Unit 2 Flashcards
(240 cards)
The 3-D conformation is able to fulfill a specific ________
Biologic function
The 3-D structure is also known as the _______ ______ that has a large number of favorable interactions within the protein
Native fold
There is a cost in _________ ________ of folding the protein into one specific native fold
Cost in conformational entropy
What are the favorable interactions in proteins?
Hydropphobic effect
Hydrogen bonds
London dispersion (Van der Waals)
Electrostatic interactions
The resonance causes the peptide bonds
- to be _______ reactive compared to esters
- to be quite ______ and nearly ______
- to exhibit a large ________ _____ in the favored trans configuration
Less reactive
Rigid and nearly planar
Dipole moment
What type of linkages are seen in primary structures?
Covalent
Secondary structures contain what linkages and structures?
H-bonds
Alpha helices, beta sheets and beta turns
In the tertiary structure, what linkages are involved? And what are the linkages between?
Covalent
H-bond
Van der Waals
And hydrophobic
Linkages between the R groups
What is a peptide bond?
A bond formed by the carbonyl group and the amide group of another molecule
Quaternary structures contain all types of linkages except _______
Covalent
Where are the molecules bonded in quaternary structure?
Between subunits (mostly using R groups)
Virtually all peptide bonds in proteins occur in ______ configuration
Trans
What constitutes the polypeptide backbone?
The bond between the N and carbonyl carbon
The alpha helix is stabilized by H bonds between ________
Nearby residues
The beta sheet is stabilized by H-bonds between ________
Adjacent segments that may not be nearby
Irregular arrangement of the polypeptide chain is called the ________ _____
Random coil
Where does trypsin cleave at?
Lysine and arginine
Cyanogen bromide cleaves at ______
Methionine
Is the alpha helix right handed or left handed?
Right handed with 3.6 residues per turn
Peptide bonds are aligned roughly ______ with the helical axis
Side chains point out and are roughly_____ with the helical axis
Parallel
Perpendicular
What are strong helix formers? And what are some examples?
Small hydrophobic residues such as Alanine and Leucine are strong helix formers
What acts as a helix breaker and why?
Proline acts as a helix breaker because the rotation around the N-Ca bond is impossible
Glycine acts as a helix breaker because the R-group supports of conformations
What affects the formation of a helix?
Attractive or repulsive interactions etween side chains 3-4 amino acids apart
What is the functional insulin part?
C-peptide