Genomes and the Flow of Biological Information

Genomes and the flow of biological information The roots of biology The diversity of life is unified by some common themes Despite their diversity at the macroscopic level, where distinctive features of organisms are readily apparent with the naked eye, the core molecular features of all organisms are remarkably similar Key themes of living A living organism must be distinct in some way from its organisms environment, that is, it must be defined by a physical barrier, which serves to operate "organism" from • Must be distinct from "environment" environment A living organism must be able to store its genome in a • Must be able to store stable way and also have a way of using this information to determine its characteristic features - its structural genome composition, how it functions, and so on • Must be able to replicate A living organism must be able to reliably replicate and pass and pass information information from one generation to the next • Require a source of energy Replication: the process wherein a complementary copy from surroundings to grow of each strand of DNA is generated by DNA polymerase Living organisms require a source of energy from their surroundings to grow and reproduce; this energy is used to drive the biological processes that keep an organism alive In modern-day organisms, the physical barrier that separates individuals from their surroundings (and so defines "self") is a lipid-based membrane, while a molecular species known as nuclei acid stores the biological information and allows for ready replication of this information (thus conferring "self" identity) Living organisms are constructed from common molecular building blocks It is thought that the entire diversity of modern-day life derives from a common original life form often referred to as the last universal common ancestor (LUCA) or progenote, whose molecular components have been conserved from generation to generation, and from species to Basic classes of species, as different organisms have evolved molecules: progenote: putative common original life form from which the entire diversity of modern-day life derives, often referred to 1. Nucleic acids as the last universal common ancestor (LUCA) 2. Proteins Nucleic acids typically have a simple, linear structure composed of 3. Lipids monomer building blocks (the nucleotides); they contain the 4. Carbohydrates instructions for life, and thus for the propagation of life Proteins are also linear polymers, composed of distinct building blocks known as amino acids, and typically fold into complex three-dimensional structures Lipids are "water-fearing" molecules that self-assemble to form the membranes that present a physical barrier to the exterior milieu, thus defining self Carbohydrates are "water-loving" molecules that play a wide range of roles in the cell, from providing energy to increasing the solubility of otherwise insoluble proteins The flow of biological information supports the maintenance of life Ultimately, a flow of information is needed to ensure that the offspring of an organism remains faithful to its parents In terms of the characteristics it exhibits The maintenance of life relies on the process of reproduction - both in the context of the growth of a specific tissue through rounds of cell division and in the development of new offspring from a parent Heritable information is stored in a simple polymer of monomer building blocks Information in all cells is stored in a repeating polymer structure called deoxyribonucleic acid (DNA), which is easily copied and transmitted to subsequent generations DNA is a type of nucleic acid and is composed of four building blocks known as nucleotides: deoxyguanosine monophosphate (G), deoxyadenosine monophosphate (A), deoxythymidine monophosphate (T), and deoxycytidine monophosphate (C) The resulting strings of letters specify genetic identity; they encode all functional molecules that must be synthesized for the cell - and ultimately the organism - to survive and propagate When two different nucleic acids have complementary sequences - that is, where A on one strand is matched by T on another, and where C on one strand is matched by G on the other - the close association of these pairs of nucleotides allows the two sequences to form extended doublestranded structures with a characteristic double-helical conformation Duplication of the information stored in DNA is facilitated by their complementarity; a complementary, fully informational strand can be made by separating the two strands and using the sequence of nucleotides in each of the two original strands to direct the synthesis of two new strands The Genome: A Working Blueprint For Life Genome: the complete DNA sequence of an organism, which serves as its instructional blueprint Transmission and maintenance of the genome are essential for life At the cellular level, the copying of the genetic information (replication), the separation (or "segregation") of the copies, and transfer into the cells of the next generation are required, even if the recipient is to remain part of the same organism - for example, a new skin cell or muscle cell In molecular terms, this means that the nucleic and, typically DNA, must be copied In its entirety, with few errors, In order to maintain the integrity of the genome - that is, the accuracy of the information contained within it The molecular machine, or enzyme, responsible for synthesizing the new DNA copies is known as DNA polymerase and, as we shall see, is very highly conserved across different organisms The genome is composed of genes and intergenic regions A gene is typically defined as a region of DNA that controls a discrete, hereditary characteristic and, as such, usually specifies the production of a functional product (a protein or RNA molecule) Different types of sequence are typically found within a given gene; some of the sequence directly encodes the product of the gene, whereas other sequences within a gene are important for specifying how and when to make the product. These regions are often referred to as coding and regulatory regions, respectively. Intragenic DNA: DNA that les between coding genes on a chromosome. These regions can contain regulatory elements, as well as transposable elements and other repeated sequences The genome is physically organized into chromosomes The large amount of DNA that constitutes a genome must be packaged in an organized way that facilitates the various key events in the life of a cell, including the replication of DNA and the expression of genes In eukaryotic chromosomes, the DNA is wrapped tightly around packaging proteins (referred to as histones) to assume a highly ordered three-dimensional structure. This highly compacted form of DNA is optimal for storage as it is very space efficient. However, highly compacted DNA does not facilitate information retrieval In addition to chromosomes, some cells have plasmids, which are extra-chromosomal pieces of DNA that can also carry important genetic information Gene number and arrangement vary greatly among organisms Although single-called bacteria generally have fewer genes than multicellular organisms, there is no simple correlation between genome size, gene number, and organism complexity It is clear that the number of different products (RNAs or proteins) that can be generated from a given gene is large. So even though the genome of a given organism may feature a seemingly modest number of genes, the same genome may, in fact, encode A huge range of different functional products Transposable element: discrete mobile DNA segment that can move between nonhomologous positions in a genome It is becoming clear that the value of the genome, in terms of governing the processes that underpin biological complexity, comes from more than just the genes from which a genome is composed. Instead it comes from a combination of gene number, the production of multiple gene products from the information carried in a single gene, and the regulatory activity of the genome's intergenic regions Bringing Genes to Life: Gene Expression Genes encoded by DNA must be "expressed" These two molecules, RNA and protein, are the principal structural and functional components of the cell and are responsible for reactions that harvest energy, synthesize cellular components, and facilitate the import and export of materials Genomes are the blueprint for life, but it is through molecular biology - the array of molecular components and processes - that this blueprint is used to direct now life at the level of a given organism proceeds Once the RNA copy of the gene has been synthesized, it is either "translated" into the corresponding protea sequence or used directly, such that the RNA molecule produced by transcription has its own specific biological function Transcription is the first step in gene expression for the production of both non-coding RNAs and proteins The process of copying the DNA sequence of interest into the corresponding RNA is referred to as transcription. The molecular machinery that is responsible for carrying out transcription is RNA polymerase and is closely related to the DNA polymerase that is responsible for replicating the genome The RNA polymerase catalyzes the synthesis of an RNA strand by joining together nucleotide monomers (single nucleotides) in a sequence dictated by the DNA template that the RNA polymerase is "reading" The initial product of a transcription event is referred to as the primary transcript. For some genes, the final functional gene product is an RNA species derived from the primary RNA transcript; such RNA species often possess regulatory functions These two classes are commonly referred to as non-coding and coding RNAs, respectively; the key distinction is that non-coding RNAs are not translated to give a protein product, whereas coding RNAs are For both non-coding and coding RNAs, the primary transcript RNA is typically subjected to a serves of events that from away and modify the RNA in a refinement process broadly referred to as RNA processing, to yield the final RNA molecule The RNA sequence is next "translated" to make functional proteins The nucleic acid code for protein synthesis is composed of the four different nucleotides, which are assembled in long linear arrays that are "read" three nucleotides at a time to specify which of the 20 different amino acids should be incorporated at a given point in the protein Distinctive sequences in the mRNA specify the start and stop sites for protein synthesis, while the successive triplet nucleotide sequences in between encode the linear sequence of amino acids that comprise the final protein product At the core of the process of translation is a functional RNA called transfer RNA (tRNA), which acts as a physical link between the coding information (in the form of a triplet nucleotide sequence that reads the codons) and the appropriate amino acid In essence, a population of tRNAs sequentially "reads" the codons in a processive march along the mRNA template, recruiting amino acids to the growing protein chain in the order specified by the mRNA template The functional repertoire of the cell is much more complex than the genome A direct consequence of the fact that RNA and protein products can be modified following their initial synthesis is that the complete set of functional RNAs and proteins is far more extensive than the set that is simply encoded by the genome Regulating Gene Expression Gene regulation: mechanisms through which the expression of a gene product is controlled in time and space Both the level and the activity of a gene product can be regulated Gene expression can be controlled by simply regulating the level of the gene product. The level can be controlled by either promoting or preventing the synthesis of the RNA product at the level of transcription or by controlling the translation of a protein Thus, a protein that is needed at only a particular stage in the development of an organism may only be synthesized just before it is needed and may then be rapidly degraded at a later stage in development The expression of key gene products is regulated at multiple levels in response to multiple signals Proteins that are frequently mutated in cancer cells, or represent the “tipping point" in the cellular decision to initiate development or to initiate A dramatic change in cell metabolism, are an example of gene products whose expression is tightly regulated, often at all possible levels Cellular Infrastructure and Gene Expression An internal membrane-bound compartment in the cell contains the genome in eukaryotes The membrane encapsulates the genetic information critical for self-propagation, together with the functioning molecules of the cell. In addition to the exterior membrane shared by all organisms, more complex organisms have additional membrane-bound compartments in their interior In prokaryotes, the chromosomal DNA is sequestered in a region called the nucleoid. By contrast, higher-complexity organisms (including those that are unicellular and multicellular) contain an internal membrane-bound structure called the nucleus where the genetic information is contained Eukaryotic cells feature multiple membrane-bound compartments with specialized functions Endoplasmic reticulum Mitochondria Lysosome Centrosomes Microtubules Ribosome Nucleus Nucleolus Cell Wall Cell Membrane Golgi body Endoplasmic reticulum: organelle found in eukaryotic cells comprising a network of tubules wherein lipids are synthesized and secreted proteins are translated, folded, modified, and then sent on their way Mitochondria: organelles found in eukaryotic cells that contain the macromolecular machinery responsible for deriving chemical energy from food precursors Centrosomes: a cytoplasmic structure that nucleates microtubules Golgi apparatus: organelle found in most eukaryotic cells that processes proteins and modifies them with sugars before packaging them for export Microtubule: long, hollow polymer of tubulin heterodimers with two distinct ends, a plus end and a minus end, which display different polymerization behaviors Ribosome: macromolecular ribonucleoprotein machine responsible for the translation of the genetic information in the mRNA into the encoded polypeptide Nucleus: membrane-bound compartment found in eukaryotic cells where the chromosomes are contained Nucleolus: structure in the nucleus where transcription of rRNAs and assembly of the ribosomes and other RNA-containing complexes occur Both mitochondria and chloroplasts contain DNA unique to these organelles that encodes certain components critical to their function. This feature led scientists to hypothesize that these organelles originated as endosymbionts, organisms living within another cell that eventually become wholly dependent on their host for existence Compartmentalization is important for facilitating chemical reactions All cellular reactions depend on interactions between molecules; by localizing various components together, their effective cellular concentrations are increased and so reactions can proceed more efficiently In addition to the chemical benefits of increased concentrations of cellular components, cells also benefit from the level of organization that accompanies compartmentalization Compartmentalization is crucial for regulating gene expression in eukaryotic cells The natural consequence of the fact that DNA in eukaryotic lens is housed in a membranebound compartment, the nucleus, is that a large amount of regulatory control of gene expression has developed, which is based on this physical separation from the rest of the cell This difference in location offers an immediate opportunity for regulation - just as you can regulate movement from one room to another in a house by locking (or unlocking) the door between them, so the physical barrier presented by the nuclear membrane provides an opportunity to regulate passage from the nucleus to the cytoplasm, such that passage can only occur if certain conditions are met This feature thus provides the cell with an opportunity for quality control - the blocking of movement of the transcript from the nucleus to the cytoplasm across the nuclear membrane which prevents inadequately processed mRNAs from encountering translational machinery Proteins that are destined for the membrane or for export from the cell have physical properties that are incompatible with passage through the membrane without specific assistance Expression of the genome Output of the genome is dictated by the interplay of genes The visual features and properties of an organism are referred to as the phenotype, while the collective DNA sequence that determines the phenotype is referred to as the genotype of the organism Haploid: containing one copy of each chromosome Diploid: containing two sets of chromosomes The importance of ploidy is that, in a haploid organism, a single version of a gene is expressed, whereas in a diploid organism, there is typically a mixed population of gene products derived from the expression of two different copies of the gene Genetic analysis has been essential in deciphering the natural function of genes Much of our understanding of biology comes from what are referred to as genetic approaches, which probe the natural function of genes by comparing so-called wild-type (normal) properties, the typical or most common form, with non-wild-type (mutant) ones Forward genetics: random mutagenesis of a population of organisms, followed by isolation of organisms with a given phenotype With a more complete understanding of genomes and their complete composition, and with sophisticated tools of gene manipulation, it has become possible to specifically disrupt a gene of interest in some organisms and to study the phenotypic consequences Reverse genetics: analysis of the consequences to the organism of directly inactivating a particular gene Genotype changes have phenotypic consequences If, in a diploid, the phenotype of the mutant gene product 18 masked by the presence of the wild-type version, then the mutation is said to be recessive By contrast, if a mutant gene product has obvious phenotypic consequences when the wild-type product is present, then the mutation is said to be dominant Mutations can be the result of very small changes in the gene (i.e. the alteration of a nucleotide), the rearrangement of large regions of the chromosome, the insertion of new segments of DNA or the deletion or excision of small or large sections of the genome In protein-coding genes, a change of one nucleotide can be sufficient to change a codon from one which encodes a particular amino acid to one encoding a different one Missense mutation: single nucleotide change in the DNA sequence that changes a codon encoding a particular amino acid to one encoding a different one Nonsense mutation: change in the DNA sequence that introduces a premature stop signal, such that only truncated gene products are made Silent mutations: change in the DNA sequence that does not result in obvious phenotypic change The origin of disease can often be traced to mutations in the organism Somatic cells: these constitute the building blocks of the body of an organism and simply transmit their genetic information to daughter cells in the same organism Germline cells: these are involved in the production of the progeny and transmit the generic information to the next generation of the organism Evolution of the Genome and the Tree of Life The evolution and diversification of life are gradual Instead, it is far more likely that these common mechanisms were passed down from our ancestors into each new species, defined as a group of organisms capable of interbreeding and producing fertile offspring, as the evolved Over time, environmental influences, such as disease, will continue to "select for" the mutant individuals and, over time, an ever-larger portion of the population will contain the mutant gene, until it becomes the norm All organisms can be grouped into three domains of life, based on sequence comparisons The bacterial domain encompasses the largest number of organisms and continues to grow as more bacteria are identified by the sampling of an increasing number of environments. These organisms are single-celled and have minimal subcellular compartmentalization Archaeal organisms share features with organisms in the bacterial domain in that they are unicellular and do not have a nuclear structure. However, core archaeal proteins typically show more sequence similarity to the corresponding proteins found in eukaryotic organisms Eukaryote organisms are distinguished by more extensive compartmentalization than found in either bacteria or archaea, including the nucleus that holds their DNA, and by possessing a cytoskeleton that helps to structure and organize their larger cell volume