Chapter 3 The Chemical Basis of Life II Organic Molecues PDF

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Chapter 3: The Chemical Basis of Life II: Organic Molecules I. The Carbon Atom and Organic Molecules A. Organic molecules contain carbon 1. Org. compounds are abundant in living organisms 2. Macromolecules are large, complex orgo. Molecules B. The Carbon 1. Need 4 electrons to fill the octet, and already have 4 in their outer shell 2. Can make up to four bonds 3. Can form nonpolar and polar bonds (based on the electronegativities of the elements a) Polar molecules are soluble in water, while non-polar is not. C. Functional Groups 1. Amino (-NH2) found in proteins, and amino acids 2. Carbonyl (Ketones) (RCOR) found in steroids, waxes and proteins 3. Aldehyde (RCOH) found in linear form of sugars and odor molecules 4. Carboxyl (RCOOH) found in amino acids and fatty acids 5. Hydroxyl (R-OH) found in steroids, alcohol, carbohydrates, and some amino acids 6. Methyl found in DNA, proteins, and carbohydrates 7. Phosphates found in nucleic acid, ATP and phospholipids 8. Sulfates found in carbohydrates, proteins, and lipids 9. Sulfhydryl- contain in the amino acid Cysteine D. Isomers 1. Structural Isomer-same molecular formula, but different bonding relationships 2. Stereoisomers- same structure, but different in 3-D shape a) Cis-trans isomer b) Enantiomers II. Formation of Organic Molecules and Macromolecules A. Polymer vs. Monomer 1. Monomer vs. Polymer a) Glucose is the monomer to starch, cellulose, and glycogen b) Amino Acids is the monomer to proteins c) Nucleotide is the monomer to Nucleic Acids 2. Polymer is formed with dehydration synthesis a) A molecule of water is removed each time the monomer is added on. b) The process is repeated to form a long polymer c) Catalyzed by enzymes 3. The breakdown of polymer is forms with hydrolysis reactions a) A molecule of water is added back, each time a monomer is releacrs b) The process is repeated to break down a long polymer B. Carbohydrates 1. General Overview on Carbohydrates a) Composed of carbon, hydrogens, and oxygen b) General molecular formula : Cn(H2O)n c) Most of the carbon atoms in the carbohydrates are linked to a hydrogen and a hydroxyl group 2. Monosaccharides a) Most common are 5 or 6 carbon sugars (1) Pentose- Ribose, and Deoxyribose (2) Hexose- Glucose (3) We could make it into a linear or ring structure (a) Different type of structure (i) D-Glucose (linear) and α- D- Glucose (ring)

Chapter 3: The Chemical Basis of Life II: Organic Molecules (ii) Structural Isomer: having different arrangement of the same elements (a) Glucose and Galactose (iii) Stereoisomers: isomers that have the 3- Dimensional (a) ∝ and β glucose (i) The beta glucose is the OH is above the ring structure (b) D- and L- glucose (i) Enantiomers with mirror image structure 3. Disaccharides a) Composed of two monosaccharides b) Joined by dehydration and condensation reaction c) The glycosidic bond is the bond that bond the two monosaccharides (1) Sucrose (Table Sugar)-- Glucose and Fructose (2) Maltose: made with two ∝ -D Glucose (3) Lactose (from Milk): made with two β-D-glucose 4. Polysaccharides a) Many monosaccharides linked together to form long polymers (1) Examples (a) Energy Storage-- starch (rice and potatoes), and glycogen (animals energy storage) (b) Structural-- cellulose (plants energy storage), chitin, glycosaminoglycans (2) Structure Formations (a) From lower to higher branched: starch, glycogen, and cellulose C. Lipids 1. General Overview of Lipids a) Predominantly of hydrogen and carbon atoms b) Nonpolar and insoluble in water c) Include fats, phospholipids, steroids, and waxes d) Tiny difference in structure can be profoundly difference in biological properties 2. Fats/Triglycerides a) Formed by bonding a glycerol with three fatty acids b) Joined by dehydrations c) Formed by ester bond, a molecule is least likely to be comprised of subunits (1) Important for energy storage and structural by providing cushioning and insulation d) Saturated and Unsaturated (1) Saturated Fatty Acids (a) All carbons are linked by a single bond (b) Ten to be a solid at room temperature (2) Unsaturated Fatty Acids (a) Contains one or more double bonds (b) Tend to be liquid at room temperature (c) Cis forms naturally, and trand is artifcally. (d) Trans UFA are linked to diseases 3. Phospholipids a) Formed from glycerol, two fatty acids, and a phosphate group b) Amphipathic molecules (1) Phosphate head: polar molecules (2) Fatty Acid Tail: non-polar molecules

Chapter 3: The Chemical Basis of Life II: Organic Molecules 4. Steroids a) Four interconnected ring of carbons atoms b) Usually insoluble in water (1) Cholesterol are examples of steroids D. Proteins 1. Composed of carbon, hydrogens, oxygen, and nitrogen, and small amounts of sulfur 2. Amino Acid a) Organic molecules that contains a carboxyl and amino groups b) Building blocks of proteins c) Difference in amino acids depends on the side chain, or the R groups 3. Polypeptide Formation a) Amino acids joined by dehydration reaction b) The Carboxyl and Amino forms a peptide bond c) Polymers of Amino Acids are known as polypeptides 4. Protein Structure and Function a) A functional proteins consist of one or more polypeptides twisted, folded, and coiled into a unique shape b) Primary Structure (1) Amino acid sequence c) Secondary Structure (1) Stretches or strains of proteins and peptides have distinct characteristics local structure that all depend on hydrogen bonding (2) The two main structure of the secondary structure is the ɑ helix, and the β- sheet, which is crucial for biological functions. d) Tertiary Structure (1) Three Dimensional Shape (2) The formation of disulfide bridge is the important aspect of stabilizing the protein tertiary structure e) Quaternary Structure (1) Formation of two or more polypeptide (2) Protein can be formed from several copies of the same polypeptide f) Five factors that promotes protein stability (1) Hydrogen bonds (2) Ionic bonds and other polar interactions (3) Hydrophobic Effects (4) Van der Waals Forces (5) Disulfide Bridges g) Protein-Protein Interactions (1) Many cellular processes involved steps which involved with two or more proteins (2) Four factors of binding process (a) Hydrogen bonds (b) Ionic bonds and other polar molecules (c) Hydrophobic Effect (d) Van der Wall effects E. Nucleic Acids 1. Responsible for the storage, expression, and transmission of genetic formation a) DNA (Deoxyribose Nucleic Acid) (1) Stores genetic information encoded in the sequence of a nucleotide monomer (2) Made with deoxyribose sugar (3) Made with adenine, thymine, cytosine, and guanine (adenine is bonded with

Chapter 3: The Chemical Basis of Life II: Organic Molecules thymine, and cytosine is bonded with guanine) (4) One form of strand (5) Double helix formed b) RNA (Ribonucleic Acid) (1) Decode DNA into instructions for linking together specific sequence of amino acids (2) Made with adenine, uracil, cytosine and guanine (adenine is bonded with uracil, and cytosine is bonded with guanine) (3) Have several forms (4) Formed with one strand c) The monomer of nucleic acid is a nucleotide (1) A nucleotide is made out of a phosphate group, five carbon sugar, and a single/double ring carbon and nitrogen atoms known as a base (2) Nitrogenous Bases (a) Pyrimidines (one-ringed carbon)- cytosine, thymine, and uracil (b) Purines (two-ringed carbon)-adenine and guanine...