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George S Espie

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Introduction to Cells (pgs 1-36) 30/05/2010 20:30:00 • All living this are made of “cells”: small, membrane-enclosed, units filled with a concentrated aqueous solution of chemicals and endowed with the extraordinary ability to create copies of themselves by growing and dividing in two • [Cells are the fundamental units of life] UNITY & DIVERSITY OF CELLS • Cells vary enormously in appearance and function (Figure 1-1 pg 3) • Some cells are clad only in a flimsy membrane & some cover this delicate layer by cloaking themselves in an outer layer of slime, building themselves rigid cell walls, or surrounding themselves with hard, mineralized material, such as that found in bone • There is a division of labour in cells (allowing some cells to become specialized to an extreme degree for particular tasks and leaving them dependent on their fellow cells for many basic requirements)* • All cells are composed of the same sorts of molecules that participate in the same types of chemical rxns • All present-day cells have apparently ‘evolved’ from the same ancestor • “Genome”-the complete set of genetic material in a cell (specifically its DNA) CELLS UNDER THE MICROSCOPE • “Light Microscope”- use visible light to illuminate specimens • “Electron Microscope”- use beams of electrons instead of beams of light as the source of illumination (making it possible to see the fine details of cells and even making some of the larger molecules visible individually) • “Transmission Electron Microscope”- type of electron microscope used to look at thin sections of tissue (similar to a light microscope, but transmits a beam of electrons instead) • “Scanning Electron Microscope”- type of electron microscope which scatter electrons off the surface of the sample and so is used to look at the surface detail of cells and other structures • “Cell Theory”- all living things are made up of cells and cells arise from pre-existing cells [proved by Louis Pasteur & his broth] • A tissue usu has to be fixed by embedding in a solid wax or resin, cut or sectioned into thin slices, and stained before it is viewed (regardless of the type of microscope) THE PROCARYOTIC CELL • ‘Pro’= before, ‘Karyon’= kernel, nut, or nucleus • Bacteria have the simplest structure and come closest to showing us life stripped down to its essentials: o No organelles o No membrane-bound nucleus to hold its DNA • Typically spherical, rod-like, or corkshrew-shaped, and small (0.1-10 μm diameter, 1000X less volume than Eukaryotes) • Have a protective coat, called a ‘cell wall’, surrounding the plasma membrane (i.e. cell membrane) • Cell reproduce quickly by dividing into two • With sufficient food, some can duplicate itself in as little as 20 min. • Fortunately for their; o Large numbers o Rapid growth rates, o And ability to exchange bits of genetic material by a process akin to sex,  Pops of prokaryotic cells can evolve fast, rapidly acquiring the ability to use new food source or to resist being killed by a new antibiotic • Most live as single-celled orgs (although some join together to form chains, clusters, or other organized multicellular structures) • In terms of chemistry, they are the most diverse and inventive class of cells • Live in a variety of conditions o Some are aerobic and some are anaerobic o Some can live entirely on inorganic substances; CO in2the atmosphere, N from N in2the atmosphere, O, H, S, & P in the air, water, and inorganic minerals o Some perform ‘photosynthesis’ (getting energy from sunlight) o Other derive their energy from the chemical reactivity of inorganic substances in the env. (E.g. Beggiatoa) • It is almost certain that chloroplasts have evolved from photosynthetic bacteria that found a home inside the plant cell’s cytoplasm • Two Domains: “Bacteria” – include most of the prokaryotes familiar from everyday life “Archaea”- usu live in hostile conditions THE EUCARYOTIC CELL • ‘Eu’ = true, ‘Karyon’ = kernel, nut or nucleus • Bigger and more elaborate (as compared with Prokaryotes) • Some live as single-celled orgs (E.g. Amoeba, Yeasts) • Other live in multicellular assemblies Main Organelles: “Nucleus” i. usu the most prominent organelle ii. enclosed within two concentric membranes that form that ‘nuclear envelope’ iii. contains molecules of DNA “Mitochondria” i. present in all Eukaryotic cells ii. contain their own DNA iii. reproduce by dividing into two iv. generators of chemical energy for the cell (i.e. power-house of the cell) v. harness energy from the oxidation of food molecules, such as sugar, to produce ATP (i.e. ‘Cellular Respiration’)  It is evident that there is a symbiotic rltnshp in which the host eukaryote and the engulfed bacterium helped one another to survive and reproduce “Chloroplast” i. large green organelles found only in the cells of plants and algae (not in the cells of animals and fungi) ii. possess internal stacks of membranes containing the green pigment ‘chlorophyll’ iii. perform ‘photosynthesis’ iv. contain their own DNA v. reproduce by dividing into two vi. thought to have evolved from bacteria- in this case from photosynthetic bacteria that were somehow engulfed by an early eukaryotic cell • Internal membranes create intracellular compartments with different functions “Endoplasmic Reticulum” (ER) i. an irregular maze of interconnected spaces enclosed by a membrane ii. is where most cell membrane components (as well as materials destined for export from the cell) are made “Golgi Apparatus” (GA) i. stacks of flattened membrane-enclosed sacs ii. receives and often chemically modifies the molecules made in the ER & then directs to the exterior of the cell or to various locations inside the cell “Lysosomes” i. small, irregularly shaped organelles in which intracellular digestion occurs [i.e. releasing nutrients from food particles and breaking down unwanted molecules for recycling or excretion] “Peroxisomes” i. small, membrane-enclosed vesicles that provide a contained env. for rxns in which Hydrogen Peroxide, a dangerously reactive chemical, is generated and degraded “Vesicles” i. involved in the transport of materials btwn one membrane-enclosed organelle and another • A continual exchange of materials takes place btwn the ER, GA, lysosomes, and the outside of the body cell • Exchange is mediated by small vesicles that pinch off from the membrane of one organelle and fuse with another • Portions of the plasma membrane tuck inward and pinch off to form vesicles that carry material captured from the external medium into the cell • These vesicles fuse with membrane-enclosed ‘endosomes’ (which mature into lysosomes, where the imported material is digested) • “Endocytosis”- process whereby large particles are engulfed by the cell • “Exocytosis” – process whereby vesicles from inside the cell fuse with the plasma membrane and release their contents into the external medium [most hormones, neurotransmitters, and other signaling molecules are secreted from cells by this process] “Cytosol” i. concentrated aqueous gel of large & small molecules ii. site of many chemical rxns that are fundamental to the cell’s existence (E.g. manufacture of proteins) “Ribosomes” i. site of ‘protein synthesis’ ii. some are free in the cytosol, while others are attached to the ER “Cytoskeleton” i. network of filaments (made of proteins) criss-crossing the cytoplasm of the eukaryotic cell ii. helps organize the internal activities of the cell iii. and underlies its movements and changes of shape  The cytoskeleton is a dynamic jungle of ropes and rods that continually being strung together and taken apart; its filaments can assemble and then disappear in a matter of minutes (due to the constant motion of the cytoplasm) Types: ‘Actin Filament’ i. thinnest of the filaments ii. present in all eukaryotic cells (E.g. Animal, Plant) iii. occur in esp large numbers inside muscle cells, where they serve as part of the machinery that generates contractile forces ‘Microtubules’ i. thickest filaments (b/c they have the form of minute hollow tubes) ii. in dividing cells, they become reorganized into a spectacular array that helps pull the duplicated chromosomes in opposite directions and distribute them equally to the two daughter cells ‘Intermediate Filaments’ i. intermediate in thickness btwn the other two ii. strengthen the cell mechanically  Together with proteins, these form a system of girders, ropes, and motors that gives the cell it’s mechanical strength, controls its shape, and drives and guides its movements ‘Cytoplasm’ i. is in constant motion! • Eukaryotic cells may have originated as predators (since they have acquired all of the distinctive features for that way of life; large size, flexible membrane, and a cytoskeleton) • “Protozoans”- single-celled, free-living, actively motile microorganisms (inc. some of the most complex cells known, e.g. amebas, flagellates, ciliates, sporozoans, etc.) MODEL ORGANISMS “Escherichia Coli” (E. Coli) i. small, rod-shaped bacterial cell ii. normally lies in the gut of humans and other vertebrates iii. can be grown easily in a simple nutrient broth in a culture bottle iv. copes well with variable chemical conditions in its env. v. reproduces quickly vi. genetic instructions are contained in a single, circular, double-stranded molecule of DNA (approx 4.6 million nucleotide pairs long and it makes 4300 different kinds of proteins)  Most of out knowledge of the fundamental mechanisms of life- inc. how cells replicate their DNA and how they decode these genetic instructions to make proteins- has come from studies of E. Coli.  Subsequent research has confirmed that these basic processes occur in the same manner in our own cells ‘Brewer’s Yeast’ (Saccharomyces Cerevisiae; A Simple Eukaryotic Cell) i. single-celled fungus ii. is closely related to animals as it is to plants iii. rigid cell wall iv. relatively immobile v. possesses mitochondria, but not chloroplasts vi. when nutrients are ample, it reproduces as quickly as a bacterium (i.e. 20 min.) vii. its nucleus contains only about 2.5 times as much DNA as E. Coli viii. good subject for genetic analysis (since it carries out all the basic tasks every eukaryotic cell must perform; e.g. cell-division cycle) ‘Arabidopsis’ i. grown indoors in large #s ii. produces thousands of offspring per plant within 8-10 weeks iii. has a genome of approx. 110 million nucleotide pairs  By examining the genetic instructions, more can be learned about the genetics, molecular biology, and evolution of flowering plants, which dominates nearly every ecosystem on land ‘World of Animals’ (A Fly, a Worm, a Fish, a Mouse, and the Human Species) • Multicellular orgs account for the majority of all named species of living org (& the majority of animal species are insects) • The foundations of classical genetics were built to a large extent on studies of a small fruit fly ‘Drosophila melanogaster’ • The genes of this insect have turned out to be amazingly similar to those of humans • Another widely studied org, smaller and simpler than Drosophila is the nematode worm ‘Caenorhabditis elegans’ (a harmless relative of the eelworms that attack the roots of crops) • 70% of human proteins have some counterpart in the worm • Studies of this specimen, have led to a detailed molecular understanding of programmed cell death (a process by which surplus cells are disposed of in all animals) • Genes of one type of animal have close counterparts in most other types of animals, apparently serving similar functions • We all have a common evolutionary origin, and under the surface it seems that we share the same molecular mechanisms • Flies, worms, fish, mice & humans thus provide a key to understanding how animals in general are made and how their cells operate HOW WE KNOW: LIFE’S COMMON MECHANISMS • By analyzing the misbehaviour of the mutant org, one can pinpoint the function for which the gene is needed, and by analyzing the DNA of the mutant one can track down the gene itself • The experiments with yeasts as well as the human cells show that proteins from different orgs can be functionally interchangeable • The molecules that orchestrate cell division in eukaryotes are so fundamentally important that they have been conserved almost unchanged over more than a billion years of eukaryotic division • Molecular machinery for reading the info encoded in DNA is also similar from cell to cell and from org to org [That is the reason as to why the yeast cells could read and use the instructions encoded in the human gene] ESSENTIAL CONCEPTS • All present-day cells are believed to have evolved from an ancestral cell that existed more than 3 billion years ago • ***Cells in a multicellular org, though they all contain the same DNA, can be very different. They turn on different sets of genes according to their developmental history and to cues they receive from the env.*** • Cells of animal and plant tissues are typically 5-20 μm in diameter & can be seen with a light microscope • The nucleus is the most prominent organelle in most plant and animal cells. It contains the genetic info of the org, stored in DNA molecules. The rest of the cell’s contents, apart from the nucleus, constitute the cytoplasm • Although the minimum # of genes needed for a viable cell is less than 400, most cells contain significantly more. Yet even such a complex org as a human has only about 24,000 protein-coding genes Chemical Components of Cells (pgs 39-69, 72-78) 30/05/2010 20:30:00  ƒIs based on carbon compounds (the study of which is known as ‘organic chemistry’)  Depends exclusively on chemical rxns that take place in a watery or aqueous solution and in the relatively narrow range of temperatures experienced on Earth  It is enormously complex  Dominated and coordinated by collections of enormous ‘polymeric molecules’ (formed from chains of chemical subunits linked end-to-end)  It is tightly regulated: cells deploy a variety of mechanisms to make sure that all their chemical rxns occur at the proper place and time  Chemistry dictates all of Biology! CHEMICAL BONDS  “Atoms”:  the smallest units of a chemical element that retains the distinctive chemical properties of that element  An atom is most stable when all of its electrons are at their lowest possible energy level and when the valence shell is filled  “Atomic Weight” or “Molecular Weight”- mass of the element relative to that of a H atom (i.e. protons + neutrons of an element)  Mass of an atom of a molecule is generally specified in ‘Daltons’, one Dalton being an a.m.u. equal to the mass of a H atom  C, H, N, & O make up 96.5% of an org’s weight  Outermost electrons determine how atoms interact *** “Ionic Bonds” i. formed when electrons are transferred from one atom to another (metal  non-metal) [It’s a type of electrostatic attraction- an attractive force that occurs btwn oppositely charged atoms] ii. “Ions”- electrically charged atoms (form during Ionic Bonding) iii. Salts (end products of ionic bonds) are highly soluble in water (dissociation into individual ions) “Covalent Bonds” i. formed when two atoms share a pair of electrons ii. in covalent bonds, the electron density helps to hold the nuclei together by opposing the mutual repulsion btwn the like charges that would otherwise force them apart iii. covalent bonds btwn multiple atoms are characterized by specific bond angles, bond lengths, and bond energies  “Bond Strength”- is measured by the amt of energy that must be supplied to break a bond (usu expressed in kcal/mole or kJ/mole)  1 kcal = 4.2 kJ  Single/Double/Triple bonds have a major influence on the 3-D shape of many macromolecules  Some molecules contain atoms that share electrons in a way that produces bonds that are intermediate in character btwn single and double bonds (E.g. Benzene)  “Polar” structure- is one in which the (+) charge is concentrated toward one end of the molecule (positive pole) and the (-) charge is concentrated toward the other end (negative pole)  Covalent bonds in which electrons are shared unequally in this way are known as ‘polar covalent bonds’  In aqueous solutions, covalent bonds are 10-100 times stronger than the other attractive forces btwn atoms, allowing their connections to define the boundaries of one molecule from another ‘Polar Covalent Bonds’  Any large molecule with many polar groups will have a pattern of partial positive and negative charges on its surface.  When this encounters a second molecule with a complementary set of charges, the two will be attracted to each other by an electrostatic attraction  When enough of these weak non-covalent bonds form btwn two large molecules, their surfaces will stick specifically to each other [Water greatly reduces the attractiveness in most biological settings] ‘Water’  Accounts for 70% of a cell’s weight  Most intracellular rxns occur in an aqueous env.  Excellent solvent for many substances b/c of its polar bonds  + When a positively charged region (H ) of one water molecule comes close to a negatively charged region of a second water molecule (O), the electrical attraction btwn them can establish a weak bond called a ‘Hydrogen Bond’ [E.g. water molecules are polar, so they can form a linkage with one another to form this type of bond] ‘Hydrogen Bonds’  Formed when a Hydrogen atom is ‘sandwiched’ btwn two electron- attracting atoms (usu ‘O’ or ‘N’)  Much weaker than covalent bonds (have less that 1/20 the strength of a strong covalent bond)  Are strongest when the three atoms are in a straight line  Hydrogen bonds formed btwn two molecules dissolved in water are relatively weak  Easily broken by the random thermal motions due to the heat energy of the molecules, so each bond lasts only an exceedingly short time ***  Substances that release protons when they dissolve in water, thus forming H3O , are called ‘Acids’  pH scale  Acids are labeled as strong or weak, depending on how fast the dissociate into their respective ions (E.g. HCl is strong; Acetic Acid is weak)  Many of the important acids in the cells are weak: their tendency to dissociate with some reluctance is a useful characteristic; it renders the surfaces of large molecules sensitive to conditions in the cellular env. ***  ‘Base’- proton acceptor which forms OH when dissolved in water (E.g. NaOH is strong; N2 is weak) “Buffers” i. weak acids & bases that can release or take up protons near pH 7 ii. keeping the env. of the cell relatively constant under a variety of conditions MOLECULES IN CELLS ‘Carbon’  If we disregard water, nearly all of the molecules in a cell are based on carbon  Has a unique role in the cell b/c of its ability to form strong covalent bonds with other carbon atoms (thus they can form chains, branches, or rings)  ‘Organic Molecules’- small & large Carbon compounds made by cells  ‘Inorganic Molecules’- all other molecules (inc. water) ‘Cells Contain Four Major Families of Small Organic Molecules’  small organic molecules of the cell are carbon compounds with molecular weights in the range of 100-1000 that contain up to 30 or so carbon atoms  usu found free in solution in the cytoplasm Uses: i. Monomer subunits in order to construct polymeric macromolecules (E.g. proteins, nucleic acids, and large polysaccharides) ii. Energy sources iii. Some may have both ***  All organic molecules are synthesized from- and are broken down into- the same set of simple compounds  Both their synthesis and their breakdown occur through sequences of simple chemical changes that are limited in variety and follow definite step-by-step rules  As a result, the compounds in a cell are chemically related and most can be classified into small # of distinct families  Four Families; the Sugars, the Fatty Acids, the Amino Acids, & the Nucleotides *REFER TO TABLE 2-2 ON PG. 51 FOR APPROX CHEMICAL COMPOSITION* ‘Sugars’ i. ***Primary source of chemical energy for cells*** ii. Simplest sugars- ‘monosaccharides’ o either contain an aldehyde group & are called ‘aldoses’, or a ketone group & are called ‘ketoses’ o General formula (CH O) where ‘n’ is usu 3-6 2 n o can be linked by covalent bonds, called ‘glycosidic bonds’ to form carbohydrates [these bonds can also attach ‘carbohydrates’ to other molecules, such as a nitrogenous base in nucleic acids] o can form ‘Polysaccharides’ (long chains- E.g. Glycogen) ‘Oligosaccharides’ (short chains) o In aqueous solution, the aldehyde or ketone group of a sugar molecule tends to react with a OH group of the same molecule, thereby closing the molecule into a ring o The OH group on the Carbon that carries the aldehyde or ketone can rapidly change from one position to the other; α & β. (* REFER TO PG. 69-TOP LEFT *) * Refer to Panel 2-3 on pg 68-69 for Illustrations * iii. 3 common disaccharides are: o maltose (glucose + glucose) o lactose (galactose + glucose) o sucrose (glucose + fructose) iv. Each of the sugars, can exist in either of two forms, callD- form (C to N, from left-to-right & theL-orm (N to C, from left-to-right) [which are mirror images of each other] o * REFER TO PG 68-69 *  “Condensation Rxns”- occur when two molecules combine to form one molecule, with the loss of a small molecule [when this is water, it is called a “dehydration rxn”]  “Hydrolysis”- involves the decomposition of a compound by reacting it with water *REFER TO FIG 2-17 ON PG. 53 FOR AN ILLUSTRATION*  Cells use simple polysaccharides composed only of glucose units- principally ‘glycogen’ in animals and ‘starch’ in plants- as long-term store of glucose, held in reserve for energy production  Sugars do not function exclusively in the production and storage of energy (but rather used for mechanical supports) [E.g. the ‘cell wall’ of plants and the ‘chitin’ of insect exoskeleton and fungi cell wall are polysaccharides] ‘Fatty Acids’ i. ***Essential function is in the formation of cell membranes*** ii. Has two chemically distinct regions: o Long hydrocarbon chain (which is hydrophobic and not very reactive chemically) o Carboxyl group (-COOH), which behaves as an acid (carboxylic - acid); it is ionized in solution (-COO ), extremely hydrophilic, and chemically reactive iii. “Amphipathic”- have both hydrophilic & hydrophobic parts iv. Almost all these molecules are covalently linked to other molecules by their carboxylic acid group v. The double bonds of some fatty acids create kinks in the molecules, interfering with their ability to pack together in a solid mass vi. Are found in cell membranes, where the tightness of their packing affects the fluidity of the membrane (most important function)* vii. Serve as a concentrated food reserve in cells viii. Can be broken down to create about 6x as much useable energy as glucose ix. Stored in the cytoplasm in the form of ‘triacylglycerol’ molecules (compounds made of 3 fatty acid chains joined to a glycerol molecule) x. Insoluble in water xi. Soluble in fat & organic solvents (E.g. benzene)  The many different fatty acids found in cells differ only in o the length of their hydrocarbon chains o and in the number and position of the C-C double bonds  “Lipids”- fatty acids & their derivatives  ‘Phospholipids’: o small molecules that, like triacylglycerols, are constructed mainly from fatty acids and glycerol o Joined to two fatty acid chains, rather than to three as in triacylglycerols o The third site on the glycerol is linked to a small hydrophilic phosphate group, which in turn is attached to a small hydrophilic compound o They are strongly amphipathic: each phospholipid molecule has a hydrophobic tail, composed of the two fatty acid chains and a hydrophilic head, where the phosphate is located ‘Amino Acids’ i. Are used to build “Proteins” o polymers of amino acids joined head-to-tail in a long chain that is then folded into a 3-D structure *** ii. All possess a carboxylic acid group and an amino group both linked to the same carbon called the ‘α- carbon’ iii. “Peptide Bond”- covalent linkage btwn two adjacent amino acids in a protein chain (formed via condensation rxns) iv. Regardless of the specific amino acids, the Polypeptide always has an amino group at one terminus (‘N-terminus’) and a carboxyl group at its other end (‘C-terminus’) v. Sequence is always read from the N-terminus to the C-terminus (three- letter abbreviations are used) vi. There are 20 amino acids vii. All amino acids (except Glycine since it’s –R group is a H ), like sugars, exist as optical isomers iD-and L-forms viii. Only L-orms are found in proteins (reason is unknown) ix.D-forms occur as part of bacterial cell walls and in some antibiotics * REFER TO PANEL 2-5 ON PG 72-73 FOR ILLUSTRATIONS * ‘Nucleotides’ (Subunits of DNA & RNA) i. Play a central part in energy transfer & are the sub-units from which the informational macromolecules , RNA & DNA, are made *** ii. Functions: genetic info (DNA), protein synthesis (RNA), carrying energy, signaling molecules in the cell (E.g. cAMP), & forming coenzymes iii. Molecule made of a Nitrogenous base, a Sugar, & a Phosphate group iv. ‘Ribonucleotides’- nucleotides containing ribose v. ‘Deoxyribonucleotides’- nucleotides containing deoxyribose vi.‘Pyramidines’ o Cytosine (C), Thymine (T), & Uracil (U) o derive from a 6-membered pyrimidine ring vii. ‘Purines’ o Adenine (A), Guanine (G) o Bear second, 5-membered ring fused to the 6- membered ring viii. ‘ATP’ (Adenosine Triphosphate, or ATP) o involved in the transfer of energy in hundreds of cellular rxns o formed through rxns that are driven by the energy released by the breakdown of foodstuffs o its 3 phosphate groups are linked in series by two “phosphoanhydride bonds” • rupture of these phosphate bonds release large amts of useful energy • the terminal phosphate group is frequently split off by hydrolysis viii. Serve as building blocks for the construction of ‘nucleic acids’ – long polymers in which nucleotide subunits are covalently linked via “phosphodiester bond” btwn the phosphate group attached to the sugar of one nucleotide and a hydroxyl group on the sugar of the next nucleotide * REFER TO FIG 2-25 ON PG. 58 FOR AN ILLUSTRATION * ix. Two main types of nucleic acids: o Ribonucleic Acids (RNA) • contain the sugar ribose & the bases A, G, C, & U • occurs in cell in the form of single-stranded polynucleotide chain • usu a more transient carrier of molecular instructions • Possible Function(s): catalytic molecule (ribozyme = ‘RNA enzyme’) o Deoxyribonucleic Acids (DNA) • contain the sugar deoxyribose & the bases A, G, C, & T • hydroxyl at the 2’ position of the ribose carbon ring is replaced by a hydrogen [so therefore it is less reactive, and more resistant to degradation] • always in the form of a double-stranded molecule • composed of two polynucleotide chains running anti- parallel to each other (held together by Hydrogen bonding btwn the bases of the two chains) • acts as a long-term repository for hereditary info x. Commonly abbreviated by a one-letter code, and the ‘sequence’ is always read from the 5’ end * REFER TO PANEL 2-6 ON PG 74-75 FOR ILLUSTRATIONS * MACROMOLECULES IN CELLS  are polymers that are constructed simply by covalently linking small organic molecules (called monomers, or subunits) into long chains, or polymers ***  most abundant of the carbon-containing molecules in a living cell  principal building blocks from which a cell is constructed  also the components that confer the most distinctive properties in living things  each polymer grows by the addition of a monomer onto one end of the polymer chain via a condensation rxn (in which a molecule of water is lost with each subunit added) o * REFER TO FIG 2-28 ON PG. 59 FOR AN ILLUSTRATION *  polymer chain is not assembled at random from these subunits; instead the subunits are added in a particular order, or sequence  non-covalent bonds specify the precise shape or ‘conformations’ of a molecule  these unique conformations- shaped by N.S.- determine the chemistry and activity of these macromolecules and dictate their interactions with other biological molecules (E.g. Most proteins & many RNA molecules fold into a particularly stable 3-D shape- otherwise they would not function in the same manner)  types of non-covalent bonds important in biological molecules: o ‘Electrostatic Attraction’ (Ionic) • Strong on their own, weak in water (due to interactions btwn the molecules & the water) • Very important (E.g. an enzyme that binds to a positively charged amino acid side chain to guide its substrate into the proper position) o ‘Hydrogen Bonding’  Holds two strands of DNA double helix together  Since they are weak, enzymes can easily unzip the helix (E.g. when a cell needs to copy its genetic material) o ‘Van der Waals Attractions’ (from dipoles)  Force of electrical attraction caused by fluctuating electrical charges that arise whenever two atoms come within a very short distance of each other (0.3-0.4 nm)  Although weaker than Hydrogen bonding, they play a key role in the attraction btwn large molecules with complementary shapes o ‘Force created by the 3-D structure of water!’  Forces hydrophobic groups together in order to minimize their disruptive effect on the hydrogen-bonded network water molecules  Also gives most proteins a compact, globular shape  This expulsion from the aqueous solution generates what is sometimes thought of as a fourth kind of weak non-covalent bond, called a ‘hydrophobic interaction’  non-covalent bonds account for much of the specificity that we associate with living cells * REFER TO FIG 4-4 ON PG 123 FOR AN ILLUSTRATION * PANEL 2-1 ‘C-H Compounds’  Carbon and hydrogen together make stable compounds (or groups) called ‘hydrocarbons’  These are non-polar (hence, they are hydrophobic),  Do not form Hydrogen bonds,  And are generally insoluble in water ‘Alternating Double Bonds’  If double bonds are on alternate carbon atoms, the bonding electrons move within the molecule, stabilizing the structure by a phenomenon called ‘resonance’ (E.g. Benzene) ‘C-O Compounds’  E.g. Alcohol (-OH group), Aldehyde (terminal-C=O group), Ketone (internal –C=O group), Carboxylic Acid (-COOH group), Esters (combining an acid and an alcohol) ‘C-N Compounds’  ‘Amines’ in water combine with an H ion to become positively charged  ‘Amides’ are formed by combining an acid and an amine (unlike amines, amides are uncharged in water [E.g. peptide bond that joins amino acids in a protein] ‘Phosphates’  Inorganic phosphatei(P) is a stable ion formed from phosphoric acid, H3PO4 -  ‘Phosphate Esters’- formed btwn a phosphate and a free OH group Protein Structure & Function (pgs 119-141, 152-153) 30/05/2010 20:30:00 • Proteins are the building blocks from which cells are assembled; they constitute most of the cell’s dry mass • Proteins also execute nearly all its myriad functions PANEL 4-1 (A few examples of some general protein functions) • ‘Enzymes’ o catalyze covalent bond breakage or formation o E.g. ‘pepsin’ – degrades dietary proteins in the stomach, DNA polymerase- copies DNA • ‘Structural Protein’ o provides mechanical support to cells and tissues o E.g. outside cells, ‘collagen’ & ‘elastic’ are common constituents of extracellular matrix and form fibers in tendons and ligaments • ‘Transport Protein’ o carries small molecules or ions o E.g. ‘hemoglobin’ carries oxygen, ‘transferrin’ carries iron • ‘Motor Protein’ o generates movement in cells and tissues o E.g. ‘kinesin’ interacts with microtubules to move organelles around the cell • ‘Storage Protein’ o stores small molecules or ions o E.g. Iron is store in the liver by binding to the small protein ‘ferritin’ • ‘Signal Protein’ o carries signals from cell to cell o E.g. ‘insulin’ controls glucose levels in the blood • ‘Receptor Protein’ o detects signals and transmits them to the cell’s response machinery o E.g. ‘rhodopsin’ in the retina detects light • ‘Gene Regulatory Protein’ o binds to DNA to switch genes on or off o E.g. ‘lactose repressor’ in bacteria silences the genes for the enzymes that degrade the sugar lactose • ‘Special-Purpose Protein’ o highly variable o E.g. ‘Antifreeze proteins’ of Arctic & Antarctic fish protect their blood against freezing THE SHAPE & STRUCTURE OF PROTEINS ‘Proteins’ i. Made from a long chain of amino acids (each linked to its neighbor via ‘peptide bond’- this involves removal of water- ‘condensation rxn’) ii. Referred to as ‘polypeptides’ or ‘polypeptide chains’ iii. In each type, the amino acids are present in a unique order, called the “amino acid sequence” (which is exactly the same from one molecule of that protein to the next) iv. “Polypeptide backbone”- made from the repeating sequence of the core atoms of the amino acids that form the chain o i.e. N-C-C-N-C-C v. ‘Side Chains’ o parts projecting from the repetitive backbone o give the amino acids its unique properties o not involved in forming the peptide bond o includes 20 vi. Long polypeptide chains are very flexible o thus proteins can in principle fold in an enormous # of ways o each folded chain is constrained by many different sets of weak non-covalent bonds that form within proteins vii. an important factor governing the folding of any protein is the distribution of its polar (hydrophilic) and non-polar (hydrophobic) amino acids o this property is assessed by the side chain o non-polar side chains tend to cluster in the interior of the folded protein (so they can avoid contact with the aqueous Cytosol that surrounds them inside a cell) o polar side chains tend to arrange themselves near the outside of the folded protein, where they can form Hydrogen bonds with water and with other polar molecules o * REFER TO FIG 4-5 ON PG 124 * o when polar amino acids are buried within the protein, they are usu hydrogen-bonded to other polar amino acids or to the polypeptide back-bone o * REFER TO FIG 4-6 ON PG 124 * ‘Proteins Fold into a Conformation of Lowest Energy’ i. Denatured proteins can recover their natural shapes on their own o thus proving that the conformation of a protein is determined solely by its ‘amino acid sequence’ ii. When proteins fold incorrectly, they sometimes form aggregates that can damage cells and even whole tissues iii. Aggregated proteins underlie a # of neurodegenerative disorders (inc. Alzheimer’s disease & Huntington’s Disease), prion diseases (E.g. scarie in sheep, mad cow disease in cattle, CJD in humans) iv. The prion protein, PrP, can adopt a misfolded form that is considered ‘infectious’ b/c it can convert properly folded PrP proteins in the infected brain into the abnormal conformation o This causes rapid spreading from cell to cell, ultimately leading to death! v. Protein folding in living cells is usu assisted by special proteins called ‘molecular chaperones’ o These prevent newly synthesized protein chains from interacting with the wrong partners o Chaperones merely make the folding process more efficient & reliable ‘Proteins come in a Wide Variety of Complicated Shapes’ • Range in size from 30 amino acids to more than 10,000; vast majority are btwn 50 & 2000 amino acids long • Proteins can be globular or fibrous; they can form filaments, sheets, rings, or spheres ‘The α Helix & the β Sheet are Common Folding Patterns’ i. ‘α helix’ o was found in the protein α-keratin, which is abundant in skin and its derivatives- such as hair, nails, & horns o ‘helix preferences’: M,A,L,E o ‘helix breakers’: P,G,S,T ii. ‘β sheet’ o found in the protein fibroin (major constituent of silk)  Both result from the Hydrogen bonding that forms btwn the N-H & C=O groups in the polypeptide backbone o Since the amino acid chains are not involved in forming these Hydrogen bonds, α helices & β sheets can be generated by many different amino acid sequences o In each case, the protein chain adopts a regular, repeating form or “motif” (i.e. recurring combination of secondary structures in different proteins) * REFER TO FIG 4-10 ON PG. 130 FOR ILLUSTRATIONS * ‘Helices Form Readily in Biological Structures’ i. It is generated when a single polypeptide chain turns around itself to form a structurally rigid cylinder o Hydrogen bonding occurs btwn every fourth amino acid, linking the C=O of one peptide bond to the N-H of another • i.e. (C=O @ ‘n’) & (N-H @ n+4) o These give rise to a regular helix with a complete turn every 3.6 amino acids ii. “coiled-coil” o forms when 2 or 3 α helices have most of their non-polar side chains on one side, so that they can twist around each other with these side chains facing inward o this minimizes exposure of hydrophobic residues to aqueous env. o * REFER TO FIGURE 4-13 ON PG 132 * ‘β Sheets Form Rigid Structures at the Core of Many Proteins’ i. formed when Hydrogen bonds form btwn segments of polypeptide chains lying side to side [these still form between N-H & C=O groups] ii. 5-10 amino acids per strand; 2-15 strands (avg. ~6) iii. can form curved surfaces, barrels, and cylinders iv. ‘Parallel’- chains runs in the same direction v. ‘Anti-parallel’- chains run in the opposite direction vi. ‘Mixed’- combination of parallel & anti-parallel chains  by convention, the arrows point toward the C-terminus of the polypeptide chain * REFER TO FIG 4-14 ON PG. 132 * ‘Proteins Have Several Levels of Organization’ i. Levels are not independent but are built one upon the next until the 3-D structure of the entire protein has been fully defined ii. ‘Primary Structure’ o amino acid sequence (linked by peptide bonds) o number 1-X from N-terminus to C-terminus o linear ii. ‘Secondary Structure’ o inc. the α helices & β sheets that form within certain segments of a polypeptide chain o other structures: turns, non-repeating (loops & coils) NOT RANDOM o created by intramolecular Hydrogen bonding iv. ‘Tertiary Structure’ o 3-D arrangement of the polypeptide o folding of all the secondary structures with respect to each other o ‘Motifs’ & ‘Domains’ are part of this structure v. ‘Quaternary Structure’ o 3-D arrangement of MULTIPLE polypeptide chains vi. ‘Protein Domain’ o a typical protein molecule is built from one or more domains, which is linked by a polypeptide chain that is often relatively unstructured o i.e. is a compact and stable folded region of polypeptide; a subunit of the tertiary structure that folds independently o usu contains 100-250 amino acids (folded into α helices & β sheets and other elements of secondary structure) o is the modular unit from which many larger proteins are constructed ‘Few of the Many Possible Polypeptide Chains Will Be Useful’ n i. For a polypeptide that is ‘n’ amino acids long, 20 different chains are possible ii. Most proteins present in cells adopt unique and stable conformations b/c with many different conformations and variable properties, it would be like a tool that unexpectedly changes its function (which is not very suitable) iii. Proteins are so precisely built that the change of even a few atoms in one amino acid can sometimes disrupt the structure of a protein thereby eliminating its function! [FIDELITY] iv. Many protein structures are so stable and effective that they have been conserved throughout evolution among many diverse orgs [STABILITY] ‘Proteins Can Be Classified into Families’  ‘Protein Families’ o A group of proteins in an org with a similar amino acid sequence [resulting through Evolution] o Usu member of these families will have related but distinct functions ‘Large Protein Molecules Often Contain More Than One Polypeptide Chain’ i. The same weak non-covalent bonds that enable a chain to fold into a specific conformation also allow proteins to bind to each other to produce large structures in the cell ii. ‘Binding Site’- any region on a protein’s surface that interacts with another molecule through sets of non-covalent bonds iii. If a binding site recognizes the surface of a second protein, the tight binding of two folded polypeptide chains at this site will create a large protein whose quaternary structure has a precise defined geometry iv. Each polypeptide chain in such a protein is called a ‘subunit’ o Each may contain more than one domain v. Other proteins contain two or more different types of polypeptide chains (E.g. Hemoglobin) * REFER TO FIG 4-19 & 4-20 ON PG. 136 FOR ILLUSTRATIONS * ‘Proteins Can Assemble into Filaments, Sheets, or Spheres’ i. A chain of identical protein molecules can be formed if the binding site on one protein molecule is complementary to another region on the surface of another protein molecule of the same type o A protein with just one binding site can form a ‘dimer’ with another identical protein o Identical proteins with two different binding sites will often form a long helical filament o If the two binding sites are disposed appropriately in relation to each other, the protein subunits will form a closed ring instead of a helix ii. Other sets of proteins associate to form extended sheets or tubes, or cage-like spherical shells * REFER TO FIG 2-21 ON PG 137 FOR AN ILLUSTRATION * ‘Some Types of Proteins Have Elongated Fibrous Shapes’ i. ‘Fibrous Proteins’ o has a simple, elongated 3-D structure o esp abundant outside the cell, where they form the gel-like extracellular matrix that helps cell bind together to form tissues o E.g. ‘α- keratin’, ‘elastin’., o ‘collagen’ • is the most abundant of these proteins in animal tissues • consists of 3 long polypeptide chains, each containing rd the non-polar amino acid Glycine at every 3 position • this structure allows the chains to wind around one another to generate a long regular triple helix with Glycine at its core • many collagen molecules bind to one another side-by- side and end-to-end to create long overlapping arrays * REFER TO FIG 4-25 ON PG. 139 FOR ILLUSTRATIONS* ‘Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages’ i. Many protein molecules are either attached to the outside of the cell’s plasma membrane or secreted as part of the extracellular matrix ii. To help maintain their structures, polypeptide chains are often stabilized by covalent cross-linkages iii. These linkages can tie together two amino acids in the same protein, or connect different polypeptide chains in a multi-subunit protein iv. Most common are S-S bonds (‘disulfide bonds’) o Form as proteins are being exported from cells o Formation is catalyzed in the ER by a special enzyme that links together two -SH groups from Cysteine side chains adjacent in the folded protein o Do not form in the cell Cytosol, where a high concentration of reducing agents converts such bonds back to Cysteine –SH groups o Do not change the conformation of a protein, but instead act as a sort of ‘atomic staple’ to reinforce its most favoured conformation HOW PROTEINS WORK ‘All Proteins Bind to Other Molecules’ i. Biological properties of a protein molecule depend on the physical interaction with other molecules o Each protein molecule can bind to just one or a few molecules out of the many thousands of different molecules it encounters ii. ‘Ligand’- any substance (an ion, a small molecule, or a macromolecule) that is bound by a protein iii. Many weak bonds are needed to enable a protein to bind tightly to a second molecule (a ligand) iv. Although the atoms buried in the interior of the protein have no direct contact with the ligand, they provide an essential scaffold that gives the surface its contours and chemical properties * REFER TO FIG 4-28 ON PG 141 FOR AN ILLUSTRATION * ‘Phosphorylation Can Control Protein Activity by Triggering a Conformational Change’ (pg. 152-153) i. Enzymes are not only regulated by the binding of small molecules ii. Another method commonly used by eukaryotic cells to regulate protein activity involves attaching a phosphate group covalently to one of its amino acid side chains iii. Since each phosphate group carries two (-) charges, the enzyme- catalyzed addition of a phosphate group to a protein can cause a major shape change by-E.g.- attracting a cluster of positively charged amino acid side chains iv. This shape change CAN, in turn, affect the binding of ligands elsewhere on the protein surface- thus altering the protein’s activity v. Removal of the phosphate group by a second enzyme returns the protein to its original shape and restores its initial activity vi. ‘Protein Phosphorylation’ o controls the activity of many different types of proteins in eukaryotic cells o can either stimulate protein activity or inhibit it, depending on the protein involved & the site at which it is being phosphorylated o involves the enzyme-catalyzed transfer of the terminal phosphate group of ATP to the hydroxyl group on a Serine, Threonine, or Tyrosine side chain of the protein o catalyzed by a ‘protein kinase’ vii. The addition & removal of these groups from specific proteins often occurs in response to signals that specify some change in a cell’s state [E.g. transporting of hormones & neurotransmitters from the cell membrane to the nucleus] viii. The reverse rxn- removal of a the phosphate group, or “dephosphorylation” is catalyzed by a ‘protein phosphatase’ ix. Cells contain hundreds of different protein kinases, each responsible for phosphorylating a different protein or set of proteins x. Cells also contain many different protein phosphatases,; some of these are highly specific and remove phosphate groups from only one or a few proteins, whereas others act on a broad range of proteins xi. For many proteins, a phosphate group is added to a particular side chain, & then removed in a continuous cycle xii. This allows proteins to switch rapidly from one state to another o the more rapidly the cycle is ‘turning’, the faster the concentration of a phosphorylated protein can change in response to a sudden stimulus that increases its rate of phosphorylation xiii. * Problem *- this costs energy with each turn of the cycle DNA & Chromosomes (pgs 171-182) 30/05/2010 20:30:00 • Life depends on the ability of cells to store, retrieve, & translate the genetic instructions required to make & maintain a living org THE STRUCTURE & FUNCTION OF DNA • ‘Chromosomes’ o thread-like structures which contains both DNA & protein o becomes visible as the cell begins to divide under a light microscope ‘A DNA Molecule Consists of Two Complementary Chains of Nucleotides’ • ‘DNA’ o consists of two long polynucleotide chains o each of these chains is composed of 4 types of nucleotide subunits (A,G,C, & T) o the two chains are held together by Hydrogen Bonding btwn the nitrogenous bases o the shapes and chemical structures of the bases allow hydrogen bonds to form efficiently only btwn A & T and btwn G & C o purine-pyramidine pair is called a ‘base pair’; this complementary base-pairing enable the base pairs to be packed in the energetically most favourable arrangement in the interior of the double helix o double-helix contains 10 base pairs per helical turn o the winding also contributes to the energetically favourable conformation of the DNA double helix * REFER TO FIGURES 5-2 & 5-6 ON PG. 173 FOR ILLUSTRATIONS * ‘The Structure of DNA Provides a Mechanism for Heredity’ i. ‘Genes’- is used to produce RNA molecules, which then direct the production of the specific protein molecules o * REFER TO FIG 5-9 ON PG 179 * ii. Organism differ from one another b/c their respective DNA molecules have different nucleotide sequences &, consequently, carry different biological messages THE STRUCTURE OF EUKARYOTIC CHROMOSOMES • Human cell contains about 2 m of DNA; yet the cell nucleus is only 5-8 μm in diameter • As a result, in eukaryotic cells, very long double-stranded DNA molecules are packaged into structures called ‘chromosomes’, which not only fit readily inside the nucleus but can be easily apportioned btwn the two daughter cell at each cell division o the complete task of packaging DNA is accomplished by specialized proteins that bind to and fold the DNA, generating a series of coils & loops that provide increasingly higher levels of organization & prevent the DNA from becoming an unmanageable tangle o It is compacted in way that allows it to remain accessible to all of the enzymes & other proteins that replicate it, repair it, and direct the expression of genes  Bacteria typically carry genes on a single, circular DNA molecule (not much is known about the packaging, etc) ‘Eukaryotic DNA Is Packaged into Multiple Chromosomes’ 9 i. Human genome contain approx. 3.2 x 10 nucleotides parceled out into 24 chromosomes o Each chromosome consists of a single, enormously long, linear DNA molecule associated with proteins that fold & pack the fine thread of DNA into a more compact structure o Each is associated with many other proteins involved in gene expression, DNA replication, & DNA repair ii. Human cells each contain two copies of each chromosome, one inherited from the father, & one from the mother (except germ cells & specialized cells that lack DNA entirely-e.g.- red blood cells) iii. ‘Homologous Chromosomes’ (homologs)- the maternal and paternal chromosomes of a pair o The only nonhomologous chromosome pairs are the sex chromosomes in males, where a Y chromosome is inherited from the father and an X chromosome from the mother iv. ‘Chromatin’- complex of DNA & protein v. Each human chromosome can be ‘painted’ a different colour (with fluorescent dyes) to allow its unambiguous identification under the light microscope o These dyes mainly distinguish btwn DNA that is rich in A-T nucleotide pairs and DNA that is G-C rich, o And they produce a striking and reliable pattern of bands along each chromosome vi. ‘Karyotype’- a display of the full set of 46 chromosomes o If parts of a chromosome are lost, or switched btwn chromosomes, these changes can be detected by changes in the banding patterns ‘Chromosomes Contain Long Strings of Genes’ i. Most important function of chromosomes is to carry the genes-the physical & functional units of heredity*** ii. ‘Genes’- defined as a segment of DNA that contains the instructions for making a particular protein iii. Chromosomes from many eukaryotes (inc. humans) contain, in addition to genes, a large excess of interspersed DNA, the majority of which does not seem to carry critical information o this is sometimes referred to as ‘junk DNA’, since its usefulness to the cell has not yet been clearly demonstrated o it may be crucial for evolution of the species, & for the proper activity of genes iv. In general, the more complex the organism, the large is its genome (not always true) v. Even closely related species with similar genome sizes can have very different #s & sizes of chromosomes (* REFER TO FIG 5-14 ON PG 182 *) i.e. there is no rltnshp btwn gene #, chromosome #, & total genome size From DNA to Protein: How Cells Read the Genome (pg 238-246) 30/05/2010 20:30:00  DNA does not direct protein synthesis itself, but acts as a manager, delegating the various tasks to a team of workers  When a particular protein is needed by the cell, the nucleotide sequence of the appropriate section of an immensely long DNA molecule in a chromosome is first copied into RNA  These RNA copies of short segments of the DNA are then used to direct the synthesis of the protein FROM DNA TO RNA  Transcription and translation are the means by which cells read out, or express, their genetic instructions- their genes  Many identical RNA copies can be made from the same gene, & each RNA molecule can direct the synthesis of many identical protein molecules  Since each cell contains only one or two copies of any particular genes, this successive amplification enables cells to rapidly synthesize large amts of protein whenever necessary  At the same time, each gene can be transcribed and translated with a different efficiency, providing the cell with a way to make vast quantities of some proteins and tiny quantites of others o * REFER TO FIG 7-2 ON PG 232 FOR AN ILLUSTRATION * ‘Portions of DNA Sequence Are Transcribed into RNA’  First step a cell takes in reading out one of its many thousands of genes is to copy the nucleotide sequence of that gene into RNA (‘Transcription’) * REFER TO FIG 7-3 ON PG 233 FOR RNA COMPOSITION & STRUCTURE * ‘Transcription Produces RNA Complementary to One Strand of DNA’  Transcription differs from DNA replication in several crucial features: o Unlike a newly formed DNA strand, the RNA strand does not remain H-bonded to the DNA template strand o RNA are single-stranded, & much shorter  ‘RNA Polymerases’ o Enzymes carrying out transcription o Catalyze the formation of the phosphodiester bonds that link the nucleotides together & form the sugar-phosphate backbone of the RNA chain o Move step-wise along the DNA, unwinding the DNA helix just ahead to expose a new region of the template strand for complementary base-pairing o As it moves along the DNA template, this enzyme displaces the newly formed RNA, allowing the two strands of DNA behind the polymerase to rewind • A short region of hybrid DNA/RNA helix, therefore forms only transiently o It uses ribonucleoside triphosphates (ATP, CTP, UTP, GTP), whose high-energy bonds provide the energy that drives the rxn forward  The almost immediate release of RNA strand from the DNA as it is synthesized means that any RNA copies can be made from the same gene in a relatively short time o The synthesis of the next RNA is usu started before the first RNA has been completed  A medium-sized gene (say, 1500 nucleotide pairs) requires approx. 50 seconds for a molecule of RNA polymerase to transcribe it  Differences btwn DNA & RNA polymerase: o “RNA Polymerase” • Catalyzes the linkage of ribonucleotides • Can start a chain without a primer (since it is not used as the permanent storage form of genetic info in cells, so mistakes in the transcripts have relatively minor consequences) 4 • Make about one mistake for every 10 nucleotides copied in the RNA o “DNA Polymerase” • Catalyzes the linkage of deoxyribonucleotides • Needs a primer to start a chain • Make about one mistake for every 10 nucleotides copied in the DNA ‘Several Types of RNA Are Produced in Cells’  Vast majority of genes in DNA specify the amino acid sequence of proteins  RNA molecules that are copied from these genes are collectively called “messenger RNA”’ (mRNA)  In eukaryotes, each contains info transcribed from just one gene, coding for a single protein  In bacteria, a set of adjacent genes is often transcribed as a single mRNA that therefore carries the info for several different proteins * REFER TO TABLE 7-1 ON PG. 236 FOR TYPES OF RNA * ‘Signals in DNA Tell RNA Polymerase Where to Start & Finish’ i. Initiation of transcription is an esp critical process b/c it is the main point at which the cell can select which proteins or RNAs are to be produced & at what rate o To begin, RNA Polymerase must be able to recognize the start of a gene and bind firmly to the DNA at this site o The way it recognizes the start site differs btwn bacteria & eukaryotes ii. When an RNA polymerase collides randomly with a piece of DNA, it sticks weakly to the double helix and then slides rapidly along iii. The enzyme latches on tightly only after it interacts with a “promoter” (which contains a specific sequence of nucleotides indicating the starting point for RNA synthesis) iv. Then it opens up the double helix immediately in front of it to expose the nucleotides on each strand of short stretch of DNA v. One of the two exposed DNA strands then acts as a template for complementary base-pairing with incoming ribonucleotides (two of which are joined together by the polymerase to begin the RNA chain) vi. Elongation occurs until the enzyme encounters a second signal DNA, the “terminator” (stop site) where the enzyme stops and releases both the DNA template & the newly made RNA chain  ‘sigma (σ) factor’ o A subunit of the bacterial polymerase that is primarily responsible for recognizing the promoter sequence on DNA o Once the polymerase has latched onto the DNA at this site, has synthesized approx. 10 nucleotides of RNA, this factor disengages, enabling the polymerase to continue on without it o After the polymerase has been released at a terminator, it re- associates with a free sigma factor and searches for a promoter, where it can begin the process of transcription again vii. Since the promoter is asymmetrical and binds the polymerase in only one orientation, DNA could not direct the synthesis of two different RNA transcripts viii. Transcription can only proceed only in the 5’-to-3’ direction o Overall, the direction of transcription with respect to the chromosome as a whole varies from gene to gene  B/c tight binding is required for RNA polymerase to begin transcription, a segment of DNA will be transcribed only if it is preceded by a promoter sequence o This ensures that only those parts of a DNA molecule that contain a gene will be transcribed into RNA ‘Initiation of Eukaryotic Gene Transcription Is a Complex Process’  Transcription initiation in eukaryotes differs in several important ways from that in bacteria: i. Have 3 types of RNA polymerases- RNA polymerase I, RNA polymerase II, & RNA polymerase III o Responsible for transcribing different types of genes Ta
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