Chapter 4: Protein 3D structure

Question 1

Which end of the polypeptide chain is the start?

Answer 1

START: amino terminal
END: carboxyl terminal

Question 2

A dipeptide is formed when…..

Answer 2

2 a.a. bond together, accompanied by the loss of H2O

Question 3

The backbone or main chain is……

Answer 3

a regular repeating part in the polypeptide chain + variable parts comprising of distinctive side chains.

Question 4

The largest protein is ….. made up of ….. a.a.

Answer 4

Titin (muscle protein), 27000

Question 5

Oligopeptides

Answer 5

made up of small number of a.a.

Question 6

Important of a.a. sequence

Answer 6

• determines 3D structure
• sequence is essential to function
• reveal evolutionary history
  + alterations can produce abnormal function & disease

Question 7

How are polypeptide chain restricted?

Answer 7

1. Peptide bond is Planer
2. double-bond character to resonance structure (prevents rotation, shortens bond length and constrains conformation of backbone)
3. peptide bond is uncharged - polymers form tightly packed globular proteins

Question 8

the 2 configurations possible for a planar peptide bond

Answer 8

Trans Config. –> 2 a-carbons are on opposite sides of the peptide bond (preferred configuration as prevents clashes between R-groups)

Cis Config. –> groups are pm the same side of peptide bond

Question 9

peptide units can rotate because ….

Answer 9

single bonds link a-carbon to amino and carbonyl group
+ peptide units can therefore rotate, taking on various orientations

Question 10

Ramachandran values

Answer 10

phi (φ) -> N – a-carbon
psi (ψ) -> Carbonyl carbon – a-carbon

Question 11

Do R-groups play a role in secondary structure?

Answer 11

NO, interactions for protein structure occur due to H-bonding of backbone

Question 12

Alpha Helix description

Answer 12

• single polypeptide coiled, H bonding on itself
• side chains projected outward

+ a.a. spaced 3-4 residues apart are spatially close in a helix.
+ helix can be clockwise or counterclockwise
+ clockwise helices are energetically more favorable (fewer clashes b/w side chains and backbone)

Question 13

Which Helix formation is typically found in proteins?

Answer 13

Clockwise (right-handed)

Question 14

Beta-pleated sheets description

Answer 14

• 2 or more polypeptide strands, not coiled (extended)
• 2 main H-bond patterns: parallel and anti-parallel

+important structural element -> fatty-acid binding

Question 15

Most proteins have compact globular shapes. Reversals in the direction of protein chains are achieved by….

Answer 15

structural elements called reverse turns and loops

Question 16

Turns and loops description

Answer 16

• exist on the surface of proteins
• role in interacting with the environment

+ loops are usually composed of a.a. with hydrophilic R-groups

Question 17

a- Keratin

Answer 17

• fibrous protein with extensive 2ndary structure
• found in hair
• 2 right handed helices intertwined to form a left-handed superhelix called a coiled coil

Question 18

Coiled-coil proteins

Answer 18

+superfamily of proteins
+2 or more helices can entwine to form stable structure
+humans have approx. 60 members of this family (including intermediate filaments and muscle proteins myosin and tropomyosin)
+ occurs by weak interaction such as van der Waals forces and Ionic interactions

+ helices may be linked by disulfide bonds formed by neighboring cysteine residues

Question 19

Collagen description

Answer 19

• fibrous protein with extensive 2ndary structure
• skin, bone, tendons, cartilage, and teeth
• super helical cable of 3 intertwined polypeptide chains
• Unique with high Gly and Pro content in each strand (hydroxyproline)

+ most abundant mammalian protein
+ Gly appears every 3rd residue
+ Gly-Pro-Pro sequence recurs frequently
+ Each helix is stabilized by steric repulsion of the pyrrolidine rings of Pro residues.
+ 3 strands stabilized by H-bonds

Question 20

Scurvy results in …..

Answer 20

lack of vitamin C (required for formation of hydroxyproline)

Question 21

Tertiary structure refers to…

Answer 21

Spatial arrangement of a.a. residues that are far apart in the sequence - level of structure is result of interactions b/w R-groups

Question 22

Interactions that can occur for tertiary structure are….

Answer 22

Disulfide bonds
H-bonds
Salt bridges
Hydrophobic interactions

Question 23

Tertiary structure is often initiated by ….

Answer 23

Hydrophobic forces
+ folding so hydrophobic residues on interior and hydrophilic residues on exterior
+ especially for globular proteins

Question 24

Globular Proteins

Answer 24

• form complicated 3D structures
• very compact with little to no empty space
• interior = hydrophobic a.a.
• exterior = charges and polar a.a.

Question 25

Myoglobin description

Answer 25

+ extremely compact molecule
+ 153 a.a.
+ capacity of Oxygen binding depends on heme
+ asymmetric because of complex folding of main chain
+ only polar residues in interior are 2 His residues

Question 26

Helix-turn-helix motifs

Answer 26

• super-secondary structure
  + a-helix separated from another helix by a turn

Question 27

protein Domains

Answer 27

• regions on a polypeptide chain that have structural/functional roles
• usually found in protein that are involved multiple functions such as catalysis, binding

+ compact globular units
+ polypeptide chains fold into 2 or more compact regions that may be connected by a flexible segment of polypeptide chain (pearls on a chain)
+ different proteins may have domain in common even if overall tertiary structures are different.

Question 28

Disulfide bonds

Answer 28

• formed by oxidation of thiols on 2 Cys
• reduction can break the bond
• increasing number of Cys usually associated with increased rigidity
• Covalent bond exists but not that stable due to red.

Question 29

Quaternary structure

Answer 29

• distinct subunits brought together in one protein molecule
  -may be multiple identical units or different units

+ the interactions among subunits are usually weak interactions (H-bonds, ionic bonds & van der Waals)
+ the simples quaternary structure is a dimer consisting of 2 identical subunits

Question 30

Hemoglobin

Answer 30

• tetramer –> α2β2 subunits