Medical Biochemistry Lecture 4 Flashcards
Primary Structure
protein adopt specific three-dimensional conformations
Native fold
has a large number of favorable interactions within the protein
What does protein. structure have?
the lowest Gibbs free energy
True or False: This structure can fulfill a specific biological function
True
Hydrophobic effect
water makes the best hydrogen bonds with itself and is disrupted by other molecules
-Hydrophobic groups aggregate, hiding their entire surface from water, which creates a structured salvation layer around the molecule
Van der Waals (London dispersion)
-attractive force due to induced dipoles in all atoms
-important to the stability in the interior of the protein
hydrogen bonds
-Interaction of N-H and C=O if the peptide bond leads to local regular structure such as alpha helices and Beta sheets
-Maximized in protein structure, allow polar molecules to traverse interior protein
Ionic interactions
-long range strong interactions between permanently charged groups
-salt-bridges, especially buried in the hydrophobic environment strongly stabilize proteins
Disulfide Bridge
-mostly in secreted proteins
-generally not found in reducing environment of cell
What are the four levels of protein structure?
Primary, Secondary, Tertiary, Quaternary
Peptide bond
partial double bond
Resonansance in peptide bonds allows a what configuration because of steric hindrance
trans
Is rotation around the peptide bond permitted?
no
Is rotation around connected on the alpha carbon permitted
yes
bulky R groups generally are on what sides?
opposite
phi
angle around alpha carbine: amide nitrogen bond
psi
angle around the alpha carbon-carbonyl carbon bond
In a fully exited polypeptide, both phi and psi are what degrees
180
The peptide are _____
but bulk-R groups on adjacent alpha carbons can interfere
planar
What two possible conformations can peptide bonds exist?
trans highly favorable except for proline( which can be found 6 percent in cis conformation in beta turns)
Secondary structures
local spatial arrangement of the polypeptide backbone
Secondary structure of alpha helix
-stabilized by H-bond between new\arby residues
-25% of amino acids in this conformation(highly variable between proteins)
Secondary structure of beta sheets
stabilized by H-bond between adjacent segments that may be far away
Random coli
irregular arrangement of the polypeptide chain
alpha helix
the helical backbone is held together by hydrogen bonds between an amide hydrogen of one amino acid and a carbonyl oxygen four amino acids away, maximizing bonds
What hand helix is 3.6 residues (5.4) per turn giving a twist?
right
Peptide bond are aligned roughly parallel with
helical axis
another characteristics of the alpha helix
sides pot out and roughly perpendicular with the helical axis
What is the inner diameter
4-5 A
What residues align nicely on top of each other
1 and 8
Peptide bond has a strong dipole movement with
- carbonyl, + amide
where does negatively charge residues occurs
near the positive end of the helix dipole
All polypeptides sequences adopt an alpha helical structures
False: Not all polypeptide sequences adopt an alpha helical structures
Small hydrophobic residues such as what are strong helix formers
Ala and Leu
What amino acid serves as a helix breaker and why?
Pro because the rotation around the N-C alpha bond is impossible
What other amino acids serves as a helix breaker and why?
Gly because the tiny R group supports other conformations
Attraction or repulsive interactions between side chains 3-4 amino acids apart will affect
formation
Why is non polar side chains along each alpha helix can be arranged?
their side chain groups contact another helix
coiled coil
this allows side groups to pack neatly only when the alpa helices interact at 18 degrees from parallel. If alpha helices remained parallel, could stain contact for only few residues
Multiple coils
helical bundle
What can an alpha helix supercoiling be
tertiary or quaternary
Beta sheets
the planarity of the peptide bond ad tetrahedral geometry of the alpha carbon create a pleated sheet-like structure
How are the side chains in beta sheets?
alternating in up and down direction
How are beta sheets in proteins?
twist in a right-handed manner
Whare the two orientation of beta sheets?
parallel and antiparallel
Parallel Beta sheets
the H-bonds strands run in the same direction; bent H-bonds(weaker)
Antiparallel B-sheets
the H-bonds stands run in opposite direction, linear H-bonds (stronger)
When does beta turns occurs?
frequently when the strands of the B sheet changes direction
How is 180 degree accomplished in a B turn?
over 4 amino acids
How is the turn stabilized?
H-bond from carbonyl oxygen to amide proton three residues down the sequence
What are common in B turns?
Proline(cis) in position 2 or a flexible glycine in position 3
Tertiary structure
overall spatial arrangement of atoms in a protein
How is tertiary structure stabilized?
numerous weak and strong interactions between amino acids side chain, often far apart in the primary sequence
What are the two major class of tertiary structure?
fibrous and globular(water or lipid soluble)
what do proteins have?
motifs(folds)
What is the strongest influence on protein folding?
Burial of hydrophobic(non polar) side chains into the core of the polypeptide’s structure
What happens in aqueous solution regarding the hydrophobic core?
proteins with a large number of non polar side groups will tend to internalize the non polar residues and be more stable than proteins containing mostly polar groups
True or False: Polar bonds can H-bond with water, and thus a smaller free energy would be gained from packing polar groups vs non polar groups
True
Change is G is more positive than non polar packing
False
Why do some alpha helices have alternating polar and non polar amino acids
to improve packing of helical bundles
Transmembrane proteins have a long stretches of how many non polar amino acids to cross the membrane?
20
