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Chapter 1

Chapter 1: Cells and Genomes.docx

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University of Toronto St. George
Melody Neumann

Chapter 1: Cells and Genomes The Universal Features of Cells on Earth - Heredity is central to the definition of life; distinguishes life from other processes in which orderly structures are generated but without the peculiarities of both parents & offspring. - Nothing less than a cell has the capacity to gather raw materials from the environment & construct a new cell in its own image complete with a new copy of hereditary information. All Cells Store Their Hereditary Information in the Same Linear Chemical Code (DNA) - All living cells on Earth store their hereditary information in the form of double-stranded molecules of DNA [long unbranched paired polymer chains formed from 4 types of monomers] - Genetic information is universally read, interpreted & copied. All Cells Replace Their Hereditary Information by Templated Polymerization - Mechanism that makes life possible depends on the structure of double stranded DNAmolecule. - Monomer = sugar (deoxyribose) + phosphate + base - Each sugar is linked to the next by the phosphate - For a single isolated strand, the monomers can be added in any order through part of the molecule that is the same for all of them. - In living cells DNAis synthesized on a template formed by a preexisting DNAstrand. o Base from existing strand binds to the base on strand being synthesized [Base-pairing rule =A-T & C-G] - The two strands twist around each other forming a double helix. - Bonds between two bases are weak when compared to the sugar-phosphate links. This allows the stands to be pulled apart without breakage of backbone.  Templated Polymerization All Cells Transcribe Portions of Their Hereditary Information Into The Same Intermediary Form (RNA) - DNA must express its information by letting it guide the synthesis of other molecules in the cell. This occurs by the production of RNAs & proteins. o Transcription (templated polymerization): segments of DNA are used as templates for synthesis of RNA o Translation: RNAdirects the synthesis of proteins - RNAhas a different backbone sugar = Ribose & a different base = Uracil (replaces Thymine) - During transcription RNA molecules are lined up & selected for polymerization on a template strand of DNA. The outcome is a polymer whose sequence represents cell’s genetic info in RNA monomers. - RNA transcripts are mass-produced & disposable and function as intermediates in the transfer of genetic information (serve as mRNA to guide synthesis of proteins according to genetic instructions stored in the DNA). - RNAmolecules are single stranded  flexible backbone o Can bend back on itself to allow one part of the molecule to form weak bonds with another part of the same molecule which is locally complimentary. This causes the RNA molecule to fold up into a specific shape (dictated by its sequence). The shape of RNA molecule in turn may enable it to recognize other molecules by binding to them selectively. All Cells Use Proteins as Catalysts - Protein molecules are long unbranched polymer chains formed by stringing together monomeric building blocks. They carry information in the form of linear sequences of symbols. They also form most of the cell’s mass (excluding water). - Monomer = amino acids; 20 types o Each amino acid is built around the same core structure through which it can be linked in a standard way to any other amino acid. o Attached to the core is a side group that gives each amino acid a distinctive chemical character. - Each protein molecule created by joining amino acids in a particular sequence folds into a precise 3D form with reactive sites on its surface. o These amino acid polymers bind with high specificity & act as enzymes (catalyze reactions that make or break covalent bonds). - Proteins maintain structure, generate movements & sense signals. - They put the cell’s genetic information into action. - Feedback loop is the basis of autocatalytic, self-reproducing behavior. o Polynucleotides specify the amino acid sequences of proteins. o Proteins catalyze many chemical reactions (including those by which new DNA molecules are synthesized) o The genetic information in DNAis used to make both RNAand proteins. All Cells Translate RNAinto Protein in the Same Way - Arbitrary features reflect frozen accidents in the early history of life (chance properties that have become deeply embedded in the constitution of all living organisms & cannot be changed without disastrous effects). - Information in mRNA is read in groups of 3 nucleotides; Codon = specifies a single amino acid in a corresponding protein. - Since there are 64 codons (4x4x4) but only 20 amino acids, there are necessarily many cases in which several codons correspond to the same amino acid. - Code is read out by tRNA. o Each tRNA attaches to an amino acid at one end & displays at its other end a specific sequence of 3 nucleotides (Anti-codon) that enables it to recognize a particular or subset of codons in mRNA. - Ribosomes are formed by 2 main chains of rRNAs & more than 50 proteins o Synthesis of protein: tRNAs charged with appropriate amino acid are brought together with an mRNA & matched up through anti-codons. Amino acids are then linked together to extend the growing protein chain & tRNAs are released. The Fragment of Genetic Information Corresponding to One Protein is One Gene - A gene is a segment of DNA sequence corresponding to a single protein or set of alternative protein variants. - The expression of individual genes is regulated; the cell adjusts the rate of transcription & translation of different genes independently according to need. - Stretches of regulatory DNA are interspersed among the segments that code for protein & these non-coding regions bind to special protein molecules that control the local rate of transcription. - Genome of the cell dictates the nature of cell’s proteins and when & where they are to be made. Life Requires Free Energy - Free energy is required for the propagation of information. o To specify information, molecules from a wild crowd are captured, arranged in a specific order, defined by some pre-existing template & linked together in a fixed relationship. o Bonds must be strong enough to resist disordering effect of thermal motion. o The process is driven forward by consumption of free energy. All Cells Function as Biochemical Factories Dealing With the Same Basic Molecular Building Blocks - All cells need to contain & manipulate a similar collection of small molecules that are universally required the synthesis of DNA, RNA& proteins. o All cells require ATP as a building block for DNA & RNA synthesis and also make & consume the molecule as a carrier of free energy. All Cells are Enclosed in a Plasma Membrane across Which Nutrients and Waste Materials Must Pass - Plasma membrane acts as a selective barrier that enables the cell to concentrate nutrients gathered from the environment & retain the products it synthesizes while excreting its waste products. - Molecules forming this membrane are amphiphilic; consisting of both hydrophilic & hydrophobic. - When placed in water, the molecules aggregate spontaneously arranging the hydrophobic portion to be in contact with one another as possible. - Amphiphilic molecules of appropriate shape aggregate in water to form a bilayer that creates small closed vesicles. o Cells produce molecules whose chemical properties cause them to self-assemble into the structure that a cell needs. - All cells have specialized proteins embedded in their membrane that transport specific molecules from one side to the other. o Transport proteins largely determine which molecules enter the cell & the catalytic proteins inside the cell determine the reactions that those molecules undergo. ALiving Cell Can Exist With Fewer Than 500 Genes - The minimum number of genes for a viable cell in today’s environment is probably not less than 200-300. - Mycoplasma genitalium has 480 genes. The Diversity of Genomes and the Tree of Life - Microorganisms make up most of the total mass of living matter on our planet. Cells Can Be Powered by a Variety of Free Energy Sources - Phototrophic organisms harvest the energy of sunlight. o By-product of their bio synthetic activities is the oxygen in the atmosphere - Lithotrophic organisms capture energy from energy-rich systems of inorganic chemicals in the environment (chemical systems far from equilibrium). o They mostly live in various inhospitable environments. o Aerobic: use molecular oxygen from environment (since O is ultimately the product of 2 living organisms, these organisms are feeding on the products of past life) o Anaerobic: little or no molecular oxygen is present (in circumstances similar to those that must have existed in the early days of life on Earth)  Hot hydrothermal vents, found deep down on the floor of the Pacific & Atlantic oceans in regions where the ocean floor is spreading as a new portion of the Earth’s crust form by gradual upwelling of material from the Earth’s interior, are the most dramatic of these sites.  A dense population of microbes lives in the neighborhood of the vent harvesting free energy from reactions between available chemicals. Other organisms such as clams, mussels & giant marine worms live off the microbes forming an entire ecosystem powered by geochemical energy. - Organotrophic organisms that get energy by feeding on other living things or the chemicals they produce. Some Cells Fix Nitrogen & Carbon Dioxide for Others - DNA, RNA& proteins are made of H, C, N, O, S & P. - Animals depend on plants for organic carbon & nitrogen compounds. Plants fix CO2 but depend on nitrogen-fixing bacteria to supply their need for nitrogen compounds. The Greatest Biochemical Diversity Exists Among Prokaryotic Cells - Eukaryotes: keep their DNA in a distinct membrane-enclosed intra-cellular compartment; the nucleus. - Prokaryotes: don’t have distinct nuclear compartment o Small & simple in outward appearance o Live mostly as independent individuals or in loosely organized communities o Spherical or rod-shaped; a few micro-meters in linear dimension o Have protective coat – cell wall o Cell interior appears as a matrix of varying texture without any discernible organized internal structure. o Many species cannot be cultured by standard laboratory techniques. The Tree of Life Has 3 Primary Branches: Bacteria, Archaea & Eukaryotes - Prokaryotes could be classified based on their biochemistry & nutritional requirements. But it is difficult to know which differences truly reflect differences of evolutionary history. - The complete DNA sequence of an organism defines its nature with almost perfect precision & in exhaustive detail. o Since DNA is subject to random changes that accumulate over time, the number of differences between DNA sequences of two organisms can provide direct, objective, quantitative indication of evolutionary distance between them. - Prokaryotes comprise of 2 distinct groups o Archaea (archaebacteria)  Are found inhabiting both extreme & not extreme environments  Resemble eukaryotes at the molecular level in their machinery for handling genetic information  Resemble bacteria more closely in their apparatus for metabolism & energy conversion o Bacteria (eubactaria) Some Genes Evolve Rapidly; Others Are Highly Conserved - Mutations: random accidents & errors that occur when storing & copying genetic information and alter the nucleotide sequence o In many cases it causes serious damage; changes are perpetuated o More probably cause no significant difference: changes may be perpetuated or not o Rarely represent a change for the better; lead to nowhere - Organisms evolve through natural selection & mutation. - Segment of DNA that doesn’t code for protein & has no significant regulatory role is free to change at a rate limited only by the frequency of random errors. - A gene that codes for protein or RNA cannot be altered easily (faulty are almost always eliminated). Therefore these genes are highly conserved. - Coding genes are the ones we should examine to trace family relationships between distantly related organisms in the tree of life. - Classification into bacteria, archaea & eukaryotes were based on analysis of one of the two main RNAcomponents of ribosome – small-subunit ribosomal RNA. Most Bacteria &Archaea Have 1000-6000 Genes - Natural selection has favored those prokaryotes that can reproduce the fastest. - Small sizes imply large ratio of surface area to volume thereby helping maximize the uptake o
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