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Chapter 2 of "Modern Biology" Text- CHEMISTRY (Review) 1 CHEMISTRY- The science of the composition, structure, properties, and reactions of matter • Structure and function of all living things are governed by the laws of chemistry • Understanding the basic principles of chemistry will give you a better understanding of all living things and how they function! • QUESTION: What examples can you give of how chemistry is involved in biology? CHEM REVIEW • Matter• Mass• Is MASS the same thing as WEIGHT? – - The pull of gravity on an object is what gives an object its "weight" – - A bowling ball having the same mass on Earth and the moon would weigh less on the moon than it does on Earth due to a gravitational pull present on the Moon. – How much do you weigh on other planets??? Find out here: http://www.exploratorium.edu/ronh/weight/ 2 Elements • Pure substances that cannot be broken down into simpler substances • Periodic Table • created in 1869 by Mendeleev • categorizes elements and shows trends • 118 elements, 92 occurring naturally •Noble or "inert" gases on far right •Alkali metals on far left (minus H) •Atomic radii increase from left to right and decrease from top to bottom 3 Biologists love CHONPS most of all! • 90% of the mass of living things are composed of combinations of 4 elements: O,C, H, & N • Throw in P and S and you can make almost any combination of organic molecules! – Carbs – Lipids – Nucleic acids – Amino acids, proteins 4 Atoms • Simplest part of an element that retains all properties of that element • Too small to see so we make up models to help us understand the structure of atoms and predict how they will act • Nucleus• Electrons (-) orbit around nucleus; very fast • Farther an E- is from the nucleus- More ENERGY! • Atomic Mass• Atomic Number• # of electrons = # of protons • - Electrons balance out + charge of protons and have very little mass 5 Compounds • Most elements do not exist by themselves in nature but rather like to combine with other elements • A molecule is formed when two or more atoms join together chemically. • A compound is a molecule that contains at least two different elements. All compounds are molecules but not all molecules are compounds. • 2 H atoms + 1 O atom = 1 H2O molecule • Chemical properties of compounds are different than the elements alone (2 gases = liquid) • “Chemical rxn’s”- chemical bonds can be broken, atoms can be rearranged, and new chemical bonds are formed! 6 States of Matter • SOLID: molecules are tightly linked; little movement and definite shape • LIQUID: molecules are less tightly linked; moves more freely than solids; conforms to container • GAS: molecules are usually not attracted to one another; move very fast; fills the entire volume of a container 7 Bonding • Most bonding takes place because atoms are most chemically stable when their outermost energy levels are filled Types of Chemical Bonds • Covalent bonds: – Strong bonds – Shared electrons, simulate a full outer orbital 8 Polar covalent bond: • Electrons are shared, but not evenly shared This creates further potential for hydrogen bonds to form between molecules 9 Hydrogen Bonds • Relatively weak, singly, but rather strong collectively 10 Ionic Bonds • Strong bonds • Create ions • Create electrical charges: when + and – charges attract, ionic bonds are created • OXIDATION: Na becomes (Na+) = loses e• REDUCTION: Cl becomes (Cl-)= gains an e- 11 Energy • Definition: • Amount of energy in the universe remains the same over time; energy can neither be created or destroyed • Energy = usable energy + dissipates (ex: heat) • Many energy forms are important in biology: – – – – – chemical energy thermal energy radiant energy electrical energy mechanical energy • Free energy: energy in a system that is available for work, for example, in a cell, it is the energy available to fuel cell processes (metabolism, etc) 12 Energy and Chemical Reactions • Exergonic rxn’s = release energy (products have less chemical energy than reactants) ex: AB + CD AC + DB + energy • Endergonic rxn’s = absorb energy (products have more chemical energy than reactants) ex: AB + CD + energy AC + DB • Activation energy: energy added to reactants to "jumpstart" the rxn • Catalysts: reduce the amount of activation energy that is needed to start the rxn. See Figure 2-7 in your book. 13 Solutions • Water is extremely important to all living things, so the chemistry of living things often involves the study of solutions! • Solution: mixture in which substances are uniformly distributed in another substance – Solutions can be mixtures of liquids, solids, or gases • Solute: • Solvent: • Concentration [ ]: measurement of the amount of solute dissolved in a fixed amount of solvent • Saturated? • Aqueous solutions: 14 Acids and Bases Dissociation: force between H2O molecules is so H2O strong that the O- atom from one H2O molecule can pull off the H+ atom from another molecule • Water dissociates into H+ and OH- equally (hydrogen and hydroxide) • Hydroxide ion formed and H+ ion is released! • Free H+ ion can react with another H2O molecule to form a hydronium ion (H3O+) • Acidity and Alkalinity is a measure of the relative amount of OH- and H+ ions in a solution! • pH= measure of how many H+ ions are in a solution • Pure water has equal OH- and H+ ions in solution; pH of 7.0 • Acidic solutions have H+ > OH- ions – pH is below 7.0 – sour • Basic solutions have H+ < OH- ions – pH is above 7.0 – slippery and bitter H+ + OH- 15 Buffers • Chemical substances that neutralize small amounts of either an acid or a base added to a solution • Most chemical rxn’s in living organisms are controlled by pH, therefore... • Buffers are very important for homeostasis. – If blood pH drops below 7.0 (acidosis), it could be fatal – If blood pH goes above 7.7 (alkalosis), it could be fatal • If our blood did not contain a buffering system, we would not be able to drink and eat acidic/basic foods! • Great chem review • http://scidiv.bcc.ctc.edu/rkr/Biology101/lectures/pdfs/Chemistry 101.pdf 16 Chapter 3 of "Modern Biology" Text BIOCHEMISTRY WHAT IS BIOCHEMISTRY? - Study of those molecules used and manufactured by living things! 17 WATER • Living things are 70-80% water by weight • Most chemical rxns in living things take place in aqueous environments (either inside or outside the cells) • Water is needed to dissolve and transport nutrients, gases, etc. around us (blood, tissue fluid, saliva, sweat, etc) 18 Water is a covalently bonded molecule that is also POLAR (has +, - regions) • 2 H+ atoms bond with an Oxygen atom at an angle • Region of the molecule where the O atom is located has a slightly neg.(-) charge, while the regions of the molecule where the two H+ atoms are have a slightly positive charge. • Oxygen has a greater “custody” of the shared electrons • In textbook see pp. 39-42 for water info 19 POLAR COVALENT BONDS: • The polar nature of water makes it the "universal" solvent • hydrophilic or hydrophobic? • What types of substances mix well with water? • Hydrogen Bonds- negative part of the water molecule (O) forms a bind with the positive charge of the H+ atoms • H-Bonds = weak when alone, strong when many! • Cause H2O molecules to cling together & to other substances! 20 Water’s polarity is responsible for some of its unique properties: Cohesion• Water molecules are attracted (+/-) to other nearby water molecules; bonds them together • Surface tension = cohesive forces between water molecules are strong enough to act as if their was a "skin" in the water surface 21 Water Properties Adhesion• Water is attracted (+/-) to other substances. • meniscus = adhesive forces between water molecules and glass 22 Water Properties Capillary Action• The climbing ability of water is due to both adhesion and cohesion • Enables water to move against the force of gravity and upward through narrow tubes • ex) Trees (Sequoias) xylem CHECK OUT THIS WEBSITE: http://www.uni.edu/~iowawet/H2OProperties.html 23 Water Properties • Water is very important in temperature regulation - resists quick temperature changes and maintains homeostasis! • H2O has a very high specific heat- which means it can absorb or lose a large amount of heat energy before its temperature changes • Thus, water has a moderating effect on temperatures 24 Organic Compounds • All compounds discovered can be classified into two broad categories: inorganic and organic • "Organic" = • The compounds of life consist of primarily 6 elements: "CHONPS" 25 Chemistry of CARBON is the chemistry of LIFE! • Carbon forms the “backbone” (framework) of all organic molecules • C has four e- in its outermost energy level, but needs 8 to fill it, so it readily forms covalent bonds! 26 • A description of carbon: "It is shamelessly promiscuous. It is the party animal of the atomic world, latching on to many other atoms (including itself) and holding tight, forming molecular conga lines of hearty robustness.“ – Bill Bryson, from “A Short History Of Nearly Everything” 27 Carbon, the basis for life • Carbon likes to bond, with other atoms and with itself • single bonds• double bonds• triple bonds28 Carbon videos NPR: It’s All About Carbon http://www.npr.org/news/specials/climate/video/ Making Carbon Bonds Breaking Carbon Bonds Carbon In Love What Do We Do? 29 Functional Groups • Clusters of atoms that influence the properties of the molecules they compose "R" stands for any group of atoms that is attached by a covalent bond to a chemical functional group -OH (hydroxyl group) is the functional group for chemicals referred to as "alcohols“ -NH4 (amino group) gives molecules slightly basic properties -COOH (carboxyl group) gives slightly acidic properties 30 Simple & Complex Molecules • Molecules are often built up from smaller, simpler molecules: MONOMERS • Monomers bond together to produce: POLYMERS • Large polymers are called: MACROMOLECULES • Monomers are bonded by condensation rxn’s (aka: dehydration synthesis): release of H2O molecules • Polymers are broken down by hydrolysis: addition of water that breaks bonds between polymers 31 There are Four Major Classes of Organic Compounds: CARBOHYDRATES (= ENERGY) • - The most abundant organic compounds in nature Monosaccharides - simple sugars; "building blocks of all carbs" • C:H:O = approx. 1:2:1 • Example: C6H12O6 • Three main monosaccharides: • glucose- main source of energy for cells • fructose- sugar in fruits and honey (the sweetest monosaccharide) • galactose- sugar in milk and yogurt – • glucose, fructose, & galactose have the same chemical formula: C6H12O6 ?! “isomers”- same chemical formula but different forms = two substances with different properties Disaccharides - two monosaccharides bonded together by condensation rxn’s ~ glycosidic bonds glucose + fructose = sucrose (common table sugar) glucose + galactose = lactose (major sugar in milk) 32 Carbs, continued Polysaccharides - several monosaccharides bonded together by condensation rxn’s; GIANT, storage molecules • Examples: glycogen (animals), starch (plant), cellulose (plant fiber), chitin (insect) • Cell stores energy it doesn’t use by converting monosaccharides into disaccharides/polysaccharides • Glycogen- stored in liver and muscles- once storage is full, glycogen turns to fat! 33 The Role of Enzymes in Starch Digestion • Monosaccharides- soluble in water & CAN pass through cell membrane by diffusion • Disaccharides- are soluble in water and CANNOT pass through the cell membrane (too BIG!) – when a cell needs energy, disaccharides are broken down into its monomers by hydrolysis! • Polysaccharides- are NOT soluble in water and CANNOT pass through the cell membrane without a series of hydrolysis rxn’s! 34 Proteins • Large and often complicated molecules • Mostly C,H,O, & N • Hundreds of thousands of different kinds in each cell • Make up skin, muscles, pigments, antibodies, hormones & enzymes • Proteins are polymers composed of amino acid monomers (20 AA groups in total) 35 Amino Acids • Central carbon atom covalently bonded to 4 other atoms • Amino Acid (general structure): • R groups give each amino acid its unique properties (acidic, basic, polar, nonpolar, etc.) • Peptide: two or more AAs bonded together by covalent bonds called peptide bonds • Polypeptide: exceptionally large chain of amino acids • Proteins are composed of one or more polypeptides • Proteins are usually bent and folded upon themselves (hydrogen bonds among individual AAs) • Protein shape is affected by temperature, pHcan be denatured! (ex: cooked egg white vs. uncooked egg white) 36 ENZYMES are important proteins • Many chemical reactions in living cells (and organisms) are regulated by ENZYMES • Enzymes are globular proteins in living systems that mediate metabolic reactions • Metabolism: the series of energy exchanges and chemical reactions that occur in living systems (cells, organisms) • catabolic activities = breakdown of larger molecules into smaller; AB ==> A + B • anabolic activities = synthesis of larger molecules from smaller ones; A + B ==> AB 37 • Enzymes act as catalysts (push, or speed up, chemical reactions) • Enzymes lower the ACTIVATION ENERGY of reactions (ex: heat required) to enable chemical bonds to form or break more easily: A + B ==> AB or AB==> A + B • Enzymes mediate the reaction in the substrate but do not take part in the reaction themselves, so enzymes can be reused again and again • Some classes of enzymes: – Proteases – Lipases – Amylases (sucrase, lactase, etc.) • most enzyme names end in -ane or -ase suffix, and most are named after the substrate upon which they act 38 • Each Enzyme acts upon a specific substrate (there are thousands of different enzymes in the body to mediate thousands of different reactions) • Enzymes have an active site, to fit with their substrate in a "lock-and-key" fashion • Sometimes, to get a good "fit", enzymes require a vitamin or mineral to fit into the active site: COENZYME • "Induced Fit Hypothesis" a change in the shape of an enzyme’s active site may occur, which allows it to bind more effectively to its substrate • Enzymes can be deactivated (DENATURED) when their 3-D active site is warped by heat or drastic pH changes (acid) 39 LIPIDS • Large, nonpolar molecules that are insoluble in H2O (hydrophobic) • Fats, waxes, oils store energy very efficiently (concentrated energy) • Ratio of C:H:O is > than in carbs; LARGE # of C-H bonds • Most lipids have "fatty acids"- long, straight carbon chains with a carboxyl group (-COOH) attached at one end Saturated: each C atom is covalently bonded to four atoms; solid at RT Unsaturated: not bonded to the maximum # of atoms that it can; usually liquid at RT 40 Lipids are divided into three categories based on their structure: 1) TRIGLYCERIDES: fats and oils - glycerol plus three fatty acids (mostly 16-18C) - Saturated- shortening, animal fat - Unsaturated: most plant oils 2) PHOSPHOLIPIDS - like fats, but with two fatty acids and a phosphate group (PO4) 3) WAXES – long fatty acid and an alcohol group 4) STEROIDS- different structure from other lipids - composed of 4 fused carbon rings - Important steroids: Cholesterol, testosterone, estrogen, progesterone, cortisol 41 NUCLEIC ACIDS • Nucleic acids are long chains (polymers)of nucleotides • Nucleotides are the monomers of nucleic acids • Each nucleotide includes a nitrogenous base (R group), a 5-carbon sugar, and a phosphate group 42 DNA: Deoxyribonucleic acid • Contains genetic information • Composed of: 1) deoxyribose sugar 2) phosphate group 3) 4 different nitrogen bases: adenine, guanine, cytosine, and thymine 43 RNA: Ribonucleic acid • Stores and transfers genetic information for making proteins from nucleus to ribosomes • Like DNA, RNA is composed of nucleotides: 1) ribose sugar 2) phosphate group 3) 4 different nitrogen bases: adenine, guanine, cytosine, and uracil • DNA IS DOUBLE STRANDED AND RNA IS SINGLE STRANDED! 44