Organic Chemistry I
Organic Chemistry I 1330
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This 6 page Class Notes was uploaded by Zaida Gomez on Tuesday September 20, 2016. The Class Notes belongs to 1330 at Texas State University taught by Aglaia Chandler in Fall 2016. Since its upload, it has received 6 views. For similar materials see Functional biology in Life and Physical Sciences at Texas State University.
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Date Created: 09/20/16
The Chemical Level of Organization: Organic Compounds Organic Compounds Hydrogen and other elements covalently bonded to carbon - Carbohydrates - Lipids - Proteins - Nucleic acid Carbon’s Bonding Behavior Outer shell of carbon has 4 electrons; can hold 8 Each carbon atom form covalent bonds with up to four atoms Carbon Compounds Carbon atoms can form single bonds with H atoms and both single and double bonds with O and N atoms Bonding Arrangements Carbons atoms can form chains or rings Other atoms project from the carbon backbone Carbon Compounds Covalently linked carbon atoms can form linear chains, branched chains and cyclic structures Functional groups (polyatomic ions) Atoms or clusters of atoms that’re covalently bonded to carbon backbone Give organic compounds their different properties Functional groups are the parts of molecules involved in chemical reactions (hydroxyl OH, amino NH3+, carboxyl COOH, phosphate Po4^3-, sulfhydryl SH) Biomolecules Macromolecules are generally polymers of simpler biomolecular units (micromolecules or monomers) Micromolecules- amino acid, carbohydrate, lipid, nucleotide Macromolecules- proteins, polysaccharides, membranes, nucleic acids (DNA, RNA) Polymers Monomers from larger molecules by condensation reactions called dehydration reactions Polymers are disassembled to monomers by hydrolysis a reaction that is essentially the reverse of dehydration reaction Carbohydrates Carbohydrates are the most abundant biological molecules They are composed of C, O, H Two monosaccharides: disaccharides (glycosidic bond) Polymers of monosaccharides units are polysaccharides Monosaccharides- (simple sugars) Oligosaccharides- (short-chained carbohydrates) Polysaccharides- (complex carbohydrates) Monosaccharides - Simplest carbohydrates - Most are sweet tasting, water soluble - Most have 5 or 6 carbon backbone - Glucose (6C) Fructose (6C) Ribose (5C) Deoxyribose (5C) Glucose and Fructose are two monosaccharides Function of Fructose- used by sperm cells as a source of energy, converted to glucose and used as a source of energy Function of Ribose- part of RNA nucleotides and ATP Function of Deoxyribose- Part of DNA nucleotides Disaccharides - Type of oligosaccharide - Two monosaccharides covalently bonded - Formed by condensation reaction Condensation of Reactions Form polymers from subunits Enzymes remove –OH from one molecule, H from another, form bond between two molecules Discarded atoms can join to form water Hydrolysis Type of cleavage reaction Breaks polymers into smaller units Enzymes split molecules into two or more parts An –OH group and an H atom derived from water are attached at exposed sites Polysaccharides Straight or branched chains of many sugar monomers Most common are composed entirely of glucose - Cellulose - Starch (ex. amylose) - Glycogen STORAGE polysaccharides- glycogen (animals) and starch (plants) STRUCTURAL polysaccharides- cellulose (plant cell walls) and Chitin (exoskeleton) Cellulose and Starch - Differ in bonding patterns between monomers Cellulose- tough indigestible, structural material in the cell wall of plants Starch- easily digested, storage form in plants Glycogen Sugar storage form in animals Stored in muscle and liver cells When blood sugar decreases, liver cells degrade glycogen, release glucose Chitin Polysaccharide: structural material for hard parts of invertebrates, cell walls of many fungi Nitrogen- containing groups attached to glucose monomers Lipids Lipids are substances of biological origin that’re soluble in organic solvents 3 functions 1. Lipids in form of a bilayer are essential components of biological membranes 2. Lipids containing hydrocarbon side chains serve as energy stores 3. Many intra- and intercellular signaling events involve lipid molecules Classification - Fatty acids - Triacylglycerols - Glycerophospholipids - Sphingolipids - Steroids - Waxes Fats Fatty acid(s) attached to glycerol Triglycerides are most common Fatty Acids Carboxyl group (-COOH) at one end Carbon backbone (up to 36 C atoms) Saturated- single bonds between carbons, chains pack tightly and form more rigid, organized aggregates Unsaturated- one or more double bonds, chains bend and pack in a less ordered way with greater potential for motion Trans Fat Unnatural compounds (obtained when oil is hydrogenated) which are known to be detrimental to health Triacyglycerols or triglycerides Fatty acid triesters of glycerol Most contain two or three different types of fatty acid residues Animal fats- high percent saturated fatty acids residues The melting temperature of a fatty acid varies with degree of saturation and chain length Most common fats in the body ROLE OF TRICYGLYCEROLS Function as energy reservoirs in animals The fat content of normal humans allows them to survive starvation for 2-3 months Insulate Saponification- formation of soaps from triacygerols Phospholipids Main components of cell membranes Amphiphilic molecules with nonpolar aliphatic tails and polar phosphoryl-X heads Waxes Long chain fatty acids linked to long chain alcohols or carbon rings Firm consistency, repel water Important in water-proofing Sterols and Derivatives No fatty acids Rigid backbone of four fused-together carbon rings Cholesterol Based on a core structure consisting of three 6-membered rings and a one 5- membered ring, all fused together Cholesterol is the most common steroid in animals and precursor for all other steroids in animals Steroid Hormones Bind to highly specific receptor proteins in the nucleus regulating gene expression and metabolism Major groups are the sex hormones and those produced by the adrenal cortex Proteins Are polymers made up of amino acid monomers linked together Amino Acids: The Legos of Life - Tiny bricks that snack together, forming the proteins on which every function of life depends Proteins- Amino acids Amino acid- a compound that contains both an amino group and a carboxyl group Alpha Amino acid in which the amino group is on the carbon adjacent to the carboxyl group all proteins are composed of 20 standard amino acids Classification of Amino Acids -The R group or side chain determines the structural range and general physical characteristics of the amino acids -The amino acids are generally grouped according to the various characteristics of their R groups - R GROUP TYPES Nonpolar- amino acids (hydrophobic) Polar- amino acids (hydrophilic) Protein synthesis Protein is a chain of amino acids linked by peptide bonds Peptide bond- type of covalent bond - Links amino group of one amino acid with carboxyl group of next - Forms through condensation reaction Peptide bond Two amino acids condense to form a dipeptide New bond is known as the peptide bond Peptides, Proteins, and Nomenclature - Amino acids polymerize to form long chains called “peptides” - Individual amino acids are called amino acid residues once they are incorporated into a peptide - Polypeptide chains are described by starting at the N-terminus and proceeding to the C-terminus Peptides - Less than 40 residues Glutathione: antioxidant, protects cells from reactive oxygen species such free radicals and peroxides Oxytocin: milk ejection, uterine muscles contraction at birth, maternal behavior, sexual arousal, bonding, increases trust and empathy (ecstasy), reduces fear, alleviates repetitive behavior (autism) Vasopressin (ADH): regulates the body’s retention of water, involved in aggression, blood pressure and temperature regulation Enkephalin: opioid peptide, natural pain killers Levels of Protein Structure 1 degree- primary- sequence 2 degree- secondary- local structures 3 degree- tertiary- overall 3 dimensional shape 4 degree- quaternary- subunit organization THE ROLE OF SEQUENCE IN PROTEIN STRUCTURE - All of the information necessary for folding the peptide chain into its “native” structure is contained in the primary amino acid structure of the peptide Primary Structure Sequence of amino acids Unique for each protein Dipeptide- Two linked amino acids Polypeptide- Three or more Backbone of polypeptide has N atoms Primary Structure and Protein Shape Primary structure influences shape in two main ways: 1. Allows hydrogen bonds to form between different amino acids along length of chain 2. Puts R groups in positions that allow them to interact Major Functions of Proteins Functions depends on 3 dimensional structure Structure depends on bonds between amino acids 1. Structure 2. Contraction 3. Transport 4. Buffers 5. Enzymes 6. Hormones 7. Antibodies Importance of Primary Sequence Many protein diseases involve a change in the primary amino acid sequence Nature of Protein Sequences Sequences and composition reflect the function of the protein Membrane proteins have more hydrophobic residues whereas fibrous proteins may have atypical sequences Homologous proteins from different organisms have homologous sequences - A small change in the primary sequence of polypeptides gives them very different biological properties Secondary Structure Hydrogen bonds form between different parts of polypeptide chain These bonds give rise to coiled or extended pattern Tertiary Structure The folding of a polypeptide chain in three dimensional space Folding as a result of interactions between R groups Quaternary Structure Some proteins are made up of more than one polypeptide chain: subunits Protein Shapes: Fibrous vs Globular Fibrous- contain polypeptide chains organized approx. Parallel along a single axis g- proteins are folded to a more or less spherical shape Fibrous Protein Contain polypeptide chains organized approx. Parallel along a single axis Characteristics- - Long fibers or large sheets - Mechanically strong - Insoluble in water and dilute salt solutions - Structural roles in nature - Tend to have only one type of secondary structure EXAMPLES Keratin of hair and wool Collagen of connective tissue of animals including cartilage, bones, teeth, skin, and blood vessels Polypeptides with Attached Organic Compounds Lipoproteins- proteins combined with cholesterol, triglycerides, phospholipids Glycoproteins- proteins combines with oligosaccharides Denaturation Disruption of three dimensional shape Breakage of weak bonds (if the bond is broken, the shape changes and the protein loses its function) causes of denaturation: -pH, temperature destroying protein shape disrupts function
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