Lecture 02

Question 1

Define primary structure of a protein

Answer 1

The linear sequence of amino acids

Question 2

Define secondary structure

Answer 2

Formed from interactions between the atoms of the peptide bond backbone

Question 3

What are the four classes of protein secondary structure?

Answer 3

Alpha-helix, beta-sheet, beta-turn, loop

Question 4

Describe an alpha-helix

Answer 4

Tightly coiled rod-like structure with backbone atoms in the center and R groups projecting outward

Question 5

How is the alpha-helix stabilized?

Answer 5

Hydrogen bonding between the carbonyl oxygen of amino acid (i) and the amide hydrogen of the peptide bond at amino acid (i + 4)

Question 6

How many amino acids per helical turn of an alpha-helix?

Answer 6

3.6

Question 7

What is the typical screw direction of alpha-helices?

Answer 7

Right-handed

Question 8

Describe the structure of beta-sheets

Answer 8

Continuous, linear segment of the primary sequence where amino acids alternate pointing the side chains in opposite directions

Question 9

What are the 2 major classes of beta-sheets?

Answer 9

Antiparallel and parallel

Question 10

How do the 2 classifications of beta-sheets differ in their H-bonds?

Answer 10

Antiparellel has linear H-bonds, parallel has bent H-bonds

Question 11

How does the primary sequence of a beta-sheet compare to an alpha-helix?

Answer 11

Beta-sheets can involve amino acids that are relatively far from each other in the primary sequence

Question 12

Describe a beta-turn and loop

Answer 12

Both link successive runs of helices or strands and indicate a directional change for the polypeptide chain.

Question 13

What amino acids are typically involved in a beta-turn?

Answer 13

Gly and Pro

Question 14

Describe the structure of a beta-turn

Answer 14

4 amino acids in which the first carbonyl oxygen and the last alpha-nitrogen H-bond.

Question 15

Loops

Answer 15

Do not follow defined patterns but contribute important functionality.

Question 16

Name the amino acids known as alpha-helix breakers

Answer 16

Proline and glycine

Question 17

Why is proline a helix breaker?

Answer 17

Rotation around the alpha-carbon-nitrogen bond is not possible due to the presence of a secondary amine

Question 18

Why is glycine a helix breaker?

Answer 18

Glycine has no R group and therefore has no preferred structure, which compromises stability

Question 19

Define tertiary structure

Answer 19

Created from interactions between the R groups of different amino acids, or an R group and atoms of the backbone

Question 20

Tertiary structure motifs

Answer 20

Alpha-helix bundles, beta-sheet barrels, alpha/beta barrels

Question 21

Give an example of proteins with a helical configuration

Answer 21

Integral membrane proteins

Question 22

Give an example of proteins with beta-barrel structures

Answer 22

Porins of the mitochondrial outer membrane

Question 23

Why is the shape of a beta-barrel significant?

Answer 23

It allows for the molecules of the cytoplasm to communicate with the outside environment

Question 24

Name 2 classes of protein tertiary structures

Answer 24

Fibrous and globular proteins

Question 25

Properties of fibrous proteins

Answer 25

Extended rod or wire shapes, insoluble in aqueous solution, disulfide links common

Question 26

Examples of fibrous proteins

Answer 26

Keratins, collagen, elastin, myosin

Question 27

Properties of globular proteins

Answer 27

Compact globe-like shape, can by hydrophilic or hydrophobic

Question 28

Define quaternary structure of a protein

Answer 28

Assembly of individual monomeric protein into a larger functional cluster

Question 29

Homo-oligomers vs. Hetero-oligomers

Answer 29

Same versus different monomers

Question 30

What is a molten globule?

Answer 30

Somewhat compact state of a protein formed during protein folding; believed to be the starting point for the exploration of tertiary structure

Question 31

What is the major force driving 3D folding?

Answer 31

Hydrophobic effect

Question 32

Define the hydrophobic effect

Answer 32

Spontaneous aggregation of hydrophobic molecules in water; driven by entropy

Question 33

Define entropy

Answer 33

The amount of disorder within a system determined by freedom of motion

Question 34

Define hydration shell

Answer 34

Caused by water molecules surrounding a solute; allows water molecules to interact with the solute from different angles

Question 35

How exactly does the hydrophobic effect increase entropy?

Answer 35

Water cannot align itself with nonpolar molecules/regions, aggregating nonpolar molecules makes the hydration shell smaller

Question 36

Describe a challenge to protein folding in vivo

Answer 36

Immature protein may come into contact with other proteins after exiting the ribosome, causing them to interact and for the immature protein to fold incorrectly

Question 37

What is the solution to the challenges associated with protein folding in vivo?

Answer 37

Molecular chaperones

Question 38

What are two ways molecular chaperones can prevent protein misfolding?

Answer 38

Either the chaperone binds to a specific region of the polypeptide of it forms a larger complex that surrounds the polypeptide and lets it fold inside

Question 39

What are 2 phenotypes caused by defective proteins?

Answer 39

Loss of function and gain of pathology

Question 40

What is an amyloid plaque?

Answer 40

Aggregate of diseased proteins

Question 41

What does the name "prion" represent?

Answer 41

Proteinacious infectious particle

Question 42

What does TSE stand for?

Answer 42

Transmissible spongiform encephalopathies

Question 43

Break down the name TSE

Answer 43

Transmissible - prion infection is transmitted by exposure to the defective protein Spongiform - creates white, vacant areas of tissues due to degeneration Encephalopathies - brain diseases

Question 44

What is the source of the prion that causes TSEs in humans?

Answer 44

PrPc, normally located at the surface of neuronal cells

Question 45

What is the function of PrPc?

Answer 45

Not clear, but it's been proposed that it may be linked to the deposition of myelin.

Question 46

What is the name of the prion form of PrPc?

Answer 46

PrPSC

Question 47

Properties of PrPSC

Answer 47

Much more stable relative to PrPc, self-associates through intermolecular beta-sheets (this causes aggregation)

Question 48

How did Kuru emerge?

Answer 48

Cannibalism; eating infected brain tissue