General Genetics - Notes with Dr. Chandlee PDF

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Notes with Dr. Chandlee...

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General Genetics & Recitation - Biology 352

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Spring 2018! Genetics: scientific study of the underlying basis of heredity (trait transmission across generations) and variation…. the branch of biology concerned with the study of genes (all aspects) and their variation.! *Watson and Crick discovered this in the 1950’s*! Gene: unit factor of heredity; physical entity in cells that is responsible for the transmission of traits from one generation to another (heredity). ! *Refinements of the gene were discovered more in the early 1990’s*! Divisions of Genetics! Approaches to genetic analysis include studies of inheritance, gene structure, function and change/variation.! 1) Transmission Genetics 1) qualitative ! 2) quantitative ! 2) Cytogenesis - ideas that we know the organization of the genetic material in the cell… leading to knowing of chromosomes. ! 3) Molecular/Biochemical Genetics - studying DNA! 4) Population Genetics - looking at genetic variants that exist in populations and how it’s maintained/changed over time, what are the forces on it, and understanding evolution.! Article Definition of a Gene: a DNA sequence (whose component segments do not necessarily need to be physically contiguous) that specifies one or more sequence-related RNAs/proteins that are both evoked by GRN’s (Genetic Regulatory Network) and participate as elements in GRN’s, often with indirect effects, or as outputs of GRN’s, the latter yielding more direct phenotypic effects.! Exon: a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence.! Intron: a segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.! GMO’s: Genetically Modified Organisms ! **The world’s first genetically engineered drug is Insulin**! Somatic Cell Nuclear Transfer: in a controversial milestone, researchers have cloned a pair of macaques (monkeys) ! Naked Foal Syndrome: hairless animal, issues with the epidermal layer of the skin which makes the animal more prone to injuries and diseases! Cell Structure is Closely Tied to Genetic Function! There are two main types of cells:! - Prokaryotic: (bacteria and archaea), usually carry a single, circular chromosome consisting of essentially naked DNA! - Eukaryotic: (protists, plants, fungi and animals)!

All cells share some common features - Plasma membrane, DNA and Ribosomes Nucleus - Found in eukaryotes! - Membrane bound compartment! - Houses genetic material, DNA! - DNA: complex array of acidic and basic proteins into thin fibers ! Nucleoid - Found in prokaryotes! - Not membrane bound!

THE MITOCHONDRIA IS THE POWERHOUSE OF THE CELL! Centrosome - no defined centrioles! Chromosome: structure within a cell that carries genetic information; the carriers of Mendel’s unit factors of heredity or genes! **The nucleus of eukaryotic cells generally carry more than one chromosome and the chromosomes are complex in their organization consisting of DNA, RNA and many proteins**! Genome: complete collection of all of the chromosomes of an organism. Consequently, the complete compliment of all of the genes carried by an individual.! Autosomes: any chromosome that is not a sex chromosome.! Sex chromosomes: a chromosome involved with determining the sex of an organism, typically one of two kinds. (XX, XY)! Centromere: the region of a chromosome to which the microtubules of the spindle attach, via the kinetochore, during cell division.!

Sexual Reproduction Homologous Chromosomes: pairs in diploid cells that are the same in size, shape, centromere placement, banding pattern and gene order.! Non-Homologous Chromosome: pairs in diploid cells that are morphologically and genetically distinct.! ! Diploid: 2N - 2 copies of every chromosome/gene (somatic cells)! Haploid: 1N - 1 copy of every chromosome/gene (germ cells)! !

MITOSIS (A) Interphase: chromosomes are extended and uncoiled forming chromatin! # !

B) Prophase: chromosomes coil up and condense; centrioles divide and move apart! !

C) Metaphase: centromeres alight on metaphase plate! !

D) Anaphase: centromeres split and daughter chromosomes migrate to opposite poles! !

E) Telophase: daughter chromosomes arrive at the poles; cytokinesis commences !

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Sister chromatids!

MEIOSIS!

2n=4……….each member of a homologous pair transmitted by a different parent so genetically similar but not identical (allelic differences)!

Gregor Mendel’s Principles of Inheritance 1) Unit factors of heredity (genes), that are responsible for trait determination, exist in pairs! 2) Different unit factors of heredity for a single trait (alleles), when present in the same individual, exhibit a relationship of dominance and recessiveness ! 3) Paired unit factors of heredity segregate away from each other during gamete formation! Terminology Gene: physical and functional unit of heredity! Locus: site or place on a chromosome where a particular gene resides! Allele: alternate forms of a gene that can exist at a single locus! Homozygous: in a diploid, situation where identical alleles occur for one or more loci! Heterozygous: in a diploid, situation where alternative alleles occur for one or more loci! Phenotype: physical appearance or form of expression for a particular trait in a specific individual! Genotype: specific allelic or genetic construction of an organism, usually represented symbolically using $ letter designations !

Example D Gene: plant height ! Locus: !

Alleles: D $ d$

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- Tall! - Dwarf!

Genotypes: DD, Dd, dd!

Setting up a Punnett Square Independent Assortment: during gamete formation, segregating pairs of unit factors of heredity for two different traits assort independently of each other ! Product Law: the probability of two (2) independent events occurring simultaneously is the product of the individual probabilities !

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Multiple Alleles ! - ABO Blood Groups! - antigens specified by a single gene that are present on the surface of red blood cells and are detectable with appropriate antibodies! - I Gene - 3 Alleles! - I^A - A antigen! - I^B - B antigen! - I^O - no antigen ! Non-mendelian allelic relationships! Allelic series! Relativity of allelic relationships ! Allelic symbols! Epistasis: One gene acts to mask or modify expression of a second gene contributing to the same trait!

_____________________________________________________________________________________________! Limits to 2-Point Linkage Analysis! 1) Limited data generated per cross! 2) Maximum recombination frequency detectable is 50%! 3) Double cross-over’s not detectable among test cross progeny ! Autosomal Recessive Traits - trait is rare in pedigree! - trait often skips generations (hidden in heterozygous carriers)! - trait affects males and females equally ! Autosomal Recessive 1) Appear equally in both sexes! 2) Generally skip generations! 3) Affected children can be born to unaffected parents! 4) When both parents heterozygous, 1/4 of the offspring are expected to be affected ! 5) Appear more frequently in consanguineous marriages ! 6) If both parents are affected, all offspring should be affected ! Autosomal Dominant 1) Appear equally in both sexes ! 2) Both affected sexes transmit to offspring of next generation ! 1) No skipping of generations! 2) Generally, affected offspring have affected parent (unless a new mutation)! 3) When one parent is affected, 1/2 of the offspring are expected to be affected! 4) Unaffected parents don’t transmit trait! X-Linked Recessive 1) More males than females affected ! 2) Affected sons can be born to unaffected mothers so can get skipping of generations ! 3) A carrier female (heterozygote) produces 1/2 affected male progeny ! 4) Trait is never passed from father to son! 5) All daughters of affected fathers are carriers (heterozygous)! 6) All sons of affected mothers should be affected (criss-cross pattern of inheritance)! X-Linked Dominant 1) Both males and females affected; females generally more than males! 2) Does not skip generations ! 1) Affected sons must have affected mother! 2) Affected daughters must have affected father or mother! 3) Affected father transmits trait to all daughters! 4) A heterozygous affected mother will pass the trait to 1/2 of sons and 1/2 of daughters ! Y-Linked 1) Only males affected! 2) Passed from father to all sons! 3) Does not skip generations! Dosage Compensation Mammals- Barr body observed in interphase nuclei of cells of female cats by M. Barr! - Sex differences for sex chromosomes in humans observed in 1959!

Lyon Hypothesis- in 1961 Mary Lyon proposes dosage compensation model to explain genetic ‘imbalance’ between males and females! Gene to Centromere Mapping centromere to locus distance based on recombination frequency (m.u.) =(1/2)(# asci with 2nd division segment) x 100% $ total number of asci ! Autosomal Recessive Traits 1) Trait is rare in pedigree! 2) Trait often skips generations (hidden in heterozygous carriers)! 3) Trait affects males and females equally! - Appear equally in both sexes ! - Generally skip generations ! - Affected children can be born to unaffected parents! - When both parents are heterozygous, 1/4 of the offspring are expected to be affected! - Appear more frequently in consanguineous marriages ! - If both parents are affected, all offspring should be affected ! Sex Determination Mechanisms - For all crocodiles, most turtles, and some lizards, sex determination is achieved according to the incubation temperature of eggs during a critical period of embryonic development! - There are three different patterns of temperature sex determination in reptiles! Testis-determining factor (TDF): is a protein encoded by a gene in the SRY that triggers testes formation! SRY Gene - encodes a transcription factor protein ! - controls the expression of other genes ! - stimulates male development! - developing testes secrete anti-Mullerian hormone and destroy female structures! - testosterone and DHT are secreted and stimulate male structures !

SRY

TDF (Transcription Factor)

Gene Activation (Autosomal and sex-linked) for development of male reproductive structures; includes genes for testosterone (androgen) and androgen receptors

Cascade continues…

X and Y Chromosomes - X Chromosome! - contains more than 1,500 genes! - larger than the Y chromosome! - acts as a homolog to Y chromosome in males! - Y Chromosome! - contains 231 genes! - many DNA segments are palindromes and may destabilize DNA! Chromosome Variation - Although most diploid species normally contain precisely two haploid chromosome sets, there are many known variations:! - a change in the total number of chromosomes! - the deletion or duplication of genes or segments of a chromosome! - rearrangements of the genetic material either within or among chromosomes (inversions and translocations)! Chromosomal Aberrations Variation in Number:! $ $

+ Aneuploids! + Polyploids!

Variation in Structure or Arrangement:! $ $ $ $

+ Deletion! + Duplication! + Inversion! + Translocation!

Monosomy: the loss of one chromosome to produce a 2n-1 complement ! $ (may have severe Phenotypic effects)! $ - Although monosomy for the X chromosome occurs in humans and individuals survive (Turner Syndrome), monosomy for any of the autosomes is usually not tolerated in humans and other animals ! $ $ ** Monosomy 21 - rare but most common **! Trisomy: Involves the addition of a chromosome to a diploid genome…(2n+1 chromosomes) for the sex chromosomes (Klinefelter Syndrome, Triplo-X) has a less dramatic phenotype than trisomies for autosomes, which are often lethal! $ - three copies of one chromosome are present, so pairing configurations are usually irregular! $ - at any particular region along the chromosome length, only two of the three homologs may $ $ $ synapse, through different regions of the trio may be paired.! - often found in spontaneously aborted fetuses, but monosomes are not.! - this suggests that abnormal gametes leading to monosomy (i.e. nullisomic gametes) may be very functionally impaired while abnormal gametes leading to trisomy (i.e. disomic gametes) are not.! Polyploids: in which more than two haploid sets of chromosomes are present, is prevalent in plans and rare in animals. + Autopolyploids ! + Allopolyploids ! - all are euploid with an N number greater than 2!

Polyploidy can originate by: the addition of one or more haploid sets of chromosomes identical to the haploid complement of the same species (autopolyploidy) or the combination of chromosome sets from different species as a consequence of interspecific matings (allopolyploidy)! Cri-du-chat: results from a segmental deletion of a small terminal portion of the short arm of chromosome 5.!

- Organisms have multiple copies of the ribosomal RNA genes (rDNA)! - this is an example of gene redundancy ! - Gene amplification is another mechanism to increase the rRNA! ———————————————————————————————! - Gene duplication may play a role in evolution.! - This hypothesis is supported by the discovery of genes that have a substantial amount of their DNA sequence in common, but whose gene products are distinct.! - Other support includes the presence of gene families, regional groups of genes whose products perform the same general function !

Paracentric Inversion! !

- An inversion involves a rearrangement of the linear gene sequence rather than the loss of genetic information! - In an inversion, a segment of a chromosome is turned around 180° within a chromosome! - An inversion requires two breaks in the chromosome and subsequent reinsertion of the inverted segment.! - An inversion may arise from chromosomal looping followed by recombination.!

Translocation is a movement of a chromosomal segment to a new location in the genome.! A reciprocal translocation:! $ - involves the exchange of segments between two non homologous chromosomes ! $ - has an unusual synapsis configuration during meiosis !

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Robertsonian translocation (or centric fusion) involves breaks at the extreme ends of the short arms of the two non homologous acrocentric chromosomes! - Familial Down syndrome is an example of this.!

Robertsonian Translocation

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For a molecule to serve as the genetic material, it must be able to: replicate, store information, express information, allow variation by mutation. * Chemical structure of genetic material is important for understanding these varied functions*

Chromosomal Theory of Inheritance - 1902: Sutton and Boveri - associated Mendelian principles of segregation and independent assortment with chromosomal segregation behavior during meiosis…..so, genes (unit factors of heredity) on chromosomes .

Searching for Genetic Material Thomas Hunt Morgan (1910) - worked with fruit flies ! - specifically eye color of these flies! ! - discovered genes are located (linked) on chromosomes ! Until 1944 Observations Favored Protein as the Genetic Material - the genetic material is physically transmitted from parent to offspring ! - proteins and nucleic acids were the major candidates for the genetic material ! - for a long time, protein was favored to be the genetic material! - it is abundant in cells! - it was the subject of the most active areas of genetic research! - DNA was thought to be too simple to be the genetic material, with only four types of nucleotides as compared to the 20 different amino acids of proteins!

Friedrich Meischer (1869) : Swiss Biochemist Isolate new substance from nuclei of pus cells: ! $ $ NUCLEIN Also found it in yeast, liver and kidney cells ! Characteristics: High phosphorous, no sulfur, acidic, polymeric ! $ $ … therefore distinct from proteins.! 2 Types: DNA or RNA ; called Nucleic Acids Chargaff’s Rules 1) A = T or A/T = 1! G=C or G/C = 1! 2) A+G = C+T or A+G/C+T = 1! purines = pyrimidines ! 3) A+T ≠ G+C or A+T/G+C ≠ 1!

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- Transfection of T2 viral DNA into bacterial cells proved conclusively that the viral DNA alone contains all the necessary information for production of mature viruses ! Indirect and Direct Evidence Supports the Concept that DNA is the Genetic Material in Eukaryotes - UV Light is capable of inducing mutations in the genetic material and is most mutagenic at a wavelength of 260 nm.! - DNA and RNA absorb UV light most strongly at 260 nm, but protein absorbs most strongly at 280 nm, a wavelength at which no significant mutagenic effects are observed.! - Again, this provides indirect evidence for DNA as the genetic material.! - The strongest direct evidence for DNA as the genetic material comes from recombinant DNA technology.! - Segments of eukaryotic DNA corresponding to specific genes are isolated and spliced into the bacterial DNA.! - The presence of the eukaryotic gene product in bacteria containing the eukaryotic gene provides direct evidence that this DNA is present and functional in the bacterial cell.!

Knowledge of Nucleic Acid Chemistry is Essential to the understanding of DNA Structure - Nucleotides are the building blocks of DNA and RNA! - The consist of! - a nitrogenous base! - a pentose sugar! - a phosphate group! - **Different types of nucleotides are used to build RNA and DNA**!

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- A nucleoside contains the nitrogenous base and the pentose sugar! - A nucleotide is a nucleoside with a phosphate group added!

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- The C-5’ position is the location of the phosphate group on a nucleotide ! - Nucleotides can have one, two, or three phosphate groups and are called NMPs, NDPs, and NTPs, respectively !

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- Nucleotides are linked by a phosphoritester bond between the phosphate group at the C-5’ position and the OH group on the C-3’ phosphate !

X-Ray Diffraction Analysis - X-rays passing through a helix diffract at angles of varying degrees to the helix making an “x” pattern, which favors an equal diameter “helix”.

- Watson and Crick proposed DNA is a -

right-handed double helix in which the two stands are antiparallel and the bases are stacked on one another.! The two strands are connected by A-T and G-C base pairing and there are 10 base pairs per helix turn.!

Major Groove and Minor Groove of DNA Hypothetical Situation: the two grooves would have similar size if dR residues were attached at 180 degrees to each other!

Alternative Forms of DNA Exist

- The Watson-Crick DNA model is of B-DNA , -

which is believed to be the biologically significant form! A-DNA is slightly more compact than B-DNA! C-DNA, D-DNA, and E-DNA are also righthanded forms of DNA that are less compact than B-DNA!

The Structure of RNA is Chemically Similar to DNA, but Single Stranded - In RNA: - the sugar ribose replaces deoxyribose of DNA - and uracil replaces thymine of DNA! - There are three classes of cellular RNAs:! - messenger RNA (mRNA) - ribosomal RNA (rRNA) - transfer RNA (tRNA) Many Analytical Techniques have been Useful during the Investigation of DNA and RNA… - Nucleic acids absorb UV light most strongly at 260 nm due to interaction between UV light and the ring of systems of the bases.!

- Nucleic acids can be separated by gradient centrifugation procedures - Sedimentation equilibrium centrifugation separates by density gradient!

CHAPTER 11 POWERPOINT

There are several questions about how DNA replication would proceed semiconservatively: - How is it unwinding of the ds helix achieved?! - What enzyme is responsible for the synthesis of new DNA using the ss template?! - Anti-parallel and ds nature of DNA complicates the replication process! 1937: Arthur Kornberg - Worked with E. coli ! - Discovered the mechanisms of DNA synthesis ! Steps to DNA Synthes...