Chapter 4

Question 1

Unlike most organic polymers, protein molecules adopt a specific…

Answer 1

3D conformation

Question 2

The protein molecules adopt a specific 3D conformation called…

Answer 2

native fold

Question 3

What kind of cost is there when folding the protein into one specific native fold?

Answer 3

entropy

Question 4

A limited number of conformations predominate under…

Answer 4

biological conditions

Question 5

What is the current conformation of a protein?

Answer 5

under present conditions, the protein will adopt the most thermodynamically stable conformation (lowest G)

Question 6

What is a native conformation?

Answer 6

proteins in any functional, folded conformations

Question 7

Strong disulfide (covalent) bonds are…

Answer 7

uncommon

Question 8

What is hydrophobic effect?

Answer 8

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

Question 9

What are secondary level hydrogen bonds?

Answer 9

elements of protein backbone from hydrogen bonds to form regular structures like beta helices and beta sheets

Question 10

What are tertiary and quaternary level hydrogen bonds?

Answer 10

R groups in the protein from hydrogen bonds between each other and other elements in the backbone

Question 11

What is london dispersion?

Answer 11

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

Question 12

What is electrostatic interactions?

Answer 12

long-range strong interactions between permanently charged groups

Question 13

The structure of the protein is partially dictated by the properties of…

Answer 13

covalent bonds between alpha-carbons, which form the backbone of a protein

Question 14

What are Ca-N and Ca-C bonds?

Answer 14

single covalent bonds, they can rotate freely when there is no steric hindrance

Question 15

What are C-N bonds?

Answer 15

have partial double bond nature, can’t freely rotate

Question 16

The lack of rotation on the C-N bond (peptide bond) forces…

Answer 16

the atoms attached by these three covalent bonds to conform with a plane

Question 17

The rigid peptide bond limit…

Answer 17

the range of conformations possible for polypeptides

Question 18

Peptide bonds have partial double bond nature due to its…

Answer 18

resonance structures

Question 19

What are the three dihedral angles that peptide conformation is defined by?

Answer 19

phi (Ca-N), psi (Ca-C) and omega (C-N)

Question 20

Rotation along the planes can only take place along the Ca…

Answer 20

which contains single bonds, with dihedra; angles phi and psi

Question 21

Amino acid side chains in polypeptides contribute to…

Answer 21

steric inference limiting the degree of rotation along phi and psi

Question 22

Secondary structures describes…

Answer 22

the local spatial arrangement of a segment in a polypeptide

Question 23

A regular secondary structure occurs when dihedral angles phi and psi remain…

Answer 23

nearly the same throughout that segment

Question 24

What are the stable secondary structures?

Answer 24

alpha helix
beta conformation
beta turn

Question 25

what is random coil?

Answer 25

structures without regular arrangements

Question 26

What are some properties of the helix?

Answer 26

tight backbone wound around and imaginary central axis

Question 27

What are some stabilization forces?

Answer 27

intrathecal h-bond between amino hydrogen (n) and carbonyl oxygen

Question 28

Not all polypeptides can form...

Answer 28

alpha helixes due to steric hindrance events that prevent formation of the required dihedral angles

Question 29

What adjacent amino acids can destabilize the helix?

Answer 29

Asn, Ser, Thr, Cys

Question 30

What amino acid is destabilizing in the alpha helix?

Answer 30

lack of H-bond donor, no phi rotation

Question 31

What amino acid is destabilizing due to high conformational flexibility?

Answer 31

Gly

Question 32

What are some properties of the beta sheet?

Answer 32

more extended conformation (zig zag) a sinlge polypeptide strand called a strand the R-groups of adjacent amino acid residues protrude in opposite direction several strand side by side, in beta conformation form a sheet

Question 33

What are stabilization forces for beta conformation and turns?

Answer 33

interstrand H-binds between adjacent backbone elements in the sheet

Question 34

Where are beta turns found?

Answer 34

found in globular proteins

Question 35

How do beta turns reverse?

Answer 35

they reverse the direction of the polymer backbone 180 degree turn

Question 36

Beta turns connect to...

Answer 36

beta strands to form an antiparallel beta sheet

Question 37

beta turns involve...

Answer 37

4 amino acid residues stabilized by a single H-bond

Question 38

What amino acids are usually found in beta turns?

Answer 38

Gly and Pro

Question 39

Every type of secondary structure can be described by...

Answer 39

their dihedral angles

Question 40

What does Ramachandran plot permit?

Answer 40

visualization of all the phi and psi angles observed in a particular protein

Question 41

A Ramachandran plot can be constructed for...

Answer 41

a single protein revealing potential secondary structures

Question 42

What amino acid is the only one that falls outside of the expected regions?

Answer 42

Gly

Question 43

Tertiary structure refers...

Answer 43

to the overall spatial arrangement of all atoms in a protein

Question 44

Amino acids that are far apart in the sequence and appear in different secondary structures interact...

Answer 44

the completely folded protein

Question 45

The spatial arrangement of two or more polypeptide chains to form a...

Answer 45

functional protein is known as the quaternary level of structure

Question 46

How are tertiary and quaternary structures stabilized?

Answer 46

by numerous weak interactions between amino acid and side chains

Question 47

What are classes of tertiary and quaternary structures?

Answer 47

fibrous, globular, membrane proteins, intrinsically disordered proteins

Question 48

What are characteristics of fibrous proteins?

Answer 48

filamentous or elongated form provide support, shape, and external protection formed by a single, repeating secondary element of structure insoluble in water high concentration of hydrophobic amino acid residues

Question 49

Where is a- Keratins found?

Answer 49

hair, nails and feathers

Question 50

What does the twisting in the quaternary structure?

Answer 50

it increases the strength of fiber

Question 51

The surfaces where the two a-helices touch contain...

Answer 51

hydrophobic amino acids

Question 52

The primary structure is rich in what amino acids?

Answer 52

Ala, Val, Leu, Ile, Met and Phe

Question 53

Where are the amino acids commonly found in the primary structure of fiber?

Answer 53

position A and D in the sequence

Question 54

The strength of fibrous proteins is enhanced by...

Answer 54

covalent cross-links between polypeptides at the quaternary level of structure

Question 55

Collagen found in...

Answer 55

cartilage, bones, tendons and skin

Question 56

What is silk fibroin?

Answer 56

the main protein in silk from moths and spiders

Question 57

What are some characteristics of globular proteins?

Answer 57

compact shape wide array of functions due to structural diversity function as enzymes, transport proteins, receptors, motor proteins, regulators and more soluble in water or bound to membranes may contain a combination of secondary level of structures