Proteins

Question 1

What interactions are involved in the protein native fold?

Answer 1

Hydrophic, hydrogen bonds, van der waals, and electrostatic interactions

Question 2

Primary structure

Answer 2

Amino acid sequence. Structure is partially dictated by the properties of the peptide bond.

Question 3

Phi rotation

Answer 3

Angle around the alpha carbon and amide nitrogen bond.

Question 4

Psi rotation

Answer 4

Angle around the alpha carbon and carbonyl carbon.

Question 5

What determines the secondary structure of the protein?

Answer 5

The organization around the peptide bond and the identity of the R groups. Refers to spatial arrangement of the polypeptide backbone.

Question 6

2 arrangements of secondary structure

Answer 6

Alpha helix and beta sheet

Question 7

Alpha helix is stabilized by…

Answer 7

Hydrogen bonds between near by residues.

Question 8

Beta sheet is stabilized by…

Answer 8

Hydrogen bonds between adjacent segments that may not be near by.

Question 9

Random coil

Answer 9

Irregular arrangement of the polypeptide chain.

Question 10

What is the helical backbone of a protein held together by?

Answer 10

Hydrogen bonds between the backbone amides of n and n+4 amino acids.

Question 11

How many residues per turn?

Answer 11

3.6

Question 12

Outside cell environment is…

Answer 12

Oxidizing, disulfide bonds form.

Question 13

Inside cell environment is…

Answer 13

Reducing.

Question 14

Protein with the lowest free energy =

Answer 14

Most stable, one with maximum weak interactions.

Question 15

How are peptide bonds aligned with the helical axis?

Answer 15

Roughly parallel. So are H-bonds.

Question 16

How are side chains aligned with the helical axis?

Answer 16

Roughly perpendicular.

Question 17

Which hydrophobic residues are strong helix formers?

Answer 17

Ones with small hydrophobic residues such as Ala and Leu.

Question 18

Which amino acids act as helix breakers?

Answer 18

Proline, because rotation around N-C bond is impossible. Glycine because tiny R group supports other conformations.

Question 19

How is the large dipole moment of the alpha helix enhanced?

Answer 19

By unpaird amides and carbonyls near the ends of the helix.

Question 20

Where do negatively charged residues occurs in the helix?

Answer 20

Near the positive end of the helix dipole.

Question 21

How do side chains sit in the beta sheet protein structure?

Answer 21

They stick out from the sheet, alternating up and down direction?

Question 22

How are beta sheets held together?

Answer 22

By the hydrogen bonding of the amide and carbonyl groups of the peptide bond from opposite strands.

Question 23

When do beta turns occur?

Answer 23

When beat sheets change direction. The 180 turn is accomplished over 4 amino acids.

Question 24

How is the beta turn stabilized?

Answer 24

By hydrogen bonds from a carbonyl oxygen to amide proton 3 residues down the sequence.

Question 25

Type I beta turn

Answer 25

Proline in position 2.

Question 26

Type II beta turn

Answer 26

Glycine in position 3.

Question 27

What is the typical connection of beta strands

Answer 27

Beta motif

Question 28

What stabilizes protein secondary structure?

Answer 28

Numerous weak interactions between amino acid side chains. Mostly hydrophobic and polar interactions, can sometimes be disulfide bonds.

Question 29

Fibrous proteins

Answer 29

Form of protein teritary structure.

Question 30

Silk fibroin

Answer 30

Antiparallel beta sheet, small Ala and Gly side chains allow for close packing.

Question 31

Globular proteins

Answer 31

Arrangement of multiple secondary structures. Composed of different motifs folded together.

Question 32

Intrinsically disordered proteins

Answer 32

Composed of amino acids whose higher concentration forces less-defined structure (Lys, Arg, Glu and Pro).

Question 33

Conjugated proteins

Answer 33

Covalently bound to a nonprotein entity

Question 34

Chromatography

Answer 34

Often used for separation of proteins in which the protein is able to remain fully folded.

Question 35

Column chromatography

Answer 35

Separation of proteins over a solid phase using a liquid phase to mobilize the proteins. Proteins with a low infinity for the solid phase will wash off first.

Question 36

Ion exchange chromatography

Answer 36

Separates based on net electric charge at a given pH. Column matrix contains bound charged groups, a proteins affinity to bind with that group is affected by pH.

Question 37

Cation exchange chromotography

Answer 37

Solid matrix in ion exchange has negative charges. Positive charges move more slowly.

Question 38

Size exclusion chromotography

Answer 38

Large proteins move faster because they don’t get stuck in the cavities.

Question 39

Affinity chromotography

Answer 39

Beads in the column have covalently attached ligands, speed at which a protein moves through the column depends on its affinity to bind to that ligand.

Question 40

SDS

Answer 40

Sodium dodecyl sulfate, a detergent to facilitate protein unfolding so they can be separated by molecular weight. Gives all proteins a uniform negative charge, so rate of movement will only depend on size.

Question 41

Isoelectric focusing

Answer 41

A pH gradient is established and proteins migrate until they reach the pH that matches its pI.

Question 42

2D electrophoresis

Answer 42

Combines isoelectric focusing and SDS. Separates identical MW that differ in pI or similar pI that differ in MW.

Question 43

Horizontal separation in 2D electrophoresis =

Answer 43

Differences in pI.

Question 44

Vertical separation in 2D electrophoresis =

Answer 44

Differences in MW.

Question 45

Specific activity ratio

Answer 45

Number of enzyme units / mg of total protein.