Amino acids, Proteins and DNA Flashcards
Describe the structure of amino acids
Has a carboxylic acid and primary amine functional group attached to the same carbon which is chiral (apart from glycine). Attached to the same carbon is R (apart from glycine).
How many naturally occurring amino acids are there?
- Only one enantiomer exists naturally.
What is a zwitterion and how do amino acids exist as these?
Ions that have both a permanent positive charge and a permanent negative charge but the compound is neutral overall. This happens at the pH value at the isoelectric point for the specific amino acid. The carboxylic acid group loses a H+ and the amine group gains H+.
Physical properties of amino acids
They are ionic compounds so have high melting points and dissolve well in polar solvents and poorly in non-polar solvents.
What happens to amino acids when the pH varies
At low pH the amine group accepts a H+ ion (is protonated) making the whole compound positive. At high pH the carboxylic acid group loses a H+ (is deprotonated) making the whole compound negative. All the groups on the side chain are subject to these effects also.
What are polypeptides?
Molecules containing up to 50 amino acids. They have the amide linkage -CONH- where the amine group from one amino acid and the carboxylic acid group from another react releasing a molecule of water.
How can proteins be broken down?
Hydrolysis. Protein is boiled with HCl (6M) for about 24h and breaks down into mixture of all the amino acids that made up the original protein. All peptide linkages are hydrolysed by the acid.
Name two shapes of proteins
Helical (spiral). Pleated sheet (zigzag)
What types of binding occur between amino acids in a protein chain?
Hydrogen bonding, ionic attractions between side chain groups. Sulfur-sulfur bonds (sulfur atoms from two amino acids can react together under suitable oxidising conditions.
Primary structure of proteins
The sequence of amino acids along a protein chain. Structure is held together by covalent bonding so is relatively stable, requires harsh conditions to break amino acids apart.
Secondary structure of proteins
Protein chain may form a helix (alpha-helix) or a folded sheet (beta-pleated sheet). Structure held together by hydrogen bonds. Hydrogen bonds much weaker than covalent bonds so structure is relatively easily disrupted by gentle heating or changes in pH.
Tertiary structure of proteins
Alpha-helix or beta-pleated sheet can itself be folded into a 3D shape. Structure held in place by a mixture of H bonding, ionic interactions, and sulfur-sulfur bonds (as well as Van der Waals).
Ways of finding structure of proteins.
X-ray diffraction can locate positions of atoms in space to determine secondary and tertiary structure. To find primary structure, first need to reflux protein with 6M HCl (hydrolysis) to break it down into all individual amino acids.
How does the active site work?
The enzyme has a cleft or crevice in it called the active site where the reaction takes place. The substrate fits precisely in the active site and is held in just the right orientation to react. The substrate must bond to it temporarily by intermolecular forces. These forces promote the movement of electrons within the substrate that lower the activation energy for the reaction.
Why is an enzyme said to be stereospecific?
The active site can often be so selective of the shape of a substrate that many enzymes only catalyse the reaction of one of a pair of enantiomers.
