Primary and Secondary Protein Structures (Zhao L2)

Question 0

What are the two main types of secondary structures in proteins?

Answer 0

1. Alpha helix

2. Beta sheet

Question 1

What is the primary structure of a protein?

Answer 1

The aa. sequence

Question 2

How many high energy bonds are required to form one peptide bond?

Answer 2

Four

2 for “charging” the tRNA (ATP –> AMP + PPi)
1 for charged tRNA to enter A site (GTP –> GDP)
1 for translocation of the whole shebang (GTP –> GDP)

Question 3

Why is the peptide bond so strong?

Answer 3

Partial double bond character

side note: Does not rotate - peptide plane :)

Question 4

Which angle is the phi angle?

Answer 4

Angle of the

alpha carbon - amide nitrogen

bond

Question 5

Which angle is the psi angle?

Answer 5

angle of the

Alpha carbon - Carbonyl carbon

bond

Question 6

What is the difference between an “peptide” and a “protein”?

Answer 6

“peptides” just refers to a really short polypeptide chain

“protein” is a longer polyeptide + possible cofactors

Question 7

What is a co-factor in the realm of proteins?

Answer 7

Functional non-amino acid component

Question 8

What is a prosthetic group in the realm of proteins?

Answer 8

A covalently attached non-amino acid component

Question 9

How many amino acids are “changed” in sickle cell anemia?

Answer 9

One!

E6V

Question 10

What is a protein polymorphism?

Answer 10

Slightly different (non-disease causing) sequence of same protein in different individuals.

Is how we get our individual traits.

Question 11

Give an example (from lecture) of a protein that is used to trace the evolutionary connections between various species.

Answer 11

Cytochrome C

Same function, similar aa sequence. The diff. in aa. seq. from species to species determines how far they are, evolutionarily, from one another.

Question 12

What is a protease or a peptidase?

Answer 12

Enzyme that hydrolyzes peptide bonds. “Digest” proteins.

Question 13

Where in the body might we need proteases/peptidases that will digest at a specific aa. but within any protein?

What are some examples of these proteases?

Answer 13

Digestive system.

Pepsin, Trypsin
Submaxillarus protease
Chymotrypsin

Question 14

What are some examples of proteases that digest only specific proteins or peptides?

Answer 14

HIV protease

Angiotensin Converting Enzyme (ACE)

Question 15

Name some examples of proteins that are synthesized in their inactive form and are later cleaved to their active state.

Answer 15

Trypsin, chymotrypsin
Insulin
Compliment enzymes
Clotting enzymes
Trxn factors
Programmed Cell Death proteins

Question 16

How is insulin activated?

Answer 16

Preproinsulin is initially synthesized and through a series of cleavage and “maturation” steps it ends up as 2 peptide chains (chain A and B) connected via disulfide bridges.

Question 17

Primary protein structure is held together by _________ bonds. Higher order protein structures are held together by ______ bonds.

Answer 17

Covalent

Noncovalent

Question 18

What is the unique secondary protein structure present in collagens?

Answer 18

Left-handed triple helix.

Question 19

What is the main non-covalent bond that shapes the alpha helix?

Answer 19

H-bond between C=O on one aa and the N-H of the aa. 4 steps down the chain.

aa i and aa i+4

Question 20

Where are the R-groups in the alpha helix?

Answer 20

R-groups point out from the helix structure.

Question 21

What class of amino acids are typically found within the alpha helix?

Answer 21

Small hydrophobic residues. (eg. Ala, Leu)

Question 22

Which two amino acids are the “helix breakers” and why?

Answer 22

Pro and Gly

Proline has a ring side chain bonded to the backbone N. Cannot form the hydrogen bonds found in the center of the helix.

Glycine is very very small and is an energy penalty to force it into an alpha helix (or beta sheet).

Question 23

The residues that point outwards on the alpha helix are in a good position to interact with what other biological molecule?

Answer 23

DNA

Question 24

What is the main non-covalent bond found in a Beta-Sheet?

Answer 24

Hydrogen bonds between C=O in one amino acid and the N-H group on a neighboring polypeptide chain.

Question 25

What are the two main classes of Beta sheets?

Answer 25

parallel and antiparallel

antiparallel: one chain N–>C, neighboring chain C—>N
parallel: both N—-> C

Both have a pleated sheet-like structure

Question 26

Where are the side chains positioned in the Beta sheet?

Answer 26

Side chains alternate pointing up and down from the main axis of the sheet.

Question 27

Give some examples of proteins composed mostly of beta sheets.

Answer 27

Fibrion - silk, spider webs

Immunoglobulin (Ig, antibody)
Fibroblast growth factor
Pepsin
HIV protease

Question 28

Describe the secondary/tertiary structure of an immunoglobin domain

Answer 28

Two beta sheets. One with 3 antiparallel beta strands, the other with 4 antiparallel beta strands.
Sheets connected by disulfide bonds.
Beta strands connected by loops and turns (where the recognition site is !)

Question 29

_______ measures the absorption (R/L polarized light) of a protein’s secondary structures.

How is this useful?

Answer 29

Circular Dichroism (CD)

Knowing the absorbances of a particular sec. structure and measuring the absorb. of a protein gives you a quantitative look at its secondary structures.

Question 30

Describe the structure of a Beta Turn

Answer 30

180 degree turn between beta strands over 4 aa’s

Stabilized by H-bond between C=O of first aa and N-H of 4th aa.

Question 31

What two amino acids are common in beta turns?

Answer 31

Pro in position 2

Glycine in position 3

Question 32

Most peptides bonds are cis or trans?

How is proline unique in this regard?

Answer 32

Most are trans

Proline can be cis (6% of the time roughly)