Chapter 6 - Proteins never end Flashcards
Peptide group
6 atoms from aan to aan+1
occupy same plane (peptide planar)
Calpha1-Calpha 2
Part of primary structure
Rotate Relative to each other
Peptide bonds
partial double bond character causes restricted conformation -> trapped in either trans or cis conformation (usually trans so that the R groups aren’t sterically hindered) -> no peptide bond rotation
Polar - O, partial negative (H-bond acceptor)
N, partial positive (H is H-bond donor)
Alpha Helix
Physical features
repeating phi and psi angles along peptide backbone -> predictable physcial features
- right handed helix
- 3.6 aa per turn
- 0.54 nm pitch (advance per turn) and 0.15 nm rise per residue
N——>C
Alpha helix
Stabilization
R-group location
Hydrogen bond stabilization: strenth in numbers; parallel to helix axis
R-group location: outside of helix; about every 4th side-chain on the same side
Possible amphipathic properties of helices
Some amino acids prefer alpha helical structure; others (pro and gly) helix breakers
Helix excludes water; van der Waals packing
Stabilizers: Ala-prefer helical phi and psi angles
disruptors - too flexible or inflexible, highly charged or bulky - gly, pro, tyr, arg, lys
Beta Sheets
Repeating phi and psi angles along extended peptide backbone -> more flexible
Interstrand hydrogen bonds and right-hand twist
Anti-Parallel (strands run in opposite direction with straigh H-bonds. 2-22 strands, avg 6 residues per strand but up to 15)
Parallel (strands run in same direction with off-set hydrogen bonds; more than 5 strands per sheet, less stable than antiparallel, can be mixed with anti-parallel sheets)
R-Groups project on alternate sides of sheet every other residue along strand
Tertiary or 3D structure
Primary stabilizing force
And other stabilizing forces
the basis of protein stability and function
hydrophobic effect (thermodynamic driving force?); 3D arrangement of secondary structures maximizes the hydrophobic effect
Additional stabilizing effect of other noncovalent forces (ionic, hydrogen bonds, and van der Waals); the sum of individual forces is greater than the parts analogy
Disulfide bond contribution to tertiary structure
Tertiary Structure
Protein folding process and the denaturing forces
a) Primary structure directs folding process (ms time frame); hydrophobic collapse; molten globule and folding chaperones (when are they needed)
b) Protein denaturation: cooperative process -> Denaturation curve and Tm
Quaternary structure
multiple subunits or polypeptides to form a single functional protein
Protein structure determination
X-ray crystallography and NMR spectroscopy (intro to techniques)
B-Sheets frequently interact in protein structures
side chains project alternately above and below B-sheet plane
Forms amphipathic sheet: hydrophobic side chains face protein interior
amphipathic alpha helices and B-sheets help form hydrophobic interior and hydrophilic surface of proteins
intermolecular h-bonds
right-handed twist to sheet (due to L-amino acid)
Variable B-structure in proteins to match function
Barrel structures or sandwiches form from twisted sheets
Form regions or compartments inside proteins for varying conditions and separate environments (i.e. channels through membrane)
Beta sheet topology (connectivity of strands)
strands may not be successsive in amino acid sequence
small loop connections between anti-parallel strands
reverse turn or B-bend to change direction
Cross-over loops occur between parallel strands
Reverse Turn Features (Type I and II)
occur at protein surfaces
Usually 4 aa arranged in 2 possible ways
- pro fits in due to rigid side-chain
- gly common due to lack of side-chain
h-bond stabilization
Helical Wheel Diagram
shows amino acid sequence influence on helix properties
every 4th amino acid in sequence is found on the same face of the helix
Alpha-Keratins
major components of hair and nails
tissue specific gene expression
coiled-coil structure - made from 2 polypeptide strands (310 residue central peptide segment)
individual strands: right-handed - overal: left-handed
7 residue pseudo repeat: abcdefg
a & d positions mostly nonpolar - align on one side of helices (hydrophobic strip)
Collagen
major component of tendons, skin, bones, and teeth - at least 19 different types
a fibrous protein
major protein in connective tissue of vertebrates
form mirrors function: include tendons (robelike fibers); skin (loosely woven fibers)
Overall role: strength, support, resilency, resistance
Higher-order Keratin Structure
N&C-termini of peptides aid protofilament formation
stepwise assembly to form macrofibrils
parallel macrofibrils form hair&nails
cys-rich cross-links form between fibers
Collagen
Basic Structure
3 left-handed helical peptides coiled around each other -> right-handed supercoil (quaternary structure - no tertiary structure)
Type I Macro: 285 kdA (good sized); 14 A wide and 3000A long
3 amino acids per turn (310) helix
rise 0.31 nm per residue (more extended than an alpha helix)
limited amino acid sequence
Collagen Triple Helix
multiple repeats of Gly-X-Y
X often Pro
Y usually 4-hydroxyproline
Gly located along central axis of a triple helix (other residues cannot fit)
Amide H from Gly forms H-bond with Carbony from Pro - interchain H-bonds
4-Hydroxyproline and 5-Hydroxylysine: post-translational enzyme
Vitamin C deficiency
hydroxylyation requiring vitamin C
hydroxyproline H-bonds between chains
hydroxylysine site of glycosylation (carbohydrate modification)
Vitamin C deficiency (scurvy) leads to lack of proper hydroxylation and defective triple helix (skin lesions, fragile blood vessels, bleeding gums)
Human and guinea pigs cannot synthesize vitamin C
Collagen Fibers
Arrangement: staggered array of tropocllagens –> basic unit in tissues
Tropocollagen
Triple helix (3 polypeptides about 800 residues each) MW=285kd
opposite twist to individual helices = greater stability
Banding pattern in EMs
stagger and overlap of molecules cause a 67 nm repeat with gap and a “hole” regions
-OH groups are glycosylated (carbohydrate)
evidence for bone nucleation site
cross-links form between fibers for additional strength
Lysyl oxidase
Converts lys or hydroxlys sidechain to a reactive aldehyde
Allysine group
and Cross-links
forms covalent cross-links between tropocollagen -> fibrils
Schiff base forms between lys NH3+ and the aldehyde group of allysine
Two allysine residues condense to form a corss-link, generally intrahelix
HIs and 5-hydroxylysine also contribute cross-links
more crosslinks accumulate with age
