Protein Structure , Enzymes And Catalysis Flashcards
What is a primary structure of protein?
Sequence of amino acids in a polypeptide chain held together by covalent bonding i.e. Peptide bond.
What is secondary protein structure?
Structural motifs in proteins a-helix and b-sheet held together by hydrogen bonds between NH and CO group of the amino acid (every 4th residue)
What is a tertiary structure of a protein?
Folding up of polypeptide chain held together by several intermolecular forces: covalent, ionic, H bonds, van der Waal and hydrophobic interactions.
What is a quaternary structure of protein?
Association of protein subunits into larger assemblies could be held together by various bonds.
Which amino acid is achiral and why?
Glycine because it has 2 of the same group (-H) attached to the alpha carbon in the amino acid molecule.
What is special about proline and what is the implication of this?
Proline forms side chain which loops back to bind to the back bone of the amino acid.
This means that proline is not present in a structure that is flexible because it would make the structure more inflexible.
What is a covalent modification?
Modification of amino acids after the polypeptide chain has been formed
Why is Val-Glu-Ala-Phe not the same as Phe-ALa-Glu-Val?
Because the sequence always synthesises from the N terminal (amino) to the C (carboxyl) terminal.
How many residues of amino acids away is the CO group H-bonded with NH group of another amino acid in the polypeptide chain?
4
Which amino acids are not normally found in the alpha helix?
Glycine and proline
Which amino acids are commonly found in the alpha helix?
ALPH - Alanine
Leucine
Phenylalanine
These are small uncharged amino acids.
Compare and contrast the DNA and protein structure.
In DNA:
- base pairs as unit
- 5’ - 3’ synthesis
- Double helix structure!!!
In protein:
- amino acids (residues) as unit
- N’ to C’ terminal synthesis of polypeptide chain
- Alpha helix, beta sheet, etc structure
Discuss why a beta sheet exists as antiparallel.
More stable conformation as the orientation of the molecules at each end makes the CO of one amino acid near to NH of another amino acid allowing hydrogen bond strengthening the structure of the beta sheet. Alternating chains go to opposite directions, hence anti parallel.
What are beta turns?
Beta turns, also known as beta bends or tight turns, are a type of secondary structure. In a beta turn, a tight loop is formed when the carbonyl oxygen of one residue forms a hydrogen bond with the amide proton of an amino acid three residues down the chain.
Glycine and proline can exist in beta turns: reverse isomers allow for sharp turns.
What are repeated motifs?
Super secondary structure found in DNA binding proteins for example, B-a-B Loop repeated many times to form a/B barrel.
