Biochem quiz 1 Protein Structure

Question 1

Peptide bond formation

Answer 1

condensation reaction that loses H20

Question 2

Properties of peptide bonds

Answer 2

rigid and planar, trans configuration, partial double bond character, polar but uncharged

Question 3

Which configuration is favored in rotation of peptide bonds?

Answer 3

Trans favored 1000:1 to CIS except for glycine and proline

C-N peptide bond is limited to 180degree rotation

Question 4

secondary structure

Answer 4

3d arrangement of main chain atoms, all polypeptide chain have secondary structure.

Question 5

alpha helix

Answer 5

main chain atoms wrapped helically around a central axis. Distance between adjacent carbons is 1.5, each turn made of 3.6 AA. Every C=O forms an H bond with the NH of the 4th amino acid in the sequence. INtra strand H bonds stabilize the alpha helix. R groups face the OUTSIDE. amphipathic helices- one phobic/phyllic

Question 6

Beta sheet

Answer 6

2 or more Beta strands held together by H bonds, antiparallel,

Question 7

Beta turns

Answer 7

beta turns connect adjacent strands of antiparallel beta sheets. H bond between main chain atoms of 1st and 4th AA

Question 8

tertiary structure

Answer 8

3D arrangement of all of the atoms in the protein. polypeptide chains, beta alpha beta loops

Question 9

List the factors that stabilize tertiary structure:

Answer 9

H bonds, ionic bonds/salt bridges, hydrophobic interactions, disulfide-covalent bonds

Question 10

Quaternary structure

Answer 10

arrangement of 2 or more polypeptide chains 2 alpha, 2 beta

Question 11

quaternary structure: name characteristics of globular proteins:

Answer 11

folded into spherical shapes, enzymes and reg. proteins, may contain several types of 2. structure. PFK, and hemoglobin.

Question 12

quaternary structure: name characteristics of fibrous proteins:

Answer 12

chains arranged in long strands. 2 and 3 structural components. Provides support, shape, and protection. Keratin and collagen

Question 13

What is denaturation?

Answer 13

Break down of proteins via urea to disrupt H bonds. Loss of regular secondary, tert, and quat structure. Loss of all function but can be restored if protein refolds to native confirmation.

Question 14

Each turn of the alpha helix is made of how many AA’s?

Answer 14

3.6

Question 15

primary structure

Answer 15

linear sequence held together by covalent peptide bonds

Question 16

What reaction forms a peptide bond?

Answer 16

condensation reaction- removal of H20

Question 17

Free ____ group at the beginning and free_____ at end of polymer chain

Answer 17

amino, carboxyl

Question 18

for which two AA does orientation prefer the cis confirmation?

Answer 18

Proline, glycine

Question 19

How does this cis preference affect confirmation?

Answer 19

proline and glycine disrupt certain common secondary structures and favor others.

Question 20

What affects differences in secondary structure?

Answer 20

rotation , more steric hinderance depending on the AA. Glycine has less steric hinderance due to its size.

Question 21

which bonds within the alpha helix stabilize the helix?

Answer 21

intra molecular Hydrogen bonds

Question 22

Do side chains on an alpha helix point inward or outward? what is the significance?

Answer 22

Side chains point outward so they can interact with other chemical groups

Question 23

what do turns and loops do in secondary structure?

Answer 23

turns and loops help connect repeating secondary structures

Question 24

zn fingers, alpha helicines, leucine zippers, helix-turn-helix

Answer 24

various combinations of secondary structure found in proteins

Question 25

what stabilizes secondary structure?

Answer 25

intra H bonds