Protein Structure

Question 1

What is the conformation of a protein?

Answer 1

The final folded structure of a protein. Proteins typically have a limited number of stable conformations

Question 2

What determines a protein’s conformation

Answer 2

Amino acid sequence

Question 3

Is proper folding of protein guaranteed? Why or why not?

Answer 3

No. Sometimes protein misfold, sometimes they require help from chaperone proteins

Question 4

What makes a protein conformation stable?

Answer 4

Gives the protein the lowest free energy.

Question 5

Can protein conformation change?

Answer 5

Yes, protein conformation can change when interacting with different molecules.

Question 6

List the four protein structures.

Answer 6

Primary, secondary, tertiary, quaternary

Question 7

What is the primary structure of a protein?

Answer 7

The linear amino acid sequence

Question 8

What is the secondary structure of a protein?

Answer 8

Small segments of peptide backbone folding to form simple structures like a helix and beta sheet.

Question 9

What is the tertiary structure of a protein?

Answer 9

The entire peptide backbone folds into the full 3D structure of the protein.

Question 10

What is the quaternary structure of a protein?

Answer 10

More than one protein combining to form a larger structure.

Question 11

In reality, does protein folding occur sequentially, with each stage occurring at their own moments in time?

Answer 11

No, typically it is all occurring simultaneously.

Question 12

Give an example of how a single amino acid change in a protein sequence can have catastrophic effects.

Answer 12

Sickles cell anemia: glutamic acid is switched for hydrophobic valine, which completely changes the shape of hemoglobin.

Question 13

What creates and stabilizes secondary structures?

Answer 13

Intramolecular hydrogen bonds between backbone

Question 14

In which ways can beta sheets be arranged?

Answer 14

Parallel, antiparallel, a combination

Question 15

Where does the R group point in an alpha helix?

Answer 15

Outwards

Question 16

What type of helix is an alpha helix?

Answer 16

Right handed

Question 17

How many amino acids per turn of an alpha helix?

Answer 17

3.6

Question 18

Explain exactly how the N-C-C backbone forms hydrogen bonds in the alpha helix.

Answer 18

Every backbone C=O group forms a hydrogen bond with the N-H group of the amino acid residue 4 residues downstream of the peptide.

Question 19

Is the primary sequence of an amino acid actually random?

Answer 19

Frequently, hydrophobic/hydrophilic amino acids are grouped on the same side of an alpha helix, resulting in one side of the helix being hydrophobic and one side hydrophylic.

Question 20

How are beta sheets held together?

Answer 20

Adjacent chains held together by hydrogen bonds between backbone residues. Hydrogen bonding occurs one every two amino acid pairs.

Question 21

How many amino acids are in one beta strand? How many strands per sheet?

Answer 21

5-10 amino acids; 2-15 strands/sheet

Question 22

How are the side chains oriented in beta sheets?

Answer 22

Alternating up and down

Question 23

What determines the folding of the tertiary structures?

Answer 23

Amino acid residues

Question 24

What is a protein domain? How many domains can a single protein have?

Answer 24

unit of protein that can fold and perform a function on its own without the help of outside molecules. There can be multiple domains within one protein.

Question 25

What happens to a protein domain when you remove it from the parent protein?

Answer 25

It retains its function.

Question 26

What is meant by domain shuffling?

Answer 26

Evolution doesn’t have to reinvent new domains for new functions, oftentimes they simply recombines previously selected domains.