Unit 5: 3-D Structure and Folding

Question 1

What is conformation

Answer 1

spatial arrangement of atoms in a protein that depends on rotation of bonds, does not involve bond breaking/making

Question 2

What does native protein mean

Answer 2

protein in any of their functional folded conformation

Question 3

primary structure

Answer 3

peptide bonds; aa sequence

Question 4

secondary structre

Answer 4

hydrogen bonds, alpha helices, beta sheets

Question 5

tertiary structure

Answer 5

interplay of side chains/R groups in folded protein

Question 6

Quaternary structure

Answer 6

non covalent interaxn btwn diff polypeptide chains

Question 7

What does X-ray crystallography measure

Answer 7

locations and intenisty of spots produced on photographic film by beam of x rays after the beam is diffracted by e- of an atom

Question 8

What are the steps involved in x-ray crystallography

Answer 8

make crystal(most difficult). diffraction pattern. e- density map. atomic model

Question 9

What is essential to fit protein to e- density map

Answer 9

sequence data

Question 10

What is nuclear magnetic resonance

Answer 10

physical phenomenon in which the nuclei in a magnetic field absorbs and re-emits electromagnetic radiation

Question 11

Disadvantage of nuclear magnetic resonance

Answer 11

only identifies structures of small portions

Question 12

advantage of nuclear magnetic resonance

Answer 12

analysis carried out on macromolecule in sln, no crystals needed. allows for movement

Question 13

Describe the planar nature of peptide bond

Answer 13

has partial double bond character, even though it is drawn as single bond. length of peptide bond supports a double bond nature of peptide linkage. charge on carbonyl )2 and amino H2 also indicate double bond nature. peptide linkage that forms btn 2 aa is planar