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Chapter 4/5 Notes

by: Allie Muro

Chapter 4/5 Notes Biology 114

Allie Muro

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week of 2/1 Chapter 4 and beginning of chapter 5
Principles of Biology
Dr. Stevan Marcus
Class Notes
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This 6 page Class Notes was uploaded by Allie Muro on Friday February 5, 2016. The Class Notes belongs to Biology 114 at University of Alabama - Tuscaloosa taught by Dr. Stevan Marcus in Spring 2016. Since its upload, it has received 23 views. For similar materials see Principles of Biology in Biology at University of Alabama - Tuscaloosa.

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Date Created: 02/05/16
Chapter 3 Hydrophilic and hydrophobic substances • On ionic or polar (or both) substances will dissolve in water • Hydrophilic- affinity for water (because it polar or charged) • Hydrophobic- does not have affinity for water • Nucleic acids, sugars, and many proteins dissolve in water because they have polar groups and, in the case of many water soluble proteins, both polar and ionic groups exposed at their surfaces • Oil molecules are hydrophobic because they have primarily non polar covalent bonds • Hydrophobic molecules related to oils are the major components of cell membranes Molecular mass and solute concentration in aqueous solutions • Molecular mass is the sum of all atomic masses of all atoms in a molecule o MM of methane (CH4) is 16à12 for C + 4x1 for H = 16 • One mole (mol) of a molecule (or compound) is its molecular mass in gram units of mass o 1 mole of CH4 = 16 grams o 1 mole of HCl = 36.5 • Molarity (M) is the number of moles of solute per liter of aqueous solution o A 1 molar aqueous solution of HCl contain 36.5 grams of HCl (H+, Cl-) per liter of water (H20) Dissociation of Water Molecules • A hydrogen atom in a hydrogen bond between two water molecules can occasionally shift from one molecule to the other o The hydrogen atom leaves its electron behind and is transferred as a proton, or hydrogen ion o The molecule with the extra proton is now a hydronium ion (H3O+), although it is often represented simply as H+ o The molecule that lost the proton is now a hydroxide ion (OH-) o Chapter 4 Important Properties of Carbon • Organic chemistry- study of compounds that contain carbon • Organic compounds range from small, simple molecules to colossal ones with substantial structural complexity • Most organic compounds contain hydrogen atoms in addition to carbon atoms • In molecules with multiple carbons, each carbon bonded to 4 other atoms has a tetrahedral shape • When 2 carbon atoms are joined by a double covalent bond, the molecule, or segment of a molecule, has a rigid flat shape and the atoms covalently bonded to the carbons are in the same plane as the carbons Molecular Diversity Arising from Variation in Carbon Skeletons • Carbon chains from the “skeletons”, or major parts of skeletons, of most organic molecules • Carbon skeletons can vary in length and may be straight, branched, or arranged in closed rings • Some carbon skeletons have double bonds • Hydrocarbons consist of only carbon and hydrogen Hydrocarbons • Organic molecules consisting of only carbon and hydrogen • Many organic molecules, such as fats, have hydrocarbon components • Hydrocarbons can undergo chemical reactions that release large amounts of energy • Are the major components of fossil fuels, which formed from the fossilized remain of dead plants and animals by exposure to heat and pressure in the earths crust over hundreds of millions of years Skeletal Formulas • Stick depictions of carbon skeletons of organic compounds in which carbon atoms of the skeleton are assumed to be bonded to hydrogen atoms, unless otherwise noted • Line ends and vertices (point of contact of two angular lines) represent carbon atoms • All atoms that are not carbon or hydrogen bonded to carbon are signified by their chemical symbol Isomers • Compounds that have the same molecular formula but different structures and chemical properties • The # of possible isomers increases as carbon skeletons increase in size o 18 variations of octane o 366,319 possible structures of icosane o *don’t need to memorize these numbers • types of isomers: o structural- have different covalent arrangements of their atoms o cis-trans – have the same covalent bonds but differ in spatial arrangements o enantiomers- isomers that are mirror images of each other Structural Isomers • differ in the covalent arrangements of their atoms • example – 2 structural isomers of butane (C4H10) cis-trans isomers • have same covalent arrangements but differ in spatial arrangements • arise from double bonded carbons because they do not allow atoms they join to rotate freely about the bond axis enantiomers • differ in spatial arrangements around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands • often designated the “L” and “D” isomers from the Latin for left and right (levo and dextro) • enantiomers cannot be superimposed on each other • important in the pharmaceutical industry o ibuprofen- effective enantiomer = S-ibuprofen, ineffective enantiomer = R- ibuprofen • 2 enantiomers of a drug may have different effects • usually only one isomer is biologically active • differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules • Chapter 4 Hydroxyl Group • Polar due to electronegative oxygen, hydrophilic (forms hydrogen bonds with water) • Written (OH) or (HO) • Compound name- many (alcohol) Carbonyl Group • Polar, hydrophilic • Sugars with ketone groups are called ketoses; those with aldehydes are called aldoses • Compound name – ketone or aldehyde • Written (C=O) Carboxyl Group • Polar and charged (hydrophilic) • Acts as an acid • Written (COOH) • Compound name- carboxyl acid or organic acid Amino Group • Charged (hydrophilic) • Acts as a base • Written (NH )2 • Compound name- amine Sulfhydryl Group • Polar (hydrophilic) • Written (SH) • 2 SH groups can react, forming a “cross-link” that helps stabilize protein structure • compound name- thiol Phosphate Group • charged (hydrophilic) • note- phosphorus atoms can violate the “octet” rule of valence electrons as in the case for phosphate • written (OPO ) 3 • contributes negative charge • when attached, confers on a molecule the ability to react with water, releasing energy • compound name- organic phosphate Methyl Group • nonpolar (hydrophobic) • written (CH 3 • affects the expression of genes • affects the shape and function of sex hormones • compound name- methylated compound Functional Group Example • the sex hormones estradiol and testosterone differ only in the presence of certain functional groups on a common ring structure • the different actions of theses two molecules produce the contrasting features of female and male animals Chapter 5 Biological Macromolecules • within cells, small organic molecules are often joined together to form larger molecules, called macromolecules • all living organisms are made up of 4 classes of macromolecules: o carbohydrates- monosaccharides, disaccharides, and polysaccharides o lipids- fats, phospholipids, sterols, etc o proteins- amino acid polymers o nucleic acids- nucleotide polymers Polymers • long molecule consisting of many similar building blocks called monomers • 2 of the 4 classes of life’s macromolecules consist only of polymers: proteins and nucleic acird • a 3 class, carbohydrates, consists of monomers, dimers, and polymers a synthesis and breakdown of polymers • monomers form larger polymers by enzyme-catalyzed dehydration reactions- covalent bonding of 2 molecules to each other through loss of a water molecule • 1 molecule provides a hydroxyl group (OH) a the other provides a hydrogen (H) • to make a polymer the dehydration is repeated as monomers are added one by one • biopolymers are disassembled to monomers by hydrolysis- the reverse of the dehydration reaction • bonds are broken by the addition of water molecules • a hydrogen from the water bonds to one monomer and the hydroxyl group bonds to the adjacent monomer Diversity of Biological Polymer • every cell has thousands of different macromolecules • macromolecules vary among cells of a single multicellular organism, very more between individual organisms within a species and very even more between species • an immense variety of polymers can be built from a small set of monomers carbohydrates serve as fuel and building material • carbohydrates include sugars and the polymers of sugars • the simplest carbohydrates are monosaccharides or single sugars • polysaccharides are sugar polymers composed of many sugar building blocks monosaccharides • have molecular formulas that are usually multiples of CH O 2e.g., glucose is C H6O12 6 • have a hydroxyl group bonded to each carbon except one, which is doubled bonded to an oxygen to form a carbonyl group • glucose is the most common monosaccharide • classified by: o the location of the carbonyl group (aldose if at the end of carbon chain or ketose if flanked by carbons within chain) o the number of carbons in the carbon skeleton • form ring structures in aqueous solutions (e.g., glucose) • serve as major fuel for cells (generate ATP) • in cellular respiration, cells extract the energy stored in glucose molecules to produce ATP


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