Organic Molecules: Hydrocarbons, Functional Groups, Biopolymers, Study notes of Chemistry

Download Organic Molecules: Hydrocarbons, Functional Groups, Biopolymers and more Study notes Chemistry in PDF only on Docsity! 1 General Characteristics of Organic Molecules The Stabilities of Organic Molecules • Carbon forms very strong bonds between H, O, N, and halogens. • Carbon also forms strong bonds with itself. • Therefore, C can form stable long chain or ring structures. • Bond strength increases from single to double to triple bond. • Carbon and hydrogen have very similar electronegativities, so the C-H bond is essentially non-polar. • Adding functional groups (e.g., C-O-H) introduces reactivity into organic molecules. General Characteristics of Organic Molecules Solubility and Acid-Base Properties of Organic Substances • Compounds with only C-C or C-H bonds are nonpolar and are soluble in nonpolar solvents and not very soluble in water. • Water soluble organic molecules have polar functional groups. • Surfactants have long nonpolar portions of the molecule with a small ionic or polar tip. • The most important organic acids are carboxylic acids with the -COOH functional group. • Basic organic molecules are usually amines, -NH2, -NHR, or - NR2 functional groups. Introduction to Hydrocarbons • Hydrocarbons are compounds with only C and H. • There are four classes: – alkanes (σ bonds, no π bonds—only single bonds) – alkenes (a mixture of σ and π bonds, but no triple bonds) – alkynes (contains triple bonds) – aromatics (have planar, ring structures with alternating single and double bonds). • Saturated compounds have only σ bonds. • Unsaturated compounds have both σ and π bonds. Introduction to Hydrocarbons 2 Alkanes Alkanes Structural Isomers • Straight chain hydrocarbons have each C atom joined in a continuous chain. • In a straight chain hydrocarbon no one C atom may be attached to more than two other C atoms. • Straight chain hydrocarbons are not linear. Each C atom is tetrahedral, so the chains are bent. • Branched chain hydrocarbons are possible for four or more C atoms, which give rise to structural isomers. • Structural isomers have different physical properties. Alkanes Structural Isomers Alkanes Naming Alkanes • To name alkanes: – Find the longest chain and use it as the name of the compound. – Number the carbon atoms starting with the end closest to the substituent. – Name and give the location of each substituent. • When two or more substituents are present list them in alphabetical order. 5 Alcohols H H H O H Methanol (CH3OH) OH Ethanol (CH3CH2OH) OH Isopropanol (CH3CHOHCH3) Rubbing alcohol OH Cholesterol (C27H46O) Carbonyls Aldehydes and Ketones • The carbonyl functional group is C=O. • Aldehydes must have at least one H atom attached to the carbonyl group: • Ketones must have two C atoms attached to the carbonyl group: R O H R O R' Carboxylic Acids • Carboxylic acids contain a carbonyl group with an - OH attached. • The carboxyl functional group is -COOH: • Carboxylic acids are weak acids. • Typical carboxylic acids are spinach, vinegar, cleaners, vitamin C, aspirin, and citrus fruits. Carboxylic Acids • Also known as fatty acids or “fats”: OH O HO O 6 Nitrogen-Functional Groups Amines and Amides • Amines are organic bases with a nitrogen: • Just as alcohols can be thought of organic forms of water, amines can be thought of organic forms of ammonia. • Amides are composites of carbonyl and amine functionalities: R C N O R' H CH3 N CH3 CH3 Biochemistry • The chemistry of living organisms is called biochemistry. • Biochemical molecules tend to be very large and difficult to synthesize. • Living organisms are highly ordered. Therefore, living organisms have very low entropy. • Most biologically important molecules are polymers, called biopolymers. • Biopolymers fall into three classes: proteins, polysaccharides (carbohydrates), and nucleic acids. Proteins Amino Acids • Proteins are large molecules present in all cells. • They are made up of α-amino acids. • There are two forms of an amino acid: one that is neutral (with -NH2 and -OH groups) and one that is zwitterionic (with -NH3+ and -O- groups). • A zwitterion has both positive and negative charge in one molecule. • There are about 20 amino acids found in most proteins. • Each amino acid is assigned a three-letter abbreviation. Amino Acids 7 Peptides and Proteins Polypeptides and Proteins • Proteins are polyamides. • When formed by amino acids, each amide group is called a peptide bond. • Peptides are formed by condensation of the -COOH group of one amino acid and the NH group of another amino acid. • Glycylalanine is abbreviated gly-ala. • Polypeptides are formed with a large number of amino acids (usually result in proteins with molecular weights between 6000 and 50 million amu). Proteins Protein Structure • Pitch is the distance between coils. • The pitch and diameter ensure no bond angles are strained and the N-H and carbonyl functional groups are optimized for H-bonding. • Tertiary structure is the three dimensional structure of the protein. Carbohydrates • Carbohydrates have empirical formula Cx(H2O)y. • Carbohydrate means hydrate of carbon. • Most abundant carbohydrate is glucose, C6H12O6. • Carbohydrates are polyhydroxy aldehydes and ketones. • Glucose is a 6 carbon aldehyde sugar and fructose 6 carbon ketone sugar. • The alcohol side of glucose can react with the aldehyde side to form a six-membered ring. Carbohydrates • Most glucose molecules are in the ring form. • Note the six-membered rings are not planar. • Focus on carbon atoms 1 and 5: if the OH groups are on opposite sides of the ring, then we have α- glucose; if they are on the same side of the ring, then we have β-glucose. • The α- and β- forms of glucose form very different compounds.