Chapter 5

Question 1

Parallel B-pleated Sheets

Answer 1

Both strands involved in H bonding run in the same direction

Question 2

Anti parallel B-pleated sheets

Answer 2

Strands involved in hydrogen bonds run in opposite directions, more stable

Question 3

B-turn

Answer 3

Necessary to change directions in order to define protein boundaries
-Proline and glycine occur frequently

Question 4

Ramachandran diagram

Answer 4

Predicts the types of secondary structures using the characteristic psi and phi angles.

Question 5

Tertiary Structure

Answer 5

Gives specific 3D shape to the polypeptide chain.

Stabilized by: Hydrophobic and hydrophilic interactions, salt bridges, H bonds and S-S bonds

Question 6

Quaternary Structure

Answer 6

Combination of 2 or more tertiaries, stabilized by the same interaction found in tertiary structure, regulatory proteins are often found as oligomers
- Hemoglobin consists of two alpha chains and two beta chains. The heme group in each subunit binds O for transport in the blood to the tissues

Question 7

Secondary structure of proteins

Answer 7

Indicates 3D spatial arrangements of the polypeptide chains

Question 8

Alpha Helix

Answer 8

• Coiled shape held in place by H bonds between amide groups and carbonyl groups.
• H bonds between the H of the N-H group and the O of the C=O of the fourth AA down the chain
• stabilized by H bonds
• disrupted by proline
• destabilized by bulky AA’s or charged AA’s in close proximity
• composed of L-amino acids, are right handed helices

Question 9

B-Pleated Sheet Structure

Answer 9

• consists of polypeptide chains arranged side by side
• parallel or antiparallel
• H bonds between chains
• R groups above/below sheet
• typical of fibrous proteins (silk)

Question 10

Proline’s affect on B-turn

Answer 10

-Proline can force formation of B-turn due to angle - promoting formation of antiparallel strands

Question 11

Glycine and B-Turn

Answer 11

Glycine can adapt to many structures due to lack of a side chain, Frequently found in position 3 of the turn

Question 12

Protein Folding

Answer 12

1. Polypeptide emerges from ribosome, short segments fold into 2’ structural units. Proline dis-trans isomerases involved in B-turn formation at this stage.
2. Appropriate arrangement of 2’ structural elements into domains by chaperones such as Hsp60 & Hsp70. Chaperones segregate hydrophobic regions into the interior away from solvent
3. Protein disulfide isomerases stabilize tertiary and quaternary structures forming the mature conformation of the protein

Question 13

Denaturation of Proteins

Answer 13

• Loss of biological activity of a protein due to disruption off its 2’, 3’, or 4’ structure while maintaining primary structure.

Question 14

Things that cause Denaturation

Answer 14

• Heat and organic compounds that break H bonds and disrupt hydrophobic interactions.
• Acids and bases that break H bonds between polar R groups and disrupt ionic bonds.
• Heavy metal ions that react with S-S bonds to form aggregates
• Agitation such as whipping that stretches peptide chains until bonds break

Question 15

Protein Folding Diseases

Answer 15

• Caused by breakdowns in the bodies ability to fold proteins
• ALS
• Alzheimer’s
• Parkinson’s
• Huntington’s
• Prions

Question 16

Endosome-Lysosome Pathway

Answer 16

Degrades extracellular and cell-surface proteins

Question 17

Ubiquitination-proteasome pathway

Answer 17

Degrades proteins from the cytoplasm, nucleus, and ER

Question 18

What 2 things have their own proteolytic system of bacterial origin?

Answer 18

Mitochondria and chloroplasts

Question 19

Ubiquitin - Proteasome Pathway Steps

Answer 19

E1 - ubiquitin activating enzyme uses ATP to activate the carboxyl group of ubiquitin’s C-terminal residue (Gly76) and forms a thioester between Gly76 of ubiquitin’s and a cysteine residue of E1
E2- ubiquitin conjugating enzyme accepts the ubiquitin from the E1 through a thioester linkage with a cysteine
E3 - ubiquitin ligase transfers the ubiquitin molecule to the epsilon NH2 group of lysine on the substrate. Ubiquitin is then added in succession to the Lysine 48 residue to form a multiubiquitin chain
- DUB enzyme recycles ubiquitin
- 26S Proteasome degrades the substrate to peptides.

Question 20

Fibrous Proteins

Answer 20

• have polypeptide chains arranged in long strands or sheets, typically of one type of 2’ . Axial ration of >10.
• Collagen
• Elastin
• Keratin( both alpha and beta)

Question 21

Globular Proteins

Answer 21

-have polypeptide chains that are folded in a spherical shape, composed of several types of 2’. Axial ration

Question 22

Collagen

Answer 22

Most abundant fibrous protein (30%) in mammals, skin, connective tissue, bone

• Helps hold cells together, provides thermal stability, mechanical strength, and involved in cell adhesion and migration.
• basic unit is tropocollagen
• 1/3 Gly, Gly-X-Y
• High in Pro

Question 23

Novel Amino Acids in Collagen

Answer 23

4-hydroxyproline, 3-hydroxyproline, and 5-hydroxylysine

• their hydroxyl groups facilitate intra-chain H bonding stabilizing 3D structure
• they are not incorporated as is but enzymatic ally after translation by post-translational processing.

Question 24

Fibrillation collagens

Answer 24

Synthesized inside fibroblasts (connective tissue) and osteoblasts (bone) and chondroblasts (cartilage).

Question 25

Lathyrism and Scurvy

Answer 25

Lathyrism- improper formation of crosslinks

Scurvy - vitamin C deficiency

Question 26

Collagen type 1 and 2

Answer 26

1 - skin, tendon, bone, cornea, lung, vasculature, and is component of scar tissue.
2 - cartilage

Question 27

Non fibrillation collagen type 4 and collagen type 3

Answer 27

4 - basement membrane collagen, found at tissue boundaries.

3 - elastic tissues such as embryonic skin, lungs, and blood vessels.

Question 28

Elastin

Answer 28

Found in elastic tissues and allows tissues in the body to resume their shape after stretching or contracting (lungs, arteries, skin, ligaments, and bladder)
-In arteries it acts as a medium for pressure wave propagation to help blood flow and is particularly abundant in large elastic blood vessels such as the aorta

Question 29

Elastin Crosslinks

Answer 29

Tropoelastin is the basic unit (gly, Val, Ala, Pro)

- Has Algol, lysinoroleucine, des onside, or isodesmosine crosslinks catalyze do by Lysyl oxidase.

Question 30

Alpha-1 antitrypsin

Answer 30

Inhibits several proteases.

• made in liver and also by monocytes and macrophages
• inhibits elastase which can destroy elastin of the alveolar walls of lungs
• Protects from emphysema
• smoking inactivates alpha-1 antitrypsin by oxidizing methionine