lecture2BIO155 - BIO115 Chemical Foundation of Biology...

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Unformatted text preview: BIO115 Chemical Foundation of Biology Jessica Pamment Levels of Biological Organization Levels 1. The biosphere 6. Organs and organ systems 2. Ecosystems 9. Organelles 3. Communities 1 µm 8. Cells 7. Tissues 4. Populations 10. Molecules 5. Organisms Atoms Overview • Elements important to life • Structure of an atom • Chemical bonds in living matter • Properties of water • Acids and bases Chemicals important to life Devil’s Garden Mystery • Observation: Patches of Amazon forest dominated by one tree species, Duroia hirsuta • These patches are known as ‘devil’s garden’ Devil’s Garden Mystery • Hypotheses: 1. Ants living in the duroia trees produce poison that kills trees of other species 1. Duroia trees themselves kill trees of other species Devil’s Garden Mystery EXPERIMENT Cedrela sapling Duroia tree Inside, unprotected Insect barrier Outside, protected Inside, protected Devil’s garden Outside, unprotected Devil’s Garden Mystery RESULTS Dead leaf tissue (cm2) after one day 16 12 8 4 0 Outside, Inside, Outside, Inside, unprotected protected unprotected protected Cedrela saplings, inside and outside devil’s gardens Devil’s Garden Mystery • Conclusion: Ants kill non­host trees by injecting leaves with formic acid. This creates space for the ants to build their home. Chemicals are all around us! ‘Natural’ doesn’t necessarily mean good: Naturally occurring toxins in food: • Lectins in raw kidney beans • Aflatoxin produced by mold grows on peanuts, raisins, corn Solanine by green potatoes/potato shoots What are elements? What are elements? • Organisms are made up of matter • Matter consists of pure elements or compounds • An element can not be broken down to other substances by chemical reactions • 92 occur in nature The Periodic Table of Elements The Periodic Table of Elements Elements Essential for Life • 96% of living matter is made up of: Carbon (C), Oxygen (O), Hydrogen (H), Nitrogen (N) • Around 4% of remaining weight is made up of: Phosphorus (P), Sulfur (S), Calcium (Ca), and Potassium (K) Trace elements: Boron (B), Copper (Cu), Iodine (I) Chemical Composition of the Human Body Carbon (C): 18.5% Oxygen (O): 65.0% Calcium (Ca): 1.5% Phosphorus (P): 1.0% Potassium (K): 0.4% Sulfur (S): 0.3% Sodium (Na): 0.2% Chlorine (Cl): 0.2% Magnesium (Mg): 0.1% Trace elements: less than 0.01% Manganese (Mn) Boron (B) Chromium (Cr) Molybdenum (Mo) Cobalt (Co) Selenium (Se) Silicon (Si) Copper (Cu) Tin (Sn) Fluorine (F) Vanadium (V) Iodine (I) Zinc (Zn) Iron (Fe) Hydrogen (H): 9.5% Nitrogen (N): 3.3% Chemical Composition of the Human Body Chemical Composition of the Human Body (a) Nitrogen deficiency (b) Iodine deficiency The Periodic Table of Elements The Periodic Table of Elements Atomic Structure • Atom is the smallest unit of matter that still retains properties of an element • Subatomic particles: neutrons, electrons, and protons • Atomic number: number of protons 2He • Mass number: sum of protons and neutrons 4He • Atoms neutral in charge have equal number of electrons as protons Helium Atom Cloud of negative charge (2 electrons) Nucleus Electrons (a) (b) Isotopes • Different atomic forms of the same element • Isotopes of the same element have the same number of protons, but differ in their number of neutrons, i.e. have different atomic masses • Radioactive isotope is one where nucleus decays spontaneously giving off particles and energy Use of Radioactive Isotopes to detect Alzheimer’s Use of Radioactive Isotopes to detect Alzheimer’s Disease The Role of Electrons • Electron configuration influences the chemical behavior of an atom • Only electrons are directly involved in the chemical reactions between atoms • Electrons are found in different electron shells, the further they are from the nucleus, the higher the energy they possess Atoms of the four elements most abundant in living Atoms of the four elements most abundant in living matter The Role of Electrons • Atoms whose outer shells are not full tend to interact with other atoms, that is, participate in chemical reactions leading to the formation of a chemical bond Chemical Bonds, the Glue of Life 1. Ionic bonds 1. Covalent bonds: nonpolar and polar 1. Hydrogen bonds Ionic Bonds • Charge­charge interactions formed between ions • Results from the transfer of electrons between atoms • Compounds formed by ionic bonds are called salts Electron Transfer and Ionic Bonding Na Cl Na Sodium atom Cl Chlorine atom Electron Transfer and Ionic Bonding Na Cl Na Cl Na Sodium atom Cl Chlorine atom Na+ Sodium ion (a cation) Cl– Chloride ion (an anion) Sodium chloride (NaCl) Covalent Bonds • Results from the sharing of a pair of valence electrons by two atoms • Elements C, H, O, and N are important to life because of their tendencies to form covalent bonds electronegativity electronegativity • Nonpolar bonds result between atoms of equal • Polar bonds result between atoms of different Covalent Bonds in Hydrogen Name and Molecular Formula Electrondistribution Diagram Lewis Dot Structure and Structural Formula Spacefilling Model (a) Hydrogen (H2) Covalent Bonds in Water Name and Molecular Formula Electrondistribution Diagram Lewis Dot Structure and Structural Formula Spacefilling Model (c) Water (H2O) Polar Covalent Bonds in a Water Molecule δ– O H H2 O H δ+ δ+ Weak Chemical Bonds • Essential to life due to reversibility • Hydrogen bonds A Hydrogen Bond Water (H2O) δ− δ+ δ δ− Ammonia (NH3) δ δ δ Hydrogen bond Chemical Reactions Chemical Reactions • 2H2 + O2 2H2O Water • Unique properties due to structure • The medium of life, makes life habitable • Exists in solid, liquid, gaseous states • Constitutes 70­95% of cells Hydrogen Bonds between Water Molecules δ– δ+ Hydrogen bond H δ+ δ– δ+ —— δ– O —— H δ+ δ– Properties of Water • Cohesion • Moderation of temperature • Expansion upon freezing • Solvent • The tendency for molecules of the same kind to stick together Cohesion • Water molecules stay together due to hydrogen bonding • Gives water structure • Allows water transport in plants Water Transport in Plants Water-conducting cells Adhesion Direction of water movement Cohesion 150 µm Moderation of Temperature • Water’s high specific heat allows it to stabilize temperature • Water’s high specific heat is due to energy being needed to break hydrogen bonds before molecules can move faster • Water has high heat of vaporization • Evaporative cooling Heat and Temperature • Related but different • Heat is the amount of energy associated with the movement of atoms/molecules in a body of matter • Temperature measures the intensity of heat, that is the average speed of molecules in that body of matter while warming up only a few degrees • Water absorbs and stores large amounts of heat Oceans can moderate Coastal Climate Santa Barbara 73° Los Angeles (Airport) 75° 70s (°F) 80s 90s 100s Pacific Ocean San Diego 72° 40 miles Burbank 90° San Bernardino 100° Riverside 96° Santa Ana Palm Springs 84° 106° Expansion upon Freezing • Water is less dense as a solid than as a liquid • Water is most dense at 4oC At 0oC water molecules are locked in a • crystal Ice forms an Insulating Barrier Ice Hydrogen bonds are stable Hydrogen bond Liquid water Hydrogen bonds break and re-form Water as a Solvent • Water is a versatile solvent due to the polarity of the water molecule • Water, a solvent, can dissolve ionic compounds (solutes) to make a solution • Water dissolves solutes essential for life –+ Cl– Cl– + – Na+ – – + + – – + – – + + + Na+ – – – Salt dissolving in Water Acids and Bases • Acidic and basic conditions affect living organisms • Behavior of substances in aqueous solutions depends on their state of ionization (to break apart into charged ions) • Water although neutral, has a tendency to ionize • Water can act as an acid and a base Acids and Bases • Acids increase the [H+] of a solution, thus decreasing the • pH HCL H+ + Cl­ • Bases decrease the [H+] of a solution, thus increasing • • the pH NH3 + H+ NH4+ NaOH Na+ + OH­ The pH The pH Scale Buffers • The internal pH of most living cells is about pH7 • Slight changes in pH affects cellular reactions • Buffers are used to maintain required range • Buffers accept H+ from solution when in excess and donate H+ when depleted Water Quality and the Environment • Alteration of water pH and temperature can affect life on earth • Sulfur Oxide from burning fossil fuels leads to acid rain • Carbon dioxide from burning fossil fuels leads to the greenhouse effect Effects of Acid Rain on a Forest 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 More acidic Acid rain Normal rain More basic Release of volcanic CO Summary • Matter is made up of elements and compounds • 25 out of the 92 elements are essential for life • Oxygen, carbon, hydrogen and nitrogen are the most abundant in living matter • Atom consists of protons and neutrons in the nucleus, and electrons in the shells • Atoms reactivity determined by outer­shell electrons Proton • Positive charge • Determines element Electron • Negative charge • Participates in chemical reactions • Outer-shell electrons determine chemical behavior Nucleus • Consists of neutrons and protons Neutron • No charge • Determines isotope Atom Summary • Strong covalent and ionic bonds, and weaker hydrogen bonds, are essential to life • Water’s polar nature results in hydrogen bonds • H bonds are responsible for water’s unusual properties • The behavior of substances in aqueous solution depends on their ionization state • Buffers are essential for pH homeostasis BIO115 The Molecules of Life Jessica Pamment Overview • • • i. ii. iii. iv. Importance of carbon Chemical groups essential to life Biomolecules Carbohydrates Lipids Proteins Nucleic Acids Properties of Carbon • The capacity to form multiple bonds and chains at low energies makes life possible • Each carbon atom can bond with as many as four atoms, allowing the formation of chains and rings Methane, the simplest hydrocarbon hydrocarbon Valences of Major Elements of Organic Compounds Hydrogen (valence = 1) H Oxygen (valence = 2) O Nitrogen (valence = 3) N Carbon (valence = 4) C Variation in Organic Molecules • Length of carbon chain • Orientation of atoms within the molecules • Functional group binding to carbon chain Variation in Carbon Skeletons Ethane (a) Length Propane 1-Butene (c) Double bonds 2-Butene Butane (b) Branching 2-Methylpropane (commonly called isobutane) Cyclohexane (d) Rings Benzene Chemical Groups • Different chemical groups can affect the properties of organic compounds by: 1. Affecting molecular structure 1. Affecting chemical reactivity Common Functional Groups Common Functional Groups Chemical Groups Most Important to Biological Processes 1. Hydroxyl ­OH 1. Carbonyl >CO 1. Carboxyl ­COOH 1. Amino ­NH2 Biomolecules • Carbohydrates, proteins and nucleic acids are polymers • Polymers are long molecules consisting of similar/identical building blocks, monomers, that are covalently bonded • Lipids are not true polymers • Basis for diversity in polymers is arrangement of units HO 1 2 3 H HO H Unlinked monomer H2O HO 1 2 Polymer 3 4 H (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 4 H Hydrolysis adds a water molecule, breaking a bond H2O HO 1 2 3 H HO H (b) Hydrolysis of a polymer Carbohydrates Carbohydrates • Literally means hydrated carbon • Sugars (monosaccharides and disaccharides) • Polymers of sugars (polysaccharides) Monosaccharides • • • i. ii. iii. Generally have the formula that are some multiple of CH2O Glucose is central to the chemistry of life Sugars can be classified: By the location of carbonyl group Size of carbon skeleton Spatial arrangement of atoms around asymmetric carbons MonosacchaMonosaccharides The Ring Structure of Glucose The Ring Structure of Glucose Disaccharides Disaccharides • Double sugar • Constructed from monosaccharides by dehydration reaction (glucose + fructose) • Most common disaccharide: sucrose • Lactose (glucose + galactose) Disaccharide Disaccharide Formation Polysaccharides • • i. ii. Polymers with up to 1000s of monosaccharides joined by glycosidic linkages Functions: Fuel storage, e.g. starch Structural, e.g. cellulose Polysaccharides Polysaccharides Structural Polysaccharides • Cellulose made by cell walls is the most abundant organic compound on Earth • Cellulose is a polymer of β glucose monomers • Polymers are straight, grouped together into strong fibrils by hydrogen bonds • Bonds in cellulose can’t be broken down by most animals; it is the fiber in our food Prokaryotes in Grazing Animals break down Cellulose Prokaryotes in Grazing Animals break down Cellulose Cell walls Cellulose microfibrils in a plant cell wall Microfibril 10 µm 0.5 µm Cellulose molecules β Glucose monomer Lipids • Not big enough to be considered macromolecules behavior • They show hydrophobic (‘water fearing’) • 1. 2. 3. Three most important types in biology: Fats Phospholipids Steroids The Synthesis and Structure of a fat, or triglyceride The Synthesis and Structure of a fat, or triglyceride Saturated Fat Stearic acid, a saturated fatty acid (a) Saturated fat Unsaturated Fat Oleic acid, an unsaturated fatty acid cis double bond causes bending (b) Unsaturated fat TYPES OF FATS Saturated Fats Unsaturated Fats Margarine INGREDIENTS: SOYBEAN OIL, FULLY HYDROGENATED COTTONSEED OIL, PARTIALLY HYDROGENATED COTTONSEED OIL AND SOYBEAN OILS, MONO AND DIGLYCERIDES, TBHO AND CITRIC ACID XANTIOXIDANTS Plant oils Trans fats Omega-3 fats Role of Fats 1. Energy storage • Weight for weight, fats provide twice as much energy as glucose • Stored in adipose cells 2. Protection of vital organs 3. Insulation Steroids • Characterized by four fused rings • Examples include hormones, cholesterol Steroids Steroids Proteins • Account for more than 50% of dry mass of most cells • Essential for almost every biological function • • • • • Functions include: Enzymes as catalysts Storage proteins Contractile proteins Antibodies as defensive proteins Some functions of Proteins Some functions of Proteins Protein Structure and Function • A protein is a chain of monomers (polypeptide) that has been folded into a 3­D structure • Depending on its folding, proteins canbe globular or fibrous • Protein function is determined by its structure • There are four levels of protein structure Amino Acids Acids Joining Joining amino acids Protein Variety Protein Variety • Made possible due to arrangement of amino acids • 20 amino acids • Each polypeptide is at least 100 amino acids • The primary structure defines the specific order of amino acids The primary The primary structure of a protein Protein Shape Protein Shape • A polypeptide is NOT a protein • A protein is a polypeptide that has folded into a 3D structure The four levels of The four levels of protein structure Requirements for Protein Folding • Specific amino acid sequence • Correct pH, temperature, and other environmental factors Denaturation and Renaturation of a Protein Denaturation Normal protein Renaturation Denatured protein Nucleic Acids • Store and transmit hereditary information • Macromolecules that exist as polynucleotide polymers • Two types: DNA and RNA Building a Protein Building a Protein DNA 1 mRNA NUCLEUS CYTOPLASM mRNA 2 Ribosome 3 Polypeptide Amino acids DNA Nucleotide DNA The nitrogenous bases of DNA DNA The structure of DNA of An RNA nucleotide nucleotide DNA vs. RNA DNA vs. RNA • Sugar: deoxyribose in DNA, ribose in RNA • Bases: RNA uses Uracil where DNA uses Thymine • RNA is usually single­stranded, DNA is double­stranded THE DOUBLE HELIX 5′ end Hydrogen bond 1 nm 3.4 nm 3′ end 3′ end 0.34 nm (a) Key features of DNA structure (b) Partial chemical structure 5′ end (c) Space-filling model Comparing the amino acid sequence of a protein among six vertebrates vertebrates Summary • Organic compounds are the building blocks of life • Carbon’s properties due to ability to form four covalent bonds • Carbohydrates, proteins, and nucleic acid are polymers of repeating units • Lipid components vary, so not polymers Summary • Carbohydrates play role in fuel storage and structure • Proteins play wide range of roles • Nucleic acids play role storing hereditary information • Lipids play a role as fuel storage, organ protection, insulation ...
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