Protein Structure

Question 1

What are three names for the bonds that hold primary structures of proteins together?

Answer 1

Covalent Bonds
Peptide Bonds
Amide Bonds

Question 2

What can an amide bond be thought of as?

Answer 2

Two amino acids joining together

Question 3

What is the name for a protein with two amino acids combining?

Answer 3

Di-peptide

Question 4

What is the name for a protein with three amino acids combining?

Answer 4

Tri-peptide

Question 5

What are the two termini on a peptide?

Answer 5

There is an N-terminus (nitrogen) and a C-terminus (carboxylic acid)

Question 6

Do proteins have a secondary structure?

Answer 6

Yes

Question 7

What is a protein’s secondary structure determined by?

Answer 7

The patterns of hydrogen bonds that can occur between linear sequences of amino acids (the primary structure)

Question 8

How many types of secondary structures are there?

Answer 8

Two

Question 9

What are the two types of secondary structures?

Answer 9

Alpha-helix

Beta-Sheets

Question 10

What do Hydrogen bonds or ionic interactions between every 3-4 amino acid’s residue cause?

Answer 10

The peptide to bend

Question 11

How do side chains act around the helix?

Answer 11

Side chains point out from the helix

Question 12

What is the structure of alpha-helices formed by peptides controlled by?

Answer 12

Amino acids structure and the geometry of the amide bond

Question 13

What hybridisation are chiral centres?

Answer 13

They are always sp3

Question 14

Describe beta-sheets

Answer 14

They are perfectly flat. They have a Zig-zag structure, where peptides are linked by H-bonds. Polypeptide chains are linked either anti-parallel or parallel to each other

Question 15

How can secondary structures be stabilised?

Answer 15

By di-sulfide bonds

Question 16

What does oxidation between the two thiol groups in a secondary structure generate?

Answer 16

A disulfide link

Question 17

What does a disulfide link between two cysteine residues cause?

Answer 17

A loop in the peptide

Question 18

When does repulsion occur in a protein?

Answer 18

When there is repulsion between adjacent groups (e.g. if they are protonated at the same pH)

Question 19

What is the tertiary structure of a protein?

Answer 19

The overall geometric shape

Question 20

What are the possible structures of tertiary proteins?

Answer 20

Some are mostly β-sheet

Many are a mix of α-helices and β-sheets.

Question 21

What do R-Sheets do in order to stabilise the protein in its final three-dimensional (or tertiary) structure?

Answer 21

Participate in both covalent and noncovalent interactions

Question 22

What is the quarternary structure of a protein?

Answer 22

The arrangement of multiple folded proteins, or coiling protein molecules in a multi-subunit complex