3D Protein Structures (Ch. 4)

Question 1

Protein stability

Answer 1

tendency to maintain a native conformation, stabilized by disulfide (covalent) bonds and, primarily, weak (noncovalent) interactions

Question 2

Weak interactions

Answer 2

noncovalent. hydrogen bonds, the hydrophobic effect, and ionic interactions.

Question 3

Hydrophobic effect

Answer 3

A type of weak, noncovalent interaction. Increase in entropy of surrounding water when nonpolar molecules are clustered together.

Question 4

Peptide bond

Answer 4

rigid, planar

Question 5

Ramachandran plot

Answer 5

psi vs. phi, which represent dihedral angles and work to define peptide conformation.

Question 6

Secondary structure

Answer 6

The local spatial arrangement of a segment of a polypeptide chain.

Question 7

Alpha-helix

Answer 7

2˚ structure. Can be left-handed or right-handed (more common). Stabilized by hydrogen bonds. Alanine shows greatest tendency to form alpha-helices. Proline is not conducive to alpha-helices.

Question 8

Beta turn

Answer 8

2˚ structure

Question 9

Beta-conformation

Answer 9

2˚ structure. Backbone of polypeptide chain is in a zigzag structure.

Question 10

Beta turn

Answer 10

2˚ structure found in globular proteins. Connect the ends of two adjacent segments in antiparallel beta-sheet. Consists of a 180˚ turn in 4 AA’s. There are two types: Type I beta-turn and Type II beta-turn.

Question 11

Beta-sheet

Answer 11

Several segments in beta-conformation, side by side. Hydrogen bonds hold the sheet together. The polypeptide chains can run parallel or anti-parallel.

Question 12

Tertiary structure

Answer 12

Overall 3D arrangement of all atoms in a protein.

Question 13

Quaternary structure

Answer 13

3D arrangement of protein subunits (2+ polypeptide chains).

Question 14

Fibrous proteins

Answer 14

with polypeptide chains arranged in long strands or sheets. Make up most support structures. The group includes alpha-Keratin, collagen, and silk fibroin.

Question 15

Fibrous proteins

Answer 15

with polypeptide chains arranged in long strands or sheets. Make up most support structures, since they provide strength and/or flexibility to the structure. The fundamental structural unit is a simple repeating secondary structure. The group includes alpha-Keratin, collagen, and silk fibroin.
Insoluble in water (lots of hydrophobic AA’s). Their strength is enhanced by covalent cross-links between chains.

Question 16

Globular proteins

Answer 16

with polypeptide chains folded into spherical shape. Make up most enzymes and regulatory proteins, transport proteins and immunoglobulins. More compact shape.

Question 17

Alpha-Keratin

Answer 17

A fibrous protein. Super strong. Only found in mammals. It is a right-handed alpha-helix. Two parallel strands form a coiled coil. Rich in hydrophobic AA residues. Disulfide bonds stabilize quaternary structure.

Question 18

Collagen

Answer 18

A fibrous protein. Strong. It is a left-handed helix (not alpha!). A coiled coil made up of three polypeptides called alpha chains.

Question 19

Collagen

Answer 19

A fibrous protein. Strong. It is a left-handed helix (not alpha!). A coiled coil made up of three polypeptides called alpha chains.

Question 20

Silk fibroin

Answer 20

A fibrous protein, produced by insects and spiders. It is usually in beta conformation, and then close packing of beta-sheets, due to large amount of Ala and Gly. Structure does not stretch, but it is flexible –> beta conformation is already stretched, and the sheets are held together by weak interactions, not covalent bonds.

Question 21

Silk fibroin

Answer 21

A fibrous protein, produced by insects and spiders. It is usually in beta conformation, and then close packing of beta-sheets, due to large amount of Ala and Gly. Structure does not stretch, but it is flexible –> beta conformation is already stretched, and the sheets are held together by weak interactions, not covalent bonds.

Question 22

Myoglobin

Answer 22

Oxygen-binding protein in muscle cells. Stores oxygen and facilitates oxygen diffusion in muscle tissue. Contains a single polypeptide chain and a heme group

Question 23

Myoglobin

Answer 23

Oxygen-binding protein in muscle cells. Stores oxygen and facilitates oxygen diffusion in muscle tissue. Contains a single polypeptide chain and a heme group. It’s predominantly alpha-helices.

Question 24

Motif

Answer 24

Aka a fold. A recognizable folding pattern involving 2+ elements of secondary structure and the connection(s) between them.

Question 25

Domain

Answer 25

A part of a polypeptide chain that is independently stable or could undergo movements as a single entity with respect to the whole protein.

Question 26

Multimer

Answer 26

A multisubunit protein.

Question 27

Oligomer

Answer 27

A multimer with just a few subunits. E.g. hemoglobin.

Question 28

Protomer

Answer 28

“repeating structural unit in such a multimeric protein”

Question 29

Protomer

Answer 29

“repeating structural unit in such a multimeric protein”

Question 30

Hemoglobin

Answer 30

A globular oligomer. A tetramer, or a dimer of alpha-beta protomers. Contains 4 polypeptide chains and 4 heme prosthetic groups, in which iron atoms are in fe2+ state. The globin consists of two alpha chains and two beta chains.

Question 31

Denaturation

Answer 31

The loss of protein function due to loss of the appropriate 3D structure. Proteins can be denatured by change in temperature or pH.

Question 32

Proteostasis

Answer 32

The continual maintenance of active cellular proteins.

Question 33

Chaperones

Answer 33

Proteins that help partially folded or incorrectly folded polypeptides by facilitating correct folding pathways. Hsp70 and chaperonins are two major families of chaperones.

Question 34

Hsp70

Answer 34

Major family of chaperone proteins.

Question 35

Chaperonins

Answer 35

Major family of chaperone proteins.

Question 36

Prion proteins

Answer 36

mad cow disease