Primary Structure

Question 1

What is the primary structure of a protein?

Answer 1

The primary structure of a protein refers to the sequence of amino acids joined together by peptide bonds.

Question 2

How many alpha-amino acids are used to make almost all proteins?

Answer 2

There are 20 alpha-amino acids from which almost all proteins are composed.

Question 3

Are there amino acids outside the canonical set of 20 used to make proteins?

Answer 3

Some proteins contain amino acids outside the canonical set of 20, but these are produced by post-translational chemical modification.

Question 4

What are peptide bonds in proteins?

Answer 4

Peptide bonds are covalent chemical bonds that link amino acids together in a protein’s primary structure.

Question 5

What is post-translational modification in proteins?

Answer 5

Post-translational modification refers to the chemical modification of a protein that occurs after it has been synthesized from RNA, including modifications to the amino acid sequence or the addition of chemical groups to the protein.

Question 6

What is the significance of a protein’s primary structure?

Answer 6

The primary structure of a protein determines its overall shape and function, as well as how it interacts with other molecules in the body.

Question 7

What is the essential structure of an alpha-amino acid?

Answer 7

The essential structure of an alpha-amino acid is an amine group (-NH2) and a carboxyl group (-COOH) attached to the same carbon (the alpha carbon).

Question 8

What is chirality?

Answer 8

Chirality is a property of molecules that have mirror-image forms (enantiomers).

Question 9

What is the chirality of naturally forming amino acids?

Answer 9

Naturally forming amino acids are L(S) enantiomers, meaning that they have a left-handed chirality.

Question 10

What is the significance of chirality in amino acids?

Answer 10

The chirality of amino acids is important because it determines how they interact with other molecules in the body and affects the function of proteins.

Question 11

Can enzymes produce D(R) amino acids?

Answer 11

Yes, some enzymes can produce D(R) amino acids, which are mirror-image forms of the naturally occurring L(S) amino acids.

Question 12

What is the only difference between each amino acid?

Answer 12

Each amino acid differs only in the identity of the substituent or R sidechain.

Question 13

What is an example of an amino acid with an R sidechain that is a hydrogen atom?

Answer 13

Glycine is an amino acid with an R sidechain that is a hydrogen atom.

Question 14

What is an example of an amino acid with an R sidechain that is a methyl group (-CH3)?

Answer 14

Alanine is an amino acid with an R sidechain that is a methyl group (-CH3).

Question 15

How does the identity of the R sidechain affect the properties of an amino acid?

Answer 15

The identity of the R sidechain can significantly affect the properties of an amino acid, such as its polarity, charge, and hydrophobicity.

Question 16

What are some other examples of amino acids and their R sidechains?

Answer 16

Some examples of amino acids and their R sidechains include serine (-CH2OH), arginine (-NH(CH2)3NH2), and phenylalanine (-C6H5).

Question 17

What determines a protein’s three-dimensional structure?

Answer 17

The physical and chemical properties of the sidechains in a protein’s amino acids determine its three-dimensional structure.

Question 18

What is the term used to describe the physical and chemical properties of the sidechains in a protein’s amino acids?

Answer 18

The term used to describe the physical and chemical properties of the sidechains in a protein’s amino acids is “physicochemical” properties.

Question 19

Why is the three-dimensional structure of a protein important?

Answer 19

The three-dimensional structure of a protein is important because it determines its function.

Question 20

What is a peptide bond?

Answer 20

A peptide bond is a covalent bond that forms between the carboxyl group (-COOH) of one amino acid and the amino group (-NH2) of another amino acid, resulting in the release of a molecule of water. Peptide bonds link amino acids together to form polypeptide chains, which can ultimately fold into proteins.

Question 21

What are the values of phi and psi in a peptide bond?

Answer 21

Phi (f) and psi (y) are angles that describe the orientation of adjacent amino acid residues in a polypeptide chain. Phi is the angle around the N-Cα bond, and psi is the angle around the Cα-C’ bond. The values of phi and psi are constrained to certain ranges based on the steric clashes of the R group.

Question 22

What is a Ramachandran plot?

Answer 22

A Ramachandran plot is a graph that displays the distribution of phi and psi angles for amino acid residues in protein structures. The plot helps to identify which combinations of phi and psi angles are energetically favorable and which are not. The plot is named after its creator, G.N. Ramachandran

Question 23

What do the white and red regions on a Ramachandran plot indicate?

Answer 23

The white areas on a Ramachandran plot correspond to conformations where atoms in the polypeptide come closer than the sum of their van der Waals radii. These regions are sterically disallowed for all amino acids except glycine. The red regions correspond to conformations where there are no steric clashes, i.e. these are the allowed regions, namely the alpha-helical and beta-sheet conformations

Question 24

What are some other forces that help shape protein structure and function?

Answer 24

In addition to peptide bonds, several other chemical forces help to shape protein structure and function. These include hydrogen bonds, hydrophobic interactions, ionic and covalent bonds, disulphide bridges, and van der Waals forces. Hydrogen bonds, in particular, play a crucial role in stabilizing the folded structure of proteins.