Chapter 6: Protein structure pt. 1 Flashcards
Primary structure (basic)
-amino acid sequence and location of disulfide bonds
- only covalent bonds
Secondary Structures (basic)
-Hydrogen bonds: between backbone amide NH of one AA and backbone carbonyl C=O of another
-3D form of LOCAL SEGMENTS of biopolymers to give regular, recurring local conformations
-forms beta and alpha sheets
(alpha helix, beta strand, beta bend, collagen triple helix, loops and turns)
Tertiary Structure (basic)
-3D structure of a polypeptide
-bonds form through the hydrophobic effect
-folds stabilized by hydrogen and disulfide
-amino acids far apart in the primary structure may be brought together
-hydrophobic inside
-hydrophilic outside
Quaternary Structure (basic)
-organization of subunits on a protein with multiple subunits (oligomer or multimer)
-bonds form through the hydrophobic effect
-have H bonding, ion pair, and all bond that the tertiary structure has but DO NOT see covalent disulfide bonds
-subunits held together by many weak, noncovalent interactions
Characteristics of peptide bonds
- 40% DB character
-trans is the most stable; almost all are trans
-NO rotation
Resonance structure of peptide bonds (rotation)
-rotation can only occur around the alpha carbon of the peptide bond
-C alpha-N: phi
-C alpha C: psi
*both occur clockwise on each side
*fully extended chain= +180 or -180
Ramachandran Plot
-calculated plot of all sterically allowed phi and psi angles for a polypeptide chain
-shows that only a limited amount permissible configurations
protein secondary struc
-3D form of LOCAL SEGMENTS of biopolymers to give regular, recurring local conformations
- in protei
Alpha Helix was proposed by…
Linus Pauling (Robert Corey)
-found that H bonds form between adjacent AA’s to give curled polypeptide helix
In the alpha helix the hydrogen bonds occur between…
n and n+4 residues
Alpha Helix facts: structure
- Carbonyls pointing up (-)
-N-term pointing downwards (+)
-R group points outward (perpendicular to axis)
-H bonds are parallel to helix axis - Pitch=5.4 A
-Residues/turns=3.6 A
-rise/AA= 1.5A/AA
-most are right handed alpha-helicies
-has dipole (polarity)
-Stable alpha-helicies end with a + charged AA to neutralize dipole movement
-can be amphipathic
alpha helix destabilizer
- Proline: its cyclic sterically destabilizes an alpha helix
- Steric/ charge repulsion by adjacent bulky like charged amino acids
- R-groups are too large (tryptophan, tyrosine)
- R-groups are too small (glycine)
alpha-Keratin: structure
-coiled coil
-motif of two amphipathic alpha helices
alpha-Keratin: key structural material in….and can detect….
-hair, nails, and skin
-detects heavy metal poisoning
alpha-Keratin: bonds and perms
-has disulfide crosslinks (S-S) w covalent bonds since it is rich in Cys
-Perm: reduce -S-S- bonds, 2RSH, curl, re-oxidize to -S-S-
Beta-Strands facts
-almost fully extended polypeptide chains
-can come from same polypeptide, completely different sections of a polypeptide or even different polypeptides
Beta-sheets facts
multiple beta strands arranged side by side
-Ramachandran plot: beta sheets are at the top left corner of the plot
Beta- strands/Sheets (x,y,z)
-Strands (x plane)
-H bonds occur between adjacent strands perpendicular to strand direction (y-axis)
-side chains (r-groups) alternate in pointing above and below the plane perpendicular to H-bonds and strands
antiparallel beta sheets
-strands run in opposite N to C-terminal direction
-stronger H bonds because they can be linear
parallel beta sheets
strands run in the same N- to C- direction direction
Beta structure facts
-extended zig-zag (ruffled) conformation
-6-12 residues usually involved
-repeating units of 2AA residues with distance of 7A
-may be amphipathic
Silk fibroin
-stronger than steel
-extended layers of anti-parallel beta sheets of Gly-Ser-GLy-Ala-Gly-Ala
*Ala alternating with Ser/Ala w/ covalent bonds
- Ala from 1 sheet interdigitates w/ Ala from another sheet
Collagen (basic)
-main structural protein in the ECM in connective tissues
-most abundant protein in mammals
-1/3 the total protein mass in large animals
-present in: bone matrix, tendons, cartilage, blood vessels, skin
Collagen: what is the general repeating unit?
G-P-P-Hyp
(Gly-Pro-Pro-Hydroxyproline)
-Gly residue is invariant (can’t change) and is located among the central axis
-Need glycine for every third residue
Collagen: bonding
-H-bonding is interchain: occurs btwn amide NH of one helix to carbonyl oxygens of another helix
interchain involving HydroxyPro (hyp) stabilizes helix
*lysine can hbond w/ hydroxypro??
-NO INTRAchain H-bonding occurs
Osteogenesis Imperfecta
-brittle bone disease
-occurs when a mutation in a gene for collagen leads to the substitution of GLY for another amino acid
-prevents the normal production of mature collagen
Scurvy (vitamin C deficiency)
-lack of hydroxypro
-not enough interchain H-bonding
-weak collagen
Formation of hydroxypro requires…
O2 and ascorbic acid (vitamin C)
-hyrdroxypro is formed by prolylhydroxylase
-hydroxylys is formed by lyslylhydroxylase
Collagen Fibrils are also strengthened by what other than hydroxyproline
-intrachain lysine-lysine
-interchain hydroxypyridinium covalent crosslinks
Collagen: cross links
-more cross links=less elastic collagen
=more brittle bones/tendons
*sign of old age
Loops and turns: general w example
-in non-regular secondary structure
-turns and loops allow chain reversal
-normally on surface of globular protein (hydrophilic)
ex: the omega loop
The beta turn (beta bend, tight turn)
-allows polypeptide in antiparallel beta-sheet to reverse direction
-carbonyl O’s are H-bonded to amide H’s btwn residues 1 and 4
-proline is often the 2nd residue in beta-bends
X-ray crystallography
-reveals 3D structure in atomic detail
-need crystals of protein
*put them in a buffer
-difficult to get for many proteins
X-ray diffraction
-beam is shone through the crystal
-once it hits the crystal the beams gets diffracted
-diffracted beams gets detected by a detector
calculating protein structure (x-ray crys/ diffraction)
- see diffraction pattern
- fourier transform
- computer fit to map protein sequence
- fixed/frozen picture of protein
*resolution measured in A=10x10^-10 (smaller angstrom the better)
2D Nosey NMR Spectroscopy
-also a way to determine the structure of protein
-Limitations: need a high concentrations of protein, time consuming, only for proteins with a low molecular weight
NMR structure of proetin
proteins are dynamic - “breathe”
-can be displaced up to 2A
Cryo-Electron Microscopy (Cryo-EM)
form of transmission electron microscopy (TEM) where the sample is studied at cryogenic temperatures
-can see membrane proteins
