KH3

Question 1

What’s another name for proteins?

Answer 1

“polypeptides”

Question 2

What’s the biological purpose of DNA and RNA?

Answer 2

To allow the synthesis of proteins which carry physical/chemical functions of cells

Question 3

What’s the average protein length? Smallest? Biggest?

Answer 3

300-400 // 40 // 30 000 (“Titin”)

Question 4

What’s the primary structure of proteins?

Answer 4

The order/sequence of their amino acids

Question 5

True or False? “Most proteins are rod-like or snake-like in shape”

Answer 5

False. They have their own unique 3D shape given by their primary structure.

Question 6

Define hydrophilic

Answer 6

“Water loving”. Polar or charged groups that interact well with water (polar solvent)

Question 7

Define hydrophobic

Answer 7

“Water fearing”. Non-polar groups that don’t interact well with water (polar solvent).

Question 8

True or False? “It’s energetically favorable to keep non-polar particles apart in a polar medium”

Answer 8

False. Coalescence/Aggregation is better since more substance gets trapped within less total particles (leaves extra to flow freely). Also favored by Van der Waals.

Question 9

From a general point of view, how do all proteins fold?

Answer 9

According to the oil drop model: hydrophilic outside and hydrophobic inside. (“Hydrophilic Shell”)

Question 10

What does the Oil Drop model not account for?

Answer 10

Endless ways of achieving a Hydrophilic Shell but proteins only really adopt one or few structures in reality (“conformations”).

Question 11

True or False? “Secondary and tertiary structures determine the path of the backbone through space”

Answer 11

True

Question 12

Briefly differentiate secondary and tertiary structures

Answer 12

Secondary : local folding // Tertiary : final shape

Question 13

What are domains in protein structure?

Answer 13

Regions of the chain that you could cut and they’d keep their shape (due to strong interactions within that area). Compact, usually longer than 40 monomers.

Question 14

Define quaternary protein structure?

Answer 14

3D shape of multiple proteins interacting together.

Question 15

True or False? “DNA directly dictates the protein function”

Answer 15

False. It’s indirect: DNA –> monomer order –> 3D shape –> function

Question 16

What’s the directionality of a protein?

Answer 16

N terminus to C terminus

Question 17

What are the two major secondary conformations?

Answer 17

Alpha-helices and beta-sheets (account for 60% of chain length)

Question 18

What holds secondary structures together?

Answer 18

Hydrogen bonds between carbonyl O and amino H.

Question 19

True or False? “Surface properties of proteins only depend on side chains”

Answer 19

True. They stick out.

Question 20

What’s the effect of side chains on protein structure?

Answer 20

They influence conformation strength and how likely they are to form (affect interactions strength).

Question 21

True or False? “Beta-sheets link adjacent, antiparallel or parallel strands through H-bonds?”

Answer 21

True, which creates large flat surfaces.

Question 22

What are interactions that contribute to tertiary structure but not secondary?

Answer 22

Ionic bonds, Van der Waals, covalent bonds (S-S, “disulfide bridge)

Question 23

True or False? “Disulfide bonds could be both intrachain and interchain (quaternary structure)”

Answer 23

True

Question 24

What are motifs in protein structure?

Answer 24

Distinct and local 3D structures: heptad repeat, Ca binding, Zinc finger. Not structurally independent (too small).

Question 25

What are the four major structural protein classes?

Answer 25

“Fibrous” (linear), “Globular”, “Integral membrane” and “Intrinsically disordered” (exist as random coils until binds to partner protein).

Question 26

What are supramolecular complexes?

Answer 26

Large “molecular machines” made of many distinct proteins.

Question 27

True or False? “Protein structure, especially tertiary, can reveal ancient evolutionary relationships”

Answer 27

True