L3 Protein Structure

Question 1

structural features of an amino acid

Answer 1

• central carbon atom
• amino group
• side chain (R/R-group)
• carboxyl group

Question 2

what are the three different categories based on chemical properties of the R group

Answer 2

1. neutral (uncharged) and nonpolar
2. neutral and polar
3. charged – acidic (negative) or basic (positive)

Question 3

polypeptide structure - what is a peptide bond

Answer 3

• covalent links between amino acid residues in a polypeptide
• form through a condensation reaction ( one water molecule is expelled)
• happens between one carboxyl group (O-) and an amino group (H)
• it has partial double-bond characteristics bc electrons are shared (makes the bond very strong and rigid)

Question 4

polypeptide structure - what are carbonyl groups

Answer 4

• C=O
• with the carbon atom bonded to two other atoms

Question 5

polypeptide structure - what are amide groups

Answer 5

• N-H
• functional group where a carbonyl carbon atom is directly linked to a nitrogen atom

Question 6

polypeptide structure - carbonyl and amide groups

Answer 6

• they are nearly coplanar and form the amide plane
• it is always in the trans configuration

Question 7

polypeptide structure - what is trans configuration

Answer 7

• most common arrangement of a peptide bond bc it is sterically favorable
• the amino acid side chains are on opposite sides of the bond

Question 8

polypeptide structure - what is cis configuration

Answer 8

• not common arrangement bc there is r group interference
• the side chains are on the same side

Question 9

define conformation

Answer 9

the arrangement of chemically bonded atoms in three dimensions

Question 10

what does the polypeptide chain conformation consist of?

Answer 10

• three repeating covalent bonds
  1) between the amide group (N-H) and central carbon (C alpha)
  2) between central carbon (C alpha) and the carbonyl group (C=O)
  3) a peptide bond between carbonyl group (C=O) and amide group (N-H)

Question 11

polypeptide chain conformation - rotational angle of bond

Answer 11

• amide group (N-H) and central carbon (C alpha) = phi (φ)
• central carbon (C alpha) and carbonyl group (C=O) = psi (ψ)
• peptide bond: amide group (N-H) and central carbon (C alpha) = omega (ω)

Question 12

polypeptide structure - what amino acids have unique properties?

Answer 12

• glycine
• proline
• cysteine

Question 13

unique properties - glycine

Answer 13

• not chiral (a type of molecule that has a non-superposable mirror image)
• has great conformational freedom (free to rotate its bonds however)

Question 14

unique properties - proline

Answer 14

• reduced hydrogen bonding potential due to absence of N-H
• least conformational freedom

Question 15

unique properties - cysteine

Answer 15

• it can form a disulfide bond by oxidation to then form cystine
• this happens bc the extracellular space has the redox potential that favors disulfide bond formation
• its common in extracellular domains of membrane proteins and in small secreted proteins (hormones)

Question 16

unique properties - cysteine and human insulin

Answer 16

• L-cysteine inhibits (restrains) insulin release
• D-cysteine controls insulin secretion

Question 17

what are the levels of protein structure

Answer 17

1. primary structure
2. secondary structure
3. tertiary structure
4. quaternary structure

Question 18

levels of protein structure - primary

Answer 18

1-D sequence of amino acids

Question 19

levels of protein structure - secondary

Answer 19

• 3-D arrangement of a short, local stretch of amino acid residues
• can be an alpha helix or a beta sheet

Question 20

levels of protein structure: secondary - alpha helix

Answer 20

• always right handed
• its stabilized by hydrogen bonds of the main chain, between the carbonyl group of one residue and amide group of another one 4 positions down

Question 21

levels of protein structure: secondary - beta sheet

Answer 21

• a pleated structure stabilized by hydrogen bonds between the main chains of amide and carbonyl groups
• the groups project laterally
• R groups project alternatively to either side of the backbone
• the strands run in parallel or anti-parallel arrangement

Question 22

levels of protein structure - tertiary structure

Answer 22

• overall 3-D folded arrangement polypeptide chain adopts under physiological conditions
• stabilized by interactions involving R groups

Question 23

levels of protein structure: tertiary structure - what are the R group interactions

Answer 23

• hydrogen bonds (OH-O or OH-N)
• hydrophobic interactions
• disulfide bonds (S-S)
• ionic bonds

Question 24

levels of protein structure - quaternary structure

Answer 24

manner in which individual folded chains associate with themselves

Question 25

explain how protein structure is heirarchial

Answer 25

- quaternary structure is based on tertiary structure, which is based on secondary structure - all three higher order structures depend on primary structure

Question 26

what are some examples of post-translational modifications

Answer 26

- phosphorylation - lipidation - ubiquitination - disulfide bond - acetylation - glycosylation

Question 27

post-translational modifications - phsophorylation

Answer 27

- can activate the protein by adding a phosphate via kinase - can turn off the protein by cleaving it off via phosphatase

Question 28

why is protein folding important

Answer 28

the amino acid sequence of a domain determines its table, functional (or native) structure

Question 29

protein folding - explain Anfinsen's experiment (1960s)

Answer 29

- studied the folding of Ribonuclease A (has 8 cystine residues that form 4 disulfide bonds)

Question 30

Anfinsen experiment (1960s) - what was the question asked

Answer 30

- can the protein refold after being denatured outside of the cell - if yes, then everything needed to fold the protein is in the primary structure

Question 31

Anfinsen experiment (1960s) - how do you unfold Ribonuclease A

Answer 31

- you will need a: 1) denaturant to disrupt hydrogen bonding (urea, guanidine hydrochloride, etc.) 2) reducing agent to disrupt the disulfide bridges (beta-mercaptoethanol, etc.)

Question 32

Anfinsen experiment (1960s) - what happened in the experiment

Answer 32

1) used urea and beta-me to denature the protein 2) then either removed denaturant and reducing against together or separately

Question 33

Anfinsen experiment (1960s) - results of taking out reducing agent then denaturant

Answer 33

- the cysteine (disulfide) bonds reform first then the hydrogen - this is a problem bc it brought it back to the tertiary structure first - results in a scrambled protein

Question 34

Anfinsen experiment (1960s) - results of taking out reducing agent and denaturant together

Answer 34

- hydrogen bonds form first - results in native conformation

Question 35

Anfinsen experiment (1960s) - was the hypothesis correct

Answer 35

- yes, the protein will refold outside of the cell - so everything needed is within the primary structure - but you need to allow the protein to form the secondary structure first

Question 36

Anfinsen experiment (1960s) - significance of results

Answer 36

1) Emphasizes hierarchical nature of protein structure 2) Polypeptides can fold correctly without additional cellular machinery 3) Nucleic acid sequence specifies not only amino acid primary sequence, but also the tertiary structure and ultimately the function of the protein

Question 37

explain why protein misfolding is important

Answer 37

- it can be "infectious" - the abnormal version (prion) induces a conformational change in the normal protein to adopt its infectious shape

Question 38

protein misfolding - what is a prion

Answer 38

- "proteinaceous infectious particles" - they are improperly folded forms of normal protein - the amino acid sequence does not differ