Basic Principles of Biological Chemistry (1-40) PDF

BIOL 150 LECTURE 4 Brief Intro to Organic Chemistry What is Organic Chemistry? A branch of chemistry dedicated to the study of the structures, synthesis and reactions of carbon-containing compounds. Organic molecules are called hydrocarbons and contain carbon bonded to hydr...

BIOL 150 LECTURE 4 Brief Intro to Organic Chemistry What is Organic Chemistry? A branch of chemistry dedicated to the study of the structures, synthesis and reactions of carbon-containing compounds. Organic molecules are called hydrocarbons and contain carbon bonded to hydrogen (as well as other elements).  Importance of Organic Compounds Carbon compounds are quite important in our life, which can be realised as: Food – starch, sugar, fats, vitamins, proteins Fuels – wood, coal, alcohol, petrol, kerosene, natural gas, diesel etc. Household and commercial articles – paper, soap, detergent, leather, rubber, paint, plastic, cosmetics, oils, furniture (wood / plastic) Textile fabrics – wool, cotton, silk, linen, rayon, nylon Drugs and disinfectants – antipyretics, analgesic, antibiotic, sulpha drugs, penicillin, quinine, aspirin etc. Poisons – opium, strychnine, CO gas Perfumes – vanillin, camphor Explosives – dynamites, picric acid, TNT Dyes – indigo, congo red, malchite green War gases – mustard gas, chloropicrin, lewisite Organic vs. Inorganic Organic molecules are made up of more than one type of element and are found in/produced by living organisms. Organic molecules contain carbon- hydrogen bonds, whereas inorganic molecules do not. Organic molecules are generally larger and more complex than inorganic molecules.  Carbon Bonding http://www.ochempal.org/wp-content/images/H/hybridization3.png Since carbon needs a total of 8 electrons to completely fill the 2p orbital, it wants to form 4 bonds with other atoms (each bond consists of one electron from carbon and one from the bonding atom). Hydrocarbons A hydrocarbon is formed when carbon bonds to hydrogen. Simplest hydrocarbon consists of 4 hydrogen atoms bonded to a carbon atom (result called methane): Carbon Skeletons A carbon skeleton is the chain, branch and/or ring of carbons that form the basis of the structure of an organic molecule. Phenol Acetone Glyceraldehyde Functional Groups Functional groups are collections of atoms in organic chemistry molecules that contribute to the chemical characteristics of the molecule Participate in predictable reactions. These groups of atoms contain oxygen or nitrogen or sometimes sulfur attached to a hydrocarbon skeleton Functional groups A functional group is a specific group of atoms within a molecule that is responsible for a characteristic of that molecule. Many biologically active molecules contain one or more functional groups. The major functional groups found in biological molecules are: Hydroxyl, Methyl, Carboxyl, Carbonyl, Amino and Phosphate.  Functional Groups http://jwblackboard.com/organic- chemistry-functional-groups-pdf What is the R? R represents the rest of the hydrocarbon chain Example: for alcohols R OH Rest of carbon chain Functional group Functional Groups: Methyl Methyl group: the smallest hydrocarbon functional group (-CH3). Methylation is a common process in biology, and is involved in regulation of gene expression, protein function and RNA metabolism. Important in fatty acid chains, insoluble in water. Methyl group The methyl group is the only non-polar functional group in the class list above. The methyl group consists of a carbon atom bound to 3 hydrogen atoms. We will treat these C-H bonds as effectively nonpolar covalent bonds. *This means that methyl groups are unable to form hydrogen bonds and will not interact with polar compounds such as water* Functional Groups: Hydroxyl Hydroxyl group: characteristic component of bases, phenols, alcohols, carboxylic and sulfonic acids, and amphoteric compounds (-OH) Ethanol (EtOH) Hydroxyl group Hydroxyl groups are very common in biological molecules. Hydroxyl groups appear on carbohydrates, on the R-groups of some amino acids, and on nucleic acids. Alcohol is an example of a molecule that contains a hydroxyl group Functional Groups: Carbonyl Carbonyl group: composed of a carbon atom double-bonded to an oxygen atom (C=O).   On an end In the middle Functional Groups: Carboxyl Carboxyl group: a set of four atoms bonded together and present in carboxylic acids, including amino acids (-COOH). Carbon atom is attached to an oxygen atom by a double bond and to a hydroxyl group (OH) by a single bond. Carboxyl group Combination of 2 functional groups attached to a single carbon atom – hydroxyl and carbonyl The carboxyl group is very versatile. In its protonated state, it can form hydrogen bonds with other polar compounds. In its deprotonated states, it can form ionic bonds with other positively charged compounds. This will have several biological consequences Found in amino acids & fatty acids Functional Groups: Amino Amino group: consists of one atom of nitrogen attached by covalent bonds two atoms of hydrogen, leaving a lone valence electron on the nitrogen which is available for bonding to another atom (–NH2). Found in all amines and amino acids. Amino group The amino group consists of a nitrogen atom attached by single bonds to hydrogen atoms. An organic compound that contains an amino group is called an amine. Like oxygen, nitrogen is also more electronegative than both carbon and hydrogen which results in the amino group displaying some polar character. Amino groups can also act as bases, which means that the nitrogen atom can bond to a third hydrogen atom. Once this occurs, the nitrogen atom gains a positive charge and can now participate in ionic bonds. Functional Groups: Sulfhydryl group: a sulfur atom and a hydrogen atom (-SH). Being the sulfur analogue of an alcohol group (-OH), this functional group is referred to either as a thiol group or a sulfhydryl group or mercaptans Smelly** Functional Groups: Phosphate Phosphate group: one of three components of a nucleotide (-PO4). Provide a source of energy for cells to do work (ATP). Presence or absence often regulates protein action. Phosphate group Phosphate groups are common in nucleic acids and on phospholipids (the term "phospho" referring to the phosphate group on the lipid). Building Organic Compounds (Polymers) Monomers and Polymers Oligomers - a few monomers joined together (less than 50).  Condensation Reaction Also called dehydration synthesis. Reaction where two substances are joined and a water molecule is lost. Campbell, N. and J Reece. Biology (Custom Ed) 2005  Hydrolysis Reaction Opposite of condensation reaction. Water is added to a substance resulting in its decomposition. Campbell, N. and J Reece. Biology (Custom Ed) 2005 Organic Molecules The four major classes of organic molecules Carbohydrates Proteins Lipids Nucleic Acids Carbohydrates composed of “carbon hydrates” ratio of one carbon molecule to one water molecule (CH2O)n. “Saccharide” is a handy synonym for carbohydrate, because it can be preceded with a prefix that indicates the size of the molecule (mono-, di-, tri- poly-). Carbohydrates Monosaccharides (glucose, fructose) Single sugars (one molecule) Disaccharides (lactose, sucrose) Combination of two monosaccharides Polysaccharides Composed of several sugars Can be many of the same monosaccharide or mixture of different ones  Carbohydrates http://cdavies.wordpress.com/2009/01/27/simple-sugars-fructose-glucose-and-sucrose/ Two Families of Carbohydrates Aldoses (monosaccharide, or simple sugar) Have a carbonyl at one end of chain Ketoses (monosaccharide, or simple sugar) Have a carbonyl anywhere else in the chain. further classified as 2-ketoses, 3-ketoses, etc. according to the position of the carbonyl. 2-ketoses are the most common: if unspecified, a ketose is a 2-ketose.  Depending on carbon number, a monosaccharide can be a: Triose (3C) Tetrose (4C) Pentose (5C) Hexose (6C) http://www.hammiverse.com/lectures/5/images/1-2.png  Whether a sugars is designated as alpha or beta is dependent on the position of the OH group on the first C http://chemistry.elmhurst.edu/vchembook/images/543alphabetaglucose.gif Alpha vs Beta Glucose Alpha and beta are both glucose isomers, but they differ only in the position of their -OH (hydroxyl) and -H (hydrogen) groups on carbon 1. Beta glucose has its -OH group above the ring. On the other hand, Alpha glucose has its -OH attached below the ring. Here are differences that you should know about alpha glucose vs. beta glucose 1. Stability Beta glucose is more stable because the body cannot easily take it apart. This stability is due to the solidly packed binding of its molecules. On the other hand, alpha glucose is less stable as you can take apart its atoms easily. Although alpha glucose is more compact, the human body can easily break the chains apart. 2. Composition Alpha glucose chains are composed of starch, while beta glucose chains are made of cellulose. Bread, pasta, potatoes, and similar foods come from starch. Typically, the tastier parts of plants are made of starch, while the hard parts of plants, such as the stem, are made of cellulose. Alpha vs Beta Glucose Metabolism Starch’s foundation is alpha glucose, and hence, the body can quickly metabolize it. On the other hand, beta glucose chains are composed of cellulose, and the body cannot break it down easily. Nevertheless, cellulose is essential for the digestive system to function correctly as they are fibers that help in food digestion.  Starch vs. Cellulose Why can we digest starch but not cellulose? Cellulose has beta glycosidic linkages and we do not have the proper glycoside hydrolases to break this linkage. http://www.vivo.colostate.edu/hbooks/pathphys/digestion/basics/foodchem.html  Carbohydrates: Disaccharides Disaccharides are formed by two monosaccharides linked by a glycosidic bond (a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.. Example: Sucrose (table sugar) Formed by one molecule of glucose and one molecule of fructose joined by a glycosidic linkage: http://hs-science-integrated.ism-online.org/2012/04/18/the-molecules-of-life/