BY 210 (Genetics Final Exam)
BY 210 (Genetics Final Exam) BY 210
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This 9 page Study Guide was uploaded by Whitney Okesanjo on Sunday June 19, 2016. The Study Guide belongs to BY 210 at University of Alabama at Birmingham taught by Shahid M. Mukhtar in Summer 2016. Since its upload, it has received 14 views. For similar materials see Genetics in Biology at University of Alabama at Birmingham.
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Date Created: 06/19/16
BY 210 Final Exam Study Guide Lecture 13, 14, 15 Statistical methods – distribution, mean variance, standard deviation, correlation Application of statistical methods are mainly heritability Mitochondria and chloroplasts are eukaryotic cytoplasmic organelles that exhibit many properties of eubacterial DNA Endosymbiont theory – mitochondria and chloroplasts are thought to be descended from bacteria that fused with nucleated cells because: o They have their own DNA o mtDNA and cpDNA are not arranged into nucleosomes mtDNA is circular and generally relatively small Introns generally absent Encodes rRNAs, tRNAs, and 13 polypeptides in humans Ancestral – retain many characteristics of their eubacterial ancestors Derived – differ from eubacterial ancestors o Inhibitors of bacterial translation block mitochondrial and chloroplast translation This does not happen in eukaryotic translation o rRna gene sequences are comparable In human mtDNA, two strands are notably different in base composition, leading to one strand being “heavier” than the other. o The “heavy” starnd is the H strand (H for heavy) and is composed of purines o The “lighter” strand is the L strand (L for light) and is composed of pyrimidines Both strands encode genes, although more are on the H strand D loop (D for displacement) – a short region (1121 bp), with 2 overlapping copies of the H strand The D loop is the site where most of the replication and transcription is controlled Replication in mtDNA is random DNA polymerase (gamma) replicates mtDNA Giant precursor mRNAs are formed off each strand and then cleaved into smaller segments Translation has more “wobble”) Extensive variation among different organisms in transcription and translation Mitochondrial genetic code varies in different organisms, thus making it an exception to the universal code In humans, there are 5 differences between the universal and mitochondrial genetic codes Uniparental inheritance – transmission through the cytoplasm rather than the nucleus mtDNA is maternally inherited in animals (through the egg only) A few sperm mitochondria enter the egg, but they are degraded and lost Allows for tracing female line back in time Homoplasmy – distinctive types of DNA within the cytoplasm of a single cell Heteroplasmy – all wild-type or all mutant-type DNA are in the cytoplasm of a single cell Myoclonic epilepsy and ragged red fiber disease (MERRF) o Mutations in mitochondrial tRNAs o Deleterious effect on ATP production o Individuals affected by MERRF are heteroplasmic o Severity of phenotype depend on percentage of mutant mtDNA Tissue distribution of mutant mitochondria and MERRF phenotype o Tissues with higher energy requirements are less tolerant of mutant mitochondria o Tissues with low energy requirements are affected only when the proportion of wild-type mitochondria is great decreased Oocyte nuclear transplantation can sidestep transmission of mitochondrial disease Chloroplast DNA exhibits many properties of eubacterial DNA o The gene structure and organization of cpDNA is similar to that of eubacterial DNA o Little is known about cpDNA replication o Transcription and translation are similar to those of eubacteria o Origins from cyanobacteria Chloroplast also exhibit cytoplasmic (maternal or rarely paternal) inheritance pattern Biparental inheritance sporadically happens Mitochondria and chloroplasts require nuclear gene products to assemble and function o Cytochroms oxidase c Functions in mitochondrial electron transport 7 subunits: 3 encoded by mitochondrial genome, 4 by nuclear genes o Nuclear genes encode majority of protein required for gene expression in mitochondria and chloroplasts Genetic material can be exchanged between nucleus, chloroplasts and mitochondria Termed “promiscuous DNA” Quantitative genetics – the genetic analysis of complex traits is known as quantitative genetics. These traits are generally influenced by polygenic inheritance (multiple genes), allele interactions and environmental factors Continuous characteristics - Variation within a population in which a graded series of intermediate phenotypes falls between the extremes. Meristic and threshold characteristics are examples of discontinuous traits that are considered quantitative o Meristic characteristics – counting quantitative features; examples are counting litter size; must be a number not a decimal o Threshold characteristics – exhibits two phenotypes or characteristics like healthy or sick o These genes are determined by multiple genes and environmental factors Quantitative genetics are different from Mendelian genetics in the in quantitative genetics, genes are unlinked Statistical methods are required for analyzing quantitative characteristics: o Population – group of interested individuals o Sample – small collection of individuals from the population o Types of distribution – symmetrical/asymmetrical bell curve (normal, skewed and bimodal) The mean provides information about the center of a distribution: o Mean – the sum of all measurements divided by the number of measurements o Variance (S^2): Variance describes how far values lie from the mean Environmental variance – genetically identical seeds grown in a variable environment Genetic variance – genetically different seeds grown in a constant environment o The average squared deviation of the observations from the mean form the variance o Standard deviation – the square root of the variance 95% - standard confidence in interval in biological science o The proportion of a trait’s variation that is due to genetics is a property of interest in heritability o Phenotype = Genotype + Environment Phenotypic variance – determines how much phenotypic differences in a population is due to genetic or environment VP = V + V + V G E GE The total phenotypic variance for a character (V p is a function of: Genetic variance (V )– the variance among the mean G phenotypes of different genotypes Environmental variance (V )– thE variance among phenotypes expressed by replicate members of the same genotype o Differences between monozygotic twins are due to environmental factors The total genetic variance for a character (V G is a function of: o Additive genetic variance (V ) – Aariation due to the additive effects of alleles o Dominance genetic variation (V ) – vDriation due to dominance relationships among alleles o Epistatic genetic variation (V) –Ivariation due to interactions among loci 2 Broad-sense heritability (H ): reflects all the genetic contributions to a population's phenotypic variance including additive, dominant, and epistatic (multi-genic interactions), as well as maternal and paternal effects. 2 Narrow-sense heritability (h ): The additive genetic portion of the phenotypic variance is known as and is defined as Population – Local groups of organisms belonging to a single species, sharing a common gene pool and can interbreed Gene pool – a gene pool is the sum of the total genes present in a population at a given time Genotypic frequency – the frequency with which different genotypes are present in a population Allele frequency – the frequency with which alleles of a particular gene are present in a population Frequency of an allele = No. copies of the alleles / No. copies of all alleles at the locus in a population. Genome sequencing: determining the order of the nucleotide bases —A, G, C, and T—in a molecule of DNA Methods: o Sanger chain termination (or dideoxy) sequencing o F. Sanger o Genome sequencing using shotgun sequence method o Exploration of genomic databases (NCBI, USCS etc.) o SNPs, mutations and types of mutations PCR Recap o https://www.youtube.com/watch?v=iQsu3Kz9NYo Primer is designed to be complementary to plasmid sequence adjacent to the unknown insert sequence. Template and primer interact through hybridization. Sanger chain sequencing o https://www.youtube.com/watch?v=vK-HlMaitnE o ddNTP- 2’,3’-dideoxynucleotide o No 3’ hydroxyl o Terminates chain when incorporated optimize the concentration of ddNTP and dNTP so that ddNTP is randomly and completely incorporated at each base Genomes are large (typically millions or billions of base pairs). The dideoxy method is good only for ~1000 bp reactions. Genomic library: Collection of cellular clones that contains copies of every sequence in the whole genome inserted into a suitable vector The Human Genome Project began using the hierarchical strategy o Construct BAC genomic library o Identify sets of overlapping BAC clones o Shear DNA from each BAC separately to make smaller clones. o Sequence DNA o Assemble sequences based on overlap. Contig - Contiguous sequence of DNA created by assembling overlapping sequenced fragments of a chromosome (BACs) Assembly - Putting sequenced fragments of DNA into their correct chromosomal positions A draft Genome: Usually available in early phase of the sequencing project Has lower accuracy than a finished sequence; some segments are missing or in the wrong order or orientation A reference sequence - not an exact match for any one person Blood (female) or sperm (male) samples taken from a large number of donors. DNA can be read in six reading frames. An open reading-frame (ORF) is a reading-frame uninterrupted by stop codons. Distance between genes is determined based on sequencing data. Distance is measured in base pairs (bp). Annotation – linking the gene sequence to information about: o Its expression o Its function o Its homology to other genes (USCS database) Homologs – evolutionary conserved genes Orthologs: homologous genes in different species that evolved from the same ‘ancestor gene’ Paralogs: homologous genes in the same organism that arose by duplication of a single gene Copy number variants (CNVs) o large blocks of duplication or deletion with population frequency of < 1% Simple sequence repeats (SSRs) o 1-10 base sequence repeated 15-100 times in tandem Single nucleotide polymorphisms o One base pair changes Deletion-insertion polymorphisms (DIPs) o Short insertions or deletions of a single or a few base pairs Transition – substituting a base of the same type. Transversion – substituting a base of the opposite type. Missense mutation – alters a codon so that it specifies a different amino acid in a protein (amino acid substitution). Nonsense mutation - converts an amino-acid-specifying codon into a stop codon. Silent mutation – alters a codon into one that codes for the same amino acid. Euploid: chromosome number is the exact multiple of the haploid number, 2n in humans Aneuploid: chromosome number is NOT the exact multiple of the haploid number Robertsonian Translocation -a translocation that occurs in maternal germ line cells and joins the long arms of two acrocentric chromosomes and creates a single large chromosome. The short arms become lost. Common mutagens include: DNA Repair mechanisms o 1-Lesion repair enzymes o Base excision repair (BER), which repairs damage to a single base caused by oxidation, alkylation, hydrolysis, or deamination. o Nucleotide excision repair (NER), which recognizes bulky, helix- distorting lesions such as pyrimidine dimers and 6,4 photoproducts. o Mismatch repair (MMR), which corrects errors of DNA replication and recombination that result in mispaired (but undamaged) nucleotides. Three mechanisms exist to repair double-strand breaks (DSBs): non-homologous end joining (NHEJ) microhomology-mediated end joining (MMEJ) homologous recombination (HR). Multiple cancer phenotypes arise from mutations in genes that regulate cell growth and division Environmental chemicals increase mutation rates and increase chances of cancer Cancer is the result of a multistep process that requires several mutations (successive mutations). Three ways cancer evades normal cell controls: o Produce cell division signals (autocrine stimulation) o Lose contact inhibition o Avoid programmed cell death Apoptosis - genetically programmed cell death (suicide). The Hayflick limit - the number of times a normal cell population will divide before it stops, presumably because the telomeres reach a critical length. o Normal cells are mortal in culture (Hayflick limit). o Cancer cells are immortal in culture (e.g. HeLa cells). Cancer usually involves several genes: o Proto-oncogenes In normal cells Code for proteins involved in the stimulus of cell division If altered, may form oncogenes Alone, do not cause malignant cancer o Require other mutations, including one in a tumor suppressor gene Mutation in oncogenes/tumor suppressor genes cause cancer Mutation DNA repair genes o Oncogenes act in a dominant fashion to promote cancer o All have a gain-of-function effect: Ras (see later part of the seminar) usually active when bound to growth factor oncogenic point mutation makes constitutively active protein c-Abl Chromosomal translocation fuses the c-abl and bcr genes Hybrid protein encodes a constitutively active tyrosine kinase Her2 Found in 20% of all breast cancers overexpressed growth factor receptor Genes that control cell division: o Control of the cell cycle Cyclin-dependent kinases (CDKs), cyclins o G -to-S transition 1 Retinoblastoma protein (RB) o G2-to-M transition Mitosis-promoting factor (MPF) o Spindle assembly checkpoint o Mutations in cell-cycle control and cancer Cyclin-dependent kinases (CDKs) – family of kinases that regulate the transition from G1 to S and from G2 to M Cyclin specifies the protein targets for CDK o Phosphorylation by CDKs can activate or inactive a protein P53 Tumor: o Activated at the G1/S checkpoint whenever the cell has DNA damage. o Inhibits cell proliferation until the DNA damage can be repaired. o If the DNA damage is irreparable, it initiates apoptosis. o About half of human tumors lack a functional p53 gene. Viruses: o Sub microscopic entities consisting of a single nucleic acid surrounded by a protein coat o Capable of replication only within the living cells of bacteria, animals or plants. o Single type of nucleic acid – either DNA or RNA but not both o Linear or circular o Not cells and not alive o Can reproduce only inside host Types of viruses o DNA viruses dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses, Bacteriophages) ssDNA viruses (+ strand or "sense") DNA (e.g. Parvoviruses) o RNA viruses dsRNA viruses (e.g. Reoviruses) (+)ssRNA viruses (+ strand or sense) RNA (e.g. Picornaviruses, Togaviruses) (−)ssRNA viruses (− strand or antisense) RNA (e.g. Orthomyxoviruses, Rhabdoviruses) o Reverse transcribing viruses ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses) dsDNA-RT viruses (e.g. Hepadnaviruses) Lytic vs Lysogenic Cycle o https://www.youtube.com/watch?v=wLoslN6d3Ec o Lytic A phage attaches to the receptor on the bacterial cell wall Viral DNA gets injected Phage DNA is replicated, transcribed/translated New phages are produced and released Bacteria are lysed (virulent phages) o Lysogenic Phage integrates into bacterial genome (Temperate phages). An integrated phage in a bacterial chromosome is called a prophage. Every time the bacterium replicates its chromosome, it also replicates the prophage. Thus, a prophage becomes part of the bacterial genome and is passed on from generation to generation (latent infection). Hope for cancer: o PVS-RIPO is a genetically engineered poliovirus that is being investigated as a new anti-cancer agent. o PVS-RIPO is a live attenuated, oral serotype 1 poliovirus vaccine that contains a heterologous internal ribosomal entry site arising from human rhinovirus (cause of the common cold) type 2. o The vaccine recognizes nectin-like molecule-5, a tumor antigen that is widely expressed in malignancies. Anti-cancer agents are: o Block carcinogen activation Flavonoids and isoflavonoids Coumarins Isothiocyanates in cruciferous vegetables Organosulfur compounds in garlic & onions o Enhance carcinogen detoxification Antioxidants in plants Isothiocyanates in cruciferous vegetables Organosulfur compounds in garlic & onions o Increase DNA repair Polyphenols in green tea Selenium (Brazilian nuts)
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