BB2 Primary Secondary Structure

Question 0

Polypeptide

Answer 0

many joined amino acids

• has direction and polarity

Question 1

Amino acids joined by

Answer 1

• peptide bond
• amide bond
• loss of water
• equilibrium prefers hydrolysis, requires input of energy

Question 2

Residues

Answer 2

amino acids in a polypeptide

Question 3

Order of residues read in order…

Answer 3

Amino Terminal to carboxyl Terminal

Question 4

Sequence

Answer 4

residue order of a protein

Question 5

Main chain of polypeptide

Answer 5

• AKA backbone
• regular, repeating part
• N H αCarbon αHydrogen Carbon Oxygen

Question 6

Peptide bond in a peptide group has

Answer 6

• partial double bond characteristics
• shortens C-N bond
• peptide group acts as single planar unit

Question 7

Only proline allows

Answer 7

• cis conformation

(steric hiderance)

Question 8

In an oxidizing environment, cysteines can pair to form

Answer 8

• disulphide bonds/bridges
(highly reactive SH group)
• resist breaks, return after stretch

Question 9

Primary Structure of protein

Answer 9

the amino acid sequence (and disulphides if any)

bonds arrangement

Question 10

Secondary Structure of a Protein

Answer 10

spatial arrangement of amino acids near to one another in the linear sequence
Hydrogen bonds

Question 11

Regular repeating structures of secondary structure

Answer 11

• alpha helix

* beta-pleated sheet

Question 12

Alpha helix

Answer 12

• regular tight coil
• right-handed
• branching at alpha carbon destabilizes
• side chains with Hbond donors or acceptors near to main chain = compete

Question 13

Rotation about axis from one residue to the next

Answer 13

100degrees
3.6 residues per turn
5 angstrom diameter

Question 14

Rise of the helix

Answer 14

distance along the axis from one residue to the next

1.5 angstrom

Question 15

Pitch of a helix

Answer 15

number of residues per turn x rise

Length of 1 complete turn along the axis

Question 16

Hydrogen bonding pattern in alpha helix

Answer 16

• carbonyl oxygen residue (i)
bonded to
• hydrogen of amide residue at (i+4)

Question 17

Myoglobin’s secondary structure consists mostly of

Answer 17

alpha helices

Question 18

Beta-pleated sheets

Answer 18

• comprised of beta-strands
• often twisted rather than flat
• 2 forms

Question 19

Antiparallel beta-pleated sheets

Answer 19

• beta-strands in sheet run in opposing directions
• more stable than parallel
• NH & CO of 1 bonded to CO & NH of anither

Question 20

Parallel beta-pleated sheets

Answer 20

• beta-strands run in same direction
• hydrogen bonding distorted = less stable
• NH Hbonded to CO of 1 AA on adjacent, CO Hbonded to NH on AA 2 down

Question 21

Concanavalin A’s secondary structure is mostly

Answer 21

beta-pleated sheets

Question 22

Beta-turns

Answer 22

• sharp turns in proteins
• keep them as compact and globular
• 4 residues, glycine is 3rd

Question 23

Most abundant animal protein

Answer 23

collagen

Question 24

Collagen helix

Answer 24

* 1000 residues * every 3rd is glycine, on inside (others = steric hinderance) * triple helix (Hbonding between strands) = super helical cable * hydrogen bonds absent * stabilizes by steric repulsion of the pyrrolidine rings of proline and hydroxyproline residues

Question 25

3-10 helix (subscript 10

Answer 25

* 3 residues in chain | * 10 residues from hydrogen bond donor to acceptor

Question 26

Mass of proteins in

Answer 26

daltons

Question 27

Cis- and trans- determined by

Answer 27

CO & NH

Question 28

Rotation specified by

Answer 28

* torsion angles | * visualized with ramachandran diagram

Question 29

Steric exclusion

Answer 29

2 atoms can't be in the same place at the same time | • powerful organizing principle

Question 30

Each residue related to the next one by

Answer 30

``` A rise (AKA translation) • 1.5A along helix • 100 degree rotation ```

Question 31

Alpha keratin

Answer 31

2 right handed alpha-helices entwined to form a left handed superhelix • alpha-helical coiled coil