Condensed Final Study Guide
Condensed Final Study Guide Biol 5A
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BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL CHAPTER 1: EVOLUTION, THE THEMES OF BIOLOGY, AND SCIENTIFIC INQUIRY Biology is the scientific study of life, with evolution, the process of change that has shaped life from its origin on Earth to today’s diversity, as its organization principle. The properties and processes of life include highly ordered structure, evolutionary adaptation, response to the environment, regulation, energy processing, reproduction, and growth and development. 1.1: The study of life reveals common themes Theme: New properties emerge at successive levels of biological organization biology today combines the strategy of reductionism, which breaks down complex systems into simpler components, with systems biology, which studies interactions of the parts of a system and models the system’s dynamic behavior structural arrangements of and interactions among components at each level of biological organization lead to emergent properties at the next level the form of a structure is well matched to its function at all levels of biological organization the cell is lowest structural level capable of performing all the activities of life the simpler and smaller prokaryotic cell, unique to bacteria and archaea, lacks a nucleus to enclose its DNA and other membrane-enclosed organelles the eukaryotic cell-with a nucleus containing DNA, and numerous organelles-is typical of all other living organisms Theme: Life’s processes involve the expression and transmission of genetic information the genetic information of a cell is coded in DNA genes are units of inheritance that transmit information from parents to offspring. They are located on chromosomes, long DNA molecules that replicate before cell division and provide identical copies to daughter cells most genes program the cell’s production of proteins, and almost all cellular structures and actions involve one or more proteins gene expression is the process by which a gene’s information is converted into a cellular product. Genes also code from RNA’s that serve other functions: playing a role in the cell’s protein manufacturing machinery and regulating gene expression the genetic instruction an organism inherits make up its genome each of the two sets of chromosomes in a human cell contains about 3 billion nucleotide pairs proteomes are whole sets of proteins encoded by a genome research developments contributing to genomics and proteomics: 1) “High throughput” technology that can analyze biological materials rapidly 2) Bioinformatics, which provides computational tools to process and analyze the resulting data 3) interdisciplinary research teams with specialists from many diverse fields Theme: Life requires the transfer and transformation of energy and matter producers transform light energy to the chemical energy in sugars, which powers the cellular activities of plants consumers eat plants and other organisms, using chemical energy in their foods to power their movement, growth, etc in each use of energy to perform work, some energy is lost to the surroundings as heat Theme: From ecosystems to molecules, interactions are important in biological systems molecular interactions within organisms are crucial to proper functioning protein enzymes catalyze cell’s chemical reactions, which are often organized into chemical pathways 1 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL many biological processes are controlled through feedback regulation, in which the product of a process regulates that process in negative feedback, the response feeds back and reduces the original stimulus in positive feedback, an end product speeds up the process 1.2: The Core Theme: Evolution accounts for the unity and diversity of life Classifying the Diversity of Life prokaryotes make up the domains Archaea and Bacteria all eukaryotes are placed in the domain Eukarya Charles Darwin and the Theory of Natural Selection natural selection: individuals with traits best suited for the environment leave more offspring; the mechanism of evolution based off of three observations 1) individuals vary in many heritable traits 2) the overproduction of offspring sets up a competition of survival 3) species are generally matched to their environments The Tree of Life diversity of species results from natural selection acting over millions of generations as populations adapted to different environments 1.3: In studying nature, scientists make observations and form and test hypotheses Science is an approach to understanding the natural world that involves inquiry, the search for explanations of natural phenomena Making Observations data: recorded observations, quantitative and qualitative using inductive reasoning to draw generalizations from collections of observations Forming and Testing Hypotheses hypothesis: tentative answer to a question or an explanation of observations, leading to predictions that can be tested -must be testable -cannot be proven to be true or incorrect -gains credibility when it is tested in various ways deductive reasoning uses “if…then” logic Theories in Science theory: broader in scope than a hypothesis, generates many specific hypotheses, supported by a larger body of evidence. It can be modified and rejected when results and new evidence no longer support it CHAPTER 2: THE CHEMICAL CONTEXT OF LIFE 2.1 Matter consists of chemical elements in pure form and in combinations called compounds Matter: anything that takes up space and has mass Elements and Compounds 2 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Elements: substances that cannot be chemically broken down to other types of matter Compound: made up of two or more elements combined in a fixed ratio The Elements of Life About 25 out of the 92 elements are essential to life Essential elements: needed for an organism to live and reproduce; Carbon, Oxygen, Hydrogen, and Nitrogen make up 96% of living matter o Most of the remaining 4% consists of Calcium, phosphorus, potassium, and sulfur Trace elements: elements required in very minute quantities such as Iron and Iodine (Mn, Co, Ni, Cu, Zn, Mo, I) *Hint: 99% of all living material consist of: CHOPKINS CaFe Mg NaCl (Carbon, Hydrogen, Oxygen, Phosphorus, Potassium, Iodine, Nitrogen, Sulfur) Evolution of Tolerance to Toxic Elements Serpentine soil contains toxic elements but some plants exhibit evolutionary adaptations that enable them to grow in such soils 2.2 An element’s properties depend on the structure of its atoms Subatomic Particles Atom: smallest unit of matter retaining the properties of that element Uncharged neutrons and positively charged protons are packed tightly together to form the atomic nucleus of an atom Negatively charged electrons form a large cloud around the positively charged nucleus Protons and neutrons have a similar mass of about 1.7 X 10^-24 gram or close to 1 dalton each Dalton: measurement unit for atomic mass Electrons have negligible mass Atomic Number and Atomic Mass Each element has a characteristic atomic number, or number of protons in each of its atoms The mass number is equal to the number of protons and neutrons in the nucleus and approximates the mass of an atom of that element in daltons Atomic mass: the total mass of an atom Isotopes Isotopes: a variance in the number of neutrons of a particular element; slightly different mases but the same chemical behaviors Radioactive isotopes: unstable isotopes, spontaneously decay, giving off particles and energy o Fixed rate of decay, referred to as its half life: amount of years it takes for 50% of the parent isotope to decay into its daughter isotope o Radiometric dating: scientists use the ratio of different isotopes to estimate how many half lives have passed since a fossil or rock was formed The Energy Levels of Electrons Energy: the capacity to cause change, to do work Potential energy: energy stored in matter as a consequence of its position or structure o Potential energy of an electrons increases as their distance from the positively charged nucleus increases 3 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Electron shells/energy level: an electron’s state of potential energy Electron Distribution and Chemical Properties The chemical behavior of an atom is determined by the number of valence electrons it has in its outermost electron shell or valence shell Valence shell of eight electrons is complete, resulting in an unreactive or inert atom Atoms with incomplete shells are chemically reactive Elements in each row or period of the periodic table of elements have the same number of electron shells and are arranged in order of increasing number of electrons Amount of energy necessary to remove an electron from its ground state is called the ionization energy o Greater the ionization energy, the more difficult it is to remove an electron o Increases from left to right and up from bottom to the top of the periodic table (except H, which has a very high ionization energy) Electron Orbitals Orbital: 3D space or volume within which an electron is most likely to be found the first electron shell can contain two electrons in a single spherical orbital, 1s orbital S –1 orbital –2 electrons P—3 orbitals—6 electrons D—5 orbitals—10 electrons F—7 orbitals—14 electrons 2.3 The formation and function of molecules depend on chemical bonding between atoms Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms These interactions usually result in atoms staying close together, held by attractions called chemical bonds Covalent Bonds Covalent bonds: when two atoms share a pair of valence electrons Molecule: two or more atoms held together by covalent bonds Electronegativity: attraction of a particular atom for shared electrons Nonpolar covalent bond: if the atoms in a molecule have similar electronegativities and the electrons remain equally shared Polar covalent bond: if one electron is more electronegative, it pulls the shared electrons closer to itself. The unequal sharing results in a polarity or separation of charges Ionic Bonds if two atoms are very different in their attraction for valence electrons, the more electronegative atom may completely transfer an electron from the other atom, resulting in the formation of charged atoms called ions cation: positively charged, atom that lost an electron anion: negatively charged, atom that gained an electron ionic bonds: holds cations and anions together because of the attraction of their opposite charges ionic compounds/salts: 3D crystalline lattice arrangements held together by electrical attractions o number of ions present in a salt crystal aren’t fixed but the atoms are present in specific ratios 4 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL o have strong ionic bonds when dry and dissolve in water Weak Chemical Bonds Ionic bonds and other weak bonds may form temporary interactions between molecules Weak bonds within many large molecules help create those molecules’ 3D functional shape Hydrogen bond: hydrogen atom that is covalently bonded to an electronegative atom has a partial positive charge and can be attracted to a different nearby electronegative atom All atoms and molecules are attracted to each other when in close contact by fleeting charge difference--van der Waals interactions Momentary uneven electron distributions produce changing positive and negative regions that create van de Waals interactions Hydrogen Bonds are weak bonds important in the chemistry of life Hydrogen bonds are attractive forces between polar molecules; when partial opposite charges in different molecules attract each other o Comparatively weak but collectively can be quite strong o Where we see hydrogen bonds: between water molecules, helping to hold DNA together, interactions between proteins Molecular Shape and Function Molecule’s shape and size affects how it interacts with other molecules In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes Biological molecules recognize and interact with each other with a specificity based on molecular shape Molecules with similar shapes can have similar biological effects 2.4: Chemical reactions make and bread chemical bonds Chemical reactions: the making or breaking of chemical bonds o Reversible o Increasing concentrations of reactants can speed up the rate of a reaction Matter is conserved in chemical reactions; same number of kinds of atoms are present in both reactants and products, although the rearrangement of electrons and atoms causes the properties of these molecules to be different Chemical equilibrium: reached when the forward and reverse reactions processed at the same rate, and the relative concentrations of reactants and products no longer change CHAPTER 3: WATER AND LIFE Water is the biological medium on Earth All living organisms require water more than any other substance Most cells are surrounded by water, and cells themselves are about 70-95% water o Red blood cells—60% water o Muscle—75% water o Plasma—92% water The abundance of water is the main reason the Earth is habitable Polar covalent bonds in water molecules result in hydrogen bonding The water molecules is a polar molecule: the opposite ends have opposite charges Polarity allows water molecules to form hydrogen bonds with each other 5 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL The hydrogen atoms pull towards the oxygen atom in water The unpaired electrons on a water molecule allow it to bond to other water molecules A single water molecule can have up to 4 other water molecules bound to it The difference between the solid and liquid form of water is the formation of H bonds and the amount of kinetic energy present Emergent properties of water contribute to Earth’s suitability for life Some of water’s properties that facilitate an environment for life are: o Cohesive/Adhesive behavior Surface tension and capillary action o Ability to moderate temperature, thermal stability Specific heat and heat of vaporization o Expansion upon freezing o Versatility as a solvent o Colorless and transparent o Low viscosity—compared to other liquids Cohesion of Water Molecules Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion Cohesion helps the transport of water against gravity in plants Adhesion is an attraction between different substances, for example, between water and plant cell walls Surface tension: measure of how hard it is to break the surface of a liquid; related to cohesion o Detergents and heat lowers the surface tension of water so they can soak into our clothes. Washing in cold water requires a wetting agent in the detergent Moderation of Temperature by Water Water absorbs heat from warmer air and releases stored heat to cooler air Water can absorb or release a large amount of heat with only a slight change in its own temperature Heat and Temperature Kinetic energy: energy of motion Heat: the measure of the total amount of kinetic energy due to molecular motion Temperature: measures the intensity of heat due to the average kinetic energy of molecules Water’s High Specific Heat The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1 degree Celsius o Specific heat of water: 1 cal/g/degrees Celsius Water resists changing its temperature because of its high specific heat o Water heats slowly and cools slowly, it has a high heat of fusion Water’s high specific heat can be traced to hydrogen bonding o Heat is absorbed when hydrogen bonds break o Heat is released when hydrogen bonds form The high specific heat of water minimizes temperature fluctuations to within limits that permit life Evaporative Cooling Heat of vaporization: the heat a liquid must absorb for 1 gram to be converted to gas 6 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL o as liquid evaporates, its remaining surface cools, a process called evaporative cooling (takes away heat) o evaporative cooling of water helps stabilize temperatures in organisms and bodies of water o a liquid with a low heat of vaporization evaporates faster, such as alcohol Floating of Ice on Water ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense if ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth ice occupies a larger volume because of its lattice structure but is less dense than liquid water Water: The Solvent of Life solution: liquid that is a homogenous mixture of substances solvent: dissolving agent of a solution solute: substance that is dissolved an aqueous solution is one in which water is the solvent water is a versatile solvent due to its polarity, which allows it to form hydrogen bonds easily when an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell water can also dissolve compounds made of nonionic polar molecules even large polar molecules such as proteins can dissolve in water if they have ionic and polar regions Hydrophobic and Hydrophilic Substances hydrophilic substance is one that has an affinity for water hydrophobic substance is one that does not have an affinity for water o oil molecules are hydrophobic because they have relatively nonpolar bonds Solute Concentrations in Aqueous Solutions most biochemical reactions occur in water chemical reactions depend on collisions of molecules and therefore on the concentration of solutes in an aqueous solution molecular mass is the sum of all of the masses of all atoms in a molecule molarity (M) is the number of moles of solute per liter of solution Acidic and Basic Conditions Affect Living Organisms a hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other o the H atom leaves its electron behind and is transferred as a proton, or hydrogen ion (H+) o the molecule with the extra proton is now a hydronium ion (H3O+) o the molecule that lost the proton is now a hydroxide ion (OH-) water is in a state of chemical equilibrium in which water molecules dissociate at the same rate at which they are being reformed changes in concentrations of H+ and OH- can drastically affect the chemistry of a cell concentrations of H+ and OH- are equal in pure water Acids and Bases 7 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL acid: any substance that increases the H+ concentration of a solution; ionize in an aqueous solution. Proton donor base: any substance that reduces the H+ concentrati0on of a solution. Proton acceptor Most biological fluids have a pH in the range of 6 to 8 Acids and bases that ionize completely are considered strong acids and bases Buffers Buffers: substances that minimize changes in concentrations of H+ and OH- in a solution o most buffers consist of an acid-base pair that reversibly combines with H+ Acidification: A Threat to Water Quality Human activities such as burning fossil fuels threaten water quality CO2 is the main product of fossil fuel combustion About 25% of human-generated CO2 is absorbed by oceans CO2 dissolved in sea water forms carbonic acid; this process is called ocean acidification As seawater acidifies, H+ ions combine with carbonate ions to produce bicarbonate Carbonate is required for calcification by many marine organisms CHAPTER 4: CARBON AND THE MOLECULAR DIVERSITY OF LIFE Organic Chemistry is the study of carbon compounds Although cells are 70-95% water, the rest consists mostly of carbon based compounds Organic compounds range from simple molecules to colossal ones Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration is the key to an atom’s characteristics Electron configuration determines the kinds and number of bonds an atom will form with other atoms The formation of bonds with Carbon Carbon can form 4 covalent bonds with a variety of atoms This tetravalence makes large, complex molecules possible In molecules with multiple carbons, each carbon bonded to 4 other atoms has a tetrahedral shape However, when two C atoms are joined by a double bond, the molecule has a flat shape Molecular Diversity Arising from Carbon Skeleton Variation Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy Isomers Compounds with the same molecular formula but different structures and properties Structural isomers have different covalent arrangements of their atoms; same chemical formula but different structures of atoms and bonds Geometric isomers have the covalent bonds to the same atoms, but differ in spatial arrangement ( cis and trans) 8 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Enantiomers are isomers that are mirror images of each other o Important in the pharmaceutical industry o Two enantiomers of a drug may have different effects o Different effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules Central carbon with 4 different groups bound to it is called the chiral center carbon; present in amino acids Functional groups are the parts of molecules involved in chemical reactions Distinctive properties of organic molecules depend not only on the carbon skeletons but also on the molecular components attached to it Certain groups of atoms are often attacked to skeletons of organic molecules. These functional groups have distinct chemical and physical properties Functional groups are the components of organic molecules that are most commonly involved in chemical reactions o The number and arrangement of functional groups give each molecule its unique properties the 7 functional groups that are most important in the chemistry of life: o hydroxyl group o carbonyl group o carboxyl group o amino group o sulfhydryl group o phosphate group o methyl group _______________________________________________________________ CHAPTER 5: STRUCTURE AND FUNCTION OF LARGE BIOLOGICAL MOLECULES How cells use organic compounds Biological organisms use the same types of building blocks All macromolecules have specific functions in cells Other than water, macromolecules make up the largest percent mass of a cell Condensation and Hydrolysis Condensation/Dehydration synthesis o two molecules combine with loss of water to form larger molecules o requires enzymes and energy; enzymatic reaction o forms a strong covalent bond o 1 OH and H removed by DNA polymerase Hydrolysis o A molecule splits into two smaller ones with the addition of water o Breaks bonds The Molecules of Life Living cells synthesize: o Carbohydrates o Lipids o Proteins o Nucleic acids *Large polymers form from smaller monomers. New properties emerge Carbohydrates Used as energy and structural molecules (structural polymers); backbone Are soluble in water to provide energy 9 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Main types: o Monosaccharides o Disaccharides o Polysaccharides Monosaccharides (CH2O) o Major cell nutrient produced during photosynthesis, raw material for other molecules o 6 Carbon sugars (hexoses) Glucose, fructose, galactose o 5 Carbon sugars (pentose) Deoxyribose, Ribose Disaccharides o Sucrose (glucose + fructose); table/cane sugar o Lactose (glucose + galactose); milk sugar, unabsorbed in intestines if individuals lack lactase—leading to diarrhea o Maltose (glucose + glucose); beer, formed during the hydrolysis of starch by amylase o Formed by condensation reactions (glycosidic linkages created) o Broken down by specific enzymes Polysaccharides (complex carbohydrates) o 100s/1000s monosaccharides long o Made of same subunit o Energy storage Starch (amylose/amylopectin) Digestible In plants only Forms ring in aqueous solutions Glycogen (highly branched) In animals only o Structural support Cellulose Forms rings in aqueous solutions Chitin Lipids Large hydrocarbons; insoluble in water Don’t form polymers Dissolve in nonpolar substances (chloroform, ether) Used for energy storage, structural, and chemical messenger Lipids with fatty acids o Glycerides o Phospholipids o Waxes Lipids with no fatty acids o Steroids Fatty Acids Carbon backbone (4-24 carbon atoms) Carboxyl group (-COOH) Methyl group makes it nonpolar Unsaturated o One or more double bonds in backbone Double bonds adds kinks Saturated 10 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL o All single bonds in backbone Triglycerides Fats/neutral fats o Three fatty acids and a glycerol molecule o Condensation reactions forms ester linkage o Most abundant lipid o Non polar; contain no charged/polar functional groups Functions o Energy storage in adipocytes o Insulation Phospholipids Glycerol backbone Two fatty acid tails (hydrophobic) Phosphate-containing head (negatively charged therefore hydrophilic) Amphipathic (both hydrophilic and hydrophobic) Main materials of cell membranes Sterols Steroids/sterols o No fatty acid tails o Four carbon ring o In eukaryotic cell membranes o Cholesterol in animal tissues Precursor to sex hormones and bile salts Waxes Long chained fatty acids linked to alcohols or carbon rings Cover plant parts (cuticle) o Help conserve water o Fend off parasites Animals o Protect, lubricate, impart pliability to skin and hair o Repel water (bird feathers, exoskeleton of insects) Amino Acids and the Primary Structure of Proteins Proteins o Enzymes (metabolism); create reactions in a timely manner o Structures (collagen and silk) o Transport and movement (lipoproteins, hemoglobin, actin/myosin, tublin) o Nutritious (egg whites, casein) o Hormones (chemical messengers, ex: insulin/growth hormone) o Immune system (antibodies) Two classes: globular and fibrous Proteins are made from a pool of amino acids Structure of Amino Acids Central carbon atom An amino group A carboxyl group A hydrogen atom One or more atoms “R group” 11 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Organisms use L form but not D Peptide Bond Formation A type of condensation reaction DNA holds instructions for RNAs, mRNA determines order of amino acids Protein Conformation Conformation (shape) is determined by genes and it determines function and is the result of linear sequence of amino acids in a polypeptide Folding, coiling and interactions of multiple polypeptide chains create a functional protein 4 levels of protein structure o Primary o Secondary o Tertiary o Quaternary Primary Structure The unique, linear sequence determined by the mRNA A change in one a.a. can affect every other level of structure One letter change may or may not have a change Secondary Level of Protein Structure Hydrogen bonding occurs between amino and carboxyl groups of amino acids Structures formed: o Alpha helix. Common in fibrous proteins, creates elastic properties o Beta Sheet. Antiparallel chains form sheet Core of many globular proteins and inelastic fibrous proteins Tertiary Level of Protein Structure Additional folding of secondary structure and bonding between R groups o Hydrogen bonds o Disulfide bridges (Strong) o Hydrophobic interactions o Ionic bonding Quaternary Level of Protein Structure Two or more polypeptide chains joined by o Weak bonds (H-bonds) o Covalent bonds between sulfur atoms and R groups Collagen (3 helical polypeptides) Insulin (2 polypeptides) Hemoglobin (4 globular polypeptides) Structural Changes by Denaturation Denaturation: altering a protein’s native conformation and activity o Usually at the secondary and tertiary structures Disruption of three dimensional shape of proteins o Temperature: thermal agitation (increasing kinetic energy) o pH and salts: additional H+/OH- or ions disrupts H-bonding, ionic and disulfide bridges o non polar solvents: protein turns “inside-out” Some proteins have organic compounds attached o Glycoproteins, lipoproteins (common on membranes) 12 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Nucleotides and the Nucleic Acids Nucleotides o Sugar—ribose or deoxyribose o Phosphate group o Bases Single or double carbon rings with Nitrogen Subunits of coenzymes o NAD+ and FAD ATP o Energy source for chemical reactions o Contains three phosphate groups Nucleic Acids—DNA and RNA Building blocks o Four kinds of nucleotides o Differ only in component bases Single Strand of Nucleic Acid A series of covalently bonded nucleotides DNA Double stranded Hydrogen bonds between strands Twisted helically Four kinds of nucleotide monomers (A, T, C, G) Encodes protein-building instructions RNA Single stranded Four kinds of nucleotide monomers (A, U, C, G) Do not encode protein-building instructions Key players in the protein-building processes mRNA, tRNA, rRNA CHAPTER 6: A TOUR OF THE CELL Cells of Living Things Prokaryotic o Usually single celled, can form colonies o No nucleus or membrane bound organelles o Metabolism through aerobic and anaerobic means o Genetic material localized (nucleoid) o Most have cell wall composed of peptidoglycan o No cytoskeleton—proteins move nutrients around o Circular DNA, one form of RNA polymerase Bacteria and archaea Eukaryotic o Kingdoms: lots in what used to be called Protista, Fungi, Plants, Animals o Nucleus membrane encloses DNA o Organelles that have membrane o RNA and protein synthesized in two different locations o Linear DNA molecules with non coding introns o More than one RNA polymerase 13 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL o Controlled—perfect at certain functions o Compartments—organelles Cell Size and Shape Surface to volume ration limits size of cells. Large cells require more raw materials o Volume (V) = cm^3 o Surface Area (SA) = cm^2 o Restrictions on size and shape Cells compartmentalize to increase SA/V, specialize reactions within, localize reactions where needed Small Compartments Isolate areas of the cell. Allows for varied conditions in different regions (pH, concentration of solutes, etc) Each smaller structure can be specialized ( a multi-departmental large company versus small business) o Allows for increase in complexity o Leads to multicellularity Provides surfaces for reactions (photosynthesis and respiration) Basic Aspects of Cell Structure and Function Plasma membrane o Lipid bilayer—same basic architecture found in all membranous organelles o Proteins Channels, transport, pumps, receptors DNA-containing region Cytoplasm o Area between outer membrane and nuclear membrane. The cytosol is the liquid/gel material containing water, gases, and macromolecules Major Cellular Components Nucleus Ribosomes Endomembrane system o Endoplasmic reticulum, smooth and rough o Golgi body o Various vesicles Mitochondria/chloroplasts Cytoskeleton Components of the Nucleus Accounts for about 6-10% of total cell volume Membrane continuous with ER Nuclear envelope: surrounds nucleus o Chromosomes: one DNA molecule and associated proteins, organized DNA o Chromatin: DNA molecules and histone proteins. Condenses to form chromosome. Nucleolus: genes for rRNA that will be assembled into ribosomal subunits. Cells may have more than one The Nuclear Envelope Double membrane system 14 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL o Two lipid bilayers. 20-40nm thick o Surrounds chromatin/nucleoplasm Nuclear pores regulate entrance/exit of ions and small proteins. Composed of a large number of proteins. It’s wider than it is thick. Passage through pore requires signal proteins and GTP Nuclear lamina made of intermediate filaments, play a role in gene regulation Ribosomes Smallest, most numerous organelle. Composition slightly different in prokaryotic and eukaryotic cells Composed of rRNA (60%) and proteins (40%). Synthesized by nucleolus o Large and small subunits Found free and bound to E.R. Differ only in what they are making Catalyzes formation of peptide bonds using RNA molecules The Endomembrane System Organelles in which lipids are assembled and proteins are produced and modified Are in direct contact or send vesicles (membrane-bound sacs) Occupy ½ of cell volume Nuclear envelope, endoplasmic reticulum, golgi apparatus, lysosomes, vacuole The Endoplasmic Reticulum Network of tubes and sacs that are continuous with nuclear membrane. Most extensive membrane system Rough (ribosome studded) and smooth o Rough: production of secretory proteins. Signal sequence on polypeptide instructs ribosome to attack to ER o Smooth: lipid production, CH2O metabolism, storage of ions (Ca+), detoxification of drugs/alcohol Proteins in membrane or within lumen catalyze reactions Golgi Bodies Enzymatic finished on proteins and lipids, and packaging in vesicles Cis (forming) face and trans (exit) face Forms glycolipids, glycoproteins through the modification of proteins produced by ER. Enzymes in lumen catalyze addition/removal of parts Produce some polysaccharides and also pectin for plant cell walls Products of golgi leave as vesicles. From cisterna to another or out of cell Lysosomes Membrane bound organelle that contains about 40 different hydrolytic enzymes responsible for the digestion of macromolecules, autolysis, intracellular digestion Dead cells no longer able to maintain H+ gradient (uses H+ pump to maintain pH of 4.8), so organelle breaks down releasing contents It works at low pHs because H+ is constantly be pumped by ATP; without it cells would die Made by ER and Golgi o Common in white blood cells Tay-Sachs is the result of faulty enzyme in lysosomes responsible for lipid breakdown in neurons Carries out hydrolysis; can break down: o Nucleic acids with enzyme nuclease 15 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL o Proteins with enzyme protease o Lipids with enzyme lipase o Carbohydrates to create usable monomers of macromolecules Vacuoles Largest in plant cells Storage of water or ions, pigments, hold food, pump out water Are larger than vesicles from golgi/ER In plants it is enclosed by Tonoplast (membrane) and provides cell with hydrostatic pressure Peroxisomes H2O2, bi-product of lipid production Contain enzymes (catalase) that break down H2O2 formed during metabolism of alcohols, fatty acids Specialized forms (glyoxysome) found in seeds and function during germination Self-replicating-imports proteins from cytosol Mitochondria Production of ATP Double-membrane system o Two distinct compartments Have their own DNA, maternal in origin Divide on their own, independent of cell Have ribosomes, produce enzymes necessary for ATP production Endosymbiont theory describes proposed origin of both mitochondria and chloroplasts Chloroplast Two outer membranes Semifluid stroma; site of carbon fixation Inner thylakoid membrane system; converts light energy into chemical energy Photosynthetic pigments found in other plastids Cytoskeleton Protein fibers that support and give shape to a cell, involved in organelle movement throughout cell, chromosome movement during cell division and large cell movements (cell motility and cytokinesis) 3 groups of fibers classified according to size: o Microtubules (thickest) o Intermediate filaments o Microfilaments (thinnest) Components of the Cytoskeleton Microtubules o Alpha and beta tubulin subunits, form hollow tube o Provide framework for cell, organized by centrosome from which they usually originate o “rail” system for organelle transport Component of centriole o Replicated prior to mitosis Form cilia and flagella o 9 + 2 arrangement (eukaryotic characteristic) 16 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Cilia and Flagella and the Structural Basis of Cell Motility Surrounded by plasma membrane Motor proteins (dynein toward – end; kinesin toward + end) on microtubules use ATP to change shape and “ratchet” past one another Movement causes bending of cilia/flagella Microfilaments (actin filaments) Solid rope of two actin proteins Thinner and more flexible than microtubules Principle component of muscle fibers Provide mechanism to support cell shape. Found just inside the cellular membrane Enable cell movement, phagocytosis and cytokinesis Intermediate Filaments Tough and durable, made of keratin Mechanically strengthen/reinforce cells or cell parts that are under stresses o Provide structure to long cells o Found in desmosomes o Give nucleus shape (nuclear lamina) Cell to Cell Junctions Plants o Plasmodesmata Perforations in cell wall that allow passage for water/solutes to adjacent cells Animals o Tight junctions: prevent leakage between cell (in stomach) o Desmosomes: mechanically attach cells to each other, serve as anchoring sites for interfilaments in cells o Gap junctions: analogous to plasmodesma, function as common pathway between cells. Cardiac muscle, nerves Plant Cell Walls Protect plants, allow for shape and prevent excess H2O uptake o Composed of cellulose Plasmodesmata connect with neighboring cells when alive Secondary cell wall inside of primary wall, forms wood Cell secretions form pectin (polysaccharide glue) which acts as adhesive o Laid down in middle lamella to hold cells together Extracellular Matrix (ECM) Intricate network of proteins and polysaccharides that are organized into a meshwork on the outside of cells o Large polysaccharides and proteoglygans form a “gel-like” material that resist compression o Proteins like collagen (most abundant protein in animals as part of bone and skin) and elasin (stretch and recoil) provide structure and strength Adhesive-like proteins (fibronectins and laminin) help cells attach to the appropriate part of the ECM CHAPTER 7: MEMBRANE STRUCTURE AND FUNCTION 17 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL The plasma membrane is the boundary of life. Like all biological membranes, it has selective permeability, allowing some materials to cross it more easily than others. According to the fluid mosaic model, biological membranes consist of various proteins that are attached to or embedded in a bilayer of amphipathic phospholipids The Fluidity of Membranes Membranes are held together by weak hydrophobic interactions o Lateral movements of phospholipids is rapid o Proteins move slower and in a directed matter (most are immobile because they are attached to the cytoskeleton and extracellular membrane) Phospholipids with unsaturated hydrocarbon tails maintain membrane fluidity at lower temperatures because the kinks in the hydrocarbon chain prevent solidification Remains fluid until phospholipids solidify at lower temperatures Steroid more common in plasma membranes of animals, cholesterol, restricts movement of phospholipids and thus reduces fluidity at warmer temperatures o Also prevents close packing of lipids and so it enhances fluidity at lower temperatures Evolution of Differences in Membrane Lipid Composition Variations in membrane-lipid composition and the ability to change the composition in response to changing temperatures are evolutionary adaptations Membrane Proteins Integral proteins: transmembrane proteins o Center is hydrophobic and outer edges are hydrophilic o Have hydrophilic channels through the center Peripheral proteins: not embedded; loosely bound to integral proteins o Support for plasma membrane Functions of Proteins 1. Transport a. Hydrophilic channel b. Change shape c. Hydrolyze ATP to pump substances 2. Enzymatic Activity a. Membrane protein may be an enzyme with active site exposed 3. Signal Transduction pathway a. Membrane protein (receptor) has binding site with specific shape b. External messenger (signaling molecule) cause proteins to change shape by binding to it 4. Cell to cell recognition a. Glycoproteins serve as identification tags specifically recognized by membrane proteins of other cells b. Short-lived 5. Intracellular joining a. Membrane proteins of adjacent cells hook through junctions b. Long-lived 6. Attachment to cytoskeleton and extracellular membrane a. Microfilaments non-covalently bound to membrane proteins b. Maintains cell shape and stabilized location of membrane proteins Diffusion Solutes move from a high concentration to a low concentration; down concentration gradient due to thermal motion 18 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Diffusion of one solute is unaffected by the concentration gradient of other solutes Passive transport: diffusion of substances across biological membranes o Permits solute to move in either direction; net movement occurs down its concentration gradient H2O Balance of Cells Without Walls Tonicity: ability of surrounding solution to cause a cell to gain or lose H2O o Depends on the solute concentration that cannot pass the membrane Osmoregulation: control of solute concentration and water balance H2O Balance of Cells with Walls Walls help maintain H2O balance Turgor pressure: opposes further uptake of water Facilitated Diffusion Passive transport of polar molecules or ions aided by proteins (proteins speed movement) Channel proteins—ion channels/aquaporin o Gated channels Carrier proteins change shape Ligand channels Active Transport Pump a solute against its gradient Uses carrier proteins (allows cell to maintain a gradient different than its surroundings) Cytoplasmic side is negatively charged and the extracellular side is positively charged Membrane potential favors passive transport of cations into the cell and anions out Two forces drive the diffusion of ions: o Chemical force (the ions’ gradient) o Electrical force (effect of membrane potential on ions’ movement) Some membrane proteins that transport ions contribute to the membrane potential Electrogenic Pump Transport protein that generates voltage across membrane by active transport of ions (stores energy for cellular work) o Na-K pump (animals): maintains osmotic balance and establishes electrochemical gradient Antiporter: results in net negative charge in cell, hydrolyzes ATP to move ions o Proton pump (plants, bacteria, fungi): actively transports H+ out of cell Cotransport Single ATP powered pump that transports specific solute and indirectly drives active transport of other solutes Plants: load sucrose made by photosynthesis in leave veins Animals: helps with diarrhea (Na levels drop as too much waste is expelled. NaCl and glucose allos solutes to be taken up by the Na-Glucose cotransporters and pass into the blood) Exocytosis Process by which the smooth and rough ER replace lipids and proteins lost from the plasma membrane 19 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Cell secretes biological molecules by fusion of a vesicle with the plasma membrane Contents of vesicles spill to the outside of the cell, vesicle becomes part of the plasma membrane Does not move water and solutes out of the cell; only removes large, insoluble particles Used by secretory cells to export products o Delivers proteins and carbohydrates from the golgi body to outside of the cell when making the plant cell wall Endocytosis Cells take in biological molecules and particulate matter by forming new vesicles from the plasma membrane Means by which large protein molecules enter cells Small area of plasma membrane sinks inward, forms pocket and pinches in Receptor Mediated Endocytosis Enables cells to acquire specific substances from the extracellular fluid Human cells taken in cholesterol for membrane and steroid synthesis o Cholesterol binds to LDL receptors on plasma membrane o Act like ligands: molecule that specifically binds to receptor site on another molecule Pinocytosis Droplets of extracellular fluid are takin into the cell in small vesicles Uptake of water and solutes into the cell by formation of vesicles at the plasma membrane CHAPTER 8: AN INTRODUCTION TO METBOLISM Metabolism: the totality of an organism’s chemical reactions; manages material and energy resources of the cell Metabolic pathway: o Begins with a specific molecule that is altered in steps, resulting in a product (can have multiple starting molecules and products) o Each step is catalyzed by enzymes o Some release energy (exergonic) to break down complex molecules—catabolic pathways (breakdown pathways) ex: cellular respiration—glucose is broken down in the presence of oxygen gas to carbon dioxide gas and water o Some consume energy (endergonic) to build complex molecules—anabolic pathways (biosynthetic pathways) Ex: photosynthesis, synthesis of amino acids and proteins o Energy released from downhill catabolic pathways is stored and used to drive uphill reactions of anabolic pathways Forms of Energy Energy: capacity to cause change o Move matter against opposing forces (gravity and forces) o Rearrange a collection of matter Kinetic energy: relative motion of objects o heat or thermal energy kinetic energy associated with the random movement of atoms or molecules 20 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Potential energy: o the energy matter possesses because of its location or structure o arrangement of electrons in bonds between atoms o chemical energy potential energy available for release in chemical reactions complex molecules have high chemical energy The Laws of Energy Transformation Thermodynamics: study of energy transformations that occur in a collection of matter o System: the particular matter under study o Surroundings: everything outside of the system o Isolated system: unable to exchange energy or matter with its surroundings o Open system: energy and matter can be transferred between the system and surroundings o Determines whether a reaction will or will not occur First Law of Thermodynamics o The energy of the universe is constant—energy can be transformed and transferred but not created or destroyed o Principle of conservation of energy Second Law of Thermodynamics o Entropy: measure of disorder or randomness o Every energy transfer or transformation increases the entropy of the universe o Spontaneous process: process that can occur without an input of energy It must increase the entropy of the universe Kinetics The speed or rates of reactions Reaction rates are affected by: o Nature of what is undergoing the reaction—reactions involving acids/salts are faster than those involving the breaking or forming of covalent bonds o Physical state o Concentration (the higher the concentration, the higher the rate of particle collisions) o Temperature o Catalyst: substance that accelerates the forward and the reverse reactions by lowering the activation energy Free Energy ∆G = energy available to do work ∆H = the total energy of the system T = temperature ∆S = change in entropy T∆S represents heat or unusable energy Free energy: the portion of the system’s energy that can perform work when temperature and pressure are uniform throughout the system o The measure of a system’s inability/tendency to change to a more stable state o It will predict if a process will be spontaneous—G and H need to be negative, while T and S will be positive 21 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL o Every spontaneous process decreases the system’s free energy, and processes with a positive or 0 G-value are non-spontaneous o The higher the G-value, the more unstable the system. The system will tend to change in order to have a lower G-value o As a reaction proceeds to equilibrium, the free energy of the mixture of reactants and products decreases G is at its lowest value Process is spontaneous and can perform work only when it is moving towards equilibrium Exergonic and Endergonic Reactions in Metabolism Exergonic reactions: proceeds with a net release of free energy o Free energy is lost o Occur spontaneously o Negative ∆G and ∆H o Positive ∆S o Increase in entropy and temperature o G = -686J; cellular respiration, hydrolysis Endergonic reactions: one that absorbs free energy from its surroundings o Stores free energy in molecules o Occurs non-spontaneously o Positive ∆G and ∆H o Negative ∆S o Decrease in entropy and temperature o G = +686J; photosynthesis, protein/DNA synthesis Equilibrium and Metabolism Reactions in isolated systems can reach equilibrium Chemical reactions of metabolism are reversible Cells that have reached metabolic equilibrium are dead (living cells are never in equilibrium) Cells are NOT isolated systems To create more order, heat is released and causes disorder in the surroundings Order is maintained by the constant input of energy (loss of order = death) Types of Work Performed by Cells Chemical work o Pushing of endergonic reactions that would not occur spontaneously (synthesis of polymers from monomers) Transport work o Pumping of substances across membranes against direction of spontaneous movement Mechanical work o Beating of cilia, contraction of muscle cells, movement of chromosomes during cellular respiration Energy coupling: the use of exergonic processes to drive energonic ones o Links +∆G with --∆G (spontaneous/exergonic with non-spontaneous/endergonic) o Uses ATP as an immediate source of energy that powers cellular work Structure and Hydrolysis of ATP ATP is used for energy coupling and to make RNA Bonds between the phosphate groups of ATP can be broken by hydrolysis 22 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL o When the terminal phosphate bond is broken, molecule of inorganic phosphate leaves ATP, becomes adenosine diphosphate (ADP) Exergonic reaction How the Hydrolysis of ATP Performs Work When ATP is hydrolyzed, the release of free energy produces heat Cells are able to use the energy released by ATP to drive endergonic chemical reactions with enzymes Phosphorylated intermediate: recipient with the phosphate group covalently bonded to o The key to coupling exergonic and endergonic reactions, more reactive than an un-phosphorylated molecule Hydrolysis of ATP is also used in transport and mechanical work o Leads to a change in protein’s shape and its ability to bind to another molecule o Sometimes involves phosphorylated intermediate o ATP is bonded non-covalently to motor protein, ATP is hydrolyzed releasing ADP and Pi, then another ATP molecule can bind—at each stage the motor protein changes shape and its ability to bind to the cytoskeleton Regeneration of ATP ATP is renewable, can be regenerated by the addition of P to ADP The energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) o ATP cycle o Formation of ATP is not spontaneous; requires the use of free energy o Catabolic pathways, light energy The Activation Energy Barrier Enzyme: molecule that acts like a catalyst, a chemical agent that speeds up a reaction without becoming consumed by the reaction Activation energy: initial investment of energy for starting a reaction, energy required to contort the reactant molecules so bonds can break o Amount of energy needed to push reactants uphill so the downhill portion can begin o Supplied as thermal energy that reactants absorb from the surroundings o When enough energy is absorbed, reactants are in the transition state (unstable) o As atoms settle into their new, more stable bonding arrangements, energy is released to the surroundings o Provides a barrier that determines the rate of the reaction How Enzymes Lower the Activation Energy Barrier Heat speeds up a reaction by allowing reactants to attain the transition state more often o Not a good method for biological molecules: High temperature denatures proteins and kills cells Heat would speed up all reactions, not just those that are needed Enzyme lowers activation energy by enabling reactant molecules to absorb enough energy to reach transition state at even moderate temperatures o Cannot change G (make endergonic into exergonic) o Hasten reactions that would eventually occur Allow for dynamic metabolism, determine which chemical processes will be going on in a cell at any particular time because they are so specific o Brings reactants closer to each other, requires less energy Substrate Specificity of Enzymes Substrate: reactant an enzyme acts upon o Enzyme forms an enzymatic substrate complex when it binds to substrate 23 BIO 5A: INTRO TO CELLULAR AND MOLECULAR BIOLOGY CONDENSED NOTES FOR FINAL Enzyme’s specificity arises from its shape, which is a consequence of its amino acid sequence Active site: restricted region of the enzyme molecule that binds to the substrate o Formed by only a few of an enzyme’s amino acids Enzymes don’t have stiff structures; change between subtle different shapes in dynamic equilibrium with slight differences in free energy As substrate enters active site, enzyme changes shape slightly due to interactions between substrate’s chemical groups on the side chains of the amino acids that form the active site o Shape change makes active site fit more snuggly around the substrate—induced fit Brings chemical groups of active site into positions that enhance their ability to catalyze chemical reactions Catalysis in the Enzyme’s Active Site Substrate held in active site by weak interactions, H bonds and ionic bonds R groups of a few amino acids of the active site catalyze conversion of substrate to product Lower activation energy and speed up a reaction o In reactions involving two or more reactants, the active site provides a template on which substrates can come together in proper orientation for reaction to occur between them o As the active site clutches its bound substrates, the enzyme may stretch the substrate molecules toward their transition state form, stressing and bending chemical bonds that must be broken o Active site may provide a microenvironment that is more conductive to a particular type of reaction than the solution itself would be without the enzyme o Direct participation of the active site in the chemical reaction Rate at which enzyme converts substrate to product depends on initial concentration of substrate o More substrate molecules, more frequently they access active sites of enzyme molecules o There is a limit as to how fast a reaction can be pushed by adding more substrate o When enzyme population is saturated, the only way to increase its rate of product formation is to add more of the enzyme Effects of Temperature and pH Rate of enzymatic reaction increases with increasing temperatures (optimal temperature) o Too high temperature disrupts hydrogen bonds that stabilize the active shape of an enzyme and it denatures as a result Optimal pH around 6-8 Cofactors Cofactors: non-protein helpers used by enzymes, may be bound tightly to an enzyme as a permanent resident or they may bind loosely and reversibly along with a substrate o Some are inorganic o If it is organic it is called a coenzyme Most vitamins are important because they act as coenzymes or raw materials from which coenzymes are made Enzyme Inhibitors Most enzym
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