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Biological Molecules The bond in table salt (NaCl) is 1. 2. 3. 4. 5. a. polar. b. ionic. c. covalent. d. double. e. nonpolar. Which of the following would NOT be used in connection with the word acid? 1. a. excess hydrogen ions 2. b. contents of the stomach 3. c. magnesium hydroxide 4. d. pH less than 7 5. e. HCl In covalent bonding, pairs of valence electrons are shared, and molecules are formed Carbon is significant because it can form 4 covalent bonds • All life is based primarily on carbon Organic Chemistry • Organic Chemistry is the chemistry of carbon • However, “Organic” does not necessarily mean “natural” • Not “chemistry of living things”- (that’s biochem) • Hydrocarbons are the most basic example – Combustible – Can form rings Carbon (always) forms 4 bonds Cadrbon forms bonds with Hydrogen, Oxyen, even itself Carbon can form double bonds 1-Butene 2-Butene Skeletons may have double bonds, which can vary in location. Carbon also forms ring structures upon itself Cyclohexane Benzene Skeletons may be arranged in rings. The variety of carbon compounds is limitless All terrestrial life is based on carbon Covalent bonds hold together the macromolecules of life • Living things create macromolecular products for structure: • 6CO2(g)+ 6H2O(l) + hν C6H12O6(s) + 6O2(g) • Macromolecules as reactants are broken down for energy: C6H12O6(s) + 6O2(g) 6CO2(g)+ 6H2O(l) All the reactions of a living thing are called its metabolism Organic molecules are good energy sources Energy is required to form covalent bonds; energy is released when bonds are broken Carbon compounds are usually combustiblethat is, they burn in the presence of oxygen FUNCTIONAL GROUPS A carbon skeleton can be modified by the addition of functional groups- familiar groups of atoms which affect the properties of the molecule hydroxide group – OH amino group – NH2 carboxyl group – COOH phosphate group – PO4 methyl group – CH3 Functional groups can radically change the function of a molecule Estradiol Female lion Testosterone Male lion Figure 3.5 Which of the following represents an amino group? 1. 2. 3. 4. 5. -OH -PO4 -CH3 - NH2 -COOH 20% 1 20% 20% 2 3 20% 4 20% 5 Announcements • Midterm next class! – Polar covalent bonds – pH – Polymers – Carbohydrates – Lipids – Proteins • Finish lab today- Hand in Wed! • Midterm in nine days! Most molecules in living things fall into four categories • • • • Carbohydrates Lipids Proteins Nucleic acids These all exhibit modular construction Modular housing Made of interchangeable parts Freight trains have modular assembly Modular assembly allows a wide variety of products from a few pieces Most biopolymers are formed by dehydration synthesis Hydrolysis is the reverse reaction (Catabolic) Metabolism • all chemical reactions in body • Anabolism- building up • Catabolism- breaking down Major Macromolecules of Life • • • • Carbohydrates Lipids Proteins Nucleic Acids Carbohydrates Carbohydrates • “Carbon” + “Hydro” • Formula (CH2O)n • Different from hydrocarbons • Soluble in water • Includes: table sugar, honey, starch, glycogen, cellulose, high fructose corn syrup • Glucose is the primary monomer A Glucose monomer can cyclize to form a ring structure Atoms in bonds are free to rotate around the bonds Glucose + Glucose = Maltose (monosaccharide + monosaccharide = disaccharide) Glucose + fructose = sucrose A polysaccharide chain can be extended to thousands- it is theoretically limitless Lipids Nonpolar molecules of living things: Fats, oils, waxes, steroids, etc. Lipids • • • • • • Non-polar High-energy molecules For energy storage Forms cell membranes Hormones Members of family include oils, fats, waxes, and cholesterol (steroids) Lipids are non-polar • Therefore, they are hydrophobic • C and H are similarly electronegative • Do not mix easily with water • C-H bond is high in energy • Lipids make good energy storage molecules Triglycerides are a primary lipid structure Dehydration synthesis links fatty acids to glycerol Fatty acids can be saturated and unsaturated (“cis” and “trans”) Monounsaturated vs. Polyunsaturated Cis- and Trans- fatty acids are isomers • Melting point is very different because of shape • Health effects are very different • Isomers- Same formula, different shape Triglycerides can be modified to form phospholipids • Phospholipids are amphipathic- having a polar and nonpolar region • Hyrophilic head, hydrophobic tails • Primary constituent of cell membranes Steroids and cholesterol are also lipids, of a different sort Estradiol Female lion Cholesterol Testosterone Male lion Many names for sugars end in the suffix A. B. C. D. E. -acid. -ose. -hyde. -ase. -ing. Proteins Amino acid polymers which make us what we are Proteins have incredible versatility of structure and function Proteins are incredibly diverse at the molecular level A few examples Insulin Rubisco ATP synthase Fibrin Nitrogenase Protein function depends greatly on shape Amino Acids • Proteins consist of subunits called amino acids Figure 2.12 Amino Acids • Exist in either of two stereoisomers: D or L. • L-forms are most often found in nature. Peptide Bonds • Peptide bonds between amino acids are formed by dehydration synthesis Figure 2.14 Proteins are made of amino acids • All amino acids have a backbone and a side group (“R” group) • Backbone: amino group, carboxyl group, central carbon • Side group: there are 20 different kinds, each with different chemical properties Some amino acids are polar, others nonpolar Others have sulfur, others are acidic, still others are basic Many are sold as nutritional supplements Amino acids are added one by one to form a polypeptide chain of a protein • Dehydration synthesis forms a peptide bond • DNA contains the instructions for the proper sequence for a specific protein DNA carries the information to make a specific protein Proteins have four levels of structure • Primary- amino acid sequence of polypeptide • Secondary- coiling of amino acid backbone • Tertiary- Polypeptide folding from amino acid side groups • Quaternary- more than one polypeptide • Protein structure depends on all these levels of interaction A protein’s Primary (1o) structure is its amino acid sequence • Determined by the sequence of amino acids • Amino acids linked by peptide bonds • Chain is called polypeptide • Sequence proceeds from “Nterminus” to “C-terminus” • Amino acid sequence determined by DNA code Levels of Protein Structure • The primary structure is a polypeptide chain Figure 2.15a Secondary (2o) structure • Hydrogen bonding between amino acid backbones • Amino group H’s H-bond with O’s from carboxyl end • 2 basic 2o 2o structures: α- helix and β-pleated sheet Alpha-helix and Beta-sheet are two important 2o structural motifs Tertiary structure • The folding interactions from amino acid side chains of a polypeptide • The folding of 2o domains upon each other • Interactions can be ionic, Hbonds, hydrophobic, or covalent • Proper 3o structure depends on pH, temperature A lightbulb filament has multiple levels of structure Quaternary structure • The interactions of multiple polypeptides to form a functional protein • Polypeptides can be the same (collagen is a homotrimer) or different (hemoglobin is a heterotetramer) Changes in the 1o structure of a protein can have far-reaching effects The tertiary structure of proteins is sensitive to denaturation • Heat or chemicals (incl. acids and bases) can temporarily or permanently change a protein’s 3o structure EnzymesCatalytic proteins Enzymes are a special kind of protein Enzymes are protein catalysts • Catalysts- things which speed up chemical reactions • Catalysts are not consumed in a reaction • -ase: The enzyme suffix Catalase How enzymes work Structure aids function An active site naturally fits substrate Enzyme specificity depends on shape Shape changes to fit substrateinduced fit LE 5-6 Enzyme available with empty active site Active site Substrate (sucrose) Substrate binds to enzyme with induced fit Glucose Enzyme (sucrase) Fructose H2O Products are released Substrate is converted to products b-galactosidase H 2O galactose lactose b-galactosidase (aka lactase in humans) glucose 11 Enzymes are catalysts made of protein. Which of these factors can slow their proper functioning? 1. 2. 3. 4. 5. Temperature pH Salts All of the above None of these Effects of Temperature and pH • Each enzyme has an optimal temperature in which it can function • Each enzyme has an optimal pH in which it can function • Tertiary structure can be radically altered by changes in pH In salad dressings, oil quickly separates from vinegar because oils are 1. 2. 3. 4. 5. heavier than water. polar. nonpolar. hydrophilic. amphiphilic. A protein containing more than one polypeptide chain exhibits the __________ level of protein structure. 1. 2. 3. 4. 5. A) primary B) secondary C) tertiary D) quaternary E) infinite Nucleic acids DNA, RNA, and ATP Nucleic acids • (Primarily) Informational molecules in cells • Include DNA, RNA, and ATP/ADP • DNA is the code to make a protein • Living things are made up of protein Nulceotides are the monomers of nucleic acid polymers • Consist of a sugar, a phosphate, and a nitrogen-containing base • Sugar can be deoxygenated • Bases contain the genetic information Hydrogen bonds hold the two sides of the DNA ladder together • DNA bases have –OH and –NH2 groups • Sides of ladder are covalently bonded • Rungs held together with H-bonds There are 4 kinds of DNA bases • Adenine and Thymine, Cytosine and Guanine • A, T, C, and G • RNA has Uracil instead of Thymine RNA’s major task is to carry out the instructions of DNA • DNA is doublestranded, RNA single • DNA has thymine, RNA has uracil ATP A nucleotide-based ATP, a single RNA nucleotide, is the basic energy currency of all cells LE 8-12 The Regeneration of ATP ATP Energy for cellular work (endergonic, energyconsuming processes) Energy from catabolism (exergonic, energyyielding processes) ADP + What powers this cycle? P i ATP energy is used in the cell for all kinds of jobs How many basic monomers are found in proteins? 1. 2. 3. 4. 5. Zero One Four Twenty Infinite How many basic monomers are found in nucleic acids? 1. 2. 3. 4. 5. Zero One Four Twenty Infinite Midterm 1 Review • • • • • • • • • • Scientific method Characteristics/Domains of living things Atomic structure- protons, neutrons electrons Valence electrons pH Functional groups Carbohydrate structure Protein structure Lipid structure Nucleic acid structure