Protein DLA- Secondary Structure

Question 1

Describe the secondary structure of proteins

Answer 1

Secondary structure can be created when there is a regular (or repeating) series of binding arrangements

For proteins, this regular arrangement is the peptide bond which links amino acid together

Question 2

Protein secondary structure include:

Answer 2

• helical structures
• beta structure(maximally extended primary sequence)
• Beta bend(or turn)

Question 3

What causes the formation of secondary structures?

Answer 3

Result from local arrangement of adjacent amino acids into an organized 3-dimensional structure

Question 4

What is the function of hydrogen bond within secondary structure?

Answer 4

The hydrogen bonds that stabilize the secondary structure are formed between the atoms that compose the peptide bonds

-hydrogen bonding is repetitive because peptide bonding is repetitive

Question 5

What type of helix do proteins have and why?

Answer 5

All amino acids in nature have an L-configuration and so form a left handed helix

Question 6

Differentiate between inter- and intra-

Answer 6

Intra- interactions WITHIN the same molecule

Inter- interactions between different molecules

Question 7

Explain where intrachain hydrogen bonds located in secondary protein structures

Answer 7

Intrachain hydrigen bonding located in the alpha-helix between the carbonyl oxygen from one amino acid is H-bonded to an alpha nitrogen of the 4th distant amino acid in the polymer

Question 8

Briefly describe the alpha-helix structure

Answer 8

• Has 3.6 residues per turn

- R groups extended outward

Question 9

What may disrupt an alpha helix?

Answer 9

1. Proline
2. Maybe glycine to a lesser extent
3. Charge repulsion: many charged amino acids that are all found on the same side, or adjacent to each other
4. Many amino acids with bulky R groups that are next to each other on the helix

Question 10

Why does proline disrupt an alpha helix?

Answer 10

Since it’s side chain forms a bond from the R group to alpha nitrogen, it causes a kink in the alpha helix that breaks it

Question 11

Why does glycine disrupt an alpha helix?

Answer 11

Since it’s R group is so small, it’s not well tolerated in the alpha helix

Question 12

Describe the characteristics of the helical wheel of the alpha helix

Answer 12

• shows how amino acid side chains are directed to the outside
  
  • May lead to constraints on the structure
  • dependent on primary structure

Question 13

How many different globular proteins are there?

Answer 13

Millions(infinite)

Question 14

What is the purpose of the “globin fold” in myoglobin?

Answer 14

The “globin fold” for myoglobin is designed to hold a porphyrin ring which has an iron atom in its center

Useful for reversible oxygen binding

Question 15

Detail the unique structure of myoglobin

Answer 15

• predominantly alpha helix(lacks beta sheet)

- myoglobin also has some turns and bends and some unorganized structure

Question 16

What does myo- mean?

Answer 16

Muscle

Question 17

Describe the B-sheet

Answer 17

• Or the beta- pleated sheet
• All of the atoms of the peptide bond are involved in hydrogen bonding
• strands visualized as broad arrows
• the beta sheet may be parallel or anti-parallel

Question 18

Differentiate parallel and anti-parallel B-sheet

Answer 18

Anti- parallel= N-terminus goes in one direction and then turns around

Parallel= two strands going in the same direction

Question 19

Parallel beta-pleated sheet has…

Answer 19

Alternating side chains

Question 20

Where do hydrogen bonds occur in beta pleated sheets?

Answer 20

Between adjacent amino acids in carboxy oxygen and amino nitrogen.

Question 21

Give an example of a protein that predominantly beta-pleated sheet

Answer 21

Silk is just about 100% beta sheet

Silk protein is bundled into fibers, spun into thread and then woven to create cloth/fabric

Question 22

What is the function of the B-bend?

Answer 22

To reverse the direction of the polypeptide

-Can link alpha helixes/beta sheets to others(infinite combinations

Question 23

Describe the structure of the B-bend.

Answer 23

• often include charged residues
• stabilized by ionic and/or H-bonds
• made of a few amino acids

Question 24

What are seupersecondary structures?

Answer 24

-result from local folding of secondary structures into small, discrete, “commonly-observed aggregates” of secondary structures

Question 25

Give 4 examples of super secondary structures

Answer 25

• B-a-B unit
• Green key
• B- meander
• B-barrel

Question 26

Give 2 examples of extended super secondary structures

Answer 26

• twisted B sheet

- B-barrel

Question 27

Give three examples of fibrous proteins

Answer 27

• silk
• collagen
• keratin

Question 28

Describe keratin as a fibrous protein and location

Answer 28

Keratin- combination of alpha helix and beta sheet

In hair, nails, horn

Question 29

Describe the collagen as a fibrous protein and it’s location

Answer 29

Collagen- in skin, tendon, bone

Most abundant protein in mammals

Question 30

Describe silk as a fibrous protein

Answer 30

In spiders, caterpillars, all. Beta sheet

Question 31

Give the general characteristics of fibrous proteins

Answer 31

• has one dominating secondary structure
• a long rod like structure
• low(or none) water solubility
• a structural role

Question 32

Why is Collagen structure so special?

Answer 32

• it does not have an alpha-helix or beta -pleated sheet

- instead has the collagen triple helix

Question 33

Why must the collagen triple helix be so tight?

Answer 33

Helix must be very tight, so where each helix contacts the other, amino acids with very small side chains are present(glycine, alanine)

Question 34

Why can collagen structure be described as repetitive?

Answer 34

Every third amino acid is glycine

Question 35

What amino acids are in a beta bend? How many residues make up a beta bend?

Answer 35

• beta bends are made up of proline and glycine

- beta bends are made up of 4 amino acid residues