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BIO130H1 (167)
Chapter 1


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University of Toronto St. George
Wolfgang Moeder

TERM TEST 1 NOTES CHAPTER ONE OF TEXTBOOK CELLS AND GENOMES  10 million, perhaps 100 million living species on earth  Most are single celled organisms  ALL CELLS STORE THEIR HEREDITARY INFO IN THE SAME LINEAR CHEMICAL CODE (DNA)  DNA – storage of hereditary information, made of long unbranched paired polymer chains, always made of the same four monomers: A T C G: adenine thymine cytosine guanine  ALL CELLS REPLICATE THEIR HEREDITARY INFORMATION BY TEMPLATED POLYMERIZATION:  Each monomer/nucleotide consists of 2 parts: sugar [deoxyribose] and a base, either ATCG  A binds to T, C binds to G; therefore two complementary sequences forming a double helix o Bonds between base pairs are weak so the strands can easily be pulled apart without breaking backbones [sugar and phosphate]; so that each strand can serve as a template for the synthesis of a fresh strand: DNA REPLICATION  ALL CELLS TRANSCRIBE PORTIONS OF THEIR HEREDITARY INFORMATION INTO THE SAME INTERMEDIARY FORM [RNA]  DNA must also express information by guiding synthesis of other molecules  Leads to the production of two other polymers, RNAs and proteins  TRANSCRIPTION – when segments of DNA are used as templates for the synthesis of RIBONUCLEIC ACID, or RNA [DNA->RNA]  TRANSLATION – when RNA molecules direct the synthesis of polymers of a different chemical class, the proteins [RNA->protein]  basically, DNA replication > RNA production > protein production  RNA backbone is made of ribose instead of deoxyribose; instead of thymine there’s Uracile  The dna segment can be used over and over again for synthesis, therefore it’s a fixed formation. RNA transcripts are mass-produced and disposable.  Since these transcripts function as intermediates, they’re called mRNAs or messenger RNA to guide proteins according to genetic instructions in DNA  RNA molecules are single stranded, therefore they are more flexible to form weak bonds with other parts of same molecule, e.g. CCCC with GGGG  ALL CELLS USE PROTEINS AS CATALYSTS [things that increase the rate of chemical reaction]  Protein molecules are long unbranched polymer chains formed by stringing together monomeric building blocks drawn from a standard repertoire that is the same for all living cells  Carry information like DNA and RNA  Monomers of protein [the A G C T equivalents] are called AMINO ACIDS, different from those of RNA and DNA and there are 20 instead of 4 types  Core around which aminos are built, and a side group that gives each amino acid a chemical character  Protein molecules are called POLYPEPTIDES and are created by joining aminos in a particular sequence where it will have reactive sides on its surface  Amino acid polymers bind with high specificity to other molecules and act as enzymes to catalyze reactions that make or break covalent bonds; they direct the vast majority of chemical processes in the cell  Other functions include maintaining structure, generating movements, sensing signals, they put the cell’s genetic info into action  Polynucleotides specify amino acid sequences of proteins > proteins catalyze reactions including the ones where DNA molecules are synthesized, creating a loop that is the basis of autocatalytic, self-reproducing behaviour of living organisms  ALL CELLS TRANSLATE RNA INTO PROTEIN THE SAME WAY  Complex process going from 4 letters genetics to 20 of proteins  Information in a sequence of messenger RNA is read out in groups of three nucleotides at a time. Each triplet, or codon codes for a single amino acid in a protein. There are 64 [4x4x4] possible codons, but only 20 amino acids... therefore, several codons correspond to the same amino acid  TRANSFER RNAS, tRNAs – codes are read out by these, a class of small RNA molecules. Each tRNA attaches to an amino acid, and displays at other end a sequence of nucleotides, ANTICODON, that enables it to recognize, through base pairing, a particular codon or subset of codons in mRNA  for synthesis of protein, succession of tRNA molecules charged with appropriate aminos have to be brought together with an mRNA molecule and matched up. Aminos then have to be linked together to extend growing protein chain, then released  process is carried out by the ribosome, formed of two main chains of RNA, called ribosomal RNAs, rRNAs and like 50 proteins  this thing latches onto the end of an mRNA molecule and then trundles along it, capturing tRNAs and stitching together the amino acids they carry to create a new protein chain  THE FRAGMENT OF GENETIC INFORMATION CORRESPONDING TO ONE PROTEIN IS ONE GENE  DNA molecules are very large because they contain the specification for thousands of proteins  Individual segments of entire DNA are transcribed into separate mRNA molecules, with each segment coding for a different protein. Each segment is called a GENE.  Complications that RNA molecules can be transcribed in more than one way so there are alternative versions of a protein  A gene is therefore defined more generally, as the segment of DNA sequence corresponding to a single protein or set of alternative protein variants  In all cells, the expression of individual genes is regulated: instead of manufacturing all proteins at once, the cell adjusts the rate of transcription and translation of genes independently, according to need  REGULATORY DNA are spread across the segments and the areas that don’t code have the purpose of binding to proteins to create a structure that controls the rate of transcription; also acting as punctuation, deciding when and where the protein begins and ends  Quantity of regulatory DNA varies, but the basic process is universal  The GENOME of the cell – all of the genetic info as embodied in the complete DNA sequence, dictates both the nature of the proteins as well as when/where they’ll be made  LIFE REQUIRES FREE ENERGY  Living cell is a dynamic chemical system that operates far from its chemical equilibrium  Cells must take in free energy. This is fundamental. When cells die, they decay towards chemical equilibrium  Genetic info is also fundamental. Free energy is required for the propagation of info. E.g. choosing between protein possibilities requires energy: molecules captured put in their proper places, bonded, linked, put on a template etc.  ALL CELLS FUNCTION AS BIOCHEMICAL FACTORIES DEALING WITH THE SAME BASIC MOLECULAR BUILDING BLOCKS  Since all cells make DNA RNA and protein, their molecules must be similar like sugars, nucleotides and amino acids  All cells require ATP atenosine triphosphate as building block for synthesis of RNA and DNA; also carries free energy and phosphate groups for other chemical reactions  While all cells operate similarly biochemically, the details of their molecules differ  Some organisms are simpler than others e.g. plants make their own organic stuff, whereas animals feed off others so their cells come ready-made  ALL CELLS ARE ENCLOSED IN A PLASMA MEMBRANCE ACROSS WHICH NUTRIENTS AND WASTE MATERIALS MUST PASS  This plasma membrane is universal and essential to cell life  Acts as a selective barrier for collecting outside nutrients and containing inside ones  Molecules forming this membrane are amphiphilic – consisting of one part that is hydrophobic and one part that is hydrophilic [water-soluble] where these molecules, when exposed would cluster the hydrophobic mol. While keeping hydrophilic exposed  Aggregate in water to form a bilayer that creates small closed vesicles  Hydrophobic tails are hydrocarbon polymers –CH2-CH2-CH2- and their assembly into a bilayered vesicle is an example of: cells produce molecules whose chemical properties cause them to self-assemble into the structures that a cell needs  Proteins in the membrane that transport nutrients; some have been so well preserved we can recognize the family resemblance between even distant organisms  Transport proteins choose which molecules enter, and the proteins inside choose the reactions of those molecules. Thus, since proteins are manufactured, the genetic info recorded in the DNA sequence dictates the entire chemistry of the cell; also its structure and behaviour  A LIVING CELL CAN EXIST WITH FEWER THAN 500 GENES  What are the minimum requirements for life?  The bacterium mycoplasma genitalium has the smallest known genomes; lives as a parasite, has only 480 genes in its genome of 580070 nucleotide pairs, representing 145018 bytes of info  Minimum number of genes viable is probably not less than 200-300, although 60 shared cells between species THE DIVERSITY OF GENOMES AND THE TREE OF LIFE  Microorganisms make up most of the living matter on earth  It’s easy to characterize organisms, easy to consider the routes by which the cells obtain matter and energy, how they depend on others, basic chemical needs  CELLS CAN BE POWERED BY A VARIETY OF FREE ENERGY SOURCES  Different ways of obtaining free energy  ORGANOTROPHIC – feeds on other things, PHOTOTROPHIC – feeds on sunlight, makes oxygen LITHOTROPIC – feeds on rock, microscopic, places where humans don’t frequent, some get energy from aerobic reactions [getting molecules in the air]; organotrophic cannot exist without the last two  SOME CELLS FIX NITROGEN AND CARBON DIOXIDE FOR OTHERS  Making living cells requires matter in addition to energy  DNA, RNA and protein consist of six elements: hydrogen, carbon, oxygen, nitrogen, phosphorus, sulfur  Plentiful in non-living environment, but not in chemical forms because they are extremely unreactive in the atmosphere  Cells depend on each other, since they differ widely in biochemistry  Cells with complementary needs have developed close associations; some have lost their individual identities and became an single composite cell  THE GREATEST BIOCHEMICAL DIVERSITY EXISTS AMONG PROCARYOTIC CELLS  Living organisms are classified on the basis cell structure into EUCARYOTES & PROCARYOTES  EUCARYOTES – has a nucleus, where DNA is kept whereas prokaryotes don’t  PRO are small, simple, outward in appearance o live independently rather than multicellular organisms, o single cytoplasmic compartment containing DNA RNA and protein o live in many niches, therefore are extremely diverse biochemically  we realize that some species can’t be cultured in the lab. 99% of pros remain to be characterized  THE TREE OF LIFE HAS THREE PRIMARY BRANCHES: BACTERIA, ARCHAEA, EUCARYOTES  It’s hard to tell what the differences are between species when they become physically similar  The answer: genome analysis. Simpler, more direct, more powerful way to determine evolutionary relationships  Prokaryotes comprise two distinct groups: bacteria [eubacteria] and archaea [archaebacteria]  Archaea inhabits env. That humans avoid e.g. bogs, sewage treatment plants, ocean depths; not easily distinguishable from bacteria, resemble eukaryotes more for genetic info
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