Biochemistry Flashcards
(43 cards)
What are helicase enzymes
Enzymes which “move” along nucleic acid phosphodiester backbone, separating the two nucleic strands, using energy from ATP hydrolysis
What is the replicaiton fork
(moves in the direction of the new strand synthesis)
Replication fork is site of active DNA synthesis, where DNA helix unwinds and DNA single strands replicate - new DNA strands are synthesised in two orientations
Which direction does DNA polymerase synthesise the new strands in
5’ to 3’ (of new DNA)
such that the 3’ to 5’ diretion is the leading strand and the 5’ to 3’ direction is the lagging strand
What is the primase enzyme
Enzyme that synthesises short RNA sequences called primers. These primers serve as a starting point for DNA synthesis
What does DNA polymerase do
DNA polymerase incorporates dNTPs into a growing DNA strand during DNA replication
dNTP is incorporated into growing strand by phosphodiester bond formation of 3’-hydroxyl terminus on growing strand and α-phosphate of incoming dNTP
What is exonuclease
Enzyme that can cleave the phosphodiester bonds present in between the nucleotides (between DNA nucleotide and RNA primer)
What does exonuclease use in its active site
Mg (II) as cofactor
what is DNA ligase and when is it used
catalyses the joining of two pieces of DNA with matching ends to form a single, unbroken molecule of DNA, which is required in DNA replication and in DNA repaire pathways
What is a nucleosome
the basic repeating unit of chromatin, comprising DNA wrapped around a core of histone proteins
What is a chromatin fiber
a higher-order (than nucleosome) structure formed by the folding and compaction of nucleosomes
what is the purpose of hierarchical organisation of DNA
ensures its compaction while allowing dynamic access for cellular processes like transcription and replication
primary structure of a protein
sequence of amino acids in the polypeptide chain
secondary structure of a protein
the local spatial arrangement of the polypeptide backbone atoms including α-helices and β-pleated sheets
tertiary structure of a protein
3 dimensional structure of an entire polypeptide chain
quaternary structure of a protein
3D spatial arrangement of individual polypeptide chain subunits as many proteins are formed by the association of 2 or more polypeptide chains
Describe the selectivity of trypsin
hydrolyses peptide bonds are basic (lysine and arginine) amino acid residues
describe the selectivity of chymotrypsin
hydrolyses peptide bonds are aromatic (phenylalanine, tryptophan, and tyrosine) amino acid residues
describe the selectivity of clostripain
hydrolyses peptide bonds after arginine amino acid residues
describe the selectivity of staphylococcal protease
can hydrolyses peptide bonds after acidic (aspartic acid and glutamic acid) amino acid residues
describe the method required to determine the primary sequence of a polypeptide
- Prepare the protein for sequencing
Reduce the proteins disulfide bonds
Separate any discrete polypeptide chains - Sequence
Fragment subunits to give small peptides
Separate and purify fragments
Determine the sequence of fragments
Repeat with different fragmentation selectivity - Organise the completed structure
Describe the effect of planar amide bonds and partial double bond character of C-N on amides
leads to restricted rotation producing cis and trans isomers of amides
which isomer of an amide is more stable
trans amides are more stable as it reduces unfavourable steric clash between C atoms in polypeptide chain
what is the exception to the increased stability of trans amides
proline (due to increased steric clash in the cis isomer compared to the trans isomer)
this is because
describe the alpha helix
helical polupeptide conformation which simultaneously allows a low energy conformation of the polypeptide backbone and stabilisation through an optimal hydrogen-bonding pattern
