lecture 5

Question 1

Amino acids are joint together by?

Answer 1

Peptide bonds

Question 2

When amino acids are bonded in a peptide or protein they are called?

Answer 2

Amino acid residues

Question 3

Each protein is made up of at least one type of chain?

Answer 3

Polypeptide

Question 4

How are amino acid residues in a polypeptide chain numbered?

Answer 4

Starting from the amino terminus to carboxyl terminus

Question 5

What causes the main chain to double back on itself forming a compact shape?

Answer 5

The globular shape

Question 6

What does the globular structure mainly comprised of?

Answer 6

Alpha helix and beta structure turns

Question 7

What are the four levels of protein structure?

Answer 7

Primary
secondary
tertiary
quaternary

Question 8

What is the primary structure?

Answer 8

amino acid sequence

Question 9

What is secondary structure?

Answer 9

Local 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues

Question 10

What is tertiary structure?

Answer 10

3D structure of a complete protein chain

Question 11

What is Quaternary structure?

Answer 11

interchain packing and structure for a protein that contains multiple protein chains

Question 12

What are the main chain atoms in a protein?

Answer 12

Nitrogen, alpha carbon, Carbon

Question 13

What is the chain angle between C’ and N?

Answer 13

Omega, either 180 or 0 degrees

Question 14

What is the chain angle between N and alphaC?

Answer 14

Phi, 0-180 degrees

Question 15

What is the chain angle C’ and alphaC?

Answer 15

psi, 0-180 degrees

Question 16

What is the phi angle?

Answer 16

Rotation angle around the N-alphaC

Question 17

What is the psi angle?

Answer 17

rotation angle around the alphaC-C’

Question 18

what is the rotation angle around the peptide bond?

Answer 18

Omega

Question 19

What degree are all the angles when the polypeptide has its conformation?

Answer 19

180 degrees

Question 20

Phi rotation can lead to what kind of collision?

Answer 20

O-O collisions

Question 21

Psi rotation can lead to what kind of collision?

Answer 21

NH-NH

Question 22

Most peptide bonds are in what formation?

Answer 22

Trans formation

Question 23

Why are peptide bonds majority trans?

Answer 23

because in the cis peptide bond there is a lot of steric crowding. The alpha carbons are on the same side

Question 24

Protein secondary structures are dominated by which two structures?

Answer 24

Alpha helix

Beta strand/sheet

Question 25

What bonds stabilise the alpha helix structures?

Answer 25

Hydrogen bonds

Question 26

What is hydrogen bonded in the alpha helix structure?

Answer 26

The carbonyl of residue and the N-H of residue, n+4

Question 27

How many residues per turn are there in an alpha helix?

Answer 27

3. 6 residues/turn | 5. 4 angstrams

Question 28

is alpha helix left or right handed?

Answer 28

Right handed

Question 29

Where do side chains point in alpha helix?

Answer 29

Out from the alpha helix to stabilise it

Question 30

What is the value of hydrogen bonds?

Answer 30

3-7kcal/mol or 12-28kJ/mol

Question 31

What residues are alpha helix breakers?

Answer 31

Glycine | Proline

Question 32

What is the alpha helix dipole?

Answer 32

~positive at N-terminus

Question 33

What are the two types of hydrogen bonding interactions in a beta sheet?

Answer 33

Parallel | Antiparallel

Question 34

Hydrogen bonding occurs between what in beta structures?

Answer 34

Adjacent chains

Question 35

What forms a beta sheet?

Answer 35

two beta strands, typically 2 to 10 strands

Question 36

what is the average strand length of a beta structure?

Answer 36

6 amino acid residues

Question 37

Beta pleated sheets have what kind of twist?

Answer 37

right handed

Question 38

Side chains point where in a beta sheet?

Answer 38

above and below the sheet

Question 39

NP-P-NP-NP-P stretch of residues commonly forms what?

Answer 39

Beta strand

Question 40

What structure exists in silk?

Answer 40

beta structure

Question 41

what are the most common turn types in beta structures?

Answer 41

Type I | Type II

Question 42

Why are protein structures difficult to display clearly?

Answer 42

Lots of atoms detailed internal cavities complicated shapes