Chapter 4: protein 3D structures
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Vanillacoffee Plus on February 23, 2012
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31 terms
Terms | Definitions |
|---|---|
 Conformation | Different arrangement of atoms in a space result of rotation about single bond. "Conformation of a protein from its amino acid sequence" |
| Configuration | different relative orientation in space that can't be altered w/o breaking/ returning covalent bond. "R&S, CIS & TRANS" Configuration: means the position or arrangement of parts; shape; outline; formation The band goes out on the field during every football game and makes many configurations |
| 1 Residue | 1 Amino acid |
| Dipeptide, tripeptide, tetrapeptide, poly | dipeptide = 1 peptide bond etc... |
| What is the nature of the peptide bond? | peptide bond is rigid and planar due to the double bond and resonance of the carboxylic acid. -indicates the implication for protein structure. -trans "configuration" -6 atoms lies in space |
| What is the primary structure of protein? | it is the sequence of amino acids in a protein. This is where the function highly depend on. |
| What evidence do we have that primary structure of proteins determine the functions? | 1. Protein with different 1* structure have different function. (oxytonin, vasopresin) 2. Genetic disease => symtoms b/c of deflective protein with altered 1* structure. Sickle cell. 3. Evolutionary conservation of key sequence patterns. |
| How do we determine primary structure? | 1.) hydrolyze, use specific reagent to ID n-terminal and c-terminal, cleave, cleave. 2.) nucleotide sequencing, or mass spec. |
| What is the secondary structure protein? | the H-bonded arrangement of the backbone of the protein and the orreintation of phi angle and psi. |
| The angle of rotation about the bond between the nitrogen atom and the -carbon atom of secondary structure is called ____ . | Phi - secondary structure only |
| The angle of rotation about the bond between the -carbon atom and the carbonyl carbon atom is called _____. | Psi- secondary structure only |
| Ramachandran plots | Are all combinations of f and c possible? Gopalasamudram Ramachandran recognized that many combinations are not found in nature, because of steric clashes between atoms. The f and c values of possible conformations can be visualized on a two-dimensional plot called a Ramachandran diagram |
| ______ exclusion, the fact that two atoms cannot be in the same place at the same time, restricts the number of possible peptide conformations and is thus a powerful organizing principle. | steric |
| 2*: characteristic of α-helix | 1. right handed stair case 2. is stabilized by h-bonding between peptide backbone group. h-bonding occurs 4 residue apart 3. Helix dipole (N-Terminus => delta+, C-terminus => delta- 4. the R-groups are pointing outward. |
| What is the stabilizing factor from primary structure? | 1. favorable interaction b/w side chains (h-bond, non-polar together "hydrophobic interaction", ionized with ionized. 2. - side chain at n-terminus, + side chain at c-terminus |
| What is the destabilizing factor from primary structure | *primary structure influence α-helix structure 1.) electrostatic repulsion e.g. Asp+Asp, 2 negative charge close to each other. 2.) Proline: limited allowed, movement of phi and psi cause kinks. Glycine: lots of phi and psi angles. Too flexible. |
| 6 characteristics of β-sheet | 1.) peptide backbone is extended in zig-zag "conformation". 2.) senses of stretches of peptide along side by side. => each strech = a β-strand => β-strands = β-sheet 3.) H-Bonding b/w peptide backbone stabilized. 4.) two arrangment can form: anti-parallel, parallel 5.) large sheet have larger curvature 6.) can have strands from distant parts of polypeptide |
| 2 characteristic of Reverse turns (β-turns) | 1.) turns can be seen at the surface of protein 2.) Glycine and proline does u turns because glycine is flexibile and proline is cis form about peptide bond. |
| Loops | - exposed to aquous environment and usually made of hydrophillic R groups. "turns" |
| Tertiary structure of protein | the overall 3-D arrangment of all atoms in the molecule |
| Tertiary water soluble protein, typically have __________ core; hydrophilic exterior | hydrophobic |
| What are the stability factor for tertiary protein? | 1. h-bonding 2. disulfide bond (cys-cys) 3. ionic (salt bridge), electrostatic attraction 4. hydrophobic interaction 5. Coordination to a metal => lone pair of e- |
| Motifs/ Suprasecondary structures | Certain combinations of secondary structure are present in many proteins and frequently exhibit similar functions. For example, an helix separated from another helix by a turn, called a helix-turn-helix unit, is found in many proteins that bind DNA |
| Domains | stretch of a protein that folds into a globular unit - folds forms the core of a domain - classification of proteins by domain structure. |
| Quaternary structure of protein | the spatial arrangement of several polypeptide chains in a multi-subunit protein |
| Terminology: dimer, trimer, tetramer, oligomer, heteromer, homomer, hetertetramer. | #of chains/ parts / subunits of a polymer heteromer: different subunits homoer: same subunits hetertetramer: different in the 4 sub units |
| Quaternary stabilizing factors? | interaction by side chains |
| 6 Ways to denature a protein | 1. heat: increase molecular vibrations, disrupt h-bonding 2. ph extremes: disrupt salt bridges ( same h-bonding) 3. detergents: interfere hydrophobic interaction 4. β-mercaptaelbanal -> breaks disulfide bonds 5. urea & guanidinium -HCL: disrupt h-bonding and hydrophobic effect 6. mechanical force |
| What is the driving force for protein folding? | - driven by hydrophobic effect (spontaneous) |
| What assists in folding? | chaperone isomerase - protein disulfide isomerase (help correct disulfide folds) - Peptide prolyl cis-trans isomerase (help proline get into cis configuration) |
| Nature of protein folding | - reversible, rapid (not random), folds are in energetically favorable conformation -primary sequence structure predicts 3* foldings |
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