BIOL150 Lecture 4 2024 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/  Carbohydrates: Disaccharides Example: Maltose (beer sugar) Formed by two molecules of Glucose: http://lactosesintolerances.blogspot.ca/2013/05/lactose-disaccharide.html  Carbohydrates: Disaccharides Example: Lactose (Milk sugar) Formed by one molecule of Galactose and one molecule of Glucose. http://lactosesintolerances.blogspot.ca/2013/05/lactose-disaccharide.html  Glycoside Linkages α glycoside bond: bond between two alpha sugars β glycoside bond: bond between two beta sugars http://image.wistatutor.com/content/feed/tvcs/untitled_45.JPG  Polysaccharides Complex carbohydrates. Made up of chains of monosaccharides that are linked together by glycosidic bonds. Ideal storage molecules for energy. Large and insoluble in water. Fold into compact shapes. Easily convert to sugars when needed. http://www.nutrientsreview.com/wp-content/uploads/2014/08/Polysaccharides-structure.jpg  Polysaccharides: Glycogen Glycogen: branched polysaccharide found in nearly all animal cells and in certain protozoa and algae. Mainly stored in the liver and muscles of humans and other vertebrates. Main form of stored carbohydrate in the body, acting as a reservoir of glucose. http://www.chemistryland.com/ElementarySchool/BuildingBlocks/BuildingOrganic.htm  Polysaccharide: Cellulose Fully permeable to water and solutes Ideal for allowing water and solutes into and out of the cell. Most abundant organic compound on Earth. About 33% of all plant matter and more than 50% of total organic carbon on planet http://www.nature.com/news/2001/010115/full/news010118-3.html  Polysaccharide: Chitin Chitin: unbranched polysaccharide, similar in structure to cellulose. Instead of (-OH), chains have (–NH-CO-CH3). Primarily found in the cuticles of arthropods, with smaller amounts being found in sponges, mollusks and annelids. Also in the cell walls of most fungi and in some http://www.swicofil.com/products/055chitosan.html green algae.  Lipids Lipids are a large class of organic compounds that are generally insoluble in water (hydrophobic). They do dissolve in nonpolar organic solvents, like chloroform, acetone or benzene. Biologically important lipids include: fats (triglycerides) phospholipids Waxes Steroids wa http://bio1151b.nicerweb.net/Locked/media/ch05/  Lipids Fats and oils are made from two kinds of molecules: Glycerol 3 carbon alcohol with a hydroxyl group on each of its carbons 3 fatty acids hydrocarbon chains with a carboxylic acid on the end Since there are three fatty acids attached, these are known as triglycerides. http://www.parl.gc.ca/content/LOP/ResearchPublications/prb0521-e.htm Lipid Structure Tail: long, non-polar hydrocarbon chain Head: hydrophilic carboxyl group http://ediblesciencefaire.files.wordpress.com/2011/05/fatty-acid-structure1.png Lipids in Soap In soap, fatty acids tails are soluble in oily dirt and their heads are soluble in water. Forms a micelle around the dirt/grease. However, when the head end is attached to glycerol to form a fat, that whole molecule is hydrophobic.  Lipids Saturated, mono-unsaturated, and poly- unsaturated refers to the number of hydrogens attached to the hydrocarbon tails of the fatty acids as compared to the number of double bonds between carbon atoms in the tail. “Saturated with hydrogen” http://aaccuratequote.com/fatty-acid-chemical-structure Saturated Fats Saturated fats In triglycerides, fatty acids contain the maximum possible amount of hydrogens Fairly straight in chain and packed closely together (solid at room temperature) Unsaturated fats Oils, mostly from plant sources, have some double bonds between some of the carbons in the hydrocarbon tail, causing bends or “kinks” in the shape of the molecules.  Phospholipids General structure: Glycerol Fatty acid Phosphate group + simple organic group (usually choline – essential nutrient) http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=41  Phospholipid Bilayer Cell membranes are formed by a two-layered arrangement of phospholipid molecules Hydrophobic lipid ends facing inward and the hydrophilic phosphate ends facing outward. All biological membranes are made of this same basic structure. http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=41  Thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many viruses are made of a lipid bilayer, as are the nuclear membrane surrounding the cell nucleus, and membranes of the membrane-bound organelles in the cell. The lipid bilayer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be. Lipid bilayers are ideally suited to this role, even though they are only a few nanometers in width, because they are impermeable to most water-soluble (hydrophilic) molecules. Bilayers are particularly impermeable to ions, which allows cells to regulate salt concentrations and pH ~Wikipedia  Lipids: Steroids Steroids: structures totally different from the other classes of lipids. Ring system of three cyclohexanes and one cyclopentane in a fused ring system. http://www.nbs.csudh.edu/chemistry/faculty/nsturm/CHE452/21_Adrenal%20Steroid17.htm Lipids: Steroids Steroids have a large number of carbon-hydrogen bonds, which make steroids non-polar. Steroids include such well known compounds as cholesterol, sex hormones, birth control pills, cortisone, and anabolic steroids.  In animals, all steroids are derived from one common precursor, lanosterol, which is modified by biosynthetic, chemical reactions to produce other steroids. Steroids serve a wide variety of functions in the body. For example, cholic acid (a bile acid) is used to help transport and excrete fats from the liver, while androsterone (a steroid hormone) activates protein synthesis in muscle. Steroids: Cholesterol Formed in brain tissue, nerve tissue, and the blood stream. It is the major compound found in gallstones and bile salts. http://depann2000.com/gallery/temp/cholesterol-molecule-structure  Steroids: Cholesterol Cholesterol can deposit on the walls of blood vessels. These deposits harden and obstruct the flow of blood. This condition, known as atherosclerosis, results in various heart diseases, strokes, and high blood pressure. http://www.webmd.com/heart-disease/atherosclerosis-19012 Steroids: Sex Hormones Primary male hormone: Testosterone Promotes the normal development of male genital organs and is synthesized from cholesterol in the testes. Promotes secondary male sexual characteristics such as deep voice, facial and body hair. Steroids: Sex Hormones Two females hormones: Estrogen and Progesterone Together, they regulate changes occurring in the uterus and ovaries, and the menstrual cycle. Estrogen is synthesized from testosterone by making the first ring aromatic which results in double bonds, the loss of a methyl group and formation of an alcohol group. Anabolic Steroids Mimic the effects of testosterone Increase protein synthesis Develop secondary male characteristics Are sometimes used therapeutically, but can be harmful long- term. Lipids: Waxes Wax: a simple lipid consisting of an ester of a long-chain alcohol and a fatty acid. Alcohol may contain from 12-32 carbon atoms. Found in nature as coatings on leaves and stems. Bees wax ➔ Proteins Proteins: natural polymer molecules Most important class of biochemical molecules. Basis for the major structural components of animal and human tissue. Types of Proteins Structural Enzymatic Transport Contractile and motor function Receptors Defense Storage (Energy) Hormonal  Proteins Proteins are polymers composed of monomers called amino acids (2-1000s). Amino acid contain: An alpha carbon base amine group ( -NH2) acidic carboxyl group ( -COOH) hydrogen atom Side chain (varies based on amino acid) http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=41  Proteins R groups: affect the way a proteins amino acids interact with one another, and how a protein interacts with other molecules. http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=41  Proteins While there are 100s of different amino acids, most organisms use only 20 to build proteins. Amino acids can be linked together by peptide bonds (covalent bonds) Dipeptide: two amino acids linked together Polypeptide: more than two. http://www.drgpdreamdot.com/protein/  Proteins http://www.freethought-forum.com/forum/showthread.php?t=11572&garpg=41 Protein Structure  Primary Structure refers to the order of the amino acids in the peptide chain. Secondary Structure is the arrangement of hydrogen bonds between the peptide nitrogens and the peptide carbonyl oxygens of different amino acid residues. Tertiary Structure three-dimensional arrangement of a polypeptide chain that has assumed its secondary structure. Disulfide bonds between cysteine residues may stabilize tertiary structure. Quaternary Structure arrangement of the subunits of a protein that has more than one polypeptide chain. Denaturation Denaturation is the disruption and possible destruction of both the secondary and tertiary structures. Disrupts alpha-helix and beta sheets and uncoils protein. Denaturation is not strong enough to break the peptide bonds in the primary structure (sequence of amino acids).  Enzymes A living system controls its activity through enzymes. A protein molecule that is a biological catalyst (speed up reactions). http://katrinalewis.edublogs.org/ 3 Characteristics of Enzymes 1. Basic function of an enzyme is to increase the rate of a reaction. Speed up cellular reactions almost a million times faster. Unaffected by reactions. 2. Act specifically with only one reactant (called a substrate) to produce products. 3. Enzymes can speed up the same chemical reaction going in the opposite directions. AB → A + B A + B → AB Enzymes Most biological reactions need the input of energy to get started, called the activation energy. Enzymes lower the activation energy required for a reaction to occur by forming temporary associations with the substrates. Without enzymes, most metabolic reactions would be too slow to maintain life.  Enzymes Proteins with a groove or pocket which forms the active site. Active site is where the substrate fits and the reaction is catalyzed. Binds to specific substrates Like a “Lock to a Key” http://wps.prenhall.com/wps/media/objects/3312/3391801/blb1406.html  Nucleic Acids Deoxyribonucleic Acid (DNA) Ribonucleic Acid (RNA) Consist of long chains of nucleotides which consist of: A pentose (5 C sugar) A phosphate group An organic (nitrogenous) base http://bio1151b.nicerweb.net/Locked/media/ch05/  Nucleic Acids http://bio1151b.nicerweb.net/Locked/media/ch05/