Biochemistry

1. Biochemistry Organic Chemistry

2. Organic molecules • Molecule made of carbon and hydrogen in a chain or a ring is considered organic • This includes carbohydrates, lipids, proteins, nucleic acids, as well as a multitude of other synthetic molecules (such as plastics) • Carbon is at the center of such a wide variety of molecules because it can form four stable covalent bonds – this allows for an infinite number of possible configurations

3. Hydrocarbons • The simplest organic molecules are made of chains or rings of only carbon and hydrogen • methane, CH4 • ethane, C2H6 • propane, C3H8 • butane, C4H10 • pentane, C5H12 • hexane, C6H14 • heptane, C7H16 • octane, C8H18 • nonane, C9H20 • decane, C10H22

4. Alkanes, alkenes, and alkynes • Hydrocarbons with only single C-C bonds are alkanes (-ane ending) • Hydrocarbons with at least one double C=C bond are alkenes (-ene ending) • Hydrocarbons with at least one triple C≡C bond are alkynes (-yne ending) • All are nonpolar, hydrophobic molecules.

5. Functional groups • Other elements are often found attached to hydrocarbons • These reactive clusters of atoms are called functional groups • They will affect the amount of intermolecular forces and thus other factors such as solubility and melting/boiling points.

6. Halides • Organic hydrocarbons with at least one halogen atom attached in place of a hydrogen • Not frequently found in living organisms • More often used in industry; as refrigerants, in production of PVC and DDT, and several pharmaceuticals such as ciproflaxin are organic halides.

7. Hydroxyl • characteristic of alcohols • electronegative oxygen atom increases the intermolecular forces • alcohols are polar molecules • more hydroxyl groups increases the melting/boiling points • compare the melting points of propanol (−126.5 °C) and glycerol (18 °C)

8. Hydroxyl • Suffix for alcohols is –ol. • Examples: • Methanol • Ethanol • Propanol • Location of hydroxyl group on longer chains is indicated in the name • Examples: • 2-propanol (isopropanol) • 1-propanol

9. Carbonyl • Carbon atom double bonded to an oxygen • Two types: aldehyde and ketone • Both are polar, and have increased boiling points and solubility compared to similar sized alkanes or alkenes • Aldehydes – carbonyl group occurs at one of the terminal carbon - names end with –al • methanal, ethanal • Ketones – carbonyl group occurs at one of the internal carbons - names end with –one • propanone, butanone

10. Carbonyl - Aldehydes • Commonly occur as natural or artificial fragrances, such as in essential oils like cinammaldehyde or vanillin • Other common examples include methanal (formaldehyde) and ethanal (acetaldehyde)

11. Carbonyl – Ketones • Used frequently as solvents in industrial processes, or in some pharmaceutical drugs, but are found in nature as animal pheromones • Examples: • acetone (propanone) • Muscone (animal scent - musk)

12. Carboxyl • A combination of hydroxyl and carbonyl groups attached to the same carbon atom • Highly polar functional groups – tend to have higher melting/boiling points than similar sized alkanes • Examples: • ethanoic acid (acetic acid or vinegar) • butanoic acid – found in rancid butter • citric acid (a tricarboxylic acid) – in citrus fruit • fatty acids – such as stearic acid or oleic acid • the acid end of all amino acids

13. Carboxyl

14. Amines • Includes nitrogen atom attached to a carbon chain or ring • Similar to an ammonia molecule, but with a carbon chain replacing one or more hydrogens. • Found in all amino acids, urea, nitrogenous bases, some insect pheromones • Methylamine – strong odour of fish • Putrescine and cadaverine – responsible for the odour of putrefying flesh (during the breakdown of amino acids)

15. Amines Methylamine Putrescine

16. Amides • Similar to amines, but with a carbonyl group attached to one of the carbon chains • Or thought of another way, they can be derived from a carboxyl group, where the –OH part of the -COOH is replaced by an –NH2 • Examples: • methanamide: HCONH2 • ethanamide: CH3CONH2 • propanamide: CH3CH2CONH2

17. Amides • Amides are weak bases and are generally less soluble than similar-sized amines • They are extremely common in nature as structural materials – in particular as proteins • Amino acids are bonded together with peptide bonds, which are essentially amide linkages

18. Sulfhydryl • Have a similar structure to hydroxyls – the oxygen is replaced with a sulfur atom • Are also referred to as thiols, they have very strong pungent odours, similar to garlic. • Skunk odour is composed of several different thiol compounds • examples: • Methanethiol • Ethanethiol • Ethanethiol is added to natural gas to make it immediately noticeable in case of a leak

19. Sulfhydryl • Thiols are important in proteins – especially ones that contain the amino acid cysteine • Two cysteines can form a covalent bond called a disulfide bond (-S-S-) in a protein • Disulfide bonds contribute to the three-dimensional structure of proteins • Coenzyme A is an important thiol used in the synthesis of fatty acids and also a critical step in the Kreb’s cycle of cellular respiration

20. Phosphate • An inorganic salt related to phosphoric acid • When attached to hydrocarbon(s), they are called organophosphates • In biological systems, phosphates are part of molecules such as phospholipids (in the plasma membrane), nucleic acids (DNA, ATP) • When phosphates are unattached to a compound (such as during the ATP-ADP cycle) they are referred to as inorganic phosphate (Pi)