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Introduction to Chemistry for Medicine / Chemistry concepts for health…
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
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 )
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.