Amino acids, proteins & DNA
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2 groups found in an amino acid
Amine (-NH2) Carboxylic acid (-COOH)
Which amino acid group acts as a base or acid?
Amine (-NH2) accepts protons as a base Carboxylic acid (-COOH) donates protons as an acid
What is a zwitterion?
Contains both a positive (–NH3+) and a negative (–COO−) charge but is overall neutral at a certain pH where both groups have reacted.
Amino acid structure in low pH
The amine group (–NH2) is protonated to (–NH3+). Molecule has an overall positive charge.
Amino acid structure in high pH
The carboxyl group (–COOH) is deprotonated to (–COO−). Molecule has an overall negative charge.
Peptide bonds structure
-CONH-
Amino acid structure after a polymer is hydrolysed with acidic conditions
An amino acid with a protonated amine group to NH3+
Amino acid structure after a polymer is hydrolysed with alkaline conditions
An amino acid with a deprotonated carboxylic group to COO-
Where does H bonding arise in the secondary structure of proteins?
Between C=O and N−H bonds from different amino acids in the polymer chain
What is tertiary structure defined as?
The 3D folding of the protein due to interactions between R groups.
Different types of R groups interactions in the tertiary structure of proteins
Hydrogen bonding (between polar groups) Disulfide (S−S) bonds Ionic bonds (between charged R groups) Hydrophobic interactions (between non-polar R groups)
How can amino acids be identified in TLC?
Protein hydrolysed and broken into its constituent amino acids. Amino acids are separated based on their solubility in the solvent. UV light is used to locate amino acids on the chromatogram. Rf calculated and compared to known values.
Why are enzymes stereospecific?
The 3D structure only had a complimentary active site to one enantiomer of the substrate
Why is computational drug design beneficial?
Proteins have very complicated shapes so enzyme structure and inhibitors can be quickly modelled. Speeding up pharmaceuticals discoveries.
Structure of a nucleotide
A phosphate group (PO43−). A pentose sugar (2-deoxyribose). A nitrogenous base (Adenine, Cytosine, Guanine, Thymine).
What bond links nucleotides to create the backbone?
Covalent
Number of H bonds between A & T, C & G
A & T = 2 C & G 3
Formula of cisplatin
[Pt(NH3)2Cl2]
Structure of cisplatin
Square planar complex Two ammonia (NH3) ligands and two chloride (Cl−) ligands Cis arrangement
How does cisplatin function?
Enters cancer cells and undergoes ligand substitution. Inside the cell, the Cl concentration is lower than in blood, causing Cl− ligands to be replaced by water. Activating cisplatin. Binds to N atoms on guanine bases in DNA, forming a platinum–DNA complex. This prevents DNA from unwinding and replicating, stopping cancer cell division.
How does activated cisplatin bind to N atoms on guanine?
Forms a co-ordinate bond to the Pt, acting as a ligand and substituing a water molecule
Advantage + disadvantage of cisplatin
Significantly increases cancer survival rates. Research is still required to find non-toxic versions of Pt