Genetics and Genomics Tutorial Notes PDF

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Ebony Williams

2018

Genetics and Genomics Week 1 Lecture -Teaching Team:  Tutors: o Cynthia. o Chris. o Yasmin. o Rod.  Guest Lecturers: o Katie. o Stephen. o Janine. -Introduction to Unit:  Designed to: o Introduce broad concepts and principles of Genetics and Genomics. o Integrate knowledge and skills to the framework of human biology, health, society, environmental science, biotechnology and bioinformatics. o Increase knowledge and skill set. o Not passive diffusion of information into your brain. o Active integration of knowledge gained with skills acquired. o Will be required to think about how small details fit into the big picture.  Topics Covered: o Chromosomes. o Sex Determination. o Prokaryotic Genetics and genomics. o RNA molecules and processing. o Gene mutations and DNA repair. o Molecular genetic analysis and biotechnology. o Genomics and proteomics. o Epigenetics and cancer genetics. o Evolutionary Genetics. o Bioinformatics. -Classes:  Lectures: o Academic Knowledge. o One lecture per week. o Up to two hours.  Workshops: o Hands-on learning on basic bioinformatics. o Application of academic knowledge in critical thinking and decision making. o Extract, analyse and communicate molecular genetics information. o Learn to work in a team as well as individually. o Eight all together. o Weeks 2-4, 7, 9-12. o 2 hours in computer lab. -Participation Requirements:  Attendance at lectures is highly recommended.

Ebony Williams

2018

 Attendance at workshop is compulsory.  Any absence from a workshop must be accounted for by supporting documentation.  Completion of the workshop activity table each week is required in order to pass the unit. -Unit Resources:  Textbook.  Campbell Essential Biology.  10 Practice Quizzes relevant to each lecture will remain open throughout the semester.  Activity table for each workshop. -What is Genetics:  Study of genes and genetic variation. -Genomics:  Study of content, organisation and function of genetic info in a whole genome. -Genome:  A complete set of genetic instructions for any organism.  Encoded in nucleic acids- either DNA or RNA. -Epigenetics:  Any inheritable influence on gene activity that doesn’t influence a change in DNA sequences. -Genetics Vs Genomics:  Genetics examines the composition, function, effects and inheritance of a single gene or small number of genes.  Genomics addresses all genes within a genome and their inter-relationships as well as their interactions with the environment in order to identify their combined influence on the development, metabolism and function of the organism. -Divisions of Genetics:  Transmission Genetics: o How an organism inherits and passes on its genetics.  Molecular Genetics: o How genetic information is replicated, encoded and expressed.  Population Genetics: o Genetic composition of populations. o How genetic composition changes over time (Evolution). o Hardy-Weinberg Equilibrium. -Divisions of Genomics:  Structural Genomics: o Determines the sequence of DNA of an entire genome.  Functional Genomics: o Determines the functions of genes by using genomic based approaches.  Comparative Genomics: o Studies how genomics evolve. -Model Genetic Organisms:  Organisms with characteristics that make them useful for genetic analysis.  Common Characteristics Include: o Short generation time. o Production of numerous progeny. o Ability to carry out controlled genetic crosses. o Ability to be reared in a lab environment. o Availability of numerous genetic variants.

Ebony Williams

2018

o Small genome. -Early Concepts of Heredity:  Pangenesis: o Genetic information travels from different parts of the body to reproductive organs.  Inheritance of Acquired Characteristics: o Acquired traits become incorporated into hereditary information.  Performationism: o Miniature organisms reside in sex cells and all traits are inherited from one parent.  Blending Inheritance: o Genes blend and mix.  Germ-plasm Theory: o All cells contain a complete set of genetic info.  Cell Theory: o All life is comprised of cells and cells arise only from cells.  Mendelian Inheritance: o Traits are inherited in accord with defined principles.

Genetics and Genomics Week 2 Lecture -What is a Chromosome:  Single DNA molecule with associated DNA-bound proteins.  In eukaryotes chromosomes are located in nucleus and are linear.  Not visible in resting cells.  Diploid organisms have 2 sets of chromosomes organised in homologous pairs. -Homologous Pairs:  Diploid cells carry 2 sets of genetic info.  Haploid cells carry 1 set of genetic info. -Essential elements of functional chromosomes:  Centromere: o Constricted region of chromosome where kinetochore assembles. o Spindle microtubules attach to kinetochore during cell division. o DNA around 110-120bp in length with 3 regions:  Regions I and III are recognition sites for protein directing spindle attachment.  Region II is A-T rich to allow for easy separation during cell division.  Telomeres: o A pair at each end. o Natural ends of chromosomes. o Repeating units of DNA (250-1500 repeats). o Repeat unit is highly conserved in vertebrates. o Has important role in replication, aging and cancer. o Most are similar in structure. o G’s and C’s towards the end of chromosomes. o G rich strands protrudes beyond C rich strands. o Special proteins can bind to single strand region to prevent degradation and chromosomes sticking together. o In some cases, overhang may fold and pair with short stretch of DNA to form a loop.  Origins of Replication:

Ebony Williams

2018

o Origin replication are sites where DNA synthesis begins. o Contains A-T rich internal repeats which make it easier for helicase to open DNA helix. o Allows primases to access strands. -Chromosome Morphology:  Metacentric.  Submetacentric.  Acrocentric.  Telocentric. -Kinetochore:  Central role is chromosome segregation.  Is a protein that binds to spindle microtubules and regulates chromosome segregation. -Telomeres, Telomerase, aging and disease:  Telomerase has both protein and RNA components.  RNA components contain 15-22 nucleotides complementary to the sequence of the G-C rich strand.  This acts as template for synthesis of additional DNA copies, preventing chromosome shortening. -Cytogenetics:  Study of chromosomes and their role in heredity. -How to prepare chromosomes:  Cells are treated with colchicine. This prevents cells for entering anaphase. Cells are then preserved chemically, spread on a microscope slide, stained, photographed and karyotypes. -Karyotype:  Complete set of chromosomes possessed by an organism.  Usually presented as a picture of metaphase.  Applications: o Detection of chromosomal mutations. o Sex determination. -Types of Chromosomes:  Microchromosomes and macrochromosomes form 2 distinct size groups.  Microchromosomes: o Are tiny chromosomes presenting in the karyotypes in all vertebrate groups, except mammals. o Any chromosome smaller than 20 mega base pairs. o Typical in avian and reptilian karyotypes. o Number found varies between species. -Chromosome Mutations:  Chromosome Rearrangement: o Duplications:  Doubling part of a chromosome.  Tandem duplication.  Displaced duplication.  Reverse duplication.  Effects:  Results in abnormal phenotypes.  Extra copies of genes don’t pair in meiosis.  Chromosome is more likely to break at duplicated regions.

Ebony Williams

2018

 Slows down cell division. Deletions:  Loss of a chromosome segment.  Effects:  Imbalances in gene product.  Expression of a normally recessive gene. o Inversions:  A segment is inverted (turned 180 degrees).  Cause breaks in some genes and may move others to new locations. o Translocations:  Movement of genetic material between nonhomologous chromosomes or within the same chromosome.  Robertsonian Translocation:  Joining 2 long arms and 2 short arms producing a large metacentric and a small chromosome.  Small chromosome is often lost in meiosis.  Cause of Down Syndrome.  Changes in the number of chromosomes: o Aneuploidy:  Change in number of individual chromosome.  Nullisomy:  Loss of both members of a homologous pair.  Monosomy:  Loss of a single chromosome.  Trisomy:  Gain of a single chromosome.  Tetrasomy:  Gain of two homologous chromosomes. o Polyploidy:  Change in number of chromosome sets.  Presence of more than 2 sets of chromosomes.  Result of failure during cell division.  Common in plants.  Autopolyploidy:  Failure during meiosis or mitosis  Allopolyploidy:  Hybridization between 2 separate species. -Fragile Sites:  Sensitive regions of chromosomes.  Associated with chromosome breakage. -Uniparental disomy and mosaicism:  Uniparental Disomy: o Both chromosomes are inherited from 1 parent.  Mosaicism: o Different cells in the same organism have different chromosome constitution. -Importance of chromosome variation:  New and extra copies of genes give rise to new functions and/or new species. o

Ebony Williams

2018

Genetics and Genomics Week 3 Lecture -Why Sex?  Sex enables creation of advantageous traits by: o Increasing variation. o Enabling evidence of parasites. -Sex-Why and How?  Costs of Sex: o Recombination. o Evading parasites.  The Basics: o Meiosis and recombination. o Gametes and fertilization.  Modes of Sex Determination: o Genetic:  Chromosomal. o Environmental. -Parthenogenesis:  Why: o Probability of transmitting alleles is 100% not 50%.  Why Not: o Genomic imprinting-need both maternal and paternal genes. -Sex Determination:  Switching of phenotype to either male or female.  Sexual reproduction alternates between haploid and diploid states.  The mechanisms directing sex differentiation. -Sex Differentiation:  The development of testis or ovaries from undifferentiated gonad. -Why study sex determination:  Provides an ideal system for studying the genetic control of organogenesis. -Sex- How?  Genotypic sex determination (GSD) is when sex is determined at fertilization independent of environment.  Environmental sex determination (ESD) is when sex is determined after fertilization by environmental factors. -GAD:  Chromosomal: o Sex is determined at conception by genes on the sex chromosomes.  Genetic Balance: o Sex determined by ratio of sex chromosomes and autosomes.  Polygenic Sex Determination: o Multiple independently segregating loci or alleles determine sex. -Sex Chromosomes and Autosomes:  Sex chromosomes contain genes that determine sex, which differ in males and females.  Autosomes are normally not involved in sex determination. -Sex Chromosomes:  XY Systems:

Ebony Williams

2018

o XX Females. o XY Males  ZW Systems: o ZZ Males. o ZW Females.  XX/XY are more common. -Multiple Sex Chromosomes:  Occurs in many species.  Thought to have evolves by sex chromosome-autosome fusion or degeneration of 1 sex chromosome.  Not yet fully understood.  In some species multiple sex chromosomes line up during meiosis to form a single X or Y chromosome. -Human Sex Chromosomes:  X is large and contains about 841 coding genes.  Y contains SRY genes. It is small and contains around 63 coding genes.  X and Y share homologous regions (Pseudoautosomal regions) which pair during meiosis. -Sex Determination in Humans:  Turner Syndrome: o Genome: XO o Female. o Sterile and short structure.  Trisomy Syndrome: o Genotype: XXX o Female o Limited fertility and tall stature.  Klinefelter Syndrome: o Genotype: XXY, XXYY or XXXY o Male. o Sterile and feminine.  Supermale Syndrome: o Genotypes: XYY o Male. o Fertile and tall.  X chromosome contains genetic info required for both sexes.  A single Y chromosome results in a male phenotype. -Androgen-Insensitivity Syndrome:  Disorder of hormone resistance in female phenotype with male genotype. -X-Inactivation:  In mammals one X chromosome randomly inactivates in female somatic cells and stays inactive over the entire lifespan. -Environmental Sec Determination (ESD):  Sex is determined after fertilization by environmental factors.  Various Factors can impact sex: o Invertebrates:  Temperature.  Nutrition.

Ebony Williams

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 Density.  Humidity.  pH.  CO2.  UV.  Metabolites.  Parasites. o Vertebrates:  Temperature.  pH.  Salinity.  Light.  Water quality.  Nutrition.  Altitude. Temp SD allows mothers to determine sex of offspring by varying temp of nest.

Genetics and Genomics Week 4 Lecture -Prokaryotic Genomes:  Mainly DNA, along with associated Proteins and RNA.  Haploid cells.  Typical chromosome is circular DNA. -Plasmids:  Small DNA molecules that replicate independently.  Not essential for normal growth, metabolism or reproduction.  Many types: o Fertility. o Resistance. o Bacteriocin. o Virulence. o Degradation of unusual substances. -DNA Replication in Bacteria:  Replication begins at origin.  DNA polymerase replicates 5’ to 3’.  Leading and lagging strands.  Bidirectional.  Gyrases and topoisomerases remove supercoils.  DNA is methylated. -Genetic recombination and Gene Transfer in Prokaryotes:  Vertical gene transfer: o Passing genes to next generation.  Horizontal gene transfer: o Donor cell contributes part of genome to recipient cell. o 3 types:  Transformation.  Transduction.  Bacterial Conjugation.

Ebony Williams

2018

-Transformation:  Recipient cell takes up DNA from environment.  Cells that take up DNA are competent: o Results from alterations in cell wall and cytoplasmic membrane. -Transduction:  Transfer of DNA from one cell to another via replicating virus.  Virus must infect both donor and recipient.  Generalised: o Transducing phage (virus) carries random DNA segment.  Specialised: o Only certain donor DNA sequences are transferred. -Conjugation:  Requires physical contact between donor and recipient cell.  Donor cell remains alive.  Mediated by conjugation (sex) Pili. -Transposons and Transposition:  Transposons: o Segments of DNA that move from one location to another. o Result in frameshift insertion called a transposition. -DNA to Protein:  Transcription: o Info in DNA is copied to mRNA.  Translation: o Polypeptides are synthesised from mRNA. -Regulation of genetic expression:  Most genes are expressed at all times, others are only transcript and translated when needed.  Basic Concepts: o Regulatory genes either initiate (Turn on) (positive control) or repress (Turn off) (negative control) the expression of a gene.  Operon: o Regulates expression of structural genes by controlling transcription.  Negative Control: o Regulatory protein binds to DNA to inhibit transcription.  Positive control: o Regulatory protein binds to DNA to stimulate transcription  Inducible Operon: o Transcription is normally off but can be induced. o Catabolic pathways.  Repressible Operon: o Transcription is normally on but can be repressed. o Anabolic pathways. o End products switches off its own production. -The lac Operon:  Present in E. coli.  Negative inducible operon.  Allows bacteria in metabolise lactose in the absence of glucose.

Ebony Williams

2018

-The trp Operon:  Present in E. coli.  Negative repressible Operon.  Allows biosynthesis of tryptophan. -Viruses:  Structure: o Not cells. o Small infectious particles consisting of nucleic acid enclosed in a protein coat. o Requires a host to provide energy and mechanisms for reproduction.  Genome: o Double or single stranded DNA or RNA.  Capsids and Envelopes: o Capsid is protein coat that encloses the genome. The coats shape allows it to attach or lock onto specific host cells. o Some have membranous envelopes that help infect hosts. These envelopes are derived from host cells membrane and contain a combination of viral and host cell molecules.  Features of Replicative Cycles: o When a virus enters a cell, the cell begins to manufacture viral proteins. o Virus uses host enzymes, ribosomes, tRNAs, amino acids, ATP and other molecules.

Genetics and Genomics Week 5 Lecture -Structure of Viruses:  Not a cell.  Small infectious particle consisting of nucleic acid enclosed in a protein coat and in some cases a membranous envelope.  They require a host to provided energy and mechanisms for viral replication.  Each has a host range, that is a limited number of host cells that it can infect.  Called counterfeit parasites. -Viral Genomes:  Can consist of either: o Double or single stranded DNA. o Double or single stranded RNA. -Capsids is the protein coat that encloses the viral genome. Its shape allows the coat to attach or lock onto host cells. -Some viruses have membranous envelopes that help them infect hosts. These envelopes are derived from the host cells membrane and contain a combination of viral and host cell molecules. -Bacteriophages are viruses that infect bacteria. They have the most complex capsids. -General features of the Viral Replicative Cycles:  Once a viral genome has entered a cell the cell begins to manufacture viral proteins.  The virus uses host enzymes, ribosomes, tRNAs, amino acids, ATP and other molecules. -RNA as Viral Genetic Material:  Broadest variety of RNA genomes is found in viruses that infect animals.  Retroviruses use reverse transcriptase to copy their RNA genome into DNA. This occurs in HIV that leads to AIDS. -Viral DNA similar to plasmids and transposons:  Viral DNA inserts itself into host genome.  During transduction in bacteria plasmid DNA inserts itself into bacteria genome.

Ebony Williams

2018

 Transposons are segments of DNA that can move within the genome of a cell. -RNA Molecules Form and Function:  Types of RNA: o Ribosomal. o Messenger. o Transfer.  Transcription: o Template strand is transcribed. o Transcription unit:  A promoter.  RNA-coding sequence.  Terminator.  Bacteria have only one type of polymerase. The sigma factor joins the core to form the holoenzymes which can build a promotor.  Eukaryotes have different polymerase molecules, each of which have different roles.  Termination: o Rho-dependent Termination:  Uses rho factor. o Rho-independent Termination:  Hairpin structure formed by inverted repeats, followed by a string of uracils.  Eukaryotic transcription is similar: o Chromatin modification needs to occur before transcription. o Basal transcription apparatus- at nucleotides to 3’ end. o Transcriptional activator proteins. o RNA polymerase II- mRNA syntheses.  Other Promoters: o Regulatory promoter. o Enhancers have their own promoters. o Polymerase I and polymerase III promoters.  RNA Polymerase II: o DNA enters through a groove and unwinds. The DNA is bent at a right angle, which positions the 3’ end at the active site and new nucleotides are added.  Post transcription modification: o Addition of 3’ cap. o Addition of poly (A) tail. o RNA splicing. o RNA editing.  Alternative splicing: o Pre-mRNA can be spliced in different ways to produce different mRNAs. o With multiple 3’ cleavage sites, there are two or more potential sites for cleavage and polyadenylation; use of different sited produces different mRNAs of different lengths. -Mid Semester Exam:  March 20th.  Room 2B04.  1:30-2:45.  Worth 30%.  25 multiple choice.

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4 out of 6 questions (with parts) worth 10 marks each. Covers weeks 1-5. Lecture 1: o Genetics is study of genes and genetic variation. o Heredity: transfer of genetic info from one generation to the next. o Variation is changes in genetic information during heredity. Lecture 2: o Lecture 3: o Lecture 4: o Lecture 5: o

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