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Midterm

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Department
Biology
Course
BIO2133
Professor
Colin Montpetit
Semester
Winter

Description
Lecture 2: genetic material, it must exhibit four characteristics: replication, storage, expression of information and variation by mutation. Forward genetic analysis: Investigators interested in studying the genetics of a trait but has no evidence that the trait is genetically based (therefore performing crosses would help resolve the question). Need to have variance to detect and study whether its responsible for a gene.If none, you would induce mutations to create the variance. As the interest is to study the genetic nature of the trait (if any), then the variance will help you design experiments to detect whether or not the trait is transmissible from one generation to the other, thus confirming the heritability of the trait and opportunities to map it in the genome. A genetic screen (often shortened to screen) is a procedure or test to identify and select individuals who possess a phenotype of interest. A genetic screen for new genes is often referred to as forward genetics as opposed to reverse genetics, the term for identifying mutant alleles in genes that are already known. Mutant alleles that are not tagged for rapid cloning are mapped and cloned by positional cloning.Biological phenomenainduce mutationsscreen variantsconfirm transmission (crosses)sequence DNA, gene function. Reverse genetics analysis: Typically, investigators have already a clue of the sequence for the trait they are interested in studying. Now the idea is to cause targeted mutations within that gene. By modifying the gene, one can then gain a sense of the role of the gene.Reverse genetics: is an approach to discovering the function of a gene by analyzing the phenotypic effects of specific gene sequences obtained by DNA sequencing. This investigative process proceeds in the opposite direction of so-called forward genetic screens of classical genetics. Simply put, while forward genetics seeks to find the genetic basis of a phenotype or trait, reverse genetics seeks to find what phenotypes arise as a result of particular genes.Putative geneinduce mutations (targeted)screen variantsgene function Mononucleotide: consists of (a) a nitrogenous base (e.g. purines – 9- member double ring; or pyrimidine, 6-member single-ring), (b) a pentose sugar, (c) and a phosphate group. Nucleic acid : A complex organic substance present in living cells, esp. DNA or RNA, whose molecules consist of many nucleotides linked in a long chain. tRNA: Transfer RNA: A small ribonucleic acid molecule with an essential role in translation. Consists of modified nucleotide bases, unique to tRNA. tRNAs contain: (1) a three-base segment (anticodon) that recognizes a codon in mRNA; (2) a binding site for the specific amino acid corresponding to the anticodon; and (3) recognition sites for interaction with ribosomes and with the enzyme that links the tRNA to its specific amino acid. Has regions where it folds back on itself due to complementary bases, forming paired stems and unpaired loops. rRNA: Ribosomal RNA: The RNA molecules that are the structural components of the ribosomal subunits. In prokaryotes, these are the 16S, 23S, and 5S molecules; in eukaryotes, they are the 18S, 28S, and 5S molecules. Chromosome: In prokaryotes, a DNA molecule containing the organism’s genome; in eukaryotes, a DNA molecule complexed with RNA and proteins to form a threadlike structure containing genetic information arranged in a linear sequence; a structure that is visible during mitosis and meiosis. Telomere: The heterochromatic terminal region of a chromosome, protecting it from deterioration. Consists of short tandem repeats. The structure that “caps” the ends of linear eukaryotic chromosomes. The heterochromatic cap structure renders chromosome ends inert in interactions with other chromosome ends and with enzymes that use double-stranded DNA ends as substrates Centromere: The specialized heterochromatic chromosomal region at which sister chromatids remain attached after replication, and the site to which spindle fibers attach to the chromosome during cell division. Location of the centromere determines the shape of the chromosome during the anaphase portion of cell division. Also known as the primary constriction Euchromatin: Chromatin or chromosomal regions that are lightly staining and are relatively uncoiled (loosely packed) the interphase portion of the cell cycle. Euchromatic regions contain most of the structural genes and are more prone to gene expression. Heterochromatin: The heavily staining, late-replicating regions of chromosomes that are prematurely condensed in interphase (tightly packed areas and almost have o gene expression). Heterochromatic areas are genetically inactive because they either lack genes or contain genes that are repressed. Also, heterochromatin replicates later during the S phase of the cell cycle than does euchromatin. C-banding: if chromosome preparations from mice were heat denatured and then treated with Giemsa stain, a unique staining pattern emerged: Only the centromeric regions of mitotic chromosomes took up the stain! The staining pattern was thus referred to as C-banding. G-banding: Involves the partial digestion of the mitotic chromosomes with the enzyme trypsin to remove protein associated with it, followed by Giemsa staining (rich A-T regions). Chromosomes can be matched up as the banding patterns are identical in homologs. The differential staining reactions reflect the heterogeneity and complexity of the chromosome along its length.Repetitive DNA sequence: A DNA sequence present in many copies in chromosome (genes for rRNA). Satellite DNA: DNA that forms a minor band when genomic DNA is centrifuged in a cesium salt gradient. This DNA usually consists of short sequences repeated many times in the genome tandem repeats and highly repetitive. Localized to the heterochromatic centromeric regions of chromosomes. 147-bp length of the 2-nm-diameter of DNA molec is wrapped around an octamer of histone proteins called nucleosome. (6x11nm). 11nm diameter fibers then packed into 30nm solenoid structure (6 nucleosomes, H1 protein in between each). This is a 6 fold increase compared to DNA. Forms a series of looped domains, condensed into chromatin 300nm fiber. This fiber is then coiled into chromatid arms. VNTRs: Belong to middle Repetitive Sequences: These non-coding repeating DNA sequences may be 15 to 100 bp long and are found within and between genes.Clusters are called minisatellites. Number of repeats of specific sequences varies among individuals and was the basis for forensics DNA fingerprinting. STRs: referred to as microsatellites, dispersed throughout genome. Middle Repetitive Sequences: Short tandem repeats 2–16 base pairs long that are found within minisatellites.(di-tri-pentanucelotides) These sequences are used to prepare DNA profiles in forensics, paternity identification. Polymorphism can happen in these, which is variation in DNA sequence between individuals, thus useful for genome analysis. SINEs: Typically come from virus infections. Repetitive Transposable sequences called short interspersed elements. are less than 500 base pairs long and may be present 500,000 times or more in the human genome(13%). belong to the Alufamily(the name is based on the presence of DNA sequences recognized by the restriction endonuclease AluI).LINEs:)Long interspersed repetitive sequences found in the genomes of higher organisms. LINEs are usually about 6 kb in length and in the human genome are present approximately 850,000 times. Aka retrotransposons Role not identified. Polytene Chromosomes: insect chromosomes, linear and huge because DNA undergoes many round of replication, without strand or cytoplasmic division This offers more copies of gene, thus more proteins(hypot). Contains puffs – areas where DNA uncoils for genetic activity. Don’t separate -> linked at the centromere. Chromosomes of 1-5k DNA strands remain in precise parallel alignment, giving rise to distinct band patterns. Lampbrush cromosomes: typically found in amphibian oocytes. Chromosome undergoe myosis and express genes simultaneously, because eggs have to survive harsh environments, also to preserve energy when it gets fertilized to undergo division. Homologs are synapsed pairs held at chiasmata. Instead of condensing, they extend.Denaturation of DNA: heat causes hydrogen bonds in DNA to break, helix unwinds and strands separates. Results in loss of function. May be caused by chemical treatment. The viscosity of the DNA decreases, and both the UV absorption and the buoyant density increase. Higher temp for G-C rich DNA (3H). Renaturation occurs if cooled down, and strands brought together to allow for reassociation. Complete match is not essential, provided there are stretches of base pairings. Lecture 3: Gene: The fundamental physical unit of heredity, whose existence can be confirmed by allelic variants and which occupies a specific chromosomal locus (the same gene will always going to be found on the same chromosome of any individual in normal situations.). A DNA sequence coding for a single polypetide.Allele: One of the possible alternative forms of a gene, often distinguished from other alleles by phenotypic effect. Transcription regulatory element: site before the promoter, where the protein (hormone ex) attaches to and either inhibits or enhance expression. Not necessarily found in the beginning of the gene, can be at the end, middle another chromosome Transcription: Transfer of genetic information from DNA by the synthesis of a complementary RNA molecule using a DNA template. Sigma subunit recognizes the promoter region. Transcription factor: general (TFIID, TFIIA, TFIIB) bind with RNAPII to the transcription initiation site. Specific – influence the rate of transcription RNA polymerase transcription: unwinds the DNA helix and enables it to separate and makes a copy of the coding strand chain starting from 5’-3’ (uses template strand copy 3’-5’)Translation initiation site: it needs to be transcribed, and it will signal to start making protein from this side. Promoter TATA Box, CAAT box etc.: another site which sigma subunit recognizes and signal to RNAPII to pass 5’ UTR Introns: info that codes for nothing and elemininated when then RNA molecule is done basically spliced out by snRNPs (U1-U6) U1 at 5’ end, U2 at branching point in the middle. U2 to 5’ end, then 5’ end (U6,U5, U2 ) to 3’ end, cutting out intron. U5 ligates strands together. Codons : A triplet of nucleotides that specifies a particular amino acid or a start or stop signal in the genetic code. Sixty-one codons specify the amino acids used in proteins, and three codons, called stop codons, signal termination of growth of the polypeptid
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