Introduction to Chemistry for Medicine / Chemistry concepts for health professionals
What is organic chemistry?
- refers to the study of carbon, its compounds and their reactions
Organic Molecules:
- Contain a limited number of elements C, H, O, N mainly (S and F are also common in drug molecules)
- Carbon bonds with other carbons to form single, double or triple bonds.
- The number of C-C bonds affects the shape and the name.
- Organic compounds can be straight chains, branching chains or cyclic in structures.
- If there are no double/triple bonds the molecule is called saturated.
- Are named systematically based on the number of carbons in the chain
- Are named based on the major functional groups
- Functional groups on molecules change their chemistry- how they react
- You will need to be able to recognise some of the common functional groups to understand the chemistry of drugs.
Polarity and Molecules:
- Molecules are polar if they contain atoms with different pull on the electrons (e.g O,N,S and halogens)
- Molecules are polar when these different atoms are arranged non-symmetrically
- Organic molecules containing O,N,S and halogens (Cl, F,l) can be polar.
Electronegativity:
- In higher electronegative atoms e.g the core of the atom is more attractive to the electron.
What is a drug?
- A medicine or other substances which has a physiological effect when ingested or otherwise introduced into the body.
What is drug target?
- A molecular structure that will undergo a specific interaction with drug(chemicals) administered to treat or diagnose a disease. The interaction has a connection with the clinical effect.
A drug target:
- Receptor
- Ion-channel
- Carrier proteins
- Enzymes
-or Other- DNA/RNA, lipids, carbohydrates
Drug Targets- Macromolecules:
- Lipids:
- cell membrane lipids
- Proteins:
- Receptors
- Enzymes
- Transport proteins (carrier proteins)
- Structural proteins (tubulin)
- Nucleic acid:
- DNA
- RNA
- Carbohydrates:
- Cell surface carbohydrates
- Antigens and recognition molecules
Macromolecules:
- Carbohydrates:
- Repeating unit= monosaccharides
- Lipids:
- Repeating units= fatty acids
-Nucleic acids: - Repeating unit= nucleotides
- Repeating units= fatty acids
- Proteins:
- Repeating unit= amino acids
Absolute fundamentals of chemical bonding:
- Every element and piece of matter is made up of atoms which are tiny and contain a centre called a nucleus.
- Inside the nucleus are proteins and neutrons- which are made up of quarks
- Quarks are tiny and bizarre.
- Protons are positively charged and all elements on the periodic table have a different number of them
- Electrons are negative particles that orbit the nucleus.
Bonds between atoms - 2 types of bonding exist
- covalent:
- Non-polar covalent (equal sharing of electrons)
- Polar covalent (unequal sharing of electrons )
- Non-polar covalent (equal sharing of electrons)
- Ionic
Covalent Bonding:
- Sharing of electrons- makes the atoms happy as they have the right number of electrons
- Electrons are always shared in pairs- all chemical bonds are made up of 2 electrons
Ionic bonding:
- One atom in the bond gives an electron to the other atom in the bond.
- Each atom has the right number of electrons
- Bonds are held together by the attraction of opposite charges.
Bonds Between atoms and molecules
- Molecules are formed when 2 or more atoms bond together - intramolecular bonding.
- But molecules also interact with each other.
- Chemical bonding also occurs between molecules- intermolecular bonding
Bonds between molecules:
- Temporary interactions=
- Ionic bonding attraction
- Hydrogen bonding
- Van der waals forces
- Ion-dipole attractions
- Dipole-dipole attractions
- Permanent interactions=
- Covalent bonding ( forms a new molecule)
Ionic Bonds: between molecules:
- Strongest forces between molecules
- opposites attract
- Closer= stronger
- Stronger in hydrophobic environments
- Attraction still strong with distance (compared to other forces)
- Ionic bonds are the most important initial interactions as a drug enters the binding site.
Hydrogen bonds:
- Weaker then ionic but stronger than Van der Waals
- Between electron-deficient H and electron-rich (N or O)
- The [e^-] deficient hydrogen is called a hydrogen bond donor ( HBD) - it donates itself
- The [e^-] rich heteroatom is called a hydrogen bond acceptor (HBA)- accepts the H
Van der Waals Forces:
- Very weak, occurs between hydrophobic regions of drug and target
- Transient= attraction of temporary dipoles due to high and low electron densities
- Interactions drop off rapidly with distance
- Drug must be close to the binding region to occur.
- The overall contribution of Van der Waals interactions can be crucial to binding.
Dipole-dipole interactions:
- Occurs if the drug and the binding site both have dipole moments (e.g a ketone functional group)
- These dipoles align with each other as the drug enter the binding site
- Dipole alignment orientates the molecules in the binding site.
- Orientation can be beneficial if other binding groups or detrimental depending on corresponding binding regions.
- The strength of the interaction decreases with distance more quickly than with electrostatic interaction but less quickly than with Van der Waals interaction
- Weaker than ionic but stronger than Van der Waals binding.
Ion-dipole interactions:
- Occurs where the charge on one molecule interacts with the dipole moment of another.
- Stronger than a dipole-dipole interaction.
- Strength of interactions falls off less rapidly with distance than for a dipole-dipole interaction.