Primary and Secondary Protein Structures (Zhao L2) Flashcards
What are the two main types of secondary structures in proteins?
- Alpha helix
2. Beta sheet
What is the primary structure of a protein?
The aa. sequence
How many high energy bonds are required to form one peptide bond?
Four
2 for “charging” the tRNA (ATP –> AMP + PPi)
1 for charged tRNA to enter A site (GTP –> GDP)
1 for translocation of the whole shebang (GTP –> GDP)
Why is the peptide bond so strong?
Partial double bond character
side note: Does not rotate - peptide plane :)
Which angle is the phi angle?
Angle of the
alpha carbon - amide nitrogen
bond
Which angle is the psi angle?
angle of the
Alpha carbon - Carbonyl carbon
bond
What is the difference between an “peptide” and a “protein”?
“peptides” just refers to a really short polypeptide chain
“protein” is a longer polyeptide + possible cofactors
What is a co-factor in the realm of proteins?
Functional non-amino acid component
What is a prosthetic group in the realm of proteins?
A covalently attached non-amino acid component
How many amino acids are “changed” in sickle cell anemia?
One!
E6V
What is a protein polymorphism?
Slightly different (non-disease causing) sequence of same protein in different individuals.
Is how we get our individual traits.
Give an example (from lecture) of a protein that is used to trace the evolutionary connections between various species.
Cytochrome C
Same function, similar aa sequence. The diff. in aa. seq. from species to species determines how far they are, evolutionarily, from one another.
What is a protease or a peptidase?
Enzyme that hydrolyzes peptide bonds. “Digest” proteins.
Where in the body might we need proteases/peptidases that will digest at a specific aa. but within any protein?
What are some examples of these proteases?
Digestive system.
Pepsin, Trypsin
Submaxillarus protease
Chymotrypsin
What are some examples of proteases that digest only specific proteins or peptides?
HIV protease
Angiotensin Converting Enzyme (ACE)
Name some examples of proteins that are synthesized in their inactive form and are later cleaved to their active state.
Trypsin, chymotrypsin Insulin Compliment enzymes Clotting enzymes Trxn factors Programmed Cell Death proteins
How is insulin activated?
Preproinsulin is initially synthesized and through a series of cleavage and “maturation” steps it ends up as 2 peptide chains (chain A and B) connected via disulfide bridges.
Primary protein structure is held together by _________ bonds. Higher order protein structures are held together by ______ bonds.
Covalent
Noncovalent
What is the unique secondary protein structure present in collagens?
Left-handed triple helix.
What is the main non-covalent bond that shapes the alpha helix?
H-bond between C=O on one aa and the N-H of the aa. 4 steps down the chain.
aa i and aa i+4
Where are the R-groups in the alpha helix?
R-groups point out from the helix structure.
What class of amino acids are typically found within the alpha helix?
Small hydrophobic residues. (eg. Ala, Leu)
Which two amino acids are the “helix breakers” and why?
Pro and Gly
Proline has a ring side chain bonded to the backbone N. Cannot form the hydrogen bonds found in the center of the helix.
Glycine is very very small and is an energy penalty to force it into an alpha helix (or beta sheet).
The residues that point outwards on the alpha helix are in a good position to interact with what other biological molecule?
DNA
