chapter 4

Question 1

protein conformation

Answer 1

a limited number of conformations predominate under biological conditions.

Question 2

hydrophobic effect

Answer 2

The release of water molecules from the structured solvation layer around the molecule as protein folds increases the net entropy.

Question 3

london dispersion

Answer 3

Medium-range weak attraction between all atoms contributes significantly to the stability in the interior of the protein

Question 4

peptide bonds structure

Answer 4

resonance causes the peptide bond to be rigid and nearly planar

Question 5

rotation around peptide bond

Answer 5

rotation can NOT occur around the peptide bond

rotation CAN occur around the bonds connected to the alpha carbon

Question 6

phi angle vs psi angle

Answer 6

phi angle= alpha carbon- amide nitrogen bond

psi angle= alpha carbon- carbonyl carbon bond

in fully extended form, both are 180 degrees

Question 7

what can limit the degree of rotation around phi and psi bonds

Answer 7

steric interference

Question 8

what AA has the most restricted angle of rotation?

the least restricted?

Answer 8

most= proline

least= glycine

Question 9

Irregular arrangement of the polypeptide chain is called the

Answer 9

random coil

Question 10

Three factors determine the secondary structure:

Answer 10

The planar nature of the peptide bond

Increased stability by maximizing H-bonds between carbonyl and amide

Spatial distribution to avoid steric strain

Question 11

2 regular arrangements of secondary structures

Answer 11

alpha helix and beta sheet

Question 12

alpha helix properties

Answer 12

R-groups face out

Right handed helix

Repeating amino acid pattern

Strong dipole moment

stabilized via H bonds between carbonyl and amino

Question 13

Beta sheet properties

Answer 13

Parallel and antiparallel

Extended conformation with limited flexibility

Repeating amino acid pattern

H bonds between chains stabilize

• need small R groups to maximize stability

Question 14

Beta turns

Answer 14

beta turns occur frequently whenever strands in beta sheets

The 180°turn is accomplished over four amino acids.

The turn is stabilized by a hydrogen bond

Identity of Cα2 and Cα3

Question 15

major classes of protein tertiary structure

Answer 15

fibrous and globular

Question 16

protein tertiary structures

Answer 16

-overall spatial arrangement of atoms in a protein.

Stabilized by numerous weak interactions between amino acid side chains

largely hydrophobic and polar interactions
can be stabilized by disulfide bonds

Question 17

Fibrous proteins

Answer 17

can be filamentous or elongated

collagen

Question 18

collagen

Answer 18

a fibrous protein found in bones, tendons, and skin.

individual collagen chains are left handed

basic unit is tropocollagen, is right handed triple helix, stabilized by H bonds

Question 19

Collagen Fibrils

Answer 19

Collagen superstructures are formed by cross-linking of collagen triple-helices to form collagen fibrils.

Crosslinks are covalent bonds between Lys or HyLys, or His amino acid residues.

Question 20

why does collagen lose flexibility with age

Answer 20

Collagen losses flexibility with age due to increase crosslinking of tropocollagen fibers

Question 21

alpha keratin

Answer 21

in hair and nails.

Right handed a-helix

left handed coil

keratin in feathers is beta

Some keratin types have disulfide bonds that harden the structure

Question 22

Silk Fibroin

Answer 22

Fibroin is the main protein in silk from moths and spiders.

Antiparallel beta sheet structure

Small side chains (Ala and Gly) allow the close packing of sheets.

Structure is stabilized by:
-hydrogen bonding within sheets
-London dispersion interactions between sheets

Question 23

α Helix, cross-linked by disulfide bonds

Answer 23

Tough, insoluble protective structures of varying hardness and flexibility

α-Keratin of hair, feathers, nails

Question 24

β Conformation

Answer 24

Soft, flexible filaments
Silk fibroin

Question 25

Collagen triple helix

Answer 25

High tensile strength, without stretch Collagen of tendons, bone matrix

Question 26

Folding Patterns of Proteins

Answer 26

motif = fold = recognizable folding pattern involving 2+ elements of secondary structures and the connection(s) -can be simple, such as in a β-α-β loop -can be elaborate, such as in a β barrel

Question 27

Domain

Answer 27

Part of a polypeptide chain that folds in a structure that functions independently from the rest of the polypeptide and in many cases can retain its structure when separate from the rest Domains within a protein can have different functions

Question 28

Protein-Folding Rules

Answer 28

burial of hydrophobic R groups requires 2+ layers of secondary structure α helices and β sheets are found in different layers adjacent amino acid segments are usually stacked adjacent the β conformation is most stable with right-handed connections

Question 29

intrinsically disordered proteins:

Answer 29

lack definable structure often lack a hydrophobic core high densities of charged residues (Lys, Arg, Glu) and Pro facilitates a protein to interact with multiple binding partners

Question 30

Protomer:

Answer 30

repeating structural unit in a multimer

Question 31

Multimer: Oligomer: Protomer:

Answer 31

Multimer: multiple subunits Oligomer: multimer with few subunits Protomer: repeating structural unit in a multimer

Question 32

proteostasis

Answer 32

continual maintenance of the active set of cellular proteins required under a given set of conditions

Question 33

denaturation

Answer 33

loss of three-dimensional structure sufficient to cause loss of function can occur by heat, pH extremes, miscible organic solvents, certain solutes, detergents often leads to protein precipitation

Question 34

Renaturation

Answer 34

process by which certain denatured globular proteins regain their native structure and biological activity Anfinsen experiment showed the amino acid sequence contains all the information required to fold the chain

Question 35

chaperone proteins

Answer 35

facilitate correct folding pathways or ideal micro environments Hsp70 = bind to hydrophobic regions chaperonins = required for the folding of proteins that do not fold spontaneously