal cross over/recombination which leads to deletion ii. Recurrence in a family c. Heterozygosity for an inversion that spans LCR region also contributes d. Absolute risk is low (1 in 7500/10000) e. Strengths are spoken language, music, and rote memorization f. Difficulties with visual spatial acuity (makes you love everyone) g. Distinct facial features including broad forehead, short nose, full cheeks, and wide mouth 2. The three genes associated with Prader-Willi syndrome and Angelman syndrome only need one functional copy h. In normal maternal imprinting, SNRPN and NDN are shut off while UBE3A is on iii. Loss of maternal copy of chromosome means full loss of UBE3A i. In paternal imprinting, UBE3A is off while SNRPN and NDN are active iv. Loss of paternal copy of chromosome means full loss of SNRPN and NDN 3. **Prader-Willi Syndrome:** loss of 15q11-13 from paternal source results in expression of UBE3A and loss of SNRPN and NDN j. Presents as hypotonia, obesity, and hypogonadism 4. **Angelman Syndrome:** loss of 15q11-13 from maternal source results in expression of SNRPN and NDN and loss of UBE3A k. Presents as developmental and intellectual deficiencies, epilepsy, and tremors 5. Prader-Willi and Angelman are companions because they both deal with imprinting l. **Imprinting:** to ensure expression of gene, mom or dad shuts their copy off (turns things off) 6. Deletion is not the same as imprinting m. Deletion in Prader-Willi and Angelman is more common because a gene is lost entirely Inversions ***LO 11. Define the following:*** 1. **Inversions:** intrachromosomal rearrangements where two breakpoints exist and the material between the breakpoints reverses orientations a. Everything is there, it's just in the wrong order (no loss/gain) b. Presence is indicated by alteration of typical banding pattern c. Consequences are based on where material is (positional effect) i. There are parts of non-coding genome needed to maintain structure so if they are moved away from the things that control it, those parts cannot function d. Balanced inversions are phenotypically normal, but still have three possibilities with preferential breakpoints: ii. Positional effects in viable offspring are limited (like X chromosome) but are possible (change in promoter or regulatory elements, etc.) iii. Pathogenic effects from breakdown within a gene (no expression) iv. Breakpoints within regulatory elements for key genes can result in altered phenotypic outcomes (like functional haploinsufficiency) e. Can be normal variants rather than abnormal chromosomes (inversions in chromosomes 1, 9, 16, and Y with breakpoints in heterochromatin) 2. **Asynapsis:** inability in homologous chromosomes to pair in meiosis (parts of chromosomes don't synapse) f. Balloons out 3. **Homosynapsis:** all parts of chromosome match 4. **Heterosynapsis:** parts of chromosomes match and parts don't g. Appear to lie adjacent but unmatched ***LO 12. Compare and contrast pericentric and paracentric inversions*** 1. **Pericentric Inversions:** two breakpoints on either side of the centromere that changes chromosome arm ratio a. Centromere is surrounded by protective heterochromatin so if the closer information to the centromere is affected, there will be problems b. Leads to duplications/deletions 2. **Paracentric Inversions:** two breakpoints on same side of centromere so only one arm is affected, and centromere position is not affected c. leads to changes in architecture ***LO 13. Diagram and explain the meiotic pairing and consequences for pericentric inversions*** 1. There are effects based on location of breakpoints in the type of synapsis a. Complications for acrocentric chromosomes i. Relocation of NOR (on short arm) to long arm b. Recombination results in formation of recombinant chromosomes ii. Relationships between size of inversion and likelihood of recombination (evidence from evaluation of spermatogenesis) with some specific exceptions observed iii. Larger inversions are more likely to recombine/inappropriately synapse 2. Altered configuration for the bivalent: homologous chromosomes align because of regions of homology and rearrangement, resulting in a loop ensuring that every part that matches lines up c. Reversed loop model with homosynapsis iv. Complementary recombinant chromosomes v. Partial trisomy for one distant and partial monosomy for the other or vice versa 1. Typically, only one (least monosomic is viable) d. Shorter segments may only exhibit partial pairing (no loop) vi. Asynapse or heterosynapse 2. No crossing over within inverted segment under these conditions vii. Only inversion undergoes synapsis (leads to further complications) 3. Recombination within the segment is possible a. Size matters because larger segment can cause bigger loss/gain and get further rearrangement ***LO 14. Diagram and explain the meiotic pairing and consequences for paracentric inversions*** 1. Practically all paracentric inversions are identified incidentally and not due to birth of an abnormal child 2. Alignment in meiosis can involve a reverse loop a. This version will have the centromeres outside the loop i. Can cause massive changes that lead to dicentric and acentric chromosomes b. Crossing over occurs within loop ii. In theory, odd number of crossings over events result in one dicentric (from stress that breaks it) and one acentric chromosome (from inability to separate properly) 1. Almost always lethal due to errors in meiosis that result iii. Monocentric recombinants have been observed in offspring of paracentric inversion carriers 2. Additional meiosis mechanisms are involved ***LO 15. Summarize the process through which dicentric and acentric chromosomes are generated*** 1. Crossing over occurs within loop a. In theory, odd number of crossings over events result in one dicentric chromosome and one acentric chromosome i. Almost always lethal due to errors in meiosis that result (inappropriate separation) b. Monocentric recombinants have been observed in offspring of paracentric inversion carriers ii. Additional meiosis mechanisms are involved Translocations ***LO 16. Define the following terms:*** 1. **Reciprocal Translocations:** two nonhomologous chromosomes exchange segment because it looks similar in some regions 2. **Balanced Carrier:** phenotypically normal chromosomes with increased risk of offspring with unbalanced karyotypes 3. **Heterozygous Translocation:** only one pair of nonhomologous chromosomes is affected a. At risk of having children with chromosomal imbalances/aneuploidy i. Carriers may have high miscarriage rate 4. **Homozygous Translocation:** both pairs of chromosomes are affected 5. **Derivative Chromosome:** rearranged chromosome that is identified based on the centromere b. Can be de novo or observed in a family going back generation 6. **Whole Arm Translocation:** breakpoints within a near/at centromere c. Moves whole arm d. P arms are short and prone to breakage or getting lost, so the q arm gets fused 7. **Robertsonian Translocation:** long arms of any two acrocentric chromosomes join to produce a single metacentric or submetacentric chromosome 8. **Quadrivalent:** four chromosomes in their duplicated form aligning and exchanging information ***LO 17. Compare and contrast reciprocal and Robertsonian Translocations and explain the difference in phenotypes expected/phenotypic considerations when they are completely autosomal vs when sex chromosome are involved*** 1. **Reciprocal Translocations:** two nonhomologous chromosomes exchange segment because it looks similar in some regions a. Nonallelic recombination b. If nonhomologous chromosomes stay together and have the right information (just in the wrong spot), they will be balanced carriers i. If they must separate, there will be a problem ii. May affect one or both chromosome copies or pairs 2. **Robertsonian Translocations:** long arms of any two acrocentric chromosomes join to produce a single metacentric or submetacentric chromosome c. All 5 acrocentric chromosomes (13, 14, 15, 21, 22) are capable of fusion events d. The close association of NORs within the nucleus may promote the formation of these locations e. **Nonhomologous Robertsonian Translocations:** long arms of any two acrocentric nonhomologous chromosomes join to produce a single metacentric or submetacentric chromosome iii. Approx. 95% (13,14 are 75% and 14, 21 are 10%) iv. Occur during oogenesis predominantly v. Most are dicentric resulting in nonrandom suppression of one centromere or both functioning together as one f. Location of breakpoint determines the type of translocation formed g. **Homologous Robertsonian Translocation:** a whole arm exchange between homologous chromosomes vi. Rare vii. May be misclassified "other" rearrangement h. Three mechanisms: viii. Unions following breaks in both short arms causing dicentric chromosome to form 1. Most common ix. Centric fusion 2. Rare x. Union following breakage in one short arm and one long arm 3. Rare i. Inheritance risk correlates with losses of gains in genetic material as well as imprinting risks xi. Because each chromosome has differently methylated regions 3. Sex chromosomes can exhibit translocations with autosomes, the other sex chromosome, or even with a homolog j. Leads to silencing of the other X or deletion if shut off 5. Must consider silencing/imprinting when considering translocations involving X h. Can mitigate or exacerbate the phenotypic outcomes 7. Frequent outcomes for translocations involving X and Y area infertility and embryonic lethality f. All de novo X autosome translocations studied thus far have been paternal in origin ***LO 18. Compare and contrast alternate, adjacent-1, and adjacent-2 segregation patterns*** 1. The quadrivalent can align and segregate in three possible segregation patterns a. **2:2 Segregation:** each daughter cell gets two of the four chromosomes involved in the quadrivalent i. Homologous chromosomes go separate in alternating patterns to give two normal, balanced cells ii. Most frequent for children of translocation heterozygotes iii. Includes alternate, adjacent-1, and adjacent 2 b. **3:1 Segregation:** demonstrates that devastations of monosomies as interchange monosomies are only ever seen at pre-implantation genetic diagnosis iv. Having varying outcomes but frequently involve trisomies and monosomies v. Can happen in all combinations but is less likely because it would involve many events c. **4:0 Segregation:** may only be of little consideration in preimplantation genetic diagnosis vi. Way too much information in one cell and none in the other 2. **Adjacent-1 Segregation:** homologous centromeres separate at anaphase I d. Gametes contain duplications and deletions e. Gets closest to dicentric state (no full monosomy or trisomy) 3. **Adjacent-2 Segregation:** homologous centromeres stay together at anaphase I f. Gametes have a segment duplication and deletion 4. The difference between adjacent-1 and adjacent-2 is that, in adjacent-1, all gametes have some losses and some gains while in adjacent-2, every cell will have derivative chromosomes and there will be associated losses and gains 5. **Alternate Segregation:** half the gametes receive both parts of the reciprocal translocation, and the other half receive both normal chromosomes g. All gametes are euploid h. Normal genetic content, but half are translocation carriers vii. Phenotypes for balanced carrier come from positional effect i. Only possibility to have fully balanced chromosome ***LO 19. Determine the consequences for each segregation pattern on offspring and identify which can produce viable offspring from a given chromosomal rearrangement*** 1. In meiosis, there is potential to form quadrivalent a. The bigger the change (more genetic material exchanged), the greater the probability of forming the quadrivalent b. The exchange is not the problem; the alignment and segregation are the problem because it changes outcomes 2. Translocations result in potential for complicated alignments and crossing over events c. Further recombination can occur further reducing the likelihood of viability d. Autosome -- sex chromosome translocations are particularly problematic i. Not intended to align or exchange material ii. Concerns with X inactivation potentially resulting in inactivation of autosomal segments and genes 1. X inactivation exhibits preferential process designed to inactivate least problematic X in these conditions 2. If both X chromosomes have been translocated material, some autosomal material will be inactivated and some critical X material will not be 3. In spermatogenesis, alternate segregation prevalence is 44% and adjacent-1 prevalence is 31% (predominant forms and more favorable phenotype) e. Adjacent-2 segregation is 13%, 3:1 segregation is 11% and 4:0 segregation is rare (very unfavorable) 4. In oogenesis, data is more problematic and variable f. Likely exhibits age related effects complicating the analysis of meiotic outcomes 5. Acrocentric chromosomes exhibit different patterns due to marked asymmetry of the quadrivalent g. Fewer alternate segregants and more 3:1 have been observed 6. Viability correlates with genes involved and severity of information lost/gained h. Severe forms undergo spontaneous pregnancy loss, perhaps even prior to implantation i. Usually, sole survivable imbalance is partial trisomy j. Viable offspring outcomes: iii. 71% adjacent-1 iv. 4% adjacent-2 v. 22% tertiary trisomy/monosomy vi. 2.5% interchange trisomy Autosomal Heredity ***LO 1. Define the following terms:*** 1. **Gene:** unit of heredity made of DNA or RNA that encodes a coherent set of potentially overlapping functional product molecules (RNA or protein) that influence phenotype a. In other words, sequence of DNA that encodes product b. Measuring or evaluating influence of phenotype may not be possible with current technology c. Cause characteristics, traits (specific properties of character), and true breeding 2. **Allele:** variations or variants of a gene (alternate form) 3. **Locus:** specific position of a gene on a chromosome 4. **Genotype:** set of alleles possessed by an individual organism 5. **Phenotype:** appearance or manifestation of a characteristic 6. **True-Breeding:** version that continues to produce same trait after several generations of self-fertilization 7. **Heterozygote:** containing more than one type of allele for a given gene 8. **Homozygote:** containing only one type of allele for a given gene 9. **Parental Generation:** first set of parents crossed 10. **Filial 1:** first generation of offspring produced from cross fertilization by parents 11. **Filial 2:** offspring produced by self-fertilization of F1 generation 12. **Dominant:** version of a gene that is observed phenotypically in the heterozygous state d. Defining dominance requires multiple experience and an analysis of multiple generations (at least 3) e. Capital letters 13. **Recessive:** version of a gene that is only observed phenotypically in the homozygous state f. Lowercase letters 14. **Monohybrid Cross:** single factor cross where a single character is observed g. Requires more than one variant h. **Monohybrids:** single character hybrids produced from a cross between two parents with different variants i. Experimental design includes true breeding plants in parental generation, offspring from both parents as filial generation 1, and self-fertilization of filial generation 1 to get filial generation 2 j. Only works if parents are fully dominant and fully recessive (true breeding strain) 15. **Dihybrid Cross:** two heterozygotes for two traits are crossed k. Useful for demonstrating law of independent assortment l. Enables visualization of all potential phenotypes for traits being evaluated 16. **Back/Test Cross:** heterozygotes for two traits are crossed to homozygotes that are recessive for both traits 17. **Punnett Squares:** allow for quick and easy determination of outcomes of crosses m. Defines likelihood of obtaining particular outcome n. Hypothesis for genotypes and expected corresponding phenotypes i. Without experimentation, there is not way to determine definitively a genotype 18. **Mendelian Inheritance:** observation of traits in offspring that matches expectations based on Mendel's rules/principles o. **Principle of Segregation:** diploids have two alleles for a given character (paternal and maternal) that separate in formation of gametes, giving equal probability of passing on either in the gametes ii. In other words, homologous chromosomes segregate/separate iii. Mechanism: two copies of same gene separate as homologous chromosomes in meiosis, so each gamete receives one copy p. **Principle of Independent Assortment:** genes for different characteristics located on different loci assort independently iv. In other words, unlinked genes (genes on separate chromosomes) assort independently of one another v. Two limitations to the rule: 1. Only applies to genes on separate chromosomes 2. Genes in proximity on the same chromosome do not sort independently (linked genes) 19. **Nonmendelian Inheritance:** linked genes located on the same chromosomes are inherited together more frequently than unlinked genes, thus they do not follow independent assortment q. Recombination enables these genes to be absorbed differently than in parental generations r. Genes can be linked in cis (dominant forms together) or trans (dominant form with recessive form of other gene) 20. **Linked Genes:** genes in proximity on the same chromosome 21. **Probability** = number of times a particular outcome occurs/total number of possible outcomes s. Predict the likelihood of having an affected child t. W u. **Random Sampling Error:** deviation between observed and expected v. **Independent Outcomes:** outcome of one does not affect the probability of another 22. **Addition Rule:** the probability of obtaining one or the other of two mutually exclusive events is the sum of their individual probabilities w. Law of segregation 23. **Multiplication Rule:** the probability of two independent events occurring simultaneously equals the product of their individual probabilities x. Applies law of independent assortment ***LO 2. Determine the expected gamete outcomes following meiosis*** 1. IN OTHER OBJECTIVES ***LO 3. Determine the expected phenotypes and genotypes of a given cross*** 1. *Outline an example of Mendel's monohybrid crosses, the results obtained, and what they indicated* a. P Generation: purple flower petals and white flower petals cross fertilized b. F1: self-fertilization of purple flower petals c. F2: 3:1 ratio of purple flower petals to white flower petals d. Results: purple is dominant for flower petals and white flower petals can only be obtained when homozygous recessive 2. *Outline an example of Mendel's dihybrid crosses, the results obtained, and what they indicated* e. TtYy x ttyy f. If TY and ty are parentals, majority of offspring will be TtYy and ttyy while fewer will be Ttyy and ttYy g. If Ty and tY are parentals, majority of offspring will be Ttyy and ttYy while fewer are TtYy and ttyy 3. *Diagram and explain why a dihybrid cross yields a 9:3:3:1 ratio* h. It follows independent assortment 4. *Explain a testcross and the importance of including recessive parental genotypes in the cross* i. Used to reveal recombination and map chromosomes/gene locations j. To see unique phenotypes, must remove masking from dominant gene to see recessive ***LO 4. Assess the consequences for genotype and phenotype with parental and recombinant chromosomes with consideration of cis and trans arrangements*** 1. Gene linkage adds to complexity of outcomes 2. Parental chromosomes differ from recombinant chromosomes in literal gene content 3. Inheritance of a recombinant chromosome provides additional variation from parental phenotypes as new combinations of genes become possible 4. Although the same gametes are always possible, the ratios will change 5. In the production of gametes, linked genes are more likely to segregate together a. In the absence of recombination, they will be together causing specific set of phenotypes to be more common 6. When looking at gene linkage, we must consider phenotypes from two traits because it's the only way to determine where recombination occurred b. See separation from vs. inheritance within c. Some gametes are possible, but outcomes will not be equal ***LO 5. Calculate probabilities for a given scenario with emphasis on phenotypic outcomes*** 1. *Differentiate between and give examples of the application of both the addition and multiplication rules* a. **Addition Rule:** the probability of obtaining one or the other of two mutually exclusive events is the sum of their individual probabilities i. Probability of two or more mutually exclusive events is determined by adding the probability of each event ii. Ex: what is the probability of rolling a 3 or 4 on single roll of die? 1. Each roll is an independent event with equal chances 2. Each independent probability is therefore 1/6 so we add the independent probabilities together 3. 1/6 +1/6 = 2/6 or 1/3 b. **Multiplication Rule:** the probability of two independent events occurring simultaneously equals the product of their individual probabilities iii. The probability of two or more independent events taking place together is determined by multiplying their individual probabilities together iv. Ex: the probability of rolling a 4 on a single roll is 1/6, but what about rolling consecutive 4s on two rolls? 4. Brings together probabilities of two separate and independent events 5. Multiplication rule says multiple independent probabilities a. 1/6 x 1/6 = 1/36 c. When to use each rule: AND vs OR v. AND is multiplication rule 6. If multiple events that are independent or combine repeated events, that's AND 7. Ex: chances first male then female will be born b. AND c. Multiplication rule of the two individual probabilities vi. OR is addition rule 8. If only one option of two is possible in a question, that's OR 9. Ex: chances of male vs female being born d. OR e. Addition rule 1 out of 2 2. *Apply these rules as appropriate for specific scenarios to define where the organism will be phenotypically dominant or recessive* d. Addition Rule in punnett squares used when saying probabilities of getting phenotypes vii. Ex: Probability of WW or Ww = Probability of WW + Probability of Ww e. Multiplication Rule -- calculate individual probabilities then multiply them viii. Can be used to predict outcome of cross involving two or more genes ix. Ex: what is probability that first three children will exhibit recessive trait if both parents are heterozygotes? 10. Aa x Aa 11. What is probability of aa? 12. What is probability of aa happening 3 times f. Probability 1 x 2 x 3 x. Ex: given AaBbCC x AabbCc, what is probability offspring will be AAbbCC? 13. Probability of AA? 14. Probability of bb? 15. Probability of Cc? 16. P = pAA x pbb x pCc 3. *Understand the application of the binomial equation* f. **Binomial Experiment:** two mutually exclusive outcomes often referred to as success and failure xi. Ex: flipping a coin where success is heads and failure is tails xii. Probability of success is p and the probability of failure is 1-p xiii. Rate of success constant is 0.5 xiv. If probability of possibility A is p, probability of possibility B is q, then probability that in n trials, A is realized s times and B is realized t times is binomial equation Sex Linked Heredity ***LO 1. Define the following terms*** 1. **Homogametic:** has gametes with same sex chromosomes (female, XX) a. Females can only produce X gametes 2. **Heterogametic:** has gametes with different sex chromosomes (male, XY) b. Males can produce both male and female gametes 3. **Hemizygous:** containing only one copy of a chromosome that can be or is typically observed in a pair c. Males only have one X so a vast majority of material on X is single gene dosage) d. At risk for haploinsufficiency 4. **Haploinsufficiency:** loss of one copy results in a situation where the remaining copy cannot compensate and make sufficient product e. Reduced function is expected due to insufficient levels of product f. Creates phenotype from loss (changes on X in male are more likely to be visible) g. Genes exclusive to Y or X in humans are not haploinsufficient as proper gene dosage is 1 i. This is why some genes on X must be inactivated h. Ex: differently methylated regions in imprinting 5. **Nondisjunction:** failure to separate chromosomes properly i. Mostly female premature sister chromatid separation 6. **Genic Determination:** genes at one or more loci determine sex without specific sex chromosomes 7. **Environmental Determination:** environment is either partially or completely responsible for sex determination j. Organism has equal chance to be either sex but cannot be both at the same time 8. **Sexual Determination:** making the decision of picking testes or ovaries ***LO 2. Compare and contrast set chromosomes and sex determination across species*** 1. **Sex Chromosomes:** chromosomes that contain the genetic information necessary to confer biological sex and influence development of secondary sexual characteristics a. In sexual reproduction, differences between the two sexes are established by key genes often located on specific sex chromosomes b. Can vary across different organisms (have varying levels of involvement) c. Do not have to involve two distinct chromosome types in the pair d. When chromosome pairing involves one biological sex having fewer chromosomes, meiosis will result in gametes that have unequal chromosome numbers 2. **Sex Determination:** development of male or female reproductive organs e. Influenced genetically or environmentally f. Genes typically located on Y chromosome confer key proteins for defining the production of testes g. Loss of genes in XY individual will result in phenotypical development as female h. No structural default exists i. Phenotypic development as a female with functional ovaries in the absence of genes is not guaranteed thus there is no actual biological default sex as previously thought i. Presence of small portions of Y chromosomes in XX individuals has been shown to be sufficient to cause phenotypical male development implying only a small portion of the chromones is needed for sex determination ***LO 3. Explain the distinction between a homogametic and heterogametic individual in XX/XY and ZZ/ZW sex determination*** 1. Heterogametic sex is two different chromosomes while homogametic sex is two of the same chromosomes 2. In chickens, the male is ZZ and the female is ZW a. In most species, heterogametic sex is female ***LO 4. Assess the outcomes for a given mating under XX/XY and ZZ/ZW organisms in terms of biological sex expectations and features associated with or influenced by sex chromosomes*** 1. In humans, males are heterogametic 2. **Pseudo-autosomal Regions:** regions of homology for sex chromosomes that look the same on 3D architecture 3. Pseudo-autosomal Regions of X and Y can pair in meiosis and have crossing over a. These regions escape X inactivation ensuring proper gene dosage for those genes b. If X is inactive, there's loss of material in common regions c. X inactivation is incomplete i. Matters in Turner and Klinefelter Syndromes because the phenotypic changes occur from parts of X not being inactivated (this is haploinsufficiency) ***LO 5. Evaluate the consequences of changes in genes, environment, and sex chromosome content for sex determination and development of secondary sexual characteristics*** 1. While biological sex is frequently determined by genes, the location of those genes can vary especially if there are no sex chromosomes a. No visible difference in the chromosomes of males and females 2. The environment plays a role in sex determination b. Ex: slipper limpets have sequential hermaphroditism (switch between sexes based on environment) c. Ex: reptiles have temperature-based sex determination (results in varied ratio of males to females) i. Turtles: warm temp for females, cold temp for males ii. Alligators: cold temp for females, warm temp for males iii. Bearded Dragon Lizards: environment influences phenotype rather than genotype 1. ZZ is male except when embryo is incubated at high temp, then ZZ is phenotypically female even though genotypical male iv. Crocodiles: sex determination is more complex because they need a test temperature of 32-33 degrees C to be males (any other temp is females) 2. Overabundance in one sex means there's a change in the ability to reproduce 3. Increased global temperatures for sex determination based on temperature is altering the ratio of females to males and disrupting reproductive potential ***LO 6. Compare and contrast the X and Y chromosome*** 1. **SRY:** gene on Y chromosome that confers testes development a. Acts a transcription factor to turn on genes associated with male sexual development b. Activation of gene occurs at roughly six weeks development c. Located near pseudo-autosomal region d. Once triggered, testes begin to form and secrete i. Testosterone promotes development of male characteristics ii. Mullerian Inhibitory Substances (MIS) suppresses female reproductive ducts 2. Prior to activation of key genes, gonads are undifferentiated e. In absence of SRY, ovaries can develop (estrogen and no MIS) f. If female reproductive system is promoted, it blocks the male (and vice versa) 3. Absence of proper gene activity can hinder development and result in sterility (no structures for sexual development) 4. Although the main components of sex determination are located on these chromosomes, autosomal genes are also important g. There are more genes associated with sexual development on the autosomes, but they require activation typically triggered by the genes on the sex chromosomes 5. X and Y also contain genes not associated with sexual development h. Inheritance of those genes do not follow Mendel's laws ***LO 7. Explain why it is necessary to have regions of similarity between the human X and Y chromosomes*** 1. **PAR1:** highly similar DNA sequences on the short arms of X and Y a. Areas for crossing over in male meiosis and resembles autosomal crossing over b. On PAR1, all genes remain active on both Xs of the female (need two copies for dosage compensation) i. Loss to Y causes phenotype in female inheriting messed up X c. High recombination frequency because of alignment ii. Malalignment can rearrange structure because important stuff can be placed close to places of alignment and moved 2. **PAR2:** region of homology at distal end of long arms that also experiences alignment at crossing over ***LO 8. Using the Morgan Fruit Fly experiments as a foundation, assess outcomes for a given mating and explain the role of reciprocal crosses in defining sex-linked inheritance*** 1. Inheritance patterns for genes on the sex chromosomes differs form that for autosomes 2. Since X chromosomes has more genes, most sex-linked inheritance is condensed to X-linked inheritance 3. **Sex-linked Inheritance:** results in differential expression of traits between males and females a. Ex: if a recessive trait is on X, males who inherit it display it while females must have both copies recessive or have preference to inactivate one X to display it 4. Morgan and his fruit flies demonstrated X linked inheritance with differential expression of traits between males and females 5. **Reciprocal Crosses:** links two parents to specifically see phenotype of X-linked inheritance b. For recessive, sex-linked appears in males more because they only get the X chromosome 6. The discrepancy between males and females' representation of the phenotype is a hallmark of X-linked or sex-linked inheritance 7. Morgan had two genetic principles c. Sex-linked inheritance is based on mutations observed in males only d. Gene linkage is based on the inheritance of genes as a single unit i. Chromosome mapping based on recombination frequencies between linked genes 8. BUT further crosses showed a low frequency of affected males that was too high to be explained by random mutation (unexpected phenotypes) e. Bridge discovered that only certain mating produced unexpected results because of nondisjunction ***LO 9. Explain X-linked inheritance in terms of human health and disease and explain the consequences for nondisjunction in terms of genotype and phenotype*** 1. Failure to properly separate chromosomes lead to inappropriate gene content in offspring a. Many genetic options produce nonviable offspring (embryonic lethal) i. YY (always) and XXX (usually) ***LO 10. Determine probabilities for offspring inheriting a particular trait (autosomal vs. linked)*** EXAMPLES Principles and Processes of Epigenetics ***LO 1. Define the following terms:*** 1. **Epigenetics:** the study of the way expression of heritable genetic traits are modified by environmental influences or other mechanisms without a change in DNA sequence a. Adding and removing yes, but not change in sequence b. Can be inherited or change in your lifetime 2. **Euchromatin:** the state of chromatin in which it is partially or fully uncoiled and genetically active 3. **Heterochromatin:** the state of chromatin in which it is tightly coiled or considered molecularly inactive 4. **Imprinting:** core phenotypic changes due to changes in gene expression without changes in core DNA sequence 5. **X-Inactivation/Lyonization:** inactivation of genes on the X chromosome that exhibit dosage effects ***LO 2. Compare and contrast euchromatin and heterochromatin and compare constitutive and facultative heterochromatin*** 1. **Euchromatin:** the state of chromatin in which it is partially or fully uncoiled and genetically active a. Loosely coiled in interphase (beads-on-a-string conformation) b. Condensed during mitosis c. Often undergoing active transcription d. Light banding e. Enables us to actively express genes 2. **Heterochromatin:** the state of chromatin in which it is tightly coiled or considered molecularly inactive c. Dark staining (seen around centromeres) d. Late replicating because structure is important so it's hard to gain access e. Highly inaccessible by replication machinery so not transcriptionally active f. Remains condensed from prophase through mitotic cycle g. Has structural significance h. **Constitutive Chromatin:** region of heterochromatin that is never transcribed i. Almost always heterochromatin ii. Plays structural roles iii. Highly repetitive sequences iv. Significant percentage of human genome (15-20%) v. Trimethylated on H3-Lys9 (even more compact) i. **Facultative Chromatin:** regions of heterochromatin that is silenced and can become active vi. Regions that become heterochromatic in certain cells/tissues vii. Trap them to shut them off viii. Ex: differentiation and development 1. All cells start them same, then differentiate so shut off genes not needed for other stuff ix. Acts as middle bridge (can become euchromatin or heterochromatin) x. Deactivated by multiple processes like changes in methylation, hypoacetylation, and changes in the timing of DNA replication 2. Monomethylation and demethylation of H3-Lys9 ***LO 3. Summarize the process of methylation and chromatin remodeling and compare DNA and histone methylation (identify the role of CRCs, histone methyltransferases, DNA methyltransferases, and histone deacetylases)*** 1. **DNA methylation:** adds methyl group to cytosine or adenine bases a. Turns things off b. Cytosine methylation is associated with heterochromatin formation and repression of gene expression c. Important process in epigenetics and in genetic disease d. Hypermethylation shuts things off even more (correlates with cancer development) e. **DNA methyltransferases:** transfer a methyl group from another molecule onto a base f. Gene silencing is mediated by DNA methylation i. Ensures genes are turned off when the cell is done with them 2. **Histone Methylation:** add methyl groups to specific histone residues g. Correlates with changes in heterochromatin and euchromatin ii. Affects more than one gene h. Affects larger areas while DNA methylation affects smaller areas 3. Heterochromatin loosens into euchromatin by increased acetylation and histone methylation (remove methyl group) 4. Euchromatin condenses into heterochromatin by histone methylation (add methyl group) and histone deacetylation 5. **Chromatin Remodeling Complexes (CRCs):** restructure chromatin (by repositioning, acetylating, methylating, and/or replacing histone variants) to increase or decrease transcription i. Use energy derived from ATP to initiate changes j. Can disrupt nucleosome structure without displacing them or reposition the nucleosomes, making key DNA binding sites accessible ***LO 4. Outline the importance of heterochromatin to gene regulation and chromosome function and the role remodeling plays in development*** 1. Thought to be junk DNA but found to have structural and functional importance a. Confer strength and protection to centromeres b. May protect against change in sequence (prevent cross over) c. May aid in alignment and separation of chromosomes during mitosis and meiosis d. Heterochromatic regions of Y chromosome have fertility factors e. Heterochromatin serves to more "permanently" turn off genes that were used in development and are no longer needed i. Role in cellular specialization and differentiation ***LO 5. Assess the consequences for gene regulation following or as induced by changes in chromatin structure*** 1. Chromatin remodeling complex has two different consequences