Lecture Overview. Hydrogen Bonds. Special Properties of Water Molecules. Universal Solvent. ph Scale Illustrated. special properties of water

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1 Lecture Overview special properties of water > water as a solvent > ph molecules of the cell > properties of carbon > carbohydrates > lipids > proteins > nucleic acids Hydrogen Bonds polarity of water allows bonding with each other hydrogen bond (always involves H) not a strong bond lasts trillionth of a second all H 2 O bonded at any given time Special Properties of Water Molecules arise because of the hydrogen bonds > exits in all three states in nature:, gas, liquid, solid > cohesion and surface tension > high temperature capacity > versatile solvent Universal Solvent definitions > solvent = dissolving agent > solute = substance that is dissolved ability to dissolve a range of substance because of its polarity negative and positive ends pull apart solute ph ph Scale Illustrated life requires a certain range of ph ph is a measure of relative amounts of hydrogen ions [H + ] and hydroxide ions [OH - ] in water logarithmic scale from 0 to 14 > ph of 0 = very acidic: [H + ] > [OH ] > ph of 7 = neutral: [H + ] = [OH ] > ph of 14 = very basic: [H + ] < [OH ] 1

2 Molecular Tour of the Cell properties of carbon carbohydrates lipids proteins nucleic acids Why is Carbon (C) So Important almost all cellular molecules contain carbon why? able to form large and diverse molecules > 4 outer electrons > tends to form covalent bonds > can form long chains Organic Compounds made by cells contain carbon more than 2 million known what are some examples? > methane > butane and isobutane > 1- and 2-butene > cyclohexane and benzene Methane single carbon 4 hydrogen atoms covalently linked hydrocarbon (carbon and hydrogen only) Butane and Isobutane 4 carbon + 10 hydrogen isomers (same molecular formula; different arrangement) carbon skeletons linear or branched 1- and 2-butene 4 carbon + 8 hydrogen singe or double-bonds 2

3 Cyclohexane and Benzene 6 carbon + 6 or 12 hydrogen carbons arranged in a ring single or double bonds liquids Functional Groups small group of atoms attached to ends of larger organic molecules determine chemical properties of molecule polar (unequal sharing of electrons with H) 4 main functional groups (Fig 4.3, p35) > hydroxyl > carbonyl > carboxyl > amino Hydroxyl Group Carbonyl Group hydrogen bonded to carbon alcohols carbon double-bonded to oxygen > located at end of chain = aldehyde > located in the middle = ketone Carboxyl Group Amino Group carbon double-bonded to oxygen and single bonded to hydroxyl group act as an acid nitrogen bonded to 2 hydrogen acts as a base 3

4 Functional Groups Summary Macromolecules small groups of atoms influence chemical properties of organic compounds organic compounds can have more than one functional group many organic compounds are large > macromolecules > polymers (composed of many small parts = monomers) examples > proteins (amino acids) > nucleic acids (nucleotides) > carbohydrates (saccharides) > lipids (fatty acids and glycerol) Synthesis of Macromolecules Breaking Down Macromolecules dehydration synthesis > unlinked monomers have hydrogen (H) and hydroxyl (OH) groups > in the process of joining 2 monomers, H 2 O is formed hydrolysis > water is used in breaking covalent bonds > e.g., breaking down food during digestion > reverse of dehydration synthesis Types of Macromolecules Carbohydrates carbohydrates > fuel and building material lipids > energy storage proteins > tools of the cell nucleic acids > information storage sugars and starches > made up of carbon (carbo) and water (hydrates) > (CH 2 0) n monomers are called monosaccharides > e.g., glucose, fructose > ends in ose = sugar > in ring structure polymerize to form: > starch - long term energy storage in plants > glycogen - long term energy storage in animals > cellulose - structural component (fiber) of cell walls 4

5 Lipids Lipids continued diverse range of compounds > hydrophobic (does not mix with water) > made of fatty acid (CH 2 ) n and glycerol (sugar) saturated and unsaturated > presence of double bonds between carbon - absent in saturated fats (solid) - present in unsaturated fats (liquid) phospholipids > major component of cell membrane waxes > barrier against water (e.g., plants) steroids > e.g., cholesterol > component of cell membranes > used in digestion of fats > synthesis of hormones Proteins wide range of functions made up of amino acids - 20 different types > amino group > carboxyl group > R group (side chain - different for each amino acid) Making Proteins Structure of Proteins polypeptide = many linked amino acids > three to thousands of linked amino acids dehydration synthesis -- peptide bond (covalent) primary structure > amino acid sequence secondary structure (folding) > dependent on amino acid sequence > coiling due to hydrogen bonding tertiary structure > 3-D shape of the protein quaternary structure > bonding interaction between protein sub-units alteration of structure affects protein function > denaturation 5

6 Nucleic Acids informational molecules two types > deoxyribonucleic acids (DNA) - inheritable > ribonucleic acids (RNA) - translators > DNA to RNA to Proteins monomers = nucleotides > sugar (5 carbon) > phosphate group > nitrogenous base - 5 types Nucleotides adenine (A) thymine (T) cytosine (C) guanine (G) uracil (U) -- instead of T in RNA Structure of DNA / RNA sugar-phosphate backbone RNA usually single stranded DNA double stranded > double helix > specific pairing of base pairs Double Helix two strands held together by hydrogen bonds > Adenine paired with Thymine > Cytosine paired with Guanine Discovery of DNA Structure structure discovered by James Watson and Francis Crick in 1953 each pairing called a base pair how many base pairs in the human DNA? Answer: about 3 billion 6

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