lecture 6- protein Flashcards
Distinct regions of a protein that fold independently of one another and often function in a semi-independent manner are called:
domains
molecular chaperones
may prevent growing proteins from making random, nonselective interactions with other proteins in various cellular compartments
the first protein whose tertiary structure was determined
myoglobin
denaturation of protein can be caused by
detergents, organic solvents, heat, certain chemical compounds, or radiation
the unfolding or disorganization of protein
denaturation
amino acid sequence will fall into the sequence that has the
lowest energy
a secondary structure will not have a noncovalent interaction with the
side chain
secondary structures will have interactions with the main chain!
stabilization of a tertiary structure of a protein will always be with
a side chain
beta sheets are very strong because of
hydrogen bonding
Protein (3 main concepts)
-mediate nearly all the processes in a cell
-diverse structure and function
-all the proteins use the same set of 20 amino acids
8 types of proteins
enzymes, structural proteins, motor proteins, receptor proteins, transport proteins, storage proteins, signal proteins, gene regulatory proteins
what is the only differing thing about amino acids?
the side chains (R)
all 20 amino acids are categorized based on their side chain properties
amino acid side chain categories
nonpolar, polar uncharged, acidic, basic
(all fairly hydrophobic)
hydrophobic side chains packed together (hydrophobic effect)
put amino acid sequence in water, hydrophobic side chains pack together, forms a pseudo 3D structure (the multenglobun??)
the pseudo 3D structure does not have noncovalent interactions!!!!
peptides
2+ amino acids joined by peptide bonds
peptides are held together by
peptide bonds formed as a result of a condensation rxn
peptide directionality convention
N-terminus to C-terminus (left to right)
shape of a protein is dictated by
amino acid sequence
side chains dictate unique properties of the amino acid which affect how the protein folds
Secondary structure: 2 most common
alpha helix= side chain outside helix (H bonding stabilizes)
beta helix= same direction or different directions
Alpha helix
- peptide backbone wraps around imaginary axis
- R group phases outwards
- intrachain H bonds stabilizes alpha helixes
how to determine is an amino acid is right or left handed?
use the right hand rule!!
follow amino acid in the way your thumb is pointing. helix should curve in same direction as your fingers
amino acid R-groups affect alpha helix stability
- electrostatic/steric interactions between adjacent side chains can affect stability of an alpha helix
- electrostatic/steric interactions between amino acids 3-4 residues away can affect the stability of an alpha helix
- proline and glycine are not usually found in helices
why is proline not found in helices?
-the nitrogen of proline is in a rigid ring which sterically interferes w the backbone
-proline in a peptide bond lacks an amide hydrogen to form hydrogen bonds
why is glycine not found in helices?
glycine is very flexible, allows for conformations that do not suit alpha helices
glycine is so small that is can’t protect the backbone hydrogen bonds from the aqueous environment
(don’t use the textbook for this info, he is the expert in this?)
proline and glycine are seen as
“helix breakers”
amphipathic helices
one side is hydrophobic, the other side is hydrophilic
proteins with alpha helices are
very strong
coils can form around eachother
(ex. keratin)
