BIOM201 Lecture 1: Functional Groups, Structures and Reactions in Medicine (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 Let’s look at Two Important Nobel prize chemists Professor Sir Geoffrey Wilkinson Professor Sir Derek Barton Nobel Prize 1973 Nobel Prize 1969 Organometallic catalysis 3D conformation of ‘Wilkinson catalyst’ organic molecules ‘Barton reaction’  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 Home BBQ “experiment” shows that life is carbon‐based ‘Carbonised’ All life is carbon‐based Atomic composition of human body ‐ Main atoms: O 5% (65% with water) C 18.5% H 2% (9.5% with water) N 3.2% (Water = 60‐70%)  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 n o b ar C f oy rt mis e h Ce h T Aliphatic Hydrocarbon Structure Comparison  ??? Unsaturated HC Mol. Formular:C2H2  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  Carbon Chain Length and Prefixes Carbon chain length and prefixes used in I.U.P.A.C. nomenclature System IUPAC: International Union of Pure and Applied Chemistry  Example: Butane and Butene Carbon chain length and prefixes used in I.U.P.A.C. nomenclature System ??? IUPAC: International Union of Pure and Applied Chemistry Why are Hydrocarbons important? DRUGS SYNTHESIS Clinical manifestations of Hydrocarbon Toxicity QUESTION TIME  Lets test your understanding? 1. The chemistry associated with carbon-carbon triple bonds are referred to as: a) Alkane chemisty 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 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 4. What is the name of the alkane with the formula C3H8? a) Methane b) Propane c) Nonane d) Decane e) Octane 5. What is meant by the term saturated, when applied to hydrocarbons? a) Molecules containing at least one C=C double bond b) That all carbon atoms are joined by C-C single bonds c) Molecules containing carbon and hydrogen atoms only d) Molecules containing at least one C ≡ C triple bond e) Molecules containing carbon and oxygen atoms only 6. Which of the following is an alkyne? a) C5H10 b) C4H10 c) C3H8 d) C7H16 e) C2H2  BIOM201- Lecture 1 Functional groups: structures and reactions Aldehydes & Ketones, Alcohols & Phenols Importance Structure Function BIOMEDICINE MEDICINE  What are Functional groups (FGs)?  How do they relate to Biochemistry? Aldehydes & Ketones, Alcohols & Phenols  Definition of these specific FGs  Nomenclature (common & IUPAC) eg. CH3OH (IUPAC) name: Methanol)  Chemical features and reactions of FGs  Examples of their role in medicine and biomedicine  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.  Functional groups (FGs)? Hydrocarbons contain varying numbers of carbon and hydrogen atoms. The hydrocarbon portions of the functionalized organic compounds are often abbreviated with the letter R and/or R’. When different atoms join onto the main chain of a hydrocarbon, they form special clusters called functional groups. These groups give the molecule unique characteristics and behaviors How does Functional groups relate to Biochemistry? These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids. Aldehydes & Ketones, Alcohols & Phenols Importance Structure Function BIOMEDICINE MEDICINE  What a ALDEHYDE? 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  Aldehydes: Class of Carbonyl Compounds Aldehydes constitute an important class of organic compounds containing the carbonyl functional group: C=O (Carbon double bonded to an oxygen). The general formula for Aldehydes: RCHO The central carbon in this group is called the Carbonyl centre. An Aldehyde is molecule that can be represented by R bond to a carbon that is double bonded to an oxygen (carbonyl group) and single bond to a hydrogen, where R represent the rest of the molecule that the functional group is attached to.  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) Provide the IUPAC name for this molecule 1. Parent chain – Longest Carbon chain 2. Change suffix from -e to -al 3. Number from carbonyl end 4. Number/name substituents 5. Label the double bond from the first starting position  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:  Solvents and perfume ingredients Production of dyes and pharmaceuticals. Aldehydes are also involved: In physiological processes. An example is 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 Simplest ketone MUST have 3 carbon atoms - the carbonyl group has carbon atom on either side Base name: longest chain closest to the C=O Replace the –e of 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 IUPAC Naming of Ketones with Double bonds Rules are the same as those for aldehydes Base name: longest chain with the C=O (6 carbons-hexane) Replace the –e of alkane name with –one (hexanone) Indicate position of C=O by number on chain so that C=O has lowest possible number is 2 (Example 1) 1 6 1 2 1,1-dichloro-2-hexanone  IUPAC Naming of the following Ketones 1. Parent name ends in –ONE 2. C=O in the middle on the molecule Butan-2-one 3. Find the longest chain containing the C=O 4. Number the C starting at the end of the pentan-2-one nearest C=O. Use a number to indicate the position of the C=O 5. Locate and number the substitutes and nonan-2-one give full name oct-5-en-2-one Homework 8 2 double bond 5  Reactions of Aldehydes & Ketones Reduction & Oxidation (Redox) Aldehydes and ketones are reduced to alcohols: Aldehydes to primary alcohols Ketones to secondary alcohols The carbonyl groups in aldehydes can be oxidized to form the next “oxidation level” compound-carboxylic acid but ketones can not.  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) is the simplest possible ketone, skin treatment for acne Ketones can also be found in the human body as Testerone 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 Carbonyl groups in drugs – anti-tumour agents  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. What are Alcohols?  Alcohols: Structure and Physical Properties Organic compound with hydroxyl or ‒OH functional group with the carbon bonded to the electronegative oxygen Alcohols have the general formula R-OH Hydroxyl group is very polar Hydrogen bonds can readily form. ALCOHOL  Naming Alcohols 1.Name the parent compound – 5 carbons = pentane 2 2.Replace the –e with –ol = pentanol 3 3.Number the parent chain with the –OH group on lowest number of 2,3-dimethyl-1-pentanol carbon = C-1 4.Identify, name, and number all substituents = dimethyl on CH3 at position 2,3  Alcohols with 2 OH-groups IUPAC: ethane-1,2-diol ‘Ethylene glycol’ = common name  Alcohols with >2 OH-groups Glycerol Glycerine (COH-COH-COH) IUPAC name: Propane-1,2,3-triol Glycerine, described in 1779 by Sheele in hydrolysis products of olive oil. Used in production of nitroglycerine (explosive) Also by-product in production of soap, anti-skin irritant, wound healing, antimicrobial, enhancing penetration, cryoprotection, etc.  Phenols: Ar-OH Phenols are compounds in which the hydroxyl group is attached to a 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) Alcohol & acid reaction - esterification 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  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  Summary: Alcohols ALCOHOL Organic compound with hydroxyl or ‒OH functional group with the carbon bonded to an oxygen Alcohols have the general formula: R-OH IUPAC naming of Alcohols 1. Name the parent compound 2. Replace the –e with –ol 3. Number the ring to minimize number of carbon with the -OH group at C1 4. Identify, name, and number all substituents  ALCOHOL Summary: Alcohols Alcohols with ≥ 1 OH GROUP 1. Ethylene glycol has 2 OH group (used as anti-freeze) 2. Glycerol has ≥ 2OH groups 3. 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 gain of oxygen and loss of hydrogen Alcohol reduction results in loss in oxygen and gain of hydrogen  Lets test your understanding? 1. Classify the compound based on the functional group present. a) Alcohol b) Ketone c) Aldehyde d) Ether e) Ester 2. What is the name of this carbonyl compound? a) 2-pentanal b) 2-pentanone c) 3-butanone d) 3-pentanone References: Fundamental of organic chemistry https://gtu.ge/Agro‐Lib/McMurry%20J.E.%20‐%20Fundamentals%20of%20Organic%20Chemistry,%207th%20ed.%20‐%202010.pdf