Ch. 6 Flashcards
Angle between Nitrogen and alpha Carbon
Phi (Φ)
Angle between alpha carbon and carbonyl carbon
Psi (Ψ)
What is the shaded area of a Ramachandran plot
most favorable Φ and Ψ angles
What are the 3 secondary structures
α-helix, β-sheets, and turns and cross overs
How are α-helices stabilized
Backbone stabilized by H-bonds spaced 4 residues apart
Residues per turn in an α-helix
3.6
Most common orientation of α-helices in nature
right handed (Φ=-60, Ψ=-50)
What effect do side chains have in an α-helix
Determines solubility in water
What amino acids can be considered helix breakers
Proline and Glycine
How are β-sheets stabilized
Backbone is stabilized by H-bonding between separate β-strands
What are β-strands composed of
tight α-helix with 2 residues per turn
Orientation of R groups in β-strands
180 apart
3 types of β-sheets
parallel (N-terminals start at same sport), anti-parallel, and mixed (both parallel and anti-parallel)
3 ways to change direction
Proline, β-turn, and cross over
What conformation around the peptide bond allows proline to have a natural turn
cis conformation
How to form β-turn
H-bond between carbonyl oxygen of a residue with the amide proton of another residue 3 AA away
Favored AAs in β-turns
Glycine (less sterics) and Proline (natural curve)
What is a cross over
short α-helical segment that connects β-strands
Two types of Fibrous proteins
keratin (hair and nails) and collagen (skin, bones, tendons, blood vessels)
Structure of the initial monomer in keratin
central right handed α-helix (rod domain)
two initial keratin monomers form a dimer called
left handed coiled coil
Why do coiled coils form
red domain is composed of heptad repeats that create a non-polar strip on the outside of the helix (hydrophobic effect)
Two coiled coils associate to form?
protofilament
Two protofilaments associate to from?
right handed protofibril
4 protofibrils form?
keratin filament
Why do protofilaments and protfibrils form
H-bonding or disulfide bonds
Structural difference between hair and nails
relative amounts of H-bonds (flexible) and disulfide bonds (rigid)
Structure of initial collagen monomer
left handed α-helix with 3.3 residues per turn
AA composition of collagen
High in Glycine and Proline
What amino acids are formed after the protein is formed
4-hydroxy proline, 3-hydroxy proline, and 5-hydroxy lysine
Enzyme that forms hydroxy proline
prolyl hydroxylase
Enzyme that forms hydroxy lysine
lysyl hyroxylase
Effect of hydroxylating proline and lysine
increases H-bonding
Key molecule in formation of hydroxy proline
Vitamin C
3 collagen monomers associate to form?
right handed triple helix (tropocollagen)
AA pattern found in collagen
Gly-X-Y
X=proline
Y=hydroxyproline
Location of glycine in tropocollagen
buried in interior b/c of glycines low sterics
What holds tropocollagen together
H-bonding in the hydroxy proline backbone
tropocollagen forms?
collagen fibers
What holds collagen fibers together
covalent crosslinks
Lysine can be oxidized to what
aldehyde form (allysine)
Lysine and allysine crosslink?
imine (schiff base)
allysine and allysine crosslink?
aldol condensation
Disrupting cross links does what to collagen
destabilizes collagen
Why does a vitamin C deficiency (scurvy) cause a diseased state
Hydroxy proline can not be made without vitamin C, disrupting the structure of collagen
Tertiary structures form the most stable structure through?
covalent and non-covalent interactions
Globular protein themes
α-helices and β-sheets in core
cavities filled with hydrophobic side chains
water stabilized the surface
What are protein domains
distinct tertiary regions connected by a flexible backbone
Levinthals paradox in relation to protein folding
protein folding is not random
What does mean that protein folding is all or nothing
remains folded until Tm then rapidly unfolds
Folding themes
- secondary structures fold first
- hydrophobic collapse
- long-range interactions
Intermediate folded shape?
molten globules
what does it mean that proteins are marginally stable
they have flexibility and motion
Why is protein folding represented as a funnel
each step leads to an intermediate lower in energy making each step easier than the last
What are molecular chaperones
proteins that help other proteins fold
Example of molecular chaperone
heat shock proteins (HSP-90)
Effects of Misfolding
loss of function and can lead to aggregation
Examples of misfolding
sickle cell, alzheimers, and cancer
What is an IUP
intrinsically unstructured protein
What AAs are found in IUPs
polar AAs and proline
Function of IUPs
can bind ligands and can increase surface area
Advantages of quaternary structure
Stability
Genetic economy
Bring catalytic sites together
Cooperativity
Example of Cooperativity in quaternary structures
ligand binding at one subunit can trigger a conformational change in another
What is Allostery
information transfer across long distances in a protein
