Protein 3D Structure - Chapter 4

Question 1

What are the four levels of protein structure?

Answer 1

Primary, secondary, tertiary, and quaternary structures.

Question 2

What is the primary structure of a protein?

Answer 2

The sequence of amino acids in a polypeptide chain.

Question 3

What type of bond forms the primary structure of proteins?

Answer 3

Each amino acid is linked to the next via peptide bonds.

Question 4

Describe the secondary structure of proteins.

Answer 4

spatial arrangement of amino acid residues near one another in the linear sequence; alpha-helix or beta strand

Question 5

Describe the structure of alpha-helices and beta sheets.

Answer 5

Alpha-helices are coiled and beta-sheets are flat, pleated structures.

Question 6

What is the tertiary structure of a protein?

Answer 6

spatial arrangement of amino acid residues that are far from each other in the linear sequence, as well as the pattern of disulfide bonds

Question 7

List some interactions that stabilize tertiary protein structure.

Answer 7

Hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.

Question 8

What is the quaternary structure?

Answer 8

The assembly of multiple polypeptide chains into a functional protein complex.

Question 9

What is an amino acid’s general structure?

Answer 9

An amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom, and a variable R group (side chain) attached to a central carbon atom.

Question 10

What are essential amino acids? List them.

Answer 10

Amino acids that cannot be synthesized by the body and must be obtained from the diet.
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

Question 11

What is a zwitterion?

Answer 11

An amino acid in its neutral form where the amino group is positively charged and the carboxyl group is negatively charged.

Question 12

What is a peptide bond?

Answer 12

A covalent bond formed between the carboxyl group of one amino acid and the amino group of another, releasing a molecule of water.

Question 13

How are protein structures experimentally determined?

Answer 13

Techniques include X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy.

Question 14

Describe the role of chaperones in protein folding?

Answer 14

They assist in the correct folding of proteins and prevent misfolding and aggregation.

Question 15

What are post-translational modifications? Where do they occur?

Answer 15

Chemical modifications made to proteins after translation, such as phosphorylation, glycosylation, and ubiquitination. They occur in the endoplasmic reticulum and the Golgi apparatus.

Question 16

Describe the impact of mutations on protein structure.

Answer 16

Mutations can alter the amino acid sequence, potentially disrupting protein folding and function. This can lead to unexpected phenotypic differences (including disease).

Question 17

What is a domain in a protein?

Answer 17

A distinct functional and structural unit within a protein, often responsible for a specific function.

Question 18

Explain the role of disulfide bridges in proteins.

Answer 18

Covalent bonds between the sulfur atoms of two cysteine residues that stabilize the protein’s tertiary and quaternary structures.

Question 19

What is denaturation of a protein?

Answer 19

The process by which a protein loses its native structure due to external stress or conditions, leading to loss of function.

Question 20

Why does the biosynthesis of peptide bonds require an input of free energy?

Answer 20

The formation of a dipeptide from two amino acids is accompanied by the loss of a water molecule. The equilibrium of this reaction is in thne direction of hydrolysis, rather than synthesis.