Chemistry & Macromolecules

Chemistry & Macromolecules - Welcome to XL2: Cells,...

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Unformatted text preview: Welcome to XL2: Cells, Tissues, and Organs Instructor: Sherry Soliman M.S., Physiological Science sksoliman@gmail.com Dates: 9/21/10­12/2/10, no meeting on 11/11/10 and 11/25/10 Days/Time: Tuesdays and Thursdays 7­10pm Lecture Room: 4216 Young Hall Lab Room: 2336 Young Hall South Required Texts • Lecture textbook: Life, The Science of Biology, 8th edition, 2008 Sadava, Heller, Orians, Purves and Hillis • Lab manual: LS 2 Laboratory Manual Pfluegl, Life Sciences 2, Cells, Tissues and Organs, Scientific American Articles FOUR Scientific American articles must be downloaded. These articles will be available on the Blackboard course website: ( http://uclaextension.blackboard.com/ ). There will be quiz questions from each article as indicated on the syllabus. Course Materials • All course material (including syllabus, lectures and Scientific American articles) will be posted on Blackboard. Grading Course grades will be based on the following: Midterm Exams (2 @ 100pts each) 200 Final Exam 180 Lab Assignments 80 Lecture/Article Quizzes (4 @ 10pts each) 40 Exams • All exams will be multiple choice and closed book. • NO MAKE UP EXAMS WILL BE GIVEN. If you area unable to take an examination because of illness or emergency, you are responsible for contacting me before the examination. You are required to have written verification from a physician regarding the illness. Labs • Attendance at laboratory is mandatory, and cannot be made up or excused!! • The laboratory component is worth 100 points total. 80 points come from the lab assignments, and 20 points come from the final exam. • Lab dates: 9/30, 10/14, 10/28, 11/9, 11/30 The Chemistry of Life & Macromolecules Lecture 1 Chapters 2 & 3 Levels of Organization Levels of Organization • Molecules are made up of atoms • Cells are built of molecules • Cells of many types are the working components of living organisms • A tissue is a group of cells with similar and coordinated functions • Organs combine several tissues that function together • Organs form systems The Chemistry of Life • What Are the Chemical Elements That Make Up Living Organisms? • How Do Atoms Bond to Form Molecules? • How Do Atoms Change Partners in Chemical Reactions? • What Properties of Water Make It So Important in Biology? Chemical elements that make up living organisms Six elements make 98% of mass of most living organisms-CHON+PS Few other elements are present in small amounts Atoms: The Constituents of Matter Isotopes of an element have the same number of protons but differ in the number of neutrons present Electron shells determine the reactivity of atoms Atoms with unfilled Outermost shells are REACTIVE Filled outermost shells STABLE •The number of electrons determines how atoms will interact • Chemical reactions: atoms bond or change bonding partners • Chemical reactions involve changes in the distribution of electrons between atoms Chemical Bonds Chemical bond-an attractive force that links two atoms together in a molecule Two main properties influence formation of bonds between atoms: 1. The state of an atom’s outermost electron shell 2. An atom’s electronegativity Covalent Bonds • Covalent bonds form by sharing one or more pairs of electrons (single, double, triple), resulting in a very stable bond • nonpolar covalent bond (equal sharing) • polar covalent bond (unequal sharing) Electronegativity the attractive force that an atomic nucleus exerts on electrons Nonpolar-H2 Polar-water H2O Ionic Bonds • Ionic bonds are formed by the electrical attraction of positive and negative ions Formation of Sodium and Chloride Ions 11 protons 11 electrons 17 protons 17 electrons 11 protons 10 electrons 17 protons 18 electrons Hydrogen bonds can form between or within molecules Hydrogen bonds • are not restricted to water molecules • may also form between a strongly electronegative atom and a hydrogen atom covalently bonded to a different electronegative atom • are weak (only 10% of the strength of covalent bond), but large numbers of them within a molecule (intramolecular) or between molecules (intermolecular) can have powerful affects on structure (e.g., proteins, DNA) Hydrogen bonds attraction between the δ– end of one molecule and the δ+ hydrogen end of another molecule Interactions between nonpolar molecules Hydrophobic interactions Van der Waals forces Figures from Chem CD- Dr. Cooper Chemical Bonds and Interactions Properties of Molecules • Polar molecules tend to be hydrophilic. • Substances that are ionic or polar often dissolve in water due to hydrogen bonds • Nonpolar molecules are called hydrophobic because they tend to aggregate with other non-polar molecules Water: Structure and Properties • Water is special, primarily because of extensive hydrogen bonding • Hydrogen Bonds Hold Water Molecules Together Water • In ice, each molecule of water is hydrogen bonded to many others in a rigid crystalline structure. These bonds take up “space”, the density of water declines with freezing, and ice floats! • This is beneficial to bottom dwellers in lakes, rivers and oceans Water Properties • Water is an excellent solvent • Water has unusual thermal properties: high specific heat high heat of vaporization high heat of fusion • cohesion • surface Tension • structure of Ice • water acts as both an acid and a base Water is an excellent solvent The hydration shells of water molecules around both positive and negative ions as they dissolve, keep these ions in solution by eliminating their ionic attraction Acids & Bases Acid releases H+ Base accepts H+ • When acids dissolve in water, they release hydrogen ions- H+ (protons) • H+ ions can attach to other molecules and change their properties • HCl is a strong acid – the dissolution is complete HCl → H+ + Cl− H+ is increased-solution is acidic Bases accept H+ ions. The OH- absorbs H+ to form water NaOH → Na+ +OH− NaOH is a strong base – the dissolution is complete Weak acids and bases: partially dissociate into ions in water −COOH → −COOH− + H+ HCO3 − + H+ → H2 CO3 pH Scale • pH is the measure of hydrogen ion concentration • It is defined as the negative logarithm of the hydrogen ion concentration in moles per liter • The pH scale indicates the strength of a solution of an acid or base. The scale values range from 1 through 14 • A pH 7 means the concentration of hydrogen ions is 1 x 10–7 M pH Scale Macromolecules: Giant Polymers There are four major types of biological macromolecules: – Proteins – Carbohydrates – Lipids – Nucleic acids Macromolecule Composition 70% WATER Polymers Vs Monomers • • • • Proteins ---> amino acids (20 different types) Carbohydrates ---> glucose, fructose, galactose Lipids ---> fatty acids and glycerols Nucleic acids ---> nucleotides Macromolecules • polymers with molecular weights > 1000 • Most are polymers of smaller molecules called monomers Most macromolecules are formed by condensation and broken down by hydrolysis Polymers are formed in condensation reactions Polymers are broken down into monomers in hydrolysis reactions Proteins • Proteins are polymers of amino acids. • They are molecules with diverse structures and functions • Each different type of protein has a characteristic amino acid composition and order • Proteins range in size from a few amino acids to thousands of them • Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids Amino Acids • There are 20 amino acids found in proteins. Each amino acid consists of an amino group, a carboxyl group, a hydrogen, and a side chain bonded to the α carbon atom • The side chains, or R groups, of amino acids may be charged, polar, or hydrophobic; there are also special cases, such as the —SH groups of cysteine, which can form disulfide bridges. The side chains give different properties to each of the amino acids Amino Acid Types These hydrophilic amino acids attract ions of opposite charges Hydrophylic amino acids with polar but uncharged side chains – form hydrogen bonds Amino Acid Types A Disulfide Bridge Amino acids polymerization Protein Structure There are four levels of protein structure: – Primary – Secondary – Tertiary – Quaternary Primary Structure Repeating units of N-C-C-N-C-C Secondary Structure Stabilized by the hydrogen bonds that form between different amino acids Tertiary Structure Tertiary structure is determined by interactions of R-groups: • disulfide bonds • aggregation of hydrophobic side chains • van der Waals forces • ionic bonds • hydrogen bonds Quaternary Structure Quaternary structure results from the interaction of subunits by hydrophobic interactions, van der Waals forces, ionic bonds, and hydrogen bonds Protein shape influences function Shape is crucial to the functioning of some proteins: – Enzymes need certain surface shapes in order to bind substrates correctly – Carrier proteins in the cell surface membrane allow substances to enter the cell – Chemical signals such as hormones bind to proteins on the cell surface membrane • Because the 3-D structure of a protein in stabilized by relatively weak bonds, environmental conditions such a temperature, pH changes, or altered salt concentrations can change the shape of the protein into an inactive formdenaturation Carbohydrates: Sugars and Sugar Polymers • Carbohydrates act as energy storage and transport molecules • They also serve as structural components Carbohydrates: molecules in which carbon is flanked by hydrogen and hydroxyl groups H—C—OH Monosaccharides – simple sugar monomers Disaccharides – 2 simple sugars linked by covalent bonds Oligosaccharides – 3 to 20 monosaccharides Polysaccharides – hundreds or thousands of monosaccharides – starch, glycogen, cellulose Carbohydrate Polymerization Polysaccarides store energy and provide structural materials Added functional groups give carbohydrates altered functions • Fructose 1, 6-biphosphate-important intermediate in cellular energy reactions • Glucosamine and galactosamine important in the extracellular matrix • Chitin-the principal structural polysaccharide in the skeletons of insects and many crustaceans and cell walls of fungi Lipids • Lipids are insoluble in water • This insolubility results from the many nonpolar covalent bonds of hydrogen and carbon in lipids • Lipids aggregate away from water, which is polar, and are attracted to each other via weak, but additive, van der Waals forces Lipids Functions Roles for lipids in organisms include: – Energy storage (fats and oils) – Cell membranes (phospholipids) – Capture of light energy (carotenoids) – Hormones and vitamins (steroids and modified fatty acids) – Thermal insulation – Electrical insulation of nerves – Water repellency (waxes and oils) Synthesis of a Triglyceride •Fats and oils are triglycerides – simple lipids – made of 3 fatty acids and 1 glycerol. Glycerol: 3 –OH groups – an alcohol •Fatty acid: nonpolar hydrocarbon with a polar carboxyl group – carboxyl bonds with hydroxyls of glycerol Saturated and Unsaturated Fatty Acids Phospholipids Phospholipid bilayer Nucleic Acids • Nucleic acids are polymers that are specialized for storage and transmission of information • Two types of nucleic acid are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Polymer of nucleotides Nucleotides Have Three Components • pentose sugar (DNA – deoxyribose sugar, RNA – ribose sugar), • a phosphate group • a nitrogen-containing base DNA bases: adenine (A), cytosine (C), guanine (G), and thymine (T); RNA bases-Uracil Nucleotide Structure Characteristics of DNA & RNA DNA • DOUBLE HELIX • Phosphate groups link sugars together • Two strands of DNA run in opposite directions • Complementary base pairing A–T C–G • Purines pair with pyrimidines by hydrogen bonding • Complementary base pairing is the basis for replication and transcription RNA • Single Stranded • Instead of thymine, RNA uses the base uracil (U) DNA & RNA Distinguishing characteristics of DNA & RNA • DNA is an informational molecule: information is encoded in the sequences of bases. All DNA molecules have the same structure – variation is in the sequence of base pairs. DNA carries hereditary information between generations • RNA uses the information to determine the sequence of amino acids in proteins Other roles for nucleotides •ATP – energy transducer in biochemical reactions •GTP – energy source in protein synthesis •cAMP – essential to the action of hormones and transmission of information in the nervous system The genome The DNA is “copied” (in a complementary way) into RNA. An RNA “message” is read in the ribosome to produce a polypeptide, with each triplet of DNA bases coding one amino acid. Thus, a sequence of 300 DNA base pairs codes a polypeptide with 100 amino acids. Humans have less than 30,000 genes, but alternate splicing of RNA messages produces somewhat more than 100,000 different polypeptides. Comparing the DNA base sequences of the same genes (and now the whole genome) in different living species provides information on evolutionary relatedness. ...
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