Chapter 5- Secondary Structure Flashcards
Primary structure definition
amino acid sequence of protein
Secondary structure definition
local spatial arrangements of the backbone atoms
Tertiary structure definition
3D structure of the entire polypeptide chain
Quaternary structure definition
Spatial arrangements of protein subunits
Peptide bonds are ____ bonds
amide bonds
Proteins result from the formation of covalent peptide bonds by
Condensation
A polymer of two amino acids is called
dipeptide
A polymer of many amino acids
polypeptide
Avg mass of amino acid
110 g/mol
Polypeptides are _____ polymers not branched
linear
The alpha H bonds and carboxyl groups run in the _____ direction
same
Amino acids are always read from the __ terminus to the __ terminus
N (amino terminus), C
In a peptide group a C–N bond is ___ than a simple amine, while a C=O bond is ____ than a simple ketone
Shorter, Longer
Peptide bond has _____ double bond character
~40%
C–N torsion angle is called __ and the C–C torsion angle is called ___
Phi, Psi
The trans configuration is more favored than the cis configuration because
the trans configuration has less steric hindrance and is more stable
the C–N bond is unable to ____
Rotate
Side chains dictate the bond angles because
different bond angles reorient to accommodate other groups around it
An alpha helix can be right-handed or left-handed which means it has
Chirality
Glycine in a peptide chain provides
- flexibility to proteins
- often found in places where proteins make sharp turns
Proline in a protein chain provides
- structure rigidity (due to cyclic side chain)
- may be found in kinks of the protein
polypeptide made of L-alpha amino acids will have n=___ and pitch =____
3.6 amino acids per turn, 5.4 A
____ and _____ of peptide bond point along the long axis (in the opposite direction)
N-H, C=O
The sum of all H bonds contributes to stability which means
more H bonds= more stability
side chains in an alpha helix point
outwards (avoids steric interference)
How do side chains affect stability?
- affecting the peptide backbone
- through side chain- side chain interactions
How many degrees between each amino acid in an alpha helix
100
interactions between side chains can lead to either the ______ or _______ of the helix
destabilization or stabilization
Steric clash means
two large bulky side chains stacked on top of each other is more likely to destabilize the helix
ASP and LYS have formed a _____ interaction
salt bridge that stabilizes the helix (different charges)
Asp and Glu have a _____ interaction
repulsion interaction that destabilizes the helix (same charges)
Aromatic amino acids can ____ which are favorable ______ ________
stack ( pi stacking), hydrophobic interactions
amino acids that tend to form an alpha helix
MALEK (met, ala, leu, glu, and lys)
Beta-branched amino acids that make them more difficult to adopt an alpha-helical conformation
Val, Ile, Thr
Amino acid that is entropically expensive and destabilizes helices
Gly
Conformationally rigid with no H bonding possible, known to destabilize helicies and may form a kink
pro
All dipoles in an alpha helix point in the ____ direction which results in a ______ ______ between the C terminal and N terminal
same, macro dipole (c end is neg and N end is pos)
Dipoles in an alpha helix result in
destabilization through entropic effects
the N terminal of an alpha helix is often capped by a _____ side chain while a ____ side chain caps a C terminal
negative, positive
Antiparallel beta sheets involve two chains running in ____ directions, the H bonds are ~ ______ to each other
opposite, parallel
Parallel beta-sheets involve two side chains running in the _____ directions, the H bonds are formed on ____
same, angles
Beta strands exhibit a _____ ______ ______ due to the chirality of the amino acids
right-handed twist
Beta turns are commonly formed by
proline and glycine
beta turns give proteins _____ and promotes the formation of _______ ______ ____
globularity, anti-parallel beta sheets
The coil/loop conformation is completely ______ and is typically found on the _____ _____ of the proteins
unstructured, outer surface
Random coils are usually ______ and ______ but do not conform to any ______ ______ ____
organized and stable, frequently recurring pattern
The stability of seconds structures is determined by
- steric repulsion minimized
- H bonding is maximized
Characteristics of Circular Dichroism Spectroscopy
- absorption spectroscopy
- provides information on the secondary structure content of proteins
- signal; originated from the amide group and the phi/ psi angles
