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Biochemistry. Organic Chemistry. 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)

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biochemistry

Biochemistry

Organic Chemistry

organic molecules
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
hydrocarbons
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
alkanes alkenes and alkynes
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.
functional groups
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.
halides
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.
hydroxyl
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)
hydroxyl1
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
carbonyl
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
carbonyl aldehydes
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)
carbonyl ketones
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)
carboxyl
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
amines
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)
amines1
Amines

Methylamine

Putrescine

amides
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
amides1
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
sulfhydryl
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
sulfhydryl1
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
phosphate
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)