nucleic acids and protein structure Flashcards
what determines macromolecular structure?
- covalent bonds
- electrostatic interactions
- hydrogen bonds
- hydrophobic interactions
- van der waals forces
what is covalent bonding?
sharing of electrons between hydrogen bonds. the strongest type
what is ionic bonding?
bond formed between charged groups with opposing charges
why are ionic bonds on the surface of a protein weaker than ionic bonds within a protein?
on the surface of a protein, charged groups are very common
what is hydrogen bonding?
electrostatic interactions between an electron lone pair and an acidic proton
what are hydrophobic interactions?
repulsion of hydrophobic molecules from water, to allow water to maximise hydrogen bonding and maximise entropic potential
what are van der waals forces?
non-specific attractive force when 2 atoms are in close proximity
what does a nucleotide consist of?
a ribose sugar, base and 5’ phosphate
in what form is DNA found, in watson + crick base pairing?
B form; a right-handed double helix where phosphates form a charged surface
what is hoogsteen base pairing?
where thymine forms additional base pairs
what is a G-quadruplex?
four guanines, with usually a K+ ion in the middle
what type of helix does RNA form?
an A form helix
why can RNA form complex structures?
due to extra hydroxyl group on the ribose
what drives the formation of helices as a secondary structure?
favourable enthalpic interactions between amino acids with the backbone 4 residues away. plus a network of hydrogen bonds, which organise the helix to be stable
what is the difference between a B-strand and B-sheet?
in a B-strand, there is one peptide backbone in a straight conformation, whereas in a B-sheet there are many
what is a recognisable structural motif? give examples
a configuration which is recognisable between structures e.g. EF hand, leucine zipper, helix-turn-helix and 4 helix bundle
how is a beta sheet formed?
linking 2 or more B-strands lying next to each other by hydrogen bonds
what is the effect of turns and loops?
these structures are often rigid and well defined, and are found on the surface of proteins, interacting with other molecules
how does the polypeptide chain fold in an aqueous environment and why?
folds so that hydrophobic groups are buried and its polar charged chains are on the outside. a system is more thermodynamically stable when hydrophobic residues are clustered together rather than extend into aqueous environment
what is an intrinsically unstructured protein? what residues are common and uncommon amongst them?
a protein which completely or in part, has no discrete three-dimensional structure under physiological conditions. these regions are rich in charged and polar amino acids with few hydrophobic residues
