Protein DLA- Secondary Structure Flashcards
Describe the secondary structure of proteins
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
Protein secondary structure include:
- helical structures
- beta structure(maximally extended primary sequence)
- Beta bend(or turn)
What causes the formation of secondary structures?
Result from local arrangement of adjacent amino acids into an organized 3-dimensional structure
What is the function of hydrogen bond within secondary structure?
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
What type of helix do proteins have and why?
All amino acids in nature have an L-configuration and so form a left handed helix
Differentiate between inter- and intra-
Intra- interactions WITHIN the same molecule
Inter- interactions between different molecules
Explain where intrachain hydrogen bonds located in secondary protein structures
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
Briefly describe the alpha-helix structure
- Has 3.6 residues per turn
- R groups extended outward
What may disrupt an alpha helix?
- Proline
- Maybe glycine to a lesser extent
- Charge repulsion: many charged amino acids that are all found on the same side, or adjacent to each other
- Many amino acids with bulky R groups that are next to each other on the helix
Why does proline disrupt an alpha helix?
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
Why does glycine disrupt an alpha helix?
Since it’s R group is so small, it’s not well tolerated in the alpha helix
Describe the characteristics of the helical wheel of the alpha helix
- shows how amino acid side chains are directed to the outside
- May lead to constraints on the structure
- dependent on primary structure
How many different globular proteins are there?
Millions(infinite)
What is the purpose of the “globin fold” in myoglobin?
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
Detail the unique structure of myoglobin
- predominantly alpha helix(lacks beta sheet)
- myoglobin also has some turns and bends and some unorganized structure
What does myo- mean?
Muscle
Describe the B-sheet
- 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
Differentiate parallel and anti-parallel B-sheet
Anti- parallel= N-terminus goes in one direction and then turns around
Parallel= two strands going in the same direction
Parallel beta-pleated sheet has…
Alternating side chains
Where do hydrogen bonds occur in beta pleated sheets?
Between adjacent amino acids in carboxy oxygen and amino nitrogen.
Give an example of a protein that predominantly beta-pleated sheet
Silk is just about 100% beta sheet
Silk protein is bundled into fibers, spun into thread and then woven to create cloth/fabric
What is the function of the B-bend?
To reverse the direction of the polypeptide
-Can link alpha helixes/beta sheets to others(infinite combinations
Describe the structure of the B-bend.
- often include charged residues
- stabilized by ionic and/or H-bonds
- made of a few amino acids
What are seupersecondary structures?
-result from local folding of secondary structures into small, discrete, “commonly-observed aggregates” of secondary structures
