nucleic acids and protein structure

Question 1

what determines macromolecular structure?

Answer 1

• covalent bonds
• electrostatic interactions
• hydrogen bonds
• hydrophobic interactions
• van der waals forces

Question 2

what is covalent bonding?

Answer 2

sharing of electrons between hydrogen bonds. the strongest type

Question 3

what is ionic bonding?

Answer 3

bond formed between charged groups with opposing charges

Question 4

why are ionic bonds on the surface of a protein weaker than ionic bonds within a protein?

Answer 4

on the surface of a protein, charged groups are very common

Question 5

what is hydrogen bonding?

Answer 5

electrostatic interactions between an electron lone pair and an acidic proton

Question 6

what are hydrophobic interactions?

Answer 6

repulsion of hydrophobic molecules from water, to allow water to maximise hydrogen bonding and maximise entropic potential

Question 7

what are van der waals forces?

Answer 7

non-specific attractive force when 2 atoms are in close proximity

Question 8

what does a nucleotide consist of?

Answer 8

a ribose sugar, base and 5’ phosphate

Question 9

in what form is DNA found, in watson + crick base pairing?

Answer 9

B form; a right-handed double helix where phosphates form a charged surface

Question 10

what is hoogsteen base pairing?

Answer 10

where thymine forms additional base pairs

Question 11

what is a G-quadruplex?

Answer 11

four guanines, with usually a K+ ion in the middle

Question 12

what type of helix does RNA form?

Answer 12

an A form helix

Question 13

why can RNA form complex structures?

Answer 13

due to extra hydroxyl group on the ribose

Question 14

what drives the formation of helices as a secondary structure?

Answer 14

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

Question 15

what is the difference between a B-strand and B-sheet?

Answer 15

in a B-strand, there is one peptide backbone in a straight conformation, whereas in a B-sheet there are many

Question 16

what is a recognisable structural motif? give examples

Answer 16

a configuration which is recognisable between structures e.g. EF hand, leucine zipper, helix-turn-helix and 4 helix bundle

Question 17

how is a beta sheet formed?

Answer 17

linking 2 or more B-strands lying next to each other by hydrogen bonds

Question 18

what is the effect of turns and loops?

Answer 18

these structures are often rigid and well defined, and are found on the surface of proteins, interacting with other molecules

Question 19

how does the polypeptide chain fold in an aqueous environment and why?

Answer 19

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

Question 20

what is an intrinsically unstructured protein? what residues are common and uncommon amongst them?

Answer 20

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