Chapter 4

Question 1

What are the 4 levels of protein structure?

Answer 1

Primary, second, tertiary, quaternary

Question 2

What does primary structure consist of?

Answer 2

Sequence of amino acids linked together by peptide bonds

Question 3

What do amino acid sequences have?

Answer 3

Direction

Question 4

How is primary structure written?

Answer 4

From the amino terminal to the carboxyl terminal, or left to right

Question 5

What are the components of a polypeptide chain?

Answer 5

Polypeptide chain consists of a regularly repeating part called backbone and variable side chains

Question 6

Explain the peptide bond in the primary structure.

Answer 6

Peptide bond has partial double-bond character.
Resonance hybrid of 2 canonical structures.
Resonance causes the peptide bonds to be quite rigid and nearly planar: rotation about the bond is prohibited.

Question 7

How are peptide bonds planar?

Answer 7

In a pair of linked amino acids, 6 atoms (C alpha, C, O, N, H, and C alpha) lie in a plane

Question 8

What are the two configurations possible for a planar peptide bond?

Answer 8

Trans and Cis.
Almost all peptide bonds in proteins are trans (there are steric clashes between R groups in the cis configuration)

Question 9

Explain how the polypeptide is made up of a series of planes linked at alpha carbons.

Answer 9

Three bonds separate sequential alpha carbons in a polypeptide chain. The N - C alpha and C alpha - C bonds can rotate. The peptide C - N bond is not free to rotate.

Question 10

Explain disulfide bonding of polypeptide chains.

Answer 10

In some proteins, polypeptide chain can be cross-linked by disulfide bonds.
Disulfide bonds form by the oxidation of 2 cysteines.
Resulting unit of 2 linked cysteines is called cystine.

Question 11

Explain secondary structures.

Answer 11

Secondary structure arises from the hydrogen bonds formed between atoms of the backbone. It is a regular local spatial arrangement of the polypeptide backbone.
2 regular arrangements are common:
- Alpha helix: stabilized by hydrogen bonds between nearby residues.
- Beta pleated sheet: stabilized by hydrogen bonds between adjacent segments that may not be nearby.
Third common arrangement in secondary structure are loops.

Question 12

Explain the alpha helix.

Answer 12

Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n+4 amino acids.
Right-handed helix with 3.6 residues (5.4 A) per turn.
Peptide bonds are aligned roughly parallel with the helical axis.
Side chains point out and are roughly perpendicular with the helical axis.

Question 13

Explain the hydrogen-bonding scheme for an alpha helix.

Answer 13

In the alpha helix, the CO group of residue i forms a hydrogen bond with the NH group of residue i+4

Question 14

How does sequence affect helix stability?

Answer 14

Not all polypeptide sequences adopt alpha-helical structures.
Small hydrophobic residues such as Alanine and Leucine are strong helix formers.
Proline acts as a helix breaker because the rotation around the N-Ca bond is impossible.
Glycine acts as a helix breaker because the tiny R group supports other conformations.
Attractive or repulsive interactions between side chains 3 to 4 amino acids apart will affect formation.

Question 15

What is ferritin?

Answer 15

Iron-storage protein; built from a bundle of alpha helices.

Question 16

Explain beta-sheets.

Answer 16

Beta-sheet is another common form of secondary structure.
Beta sheets are formed by adjacent beta-sheets.
In contrast to an alpha-helix, the polypeptide in a beta-strand is fully extended.
Side chains are alternatively above and below the plane of the strand.
Planarity of the peptide bond and tetrahedral geometry of the beta carbon create a pleated sheet-like structure.
Sheet-like arrangement of the backbone is held together by hydrogen bonds between the backbone amides in different strands.
Side chains protrude from the sheet, alternating in an up-and-down.

Question 17

Explain parallel and antiparallel beta sheets.

Answer 17

Multi beta-strand interactions are called sheets.
Sheets are held together by the hydrogen bonding of amine and carbonyl groups of the peptide bond from opposite strands.
Two major orientations of beta sheets, antiparallel and parallel, are determined by the directionality of the strands within.
In parallel beta sheets, the H-bonded strands run in the same direction: hydrogen bonds between strands are bent (weaker).
In antiparallel beta sheets, the H-bonded strands run in opposite directions: hydrogen bonds between strands are linear (stronger).

Question 18

What is fibroin?

Answer 18

Protein of silk, produced by insects and spiders. Consists of layers of antiparallel beta-sheets.

Question 19

Explain beta turns.

Answer 19

Beta turns occur frequently whenever strands in beta sheets change the direction.
The 180 degree turn is accomplished over 4 amino acids.
Turn is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three reisidues down the sequence.
Proline in position 2 or glycine in position 3 are common in beta turns.

Question 20

What is protein tertiary structure?

Answer 20

Tertiary structure refers to the spatial arrangement of amino acids that are far apart in the primary structure.
Stabilized by numerous weak interactions between amino acid side chains.
- Largely hydrophobic and polar interactions.
- Can be stabilized by disulfide bonds.
Interacting amino acids are not necessarily next to each other in the primary sequence.

Question 21

What are water-soluble globular proteins?

Answer 21

Globular proteins, such as myoglobin, form complicated three-dimensional structures.
Globular proteins are very compact. There is little or no empty space in the interior of globular proteins.
Interior of globular proteins consists mainly of hydrophobic amino acids.
Exterior of globular proteins consists of charged and polar amino acids.

Question 22

What is quaternary structure?

Answer 22

Many proteins are composed of multiple polypeptide chains called subunits.
Proteins are said to display quaternary structure.

Question 23

What are the fibrous proteins and what do they do?

Answer 23

Fibrous proteins provide structural support for cells and tissues.
Fibroin: protein of silk, produced by insects and spiders. - Consists of layers of antiparallel beta-sheets.
Alpha-Keratin: structural protein found in horns, wool, and hair of mammals.
- Composed of 2 right-handed alpha-helices intertwined to form a left-handed super helix called a coiled-coil.
- Belongs to the protein family named Intermediate Filaments (IF). Other IF proteins are found in the cytoskeletons of animal cells.
Collagen: main protein of connective tissue.
- Component of skin, bone, tendons, cartilage, and teeth.
- Consists of three intertwined helical polypeptide chains that form a super helical cable. Helical polypeptide chains of collagen are not alpha-helices.

Question 24

What is alpha-keratin?

Answer 24

Alpha-keratins are the major proteins of hair, fingernails, claws, horns, hooves, and much of the outer layer of skin.
Alpha-keratins are members of a broad group of Intermediate Filament proteins.
Intermediate filaments are part of the cytoskeleton.
Alpha-keratin consists of two right-handed alpha-helices intertwined to form a left-handed superhelix called a coiled coil.

Question 25

What is collagen and its structre?

Answer 25

Collagen: main fibrous protein of connective tissue.
Different type of helix is present in collagen - left-handed.
Three polypeptides are super twisted about each other.
Helical polypeptide chains of collagen are not alpha-helices.
Helices in collagen are not stabilized by hydrogen bonds. They are stabilized by steric repulsion of the pyrrolidine rings of proline. Three intertwined chains interact with one another with hydrogens bonds.
Interior of the superhelical cable is crowded, and only glycine can fit in the interior.

Question 26

Explain the clinical insight about defects in collagen structure result in pathological conditions.

Answer 26

Hydroxyproline, modified version of proline where a hydroxyl group replaces a hydrogen, is important for the stabilization of collagen.
Vitamin C is required for the formation of hydroxyproline. Lack of vitamin C results in scurvy because the body can’t produce hydroxyproline.

Question 27

Explain intrinsically disordered proteins.

Answer 27

Over 30% of proteins have this.
Contain protein segments that lack definable structure.
Composed of amino acids whose higher concentration forces less-defined structure.
- Lys, Arg, Glu, and Pro.
Disordered regions can conform to many different proteins, facilitating interaction with numerous different partner proteins.