Unit 1 Flashcards
What does the ionisation state of a drug depend on and what will this influence?
The ionisation state of a dug depends on the pH of the medium in which it is dissolved in which in turn influences the solubility of the drug, the way in which it is formulated as a medicine, its absorption and distribution within the body and its pharmacological activity.
Describe how double bonds and triple bonds are formed and their bond angle.
Double bonds also known as alkenes are formed from 1s orbital and 2p orbitals creating 3 sp² orbitals with a bond angle of 120. However triple bonds are formed from 1s orbital and 1p orbital creating 2 sp orbital with an angle of 180.
Describe how sigma and pi bonds are formed.
Sigma bonds are formed by the overlap of sp^n hybrid orbitals. The single bond frameworks the molecule where the electron density is concentrated between the nuclei. However, pi bonds are formed by the overlap of p orbitals. This contains double and triple bonds and restrict rotation.
What effect does stereochemistry have on a drug?
Stereochemistry can effect the the clinical efficiency as the drug depends on the three dimensional structure. It can also have an effect on its toxicity and side effects.
What defines a chiral compound?
If all four attached groups of the sp^3 atom are different, then the molecule cannot be superimposed onto its mirror image (the two isomers are different compounds). These separate chiral isomers are a pair of enantiomers.
What are the possible effects of the mirror image compound?
The mirror image can be either inactive or have other effects such as producing side effects, countering the effect of the drug or being metabolised into a toxic product.
What is diastereoisomers?
These are stereoisomers of each other but are not specifically mirror images of each other.
What are the two types of diastereoisomers?
1) Cis-trans diastereoisomers: found in molecules with double bonds and saturated rings.
2) Chiral diastereoisomers: chiral isomers which are not enantiomers and therefore different in physical, chemical and biological properties. They are only found in molecules with multiple chiral centres.
What is a racemic mixture (racemate)?
An equal mixture of both enantiomers of a compound, has no measurable optical rotation.
What is bond polarity?
This is the sharing of electrons between atoms often unevenly causing partial negative and positive charges.
How does hydrogen bonding occur?
This is when a strongly electronegative atom (oxygen, nitrogen and halogens) approaches a hydrogen atom which is covalently attached to a second strongly electronegative atom. For example, hydrogen bonding can occur between a carbonyl and an amino acid.
Which atom in a hydrogen bond is classed as an acceptor and which one is classed as a donor?
The acceptor in the hydrogen bond is the hydrogen atom attached to the electronegative atom and the donor is the electronegative atom (O, N or F) with one or more lone airs of electrons.
What are some properties of hydrogen bonding?
The hydrogen bond has an optimum length and is linear. This results in the bond being relatively constrained and therefore constrains the distances and orientation between molecules. This allows the hydrogen bond to determine the structure of the proteins and holding together the double stranded DNA molecule. The hydrogen bond is also relatively strong.
How do you identify charge-charge (ionic) interaction?
Any group or atom in a molecule which carries a charge, as a result of either the electronegativity difference between atoms, the presence of an acidic or basic group or an atom with a lone pair of electrons. The interaction can either be attractive with an oppositely charged group or repulsive with a similarly charged group.
What is the difference between hydrophobic and hydrophilic groups?
Hydrophobic molecules are insoluble in water whereas hydrophilic molecules are soluble in water. These molecules can be identified by the presence of polar groups such as carboxylic acid, amine and hydroxyl, making the molecule hydrophilic and the absence of these makes the molecule hydrophobic.
What are the five major groups of amino acids?
- Non-polar (straight or branched chains, may or may not be cyclic).
- Aromatic
- Uncharged polar
- Charged
- Sulphur-containing
Why are amino acids amphoteric?
They contain at least 2 ionisable side chains which can make them react as either acids or basis depending on the pH of the medium. In acidic media (below pKa) the carboxylic group is unionised while the amino group is ionised. In basic media the opposite is true.
What structural elements constitute an amino acid?
Nitrogen and hydrogen
What differentiates polar and non-polar amino acids?
Non-polar amino acids contain mostly hydrocarbons whereas polar amino acids contain a charge.
How are amino acids joined together and what is the resulting molecule known as and consists of what?
Amino acids are joined together by losing a water molecule and the resulting molecule is known as a dipeptide and consists of two amino acids linked through CO-NH amide linkage also known as a peptide bond.
How are specialised protein structure established?
Specialised protein structure is formed after the formation of a new protein (translation) where a few amino acid residues are modified. An example includes 4-hydroxyproline and 5-hydroxyproline which are modified versions of the amino acids proline and lysine, an essential components of collagen.
What is the function of amino acids and their derivatives?
They are chemical messengers between body cells or as intermediates in various metabolic processes. This includes the roles of y-aminobutyric acid (GABA a derisive of the amino acid glutamate) and dopamine (derivative of tyrosine).
What are the 6 categories of proteins and what is there functions?
- Structural proteins: structural support and framework
- Movement proteins: components in muscles
- Transporter: in cell membranes allow the movement of molecules in and out of the cells.
- Metabolic: Catalyses the breakdown & synthesis of biological macromolecules to maintain cellular function.
- Communication: binding of hormones & neurotransmitters to specific cellular receptors.
- Defence & Protection: contribute to the barrier properties of skin such as keratin in immune system.
Describe the four structure of proteins?
- Primary: Simple linear sequence of amino acids
- Secondary: Contains regions of amino acid chains that are stabilised by hydrogen bonds from the polypeptide backbone, creating alpha helix & beta pleated sheets.
- Tertiary: Complex coiling & folding of secondary structure which forms final three-dimensional structure and results in the interaction between the polypeptide chain & surrounding water molecules.
- Quaternary: Interaction between individual polypeptides to form a multi-subunit protein complex.
