3-D Structure and Function of Proteins

Question 1

Proteomics

Answer 1

Study of large sets of proteins, often those produced by a cell

Question 2

Primary structure

Answer 2

Linear sequence of amino acid residues

Question 3

Secondary structure

Answer 3

Structures created by H-bonding between amino acid residues in peptide chain

Question 4

Tertiary structure

Answer 4

Completely folded and compacted polypeptide chain

Question 5

Quaternary structure

Answer 5

Several polypeptides come together

Question 6

X-ray crystallography

Answer 6

Technique used for determining 3-D structure of protein

Electromagnetic waves of similar size to regularity of crystal pass through crystal and create diffraction pattern

Question 7

Protein Data Bank

Answer 7

Data bank through which thousands of solved 3-D protein crystal structures can be accessed

Question 8

Space-filling models

Answer 8

Use Van der Waals radii to illustrate overall shape and surface topography of protein
Looks like blob of balls

Question 9

Ribbon structures

Answer 9

Simplified model of protein (shows some aspects of secondary structure) used to show binding domains

Question 10

Ball-and-stick structures

Answer 10

Highly detailed model of protein that shows H-bonding and other molecular interactions
Combines aspects of space-filling models and ribbon structures

Question 11

Flexibility of proteins

Answer 11

Proteins don’t have static, immovable structures

Question 12

Phi bond

Answer 12

Rotation around N-alpha C bond

Question 13

Psi bond

Answer 13

Rotation around alpha C-carboxyl C bond

Question 14

Ramachandran plot

Answer 14

Graphical representation of types of secondary structures allowed in polypeptides

Question 15

Alpha helix

Answer 15

Corkscrew-type secondary structure
Sidechains oriented outward from helix axis
Can be amphipathic (different sides of helix can have sidechains with different polarities)

Question 16

Beta sheets

Answer 16

Flat secondary structure
Stable due to interstrand H-bonding
More flexibility in bond angles than alpha helices
Amino acid sidechains point alternatively above and below the plane
Each strand in sheet has a slight right hand twist
Can be amphipathic

Question 17

2 types of beta sheets

Answer 17

Parallel and anti-parallel

Question 18

Loops

Answer 18

Segments of non-regular structure that connect proteins

Contain hydrophilic residues and are found at or near the surface of proteins

Question 19

Turns

Answer 19

Short loops (<5 residues)
Often cause an abrupt change in chain direction

Question 20

Motifs

Answer 20

Combination of alpha helices, beta sheets, and loops to form tertiary structure of proteins

Question 21

Domains

Answer 21

Independently folded, compact globular units
Made up of motifs
Show structural similarity across species

Question 22

Chemical denaturation agents

Answer 22

Chaotropic agents (urea, guanidinium salts)
Detergents (SDS)

Question 23

Beta-mercaptoethanol

Answer 23

Denatures proteins by cleaving disulfide bonds

Question 24

Renaturation of proteins

Answer 24

Rare- some small proteins can spontaneously reform their native conformations, but most cannot

Question 25

Dictation of protein folding

Answer 25

Controlled by amino acid sequence

Question 26

Molecular chaperones

Answer 26

Assist in protein folding