BIOM201 Lecture 1 Functional Groups PDF

Biochemistry course: Lecture 1: BIO201 Functional groups: Structures, Reactions and their role in Medicine Dr. Shona Pedersen, Associate Professor in Biochemistry College of Medicine, Qatar University Room 127A, Ph: 4403 7879...

Biochemistry course: Lecture 1: BIO201 Functional groups: Structures, Reactions and their role in Medicine Dr. Shona Pedersen, Associate Professor in Biochemistry College of Medicine, Qatar University Room 127A, Ph: 4403 7879 [email protected] 21 January 2024  Breaking the ice: The Types of Learners Try to understand which type of learner you are, and adjust your way of learning. Prepare lecture notes depending on which type of learner you are. Remember to go through the notes of the lecture on the same day e.g. in the evening. Go through the notes again in the next 2-3 days, and definitely before the next lecture.  What is Biochemistry? Best way to understand how life works in a fundamental way. Sub-atomic Life Organism Cells Reactions Molecules Atoms particles Biology Biochemistry Chemistry Chemistry shapes the way reactions and processes work in nature, biochemistry takes the knowledge from chemistry to study the fundamental processes that makes our up biology.  What is importance of Biochemistry in Medicine? Biochemistry is a valuable subject in medicine, without this there would have been no advancements in the field. Biochemistry helps to understand the biochemical changes and related physiological alteration in the body during infection / disease.  Level of understanding in BIOM201 - from Basic up to Advanced levels Examples Impact of drugs Advanced Electron tunneling in the reaction of the respiratory chain Basic Intermediate Main biochemical reactions in a Chemistry of main human cell molecules of life  Cells consist of: Peptides & Proteins What is the most common chemical Sugars & Carbohydrates element in the major macromolecules of a cell? Lipids & Fats Nucleic Acids (DNA & RNA) Metabolites  Chemical Composition of the Human Body CHNOPS Helmenstine, Anne Marie, Ph.D. "Chemical Composition of the Human Body." ThoughtCo, Apr. 5, 2023, thoughtco.com/chemical- composition-of-the-human-body-603995.  What do you know about hydrocarbons 1.What are hydrocarbons? 2.What famous molecules contains hydrocarbons?  What are Hydrocarbons (HC)? Hydrocarbons are organic molecules consisting ONLY carbon and hydrogen atoms. Many organic molecules, such as fats, have HC components. HCs can undergo reactions that release a large amount of energy. They are broadly categorized into four distinct subgroups. Hydrocarbon Classification Hydrocarbons contain only carbon & hydrogen Hydrocarbons Aliphatic Aromatic Ring structure (Benzene) Alkanes Alkynes Alkenes Hydrocarbon Classification Hydrocarbons contain only carbon & hydrogen n o b ar C f oy rt mis e h Ce h T  Aliphatic Hydrocarbon Structure Comparison Saturated Unsaturated Unsaturated OmoreH) (t) (less  IUPAC (International Union of Pure and Applied Chemistry) Aim of IUPAC: Is to ensure that every organic compound has a unique, unambiguous name. IUPAC.ORG  Example: Butane and Butene Carbon chain length and prefixes used in I.U.P.A.C. nomenclature System butyne an alkyne Cutten-z Structural Formula Molecular Formula C4H6 General Formula CnH2n-2 IUPAC: International Union of Pure and Applied Chemistry  Why are Hydrocarbons important? because they are used - DRUGS SYNTHESIS Clinical manifestations of Hydrocarbon Toxicity Pulmonary Tachypnea-shallow breathing Cardiac Ventricular dysrhythmias Central Nervous Slurred speech Peripheral Nervous Problems with the extremeties GI and Hepatic Nausea and Vomitting Hematologic Anemia Dermal Local erythema QUESTION TIME  Lets test your understanding? 1. The chemistry associated with carbon-carbon triple bonds are referred to as: a) Alkane chemisty O b) Alkyne chemistry c) Alkene chemisty d) Cycloalkane chemistry e) Aromatic chemistry 2. Which has the least carbon-carbon bond length? a) Butane b) Butene O c) Butyne d) Benzene e) Heptane 3. What is the general formula for an alkane? & a) CnH2n+2 b) CnH2n-2 c) CnH2n d) CnH2n-1 e) CnH2n Functional groups  What are Functional groups? Since FGs are covalently bonded sets of atoms that can “functionalize” a compound by enabling it to adopt different physical and chemical properties. FGs allows for the quick identification of the atoms in a molecule, which is useful in chemistry and biochemistry. Cl, OH and O are specific groups of atoms within a molecule that exhibit characteristic chemical behavior. Molecules containing the same functional groups often display similar physical and chemical properties. How does Functional groups relate to Biochemistry? These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids. Map of functional groups: FGs = 0 cot Carbonyl Hydroxyl + Carboxyl = Ester Ether Amine Alcohol Phenol Hydroxyl from Alcohol Carboxyl from Carboxylic acid + Amide  Functional groups 1. Aldehydes & Ketones (carbonyl, C=O) 2. Alcohols & Phenols (hydroxyl, OH) Importance Structure Function BIOMEDICINE MEDICINE  Aldehydes: Class of Carbonyl Compounds Aldehydes constitute an important class of organic compounds containing the carbonyl functional group: C=O (Carbon double bonded to oxygen). The general formula for Aldehydes: RCHO The central carbon in this group is called the Carbonyl centre. R represents the rest of the molecule to which the FG is attached. An Aldehyde is a molecule represented by an R bond to a carbon double bonded to an oxygen (carbonyl group) and a single bond to a hydrogen.  What are ALDEHYDES? They are reactive species that generally toxic to the body. The only structural difference between hydrocarbon and aldehydes is the presence of the carbonyl group (C=O) present in aldehydes. Used to make synthetic resins and to create dyes, flavourings, perfumes, and other chemicals. Others are used as preservatives and as disinfectants. IUPAC & Common names and Formulas for several Aldehydes [ methan + al = - S - & /  IUPAC Nomenclature and Common Names: ALDEHYDES Naming Aldehydes Find longest continuous carbon chain (parent chain and bonds) Replace the final –e of alkane name with suffix –al Number to give aldehyde GROUP number 1 (carbonyl carbon) Number and name all substituents-start with the prefix Methane-Methanal Ethane-Ethanal  Naming Aldehydes with double bonds Provide the IUPAC name for this molecule 1. Parent chain – 7 carbons, 1 double bond = heptene 2. Change suffix from -e to -al = heptenal 3. Number from carbonyl end 4. Number/name substituents = 2,6-dimethyl 5. Label the double bond from the first starting position 7 5 3 6 4 2 1 2,6-Dimethyl-5-heptenal  Let’s Look at some examples on IUPAC naming of Aldehydes (-al) Additional rules -Number the Cs starting at the end nearest to the C=O -OH is named hydroxy as a secondary group -Aldehydes are named oxo if the there are two C=0 groups -The first C=0 always represent the functional group (based on the lowest number) -Halogens (Chloride, Bromide etc.) 3-chloropropanal 3-oxohexanal 5-hydroxy-3-oxohexanal Some Medical and Biomedical uses of Aldehydes Aldehydes are also useful as: Production of dyes and pharmaceuticals + Solvents and perfume Aldehydes are also involved: In physiological processes. Ex: retinal (vitamin A aldehyde), important in human vision. In facilitating easy metabolism of carbohydrates in the human body. It does this by providing a medium of interchange of the carbon atoms found in proteins, carbohydrates, and lipids in the body Formaldehyde (methanal-formalin) has a lethal effect on viruses but can be used to preserve biological tissue and anatomical specimes. Acetaldehyde is produced when one’s liver metabolizes ethanol (drinking alcohol) and causes symptoms of hangover  Ketones: Class of Carbonyl Compounds C=O Ketones constitute an important class of organic compounds containing the carbonyl functional group: C=O. Ketones: carbonyl center, where R and R' can be a variety of carbon-containing substituents: RCOR' When carbonyl center are joined by two other carbon atoms then the compound formed is a ketone. IUPAC Nomenclature and Common Names: Ketones The simplest ketone MUST have 3 carbon atoms Base name: longest chain closest to the C=O Replace the –e of the alkane name with –one Indicate position of C=O by number on chain so that C=O has lowest possible number Propane-Propanone Butane-Butanone/But-2-one Octane- 4-Octanone/Oct-4-one  Some Medical and Biomedical uses of Ketones High levels of ketones in your blood or urine can mean you are at risk of developing diabetic ketoacidosis-this is life-threatening. Having ketones can indicate that your body needs more insulin Propanone (Acetone) (the simplest possible ketone): skin treatment for acne Ketones can also be found in the body: as Testosterone and progesterone. Aldosterone is secreted in blood sodium levels are too low so that the kidney can retain sodium ions. Aldosterone also controls swelling in tissues Acetone  Reactions of Aldehydes & Ketones Reduction & Oxidation (Redox) Reduction: Aldehydes and ketones are reduced to alcohols: Aldehydes to primary alcohols Ketones to secondary alcohols Oxidation: Aldehydes can be oxidized, but ketones cannot. WHY? The carbonyl groups in aldehydes can be oxidized to form the next “oxidation level” compound-carboxylic acid but ketones can not.  Reactions of Aldehydes & Ketones reduction Primary aldehyde alcohol Carboxylic acid reduction Secondary ketone alcohol  Let’s Recap: Aldehydes (-al) and Ketones (-one) ALDEHYDES KETONES IUPAC naming of Aldehydes (-al) and Ketones (-one) RCHO RCOR' Aldehydes contain at least one hydrogen atom attached to the carbonyl carbon atom. Ketones contain two carbon groups attached to the carbonyl carbon atom but no hydrogens. Additional rules -Number the Cs starting at the end nearest to Aldehydes and ketones are reduced to the C=O alcohols: Aldehydes to primary alcohols -OH is named hydroxy as a secondary group and Ketones to secondary alcohols. -Aldehydes are named oxo if the there are two C=0 groups. The carbonyl groups in ALDEHYDES can The first C=0 always represent the functional be oxidized to form carboxylic acid but group (based on the lowest number) ketones can not. Map of functional groups: FGs Carbonyl Hydroxyl + Carboxyl = Ester Ether Amine Alcohol Phenol Hydroxyl from Alcohol + Carboxyl from Carboxylic acid Amide What are Alcohols?  Alcohols: Structure and Physical Properties Organic compound with the electronegative oxygen Alcohols have the general formula R-OH Hydroxyl group is very polar Hydrogen bonds can readily form. ALCOHOL  Alcohols with 2 OH-groups IUPAC: ethane-1,2-diol Common name: ‘Ethylene glycol’  Medically Important Alcohols Methanol Pharmaceutical manufacture (toxic, can cause blindness and death if ingested) Ethanol Disinfection, sterilization Ethylene glycol (1,2-ethanediol) Glycerol (1,2,3-propanetriol) Used for its viscosity. Derivatives are important drugs  Phenols: Ar-OH Phenols are compounds in which the hydroxyl group is attached to a benzene ring (so they are alcohols WITH benzene ring) Polar compounds due to the hydroxyl group Simple phenols are water soluble Components of flavorings & fragrances Phenols have the formula Ar-OH Ar must be an aromatic ring (e.g., benzene)  lide S urtant imp Summary of alcohol redox reactions Oxidation Reduction gain of oxygen loss of oxygen loss of hydrogen gain of hydrogen More oxidized form H H H OH R C H R C OH R C O R C O H H Alkane Alcohol Aldehyde Acid More reduced form  Summary: Alcohols ALCOHOL Organic compound with functional group with the carbon bonded to an oxygen. Alcohols have the general formula: R-OH Alcohols 1. Ethylene glycol has 2 OH group (used as an anti-freeze) 2. Phenols is an aromatic alcohol (Ar-OH)-hydroxyl group is attached to a benzene ring Types of reactions of Alcohols Oxidation (Aldehydes, ketones, and acids), esterification (esters) Reduction (Alkanes), Dehydration (alkenes) Alcohol Redox reactions: Alcohol Oxidation results in a gain of oxygen and a loss of hydrogen Alcohol reduction results in the loss of oxygen and the gain of hydrogen Map of functional groups: FGs Carboxy Carbonyl Hydroxyl + l = Ester Ether Amine Thiols Alcohol Phenol + Hydroxyl from Alcohol Carboxyl from Carboxylic acid Amide  Carboxylic acid, Esters, Ethers Amines, Amides & Thiols CARBOXYLIC ESTERS AMIDES ACIDS Importance THIOLS ETHERS AMINES Structure Function BIOMEDICINE Map of functional groups: FGs Carboxylic acid Ester Ether Amine Thiols yl Hydroxyl from Alcohol Carboxyl from Carboxylic acid + Amide  Carboxylic Acid Structure Carboxylic acid functional groups consist of two polar functional groups Carbonyl group Hydroxyl group They have a general formula: R-COOH CARBOXYLIC ACID R-COOH Names and Structures of Common Carboxylic Acids (Ending with oic, followed by the word acid) - oic acid - - (oic acid)  Carboxylic Acid-Base: Reactions Carboxylic acids behave as acids - they deprotonate to form a carboxylate ion and hydrogen ion Carboxylic acids react with strong bases to form carboxylate salts By a process of neutralization: Acid protons (H+) are removed from the –OH- to form H2O and carboxylate ion ( -COO-). Carboxylic acid: Role in Medicine Aspirin- treat pain and reduce fever Anti-inflammatory drugs and inflammation Diet supplements  Summary: Carboxylic Acid (oic/dioic + acid) Structure of Carboxylic acid Carboxylic acid consists of two polar FGS: Carbonyl and CARBOXYLIC ACIDS Hydroxyl group Carboxylic acid has the general formula: R-COOH Aromatic (AR-COOH) and aliphatic R-COOH Carboxylic acids 1 Carboxyl group Nomenclature of Carboxylic acid For one Carboxyl group –e replaced with –oic +acid For two Carboxyl groups the suffix is –dioic +acid 2 Carboxyl groups Reactions of carboxylic acid They can behave as acids - deprotonate to form a carboxylate anion and hydrogen ion. They react with strong bases to form carboxylate salts and water by the process of neutralization. Map of functional groups: FGs Hydroxyl + Carboxyl = Ester Ether Amine Thiols Hydroxyl from Alcohol Carboxyl from Carboxylic acid + Amide  Esters: Structure and Nomenclature Formed from an alcohol + a carboxylic acid by ESTERIFICATION Esters’s name consists of: - Alcohol part (-yl) - Carboxylic acid part (-oate) General formula for Esters: RCOOR’ ESTERS RCOOR = 1 2 1  Esters: Reactions Carboxylic acid & alcohol = condensation reaction ester & water Ester & water = hydrolysis Carboxylic acid & alcohol Role of Esters in Medicine as approved drugs C: heart disease T: hypertension O: influenza P: anaesthetic M: ADHD L: glaucoma  Summary of the functional groups so far Aldehydes contain at least one hydrogen FGs with Carbonyl groups ALDEHYDES KETONES R-CHO R-COR atom attached to the carbonyl carbon atom Ketones contain two carbon groups attached to the carbonyl carbon atom-no ESTERS CARBOXYLIC ACIDS hydrogen R-COOR R-COOH Carboxylic acids contain a hydroxyl group attached to the carbonyl carbon atom Esters contain an oxygen atom attached to ALCOHOLS the carbonyl carbon atom. Alcohols has an hydroxyl functional group with the carbon bonded to the oxygen. R-COH Map of functional groups: FGs Carboxylic acid Ester Ether Amine Thiols + Amide  Ethers: Structure and Nomenclature Ethers have the formula R-O-R’, very similar to alcohols Ethers are organic compounds that contain an oxygen atom bonded to two alkyl or aryl groups where represent the alkyl or aryl groups. 1 ETHERS 2 Two aryl groups Two alkyl groups  Symmetrical & Asymmetrical Ethers Ethers can be further classified into: Symmetrical and Asymmetrical Dimethyl ether Ethyl methyl ether Diphenyl ether Methyl phenyl ether Simple/Symmetrical ethers: Have the same alkyl or aryl groups on both sides of the oxygen atom. Mixed/Asymmetrical ethers: Have different alkyl or aryl groups on either side of the oxygen atom  Ethers in Medicine Ethers are used as inhalational anesthetics Fluroxene: Synthesized in 1951, clinical use in 1954 but withdrawn in 1974 Why? Interfered with nerve impulse transmission What was the solution? Halogenated ethers are now used routinely as general anesthetics-Less flammable-Safer to store and work with. Esters (R-COOR) vs. Ethers (ROR/ROR’) vs Alcohol (ROH) ESTERS ETHERS ALCOHOLS Esters contain an oxygen atom attached to another carbon group connected to the carbonyl carbon atom. Ethers contain an oxygen atom bonded to which can represent either alkyl or aryl groups Alcohols have a hydroxyl functional group with the carbon bonded to the oxygen Map of functional groups: FGs Carboxy Ester Ether Amine Thiols l + Amide  Thiols (R-S-H) Thiols (R-S-H) are sulfur equivalents of alcohols, where the Sulphur replaces the Oxygen of alcohols (R-0-H) Chemical reaction of Thiols It can oxidize to form S-S bond-disulfide bridges, a common mechanism used in nature to stabilize many proteins. Map of functional groups: FGs Carboxylic acid Ester Ether Amine Thiols + Amide  Amines The most important type of organic base found in nature AMINES and are derivatives of ammonia NH3+ The functional group is amino (NH2) and General formula, RNH2 Contain N attached to one or more alkyl (Aliphatic amine) or aromatic groups (Aromatic amines). Amines can form hydrogen bonds, but not as strongly as alcohols  Amines: Reactions 1. Amines with OH groups Amines accept H+ when dissolved in water Nitrogen’s lone pair electrons can be shared with a proton from water An alkylammonium ion is produced Hydroxide ions are also formed, making solutions basic 2. Amines with HCl Amines form salts by accepting a proton from strong mineral acids Map of functional groups: FGs Carboxylic acid Ester Ether Amine Thiols + Amide  Amides Amides Amides are formed in a reaction between a carboxylic acid group and an amine (or ammonia) The amide bond is the bond formed between: Hydroxyl group of a carboxylic group (-COOH) Hydrogen of an amino group (-NH2) Amide bonds between amino acids Amino acid 1 Amino acid 2  Differences Between Amide and Peptide Bond An amide bond occurs between a hydroxyl group of a carboxylic group (-COOH) of one molecule and a hydrogen of an amino group (-NH2) of another molecule. Whereas, the peptide bond is a type of amide bond that occurs between two amino acids during the synthesis of a polypeptide chain. Amino acid 1 Amino acid 2  Hydrolysis of amide bonds Amides hydrolyze with Strong Acid to produce Carboxylic acid and Amine salts Strong Base to produce Carboxylic acid salt and Amine ALDEHYDES KETONES CARBOXYLIC ACIDS ESTERS AMIDES ETHERS ALCOHOLS AMINES Map of functional groups: FGs Carbonyl Hydroxyl + Carboxy l = Ester Ether Amine Thiols Alcohol Phenol Hydroxyl from Alcohol + Carboxyl from Carboxylic acid Amide References: Fundamental of organic chemistry https://gtu.ge/Agro-Lib/McMurry%20J.E.%20-%20Fundamentals%20of%20Organic% 20Chemistry,%207th%20ed.%20-%202010.pdf