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Notes February 22-26

by: Joseph Merritt Ramsey

Notes February 22-26 CELL 2050

Marketplace > Tulane University > Science > CELL 2050 > Notes February 22 26
Joseph Merritt Ramsey

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Class Notes, Eukaryotic Chromosomes and Linkage
Dr. Meenakshi Vijayaraghavan
Class Notes
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This 15 page Class Notes was uploaded by Joseph Merritt Ramsey on Monday March 7, 2016. The Class Notes belongs to CELL 2050 at Tulane University taught by Dr. Meenakshi Vijayaraghavan in Winter 2016. Since its upload, it has received 31 views. For similar materials see Genetics in Science at Tulane University.


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Date Created: 03/07/16
February 22, 2016 Chapter 10: Chromosome Organization and Molecular Structure  Chromosome Overview  Viruses   Bacteria  Eukaryotes o Chromosome Overview o Important Characteristics of the Chromosome  1. Origins of Replication  2. Centromere  3. Telomeres o Repetitive Sequencing  Sequence Complexity –   Types of Repetition:  How do we test for repetitive sequences? The process utilizes  Cleavage and Density properties of DNA o Compaction in Eukaryotes  Why do they need to compact?  Process Overview  Compaction Comparison – Heterochromatin vs. Euchromatin  The Role of the Nuclear Matrix  MARs and SARs  So what does it do? o 1. Compaction  Radial Loops are present in Euchromatin  and Heterochromatin, so matrix binding is needed (and Linker Proteins)  Anywhere Radial Loops forms, MARs and  SARs are present  Form in both Euchromatin (30nm Level)  and Heterochromatin o 2. Chromosome Territory  It is also necessary to defining the  chromosome territory o 3. Gene Transcription  Manipulations can unwind DNA (using  saline solution), but Matrix binding  remains  So Radial Loops can be accessed  Chromatin Overview  Heterochromatin o 700nm Diameter Loops o Dark Stain o Constitutive is always coiled (Centromere,  Telomere, tandem repeats) o Facultative can fluctuate with Euchromatic  Euchromatin o 30nm Level of Compaction, 300nm Diameter  Loops Light Stain o The Dividing Cell  The first stage of the cell is the 300nm to 700nm  Importance of the Metaphase Step  Max compaction is achieved in Metaphase (1400nm  fibers)  This is the ultimate level  Fewer Bands are present at Metaphase (300) than  Prophase (2,000)  Importance of Proteins  Two proteins play a critical role in Metaphase  Condensing o These are “Structural Maintenance of  Chromosome” proteins (SMC) o They maintain chromosomeal structure through  the various cycle phases o General Structure  They have a Head, Arm, Hinge  Dimer, head and hinge, connected by arm o ATP Involvement  Head has binding site region  Hydrolysis occurs o Two of these dimerize to form a tetramer o They Fold, Tether, and Manipulate  Condensin o Present in the cytoplasm o At Prometaphase the Nuclear Membrane is  broken down and condensing comes in direct  contact with DNA o Works to compact DNA (so works with  Topoisomerase I)  Cohesin o Involved with the cohesion process (attaching  the two forms) o As soon as sister chromatid replication occurs,  cohesin acts (this is the S­Phase) o Biggest job is to prevent Premature Separation o Features:  I. Does not occur between homologues  (not with the Synaptonemal Complex)  II. Begins to break down in the middle of  metaphase (getting ready for separated)  III. Fully separated by Anaphase  Promotion Complex (done by Separase,  some was still remaining) o Important to note the Synaptonemal Complex is  between Homologues Chapter 8: Chromosome Structure and Number  Overview of Mutations o Genetic Mutation – single gene, single protein; small sequence  change; Allelic Mutation o Chromosome Mutation – array of proteins and genes in large  sequences  1. Structure – Aberration  2. Number – Genome Mutation  Cytogenetics o Definition – examination of the chromosomal compaction and  composition of an organism o Process for Examination  1. Addition of Division Inducing Agent (condenses and  duplicates Chromosomes)  2. Allowance of Replication  3. Centrifuge to Stop Replication and Collect Sample (forms  sample pellet)  4. Addition of Hypotonic Solution (swells up cells)  5. Drop Cells on a Slide and Fix Them (no more changes can  occur)  6. Stain Cells With Geimsa (stains different components  differently)  7. Addition of Trypsin (breaks down histones, reveals DNA  bands)  8. Photo Imaging (computer or camera)  9. Karyotype Arrangement o Karyotype Arrangement – the entire chromosome complement of an  organism arranged from tallest to shortest  Homologue Identification  1. Size o While size can help identify Homologues, it is no  suggestive of overall genomic complexity of an  organism  2. Centromere Position o 1. Meta­Centric – in the middle o 2. Sub­Met­Centric – closer to the middle o 3. Acro­Centric – closer to one end; ‘p’ is short,  ‘q’ is long o 4. Telo­Centric – only one arm  3. Banding Patterns o Banding is induced by the addition of the  Trypsin o This can identify and differentiate based on Loci, not based on Alleles  Mutations o General Types  1. Loss of Genetic Material  2. No Loss of Genetic Material o Material Loss is a Common Form  Deletion/Deficiency vs. Duplication/Addition (Loss/Gain)  Inversion (No Loss/Gain)  Translocation (No Loss/Gain)  Mutation Types o 1. Deletion (Break Occurs in the Chromosome)  Terminal (end is lost) vs. Interstitial (section is lost)  An overall expression imbalance occurs  Can de expressed as:  I. Haploinsufficiency o A  deletion occurs in the Dominant Allele  Location o So the expressing gene is lost  II. Pseudo­Dominance o Dominant Allele (Cystic Fibrosis) is present,  giving normal phenotype o But if the normal phenotype is removed, only the recessive sick copy is left o So the recessive allele is enough  III. Recessive Parity o Consider why imprinting makes a difference –  one functioning gene is already lost  Why does Deletion occur?  One form is Chromosomal breaking  But Paralogs can also lead to Improper Crossing  Over and a deletion  The locations are misaligned because of the  similarities o So there is always a loss and always a gain  (deletion or addition) o  But never both o Homologue separation  This means that even if this were to occur every time,  only 50% of the final gametes would have the problem o The process only occurs between two of the  homologues during Prophase I o The remaining 50% will be split 50/50 (delete,  add) o 2. Duplication  Imbalance is the Key Idea  Differentiates it from Deletions – they still have the  whole genome present  But now they have more of a given protein present  How Does Duplication Occur?  Misaligned Crossover occurs again  Places homologue gene onto the adjacent homologue  But it is not always detrimental  To What Does Duplication Lead?  I. Paralogs o Peripheral Neuropathy is an example  (Demyelination affecting motor function)  Chromosome 17 duplication  Big toe and muscle myelination degrades  II. Gene Families o Globin is an example  Myoglobin (precursor) placed itself on 22  Alpha Globin on 16  Beta Globin on 11 o Various forms are active – has an evolutionary  significance o Globin Timeline  Fetus – Zeta/Epsilon  Developing Second & Third Trimester –  Alpha/Gamma  Adult – Alpha/Beta  III. Copy Number Variation o Segmental duplication occurs again  It confuses the alignment process during  replication  So crossing over is supposed to occur  between allelic locations, but instead it  occurs between Homologues in different  locations o Variable Genes  Small Segment of DNA (1000bp) present  multiple times  Variation of variable gene in the  population o Nonallelic Homologue recombination  Transposable Elements are an Example  Different chromosomes can align due to duplicated  regions  Small Chromosome (21) and Large Chromosome (22)  could have homologues that swap  You have to have   Similar Centromere   Homologues February 24, 2016 Chapter 8: Chromosome Structure and Number  Overview of Mutations o Genetic Mutation o Chromosome Mutation  Cytogenetics  Mutations o General Types o Material Loss is a Common Form o Mutation Types  1. Deletion  2. Duplicaiton  To What Does Duplication Lead? o I. Paralogs o II. Gene Families o III. Copy Number Variation  Transposable Elements are an Example o Different chromosomes can align due to  duplicated regions  3. Inversion Pericentric Paracentric  Centromere is involved  Centromere is not involved o Centromere also flips o Much more harmful – can   result in multiple chromosomes  Dicentric Bridges and  Monocentric Fragments occur  Total content remains consistent o Often times they remain functional and no real  changes occur o In 2% of cases you can detect it Cytogenetically o And often defects occur as well  But what if it affects the Phenotype? What if function  is lost? o 1. Point Break Effect  The break occurs in the  middle of a gene,  rendering it useless  Proper protein can no longer be created o 2. Location Effect  Regulatory sequences are relocated  Promotor sequence can be moved  Imprinting sequence can be moved  Inversion Heterozygotes o In these individuals, one chromosome has  inversion and the other doesn’t o So, considering expression, the genes from the  proper chromosome can compensate  As long as the break hasn’t occurred o This only plays a role during gametogenesis  In this context, 2 Gametes will inherit the  inverted chromosome  And other mechanistic errors occur as well  What are the differences? (Always occurs during  Synapsis during Prophase I) o Differences occur during the Loop Formation,  Homologous pair up o And after this the Centromeres are connected to  Kinotechore microtubules  So Acentric Fragments are simply lost  And Dicetric Bridges are ripped apart  4. Translocation – no net loss or gain of gene content occurs;  usually occurs as an improper repair mechanism (so  dysfunctional telomere)  1) Simple – one break occurs o Normally, a small Break Occurs and the  Telomere responds  But in this case the Telomere is not  properly functioning and the broken  portion gets moved o Simple and balanced has no loss of gene  function o Dysfunction Comes as a Result of:  A. Point Break Effect   B. Location Effect  2) Reciprocal – two breaks occur o Often times balanced translocation occurs with  two breaks o Unbalanced can be very deleterious to the  organism  Genes are lost, severe effects can result  13/14 and 14/21 Translocations are good  examples  Caner, Infertility, XX Male Syndrome all  occur  SRY is cleaved and connected to  female  3) Robertsonian – also known as Centric Fusion o As per the name, the Centromere’s of two fuse  together o Most common in the 14/21 Chromosomes  Known as Familial Down Syndrome (14  (long)­21(small) Translocation)  Breaks happen in the Centromeres in  Acrocentric Chromosomes  “p” arms are removed and a new  chromosome is created with the whole set  of #21 genes (psuedotrisomy) o Forms one Metacentric Chromosome o Occurs during Crossing Over, so Four  Chromatids are present (and then two become  one) o Translocation Mechanisms In Gametogenesis – Individuals with  Balanced Translocation Have a Greater Risk of Gamete  Translocation It all depends on segregation patterns in Meiosis I Misaligned crossover occurs, nonhomologous crossovers This occurs because of previously translocated homologues now present on different Chromosomes:  1. Alternate Segregation (Balanced)  Balanced Translocated Stay Together  Chromosomes on opposite sides segregate into the  same cell  Balanced­2 Segregates with Balanced­1  All the gametes are fine (they are balanced, two normal and two trans)  2. Adjacent 1 (Unbalanced)  Centromere of Normal­2 goes with Translocated­1  Adjacent non­homologous chromosomes segregate into same cell  Centromere of Two goes with One  All four will have deletions and duplications o No viable gametes  3. Adjacent 2 (Unbalanced)  Centromere of 2 Pairs with Centromere of 2  Adjacent Homologous Chromosomes Segregate into the same cell  Centromere of Two goes with centromere of Two and  vice versa and vice versa  Chromosome Number Variation o Terminology  1. Aneuploidy – a single additional chromosome is  present/taken away  2. Eupoidy – normal number is present  3. Polyploidy – a set of chromosomes is removed or added o Differentiation Polyploidy Anneuploidy  Sets of Chromosomes  Individual Chromosomes  2n (diploid), 3n (triploid), etc.  Genomic number changes, almost  always deleterious effects o Because each gene will now  have 150% production  Ex: Jimson Weed o Diploid Number is 2n o No Sex Determining, so 12  Chromosomes present in total o So with 12 Autosomes, there are 12 possible trisomies  2n+1, 2n­1 o Aneuploidy Diseases 1/800 Trisomy 21 Down Syndrome Mental retardation, structural developmental issues Trisomy 18 1/6,000 Edward Syndrome Mental and physical  retardation, extreme muscle  tone Trisomy 13 1/15,000 Patau Syndrome Mental and physical  retardation, organ defects,  early death (2­3 days) Trisomy 1 Fetal Death Fetal Death XXY (Male) 1/1,000 Klinefelter  Sexual immaturity, breast  Syndrome swelling XYY (Male) 1/1,000 Jacobs Syndrome Tall XXX (Female) 1/1,500 Triple X Syndrome Tall and Thin, Menstrual  Irregularity X0 (Female) 1/5,000 Turner Syndrome Short stature, sexually  undeveloped


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