BMSC 200 (Slide 4) 3D structures

tasnimjaisee's version from 2017-10-02 16:38


Question Answer
Protein SizeTypically 100-1,000 amino acids in length
3d structure of protein is determined by?Amino acid sequence
The function of a protein depends on its?structure
An isolated protein usually exists in what form?In 1/small number of stable structural forms
The most important forces stabilizing specific structures of a given protein are?non-covalent
Native proteins are only which type of stable?marginally stable (stability is defined as the tendency to maintain a native conformation).
The protein conformation with lowest free energy (the most stable) is usually the one with?the maximum number of weak interactions
The stability of a protein is defined as?Difference in free energies of folded & unfolded states
Folded proteins occupy which type of energy state?Low-energy state that makes the native structure most stable
Denaturationdisruption of native conformation with loss of activity - Energy required is small (equivalent to a few hydrogen bonds) - Reversible
Primary Structure Only linear arrangement of amino acids - determined by investigating protein/corresponding gene
Secondary StructureMaintained by main chain hydrogen bonds between amide hydrogen & carbonyl oxygen groups - Important: a-Helicies and b-Sheets
To represent a viable form of secondary structure the folding pattern mustOptimize hydrogen bond potential of main-chain carbonyl & amide groups - Represent favored conformation of polypeptide chain
Peptide bond have which hydrogen bonds?Equal number of hydrogen bond donors & hydrogen bond acceptors
ConfigurationSpatial arrangement of atoms around double bonds/chiral centers - Only changed by breaking bonds
ConformationSpatial arrangement of groups that are in different positions in space w/o breaking bonds - Structural state that are achieved w/o breaking covalent bonds
Rotation around C-N bond is restricted due to?The partial double-bond nature of the peptide bond
Most residues within biological peptides and proteins tend to be in cis or trans configuration?trans configuration
Each α-carbon is held within?Main-chain through single bonds - Complete freedom of rotation - Phi (Φ) Cα-N and Psi (ψ) Cα-C
Ramachadran plotIllustrates all possible combinations of phi and psi & highlights combinations that are observed in actual proteins
The most favored conformations define the?common secondary structures (lowest energy conformations)
Secondary Structure (α-Helix) 3.6 residues/turn - (n+4) - Stabilized by hydrogen bonds parallel to helix axis - Point toward the C-terminus
Proline because of its rigidity, makes it a?Helix breaker & is not found in α-helicies
Glycine because of the flexibility makes it?Uncommon in α-helicies
Residues separated by 3-4 positions in the primary structure are?close together in helical structure
Charged residues separated by 3-4 positions in the primary structure are?away from each other
Aromatic residues separated by 3 or 4 positions do what action?enable hydrophibic interactions
A small ____ ____ are in each peptide bondElectrical dipole
As a result, the helix has a net dipole, helix N terminus carries ___ charge, the C terminus carries partial ____ charge + and -
Residues which are four residues away from each other in the primary sequence will be on ____ side of an alpha-helixSame
Positioning of hydrophobic & hydrophilic residues with primary structure generates?amphipathic helix with hydrophobic and hydrophilic faces
Tertiary Structurefinal folding patter of single polypeptide
Secondary Structure β Sheets FactsMultiple β strands arranged side-by-side - Made up of β strands
Secondary Structure β Sheets FactsMultiple β strands arranged side-by-side - Made up of β strands - Fully extended polypeptide chains - Side chains move above and below strands - Stabilized by Hbonds C=O and -NH
Parallel β sheetsstrands run in the same direction
Anti-Parallel β sheetsstrands run in the opposite direction - More stable because of hydrogen bonding geometry
Side chains within polypeptide chain tend to be cis or trans?Trans
alternating polar and non-polar residues within the primary structure will give rise to what type of beta sheet?an amphipathic beta sheet
Tertiary structure represents the final ____ ____ of a single polypeptide chainFolding pattern
Amino acid sequence determines which structure?tertiary
Quaternary Structurefolding pattern with multiple polypeptidesSubunit are separate polypeptide chains - multiple subunits of the same/different polypeptides - Subunits often associate by non-covalent interactions - Specific & discrete interactions
Biological advantages associated with quaternary structureStabilizes and prolongs life of proteins
Fibrous ProteinsKeratin • Collagen • Silk
Globular ProteinsMyoglobin • Hemoglobin
Primary Structure of KeratinPseudo-seven repeat - A & D are hydrophobic
Secondary Structure of Keratin: Right-handed amphipathic alpha-helicies - Residues from A & D are on the same face of the helix; hydrophobic strip along helix length
Question Answer
Tertiary Structure of keratindominated by polypeptide strand presenting an alpha-helical rod - Hydrophobic strip running length of this rod is looking for a hydrophobic environment
Quaternary Structure of Keratine: Pseudo7 repeat generates hydrophobic surfaces along helix length - Hydrophobic surfaces interact to form coiled-coil - Coiled-coil of keratin involves 2 right-handed helicies wrap around each other in a left-handed fashion
Question Answer
Strength of the structures produced from keratin arise from?Successive linking of individual units into higher-order structures
Individual units of Keratin linked together through which bonds?Disulfide
Collagen makes up which % of proteins?25%
Primary Structure of CollagenMultiple repeats of Gly-X-Y where X is often proline or hydroxyproline
Secondary Structure of CollagenFormation of left-handed helicies of three residues per turn
Tertiary Structure of CollagenNearly the full length of the polypeptide is helical.
Quaternar Structure of CollagenFormation of coiled-coils. Three left-handed helicies wrapping around each other in a right-handed fashion.
Individual units of Collagen linked together through which bonds?Amino acid residues undergoing post-translational modification (hydroxyproline, hydroxylysine).