Starter for Cells and Genomes.pdf

Cells & Genomes: A Starter for Genetics Cell – the basic structural and functional unit of all living things. Genome – the set of hereditary information encoded in the DNA of an organism, including both protein-coding & non-protein coding sequences. Gene – A DNA sequence coding for a single pol...

Cells & Genomes: A Starter for Genetics Cell – the basic structural and functional unit of all living things. Genome – the set of hereditary information encoded in the DNA of an organism, including both protein-coding & non-protein coding sequences. Gene – A DNA sequence coding for a single polypeptide. The fundamental physical unit of heredity w/c occupies a specific chromosomal locus. The 3 primary branches of the tree of Life Prokaryotes: Bacteria (or Eubacteria) Ex. E. coli Bacillus  lack cell wall & contain a genome w/ fewer than 500 genes Mycoplasma (Bacteria), the smallest known cells (0.2 µm diameter) Bacteria present in every habitat on Earth, from ice shelf of antarctic to the driest African deserts to internal confines of plants & animals The 3 primary branches of the tree of Life Prokaryotes: Archaea (or archaebacteria) Ex. Methanothermobacter Methanococcus Archaebacteria - those that can thrive in extreme conditions: extremely high temperatures extremely salty extremely acidic Arhaea - often found inhabiting environments that humans avoid, such as: bogs sewage treatment plant ocean depths salt brines  Hot acid springs soils lakes  Cyanobacteria Synechocystis (Unicellular) Anabaena (Filamentous) Spirulina Most Bacteria & Archaea have 1000 – 6000 Genes Bacteria & Archaebacteria have small genomes, w/ genes packed closely together & minimum quantities of regulatory DNA between them. Small genome size has made it made it easy to use modern DNA sequencing techniques to determine complete genome sequences. (Contain between 106 & 107 nucleotide pairs, encoding 1,000 – 6,000 genes) Eukaryotes Animals plants Fungi Filamentous fungi Mushrooms  yeast (S. cerevisiae) Protists paramecium amoeba euglena algae (plant- like protists) protozoans Model Orgnisms for Cell and Molecular Biology Mus musculus Human & mouse: similar genes & similar development – have similar patches on foreheads. Both have mutations in the Kit gene needed for development & maintenance of pigment cells.  Arabidopsis thaliana Small weed, Thale cress (Arabidopsis thaliana), can be grown indoors in large numbers. Produces thousands of offsprings per plant after 8-10 wks. Genome size is 220 million nucleotide pairs, 17 X the size of yeast.  Drosophila melanogaster Model for genetic studies – proof of the existence of genes that are carried on chromosomes. Used D. melanogaster for research & discovered the period gene (PE) affecting circadian rhythm. Polytene chromosome of Drosophila melanogaster – Giant chromosome, due to many rounds of DNA replication without an intervening cell division.  Caenorhabditis elegans About 1 mm. long. Mostly hermaphroditic (producing both eggs and sperm). W/ a life cycle of only a few days, an ability to survive in a freezer and a simple body plan. Model for cell division and cell death. Zea mays  Escherichia coli Rod shaped bacteria, lives in the gut of humans & other vertebrates, can be grown easily in a simple nutrient broth in a culture bottle. Standard lab strain is E. coli K-12.  Saccharomyces cerivisiae Small, single-celled fungi. Easy to grow in a simple nutrient medium. Can reproduce either vegetatively or sexually. Has a very small genome.  Danio rerio Has a generation time of only 3 months. Transparent for the first 2 weeks of its life, one can watch the behavior of individual cells in the living organism. Xenopus laevis – model for vertebrate development (w/ a duplicated genome, twice as much DNA per cell).  No gene is ever entirely new. “New genes” can can occur thru: 1. Intragenic mutation: an existing gene can be randomly modified by changes in its DNA sequence, thru various types of error that occur in DNA replication 2. Gene duplication - existing gene can be duplicated to create a pair of identical genes w/in a single cell; the 2 genes may diverge in the course of time. Gene Duplications Give Rise to Families of Related Genes w/in a Single Cell A cell duplicates its whole genome each time it divides into 2 daughter cells. Accidents result in inappropriate duplication of just part of the genome, w/ retention of original & duplicate segments in a single cell.  Once a gene has been duplicated, one of the 2 gene copies is free to mutate & become specialized to perform a different function w/in the same cell. Repeated rounds of duplication & divergence, over millions of years, have enabled 1 gene to give rise to a family of genes found in a single genome. DNA sequence of prokaryotic genomes reveal examples of such gene families: Bacillus subtilis, 47% of genes have one or more obvious relatives.  Genes gradually differ in the course of time, but are likely to continue to have corresponding functions in 2 related species Orthologs – Genes related by descent in 2 separate species derived from the same ancestral gene. Paralogs - Related genes that have resulted from a gene duplication event w/in a single genome - & are likely to have diverged in their function. 3. DNA segment shuffling – 2 or more existing genes can break & rejoin to make a hybrid gene consisting of DNA segments that originally belonged to separate genes. 4. Horizontal (intercellular) transfer: DNA is transferred from the genome of one cell to that of another – even to that of another species. (Contrast w/ the usual vertical transfer). Prokaryotes – provide good examples of horizontal transfer of genes from one species to another. Viruses – (Bacteriophages) Vectors for gene transfer. A virus will replicate in one cell, emerge from it w/ a capsule & then enter & infect another cell, w/c maybe of the same or a different species.  By virus-mediated transfer, bacteria & archaea can acquire genes from neighboring cells easily. Genes that confer resistance to antibiotic or an ability to produce a toxin, can be transferred from species to species & provide recipient bacterium w/ selective advantage.  New & dangerous strains of bacteria have been observed to evolve in bacterial ecosystems that inhabit hospitals or various niches in the human body. Horizontal gene transfer is responsible for the spread, over the past 40 years, of penicillin-resistant strains of Neisseria gonorrhoeae (that causes gonorrhoea).  About 18% of all of the genes in present-day genome of E. coli have been acquired by horizontal transfer from another species w/in the past 100 million years.  Horizontal transfer of genes between eukaryotic cells of different species are rare. (but massive transfers from bacteria to eukaryotic genomes have occurred in mitochondria & chloroplasts)  In Eukaryotes, sexual reproduction causes large-scale horizontal transfer of genetic information between 2 initially separate cell lineages – Father & Mother. Key feature of sexual reproduction in Eukaryotes: Genetic exchange occurs only between individuals of the same species. Result: individuals who are related more closely to one set of relatives w/ respect to some genes & more closely to another set of relatives w/ respect to others.  These types of changes leave a characteristic trace in the DNA sequence of the organism, & there is evidence that all 4 processes have frequently occurred. The Function of a Gene Can often Be Deduced from Its Sequence If sequence of newly discovered gene has been determined, one can search for the entire computer database of known gene sequences for genes related to it.  The function of one or more of these genes will have already been determined experimentally. Gene sequences determine gene function: one can make a guess at the function of a new gene (it is likely to be similar to that of already known homologs). Gene families classified by Function Common to All 3 Domains of the Living World: Information processing Cellular processes & signaling Metabolism Poorly characterized Mutation - the process that produces an alteration in DNA or chromosome structure; in genes, the source of new alleles. Mutations Reveal the Functions of Genes The analysis of gene functions depends on Genetics & Biochemistry. Genetics starts w/ the study of mutants: one either finds or make an organism in w/c a gene is altered & examine the effects of the organism’s structure & function. Biochemistry – directly examines functions of molecules from an organism & then study their chemical activities. Genetics & biochemistry used in combination w/ cell biology provide the best way to relate genes & molecules to the structure & function of an organism.  DNA sequence information & the powerful tools of molecular biology have accelerated progress. Specific subregions w/in the gene can be identified that have been preserved or unchanged over the course of time. These are the CONSERVED REGIONS These CONSERVED REGIONS are likely to be the most important parts of the gene in terms of function.  contributions of the CONSERVED REGIONS can be tested by creating mutations of specific sites w/in the gene, or by constructing artificial hybrid genes that combine part of one gene w/ part of another. Human Genome Project - an international scientific research project w/ the goal of determining the sequence of nucleotide base pairs making up human DNA, & of identifying & mapping all of the genes of the human genome from both a physical & a functional standpoint. Information from Human Genome Project & other areas of genetics is now having far-reaching effects on our daily lives. Ex: researchers & clinicians are using genomic information to improve the quality of medical care via translational medicine. Translational medicine- a process in w/c genetic findings are directly “translated” into new & improved methods of diagnosis & treatment. One important area of focus is cardiovascular disease, w/c is the leading cause of death worldwide. One of key risk factors for development of heart disease is presence of elevated blood levels of “bad” cholesterol (low- density lipoprotein cholesterol, or LDL cholesterol).  Statin drugs - effective in lowering blood levels of LDL cholesterol & reducing risk of heart disease, but up to 50 % of treated individuals remain at risk … & serious side-effects prevent others from using these drugs. Pharmaceutical firms - developing a new generation of more effective cholesterol-lowering drugs. But, bringing a new drug to market is costly & can run over $1 billion, & many drugs (up to 1 in 3) fail clinical trials & are withdrawn. Human genetics - now playing a vital role in drug development. Blood levels of LDL in a population vary over a 3-fold range, & about 50 % of this variation is genetic. The role PCSK9 gene, in controlling LDL levels is an outstanding example of how a genetic approach has been successful in identifying drug targets & improving chance that a new drug will be successful. Rapid transfer of basic research on PCSK9 to drug development & its use in treating patients is an original example of translational medicine.  After PCSK9 gene was identified, several mutant forms of this gene were found associated w/ extremely high levels of LDL cholesterol, resulting in a condition, familial hypercholesterolemia (FH). Scientists wondered if other mutations in PCSK9 might have opposite effect & drastically lower LDL cholesterol levels. s Hence, they focused on data from Dallas Heart Study, w/c gave detailed information, including LDL levels & DNA samples, from 3500 individuals. DNA sequencing of PSCK9 gene from people w/ extremely low LDL levels identified 2 mutations that reduced blood levels of LDL by 40 %. Carriers of these mutations had an 88% lower risk of heart disease.  PCSK9 protein binds to LDL receptors on liver cells, moving receptors into cell & are broken down. But, if PCSK9 protein does not bind to LDL receptor, receptor is returned to cell surface & can remove more LDL from bloodstream. Carriers of the 2 mutations have much lower PCSK9 protein levels. Thus, liver cells in these individuals have more LDL receptors, w/c in turn, remove more LDL from the blood. pharmaceutical firms have developed antibody-based drugs that bind to PCKS9 protein & prevent its interaction w/ LDL receptors, w/c in turn, lowers LDL cholesterol levels.  Clinical trials show that LDL blood levels can be reduced up to 70 % in the test population, & one of these drugs has been shown to reduce heart attacks & strokes by 50%. It is expected that the drugs will soon be available to treat elevated cholesterol levels.  PCSK9 gene study shows that pairing genetic research w/ drug development play a critical & exciting role in speeding the drive of research findings into medical practice. Genetics has a Rich & Vibrant History It’s not known when people 1st knew the hereditary nature of traits, but archaeological evidence… records successful domestication of animals & cultivation of plants many years ago thru artificial selection of genetic variants from wild populations. Genetics has a Rich & Vibrant History In 8000 & 1000 b.c., animals were domesticated & selective breeding of these species soon followed. Genetics has a Rich & Vibrant History Cultivation of many plants began in 5000 b.c. Such evidence documents our ancestors’ successful attempts to manipulate the genetic composition of species. In the Golden Age of Greek culture, writings of the Hippocratic School of Medicine (500–400 b.c.) & of Aristotle (384– 322 b.c.) discussed heredity as it relates to humans. The Hippocratic treatise On the Seed argued that active “humors” in various parts of the body served as the bearers of hereditary traits. Active “humors” - from various parts of the male body to the semen & passed on to offspring, humors could be healthy or diseased, w/ diseased humors accounting for the appearance of newborns w/ congenital disorders or deformities. Belief: “humors” could be altered in individuals before passing on to offspring, explains how newborns could “inherit” traits that their parents had “acquired” in response to their environment. Aristotle: male semen contained “vital heat” w/ the capacity to produce offspring of the same “form” (i.e., basic structure & capacities) as the parent. Aristotle: “vital heat” cooked & shaped menstrual blood produced by female, w/c was the “physical substance” that gave rise to an offspring.  Embryo developed not because it already contained parts of an adult in miniature form but because of the shaping power of the vital heat.  The ideas of Hippocrates & Aristotle appear primitive & naive, but we should understand that prior to 1800s neither sperm eggs had been observed nor in mammals. In 1600 & 1850- strides provided insight into biological basis of life. In 1600s, William Harvey proposed theory of epigenesis: the organism develops from fertilized embryo by a succession of developmental events that transform embryo into an adult.  The theory of epigenesis conflicted w/ the preformation theory, w/c stated that the sperm or the fertilized egg contains a complete miniature adult, a homunculus In 1830, Matthias Schleiden & Theodor Schwann proposed the cell theory, stating that all organisms are composed of cells derived from pre-existing cells.  Spontaneous generation, the creation of living organisms from nonliving components, was disproved by Louis Pasteur. Living organisms were derived from preexisting organisms & consist of cells. Charles Darwin & Evolution Charles Darwin - published “The Origin of Species” in 1859, described his ideas about evolution. His geological, geographical & biological observations convinced him thatexisting species arose by descent w/ modification from ancestral species.  Darwin’s voyage on HMS Beagle (1831– 1836), led him to formulate: theory of natural selection, w/c presented an explanation of the mechanism of evolutionary change. Alfred Russell Wallace natural selection: based on observation that populations tend to contain more offspring than environment can support, leading to struggle for survival among individuals. Individuals w/ heritable traits are better able to survive & reproduce than those w/ less adaptive traits. Natural selection Over time, advantageous variations, even very slight ones, will accumulate. If a population carrying inherited variations becomes reproductively isolated, a new species may result. Darwin lacked understanding of genetic basis of variation & inheritance, a gap that left his theory open to criticism into the 20th century. Gregor Johann Mendel (1866) showed how traits were passed on from generation to generation in pea plants & offered a general model of how traits are inherited. His research was little known until partially duplicated & enlightened by Carl Correns, Hugo de Vries & Erich Tschermak in 1900.  Mendel used quantitative data analysis to his results & showed that traits are passed from parents to offspring in predictable ways. concluded that each trait is controlled by pair of factors ( genes) & that during gamete formation (meiosis), members of a gene pair separate from each other. Mendel’s work became recognized (1900) explaining transmission of traits in pea plants & all other higher organisms. His work forms the foundation for Genetics, w/c is defined as the branch of biology concerned w/ the study of heredity & variation. 20 years after Mendel, researchers identified chromosomes & establish that most eukaryotes have a characteristic number of chromosomes called diploid number (2n) in most of their cells. Chromosomes in diploid cells exist in pairs (homologous chromosomes).  The Chromosome Theory of Inheritance (Walter Sutton & Theodore Boveri, 20th Century) - states that inherited traits are controlled by genes residing on chromosomes faithfully transmitted thru gametes, maintaining genetic continuity from generation to generation. Genetic Variation Scientists study inheritance of traits in fruit fly, Drosophila melanogaster. White-eyed fly was discovered among normal (wild-type) red-eyed flies. This variant was produced by a mutation in 1 of the genes controlling eye color. Mutations are any heritable change in the DNA sequence & are the source of all genetic variation. Genetic Variation The white-eye variant discovered in Drosophila is an allele of a gene controlling eye color. Alleles are defined as alternative forms of a gene. Different alleles may produce differences in observable features, or phenotype, of an organism.  The set of alleles for a given trait carried by an organism is the genotype. Using mutant genes as markers, geneticists can map the location of genes on chromosomes. The Chemical Nature of Genes: DNA or Proteins? 1920s: proteins & DNA were the major chemical components of chromosomes. Because of proteins’ universal distribution in the nucleus & cytoplasm, researchers thought proteins were the carriers of genetic information. In 1944 - Avery, MacLeod & McCarty (Rockefeller Institute, NY) proved that DNA was the carrier of genetic information in bacteria but failed to convince influential scientists Further evidence for the role of DNA as a carrier of genetic information came from scientists who worked w/ viruses (Hershey & Chase). This evidence provided solid proof that DNA, not protein, is the genetic material, setting the stage for work to establish structure of DNA (Hershey & Chase, 1952)  The Structure of DNA & RNA A 20th century great discovery by James Watson & Francis Crick (1953) is the structure of DNA. DNA is a long, ladder-like macromolecule that twists to form a double helix. Each linear strand of the helix is made up of nucleotides. Maurice Wilkins, Watson & Crick were awarded a Nobel Prize in 1962 for their work on the structure of DNA. James Watson, Francis Crick, Maurice Wilkins & Rosalind Franklin (1962 Nobel Prize)  RNA DNA but contains a different - similar to sugar (ribose) in its nucleotides & contains nitrogenous base uracil in place of thymine. RNA, is generally a single-stranded molecule. Gene Expression: From DNA to phenotype Proteins & biological function The diversity of proteins & the biological functions they perform…. affect the diversity of life itself. It arises from 20 different amino acids. A protein’s shape & chemical behavior are determined by its linear sequence of amino acids Enzymes – form the largest category of proteins; biological catalysts, lowering energy of activation in a reaction & allowing cellular metabolism to proceed at body temperature. Proteins- critical components of cells & organisms, includes: hemoglobin - the oxygen binding molecule in red blood cells. insulin – a pancreatic hormone collagen – connective tissue molecule actin & myosin – contractile muscle proteins The biochemical or structural properties of a protein play a role in producing a phenotype. Mutation – alters a gene, it may modify or eliminate the encoded protein’s usual function & cause an altered phenotype. Mutation in a gene encoding B-globin Sickle cell anemia causes amino acid substitution in 1 of the 146 amino acids in the protein. Individuals w/ 2 mutant copies of Beta- globin gene have sickle cell anemia. ss (2 copies of the mutant Beta globin gene) have sickle cell anemia  cause hemoglobin molecules in RBC to polymerize when blood’s oxygen concentration is low, forming long chains of hemoglobin that distort shape of RBC. Mutant Beta- globin proteins Deformed cells are fragile & break easily, reducing the number of red blood cells in circulation. Sickle-shaped blood cells block blood flow in capillaries & small blood vessels, causing severe pain & damage to the heart, brain & muscles. (Close relationship between genotype & phenotype). Development Recombinant DNA of Technology Began the Era of DNA Cloning: Restriction enzymes, vectors, recombinant DNA, clones. Biotechnology: the impact is continually expanding Use of recombinant DNA technology & other molecular techniques to make products is called biotechnology. Products of biotechnology: health care, agriculture, supermarket, drug development GM crops – resistant to herbicides, insects & nutritional enhancement. Dolly (cloned) sheep Bioinformatics Genomics Proteomics