Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
34 Cards in this Set
- Front
- Back
|
NH2 terminal orlysine chain
|
Acid form:
R-NH3+ ammonium Base form: R-NH2 + H+ Pka 7.6-10.6 |
|
|
COOH terminal or Glu, Asp
|
Acid:
R-COOH carboxylic acid Base: R-Coo- + H+ Pka 3.0-5.5 |
|
|
Arginine
|
Acid: Guanidinium
Base: Guauidino Pka 11.5-12.5 |
|
|
Histidine
|
Acid: Imidozolium
Base: Imidozole Pka 6.0-7.0 |
|
|
Tyrosine
|
Acid: Phenol
Base: Phenolate Pka 9.5-10.5 |
|
|
Dissociation constant
|
COOH «COO- + H+
pka 2.0-2.5 NH3+ « NH2 + H+ Pka 9.0-10.0 The third dissociation constant comes from ionizible groups on side chain pH= pka + log [conj base]/[conj acid] pH= pka + log[conj acid]/ [conj base] |
|
|
pI on protein
|
at pH < pI, The molecule is positively charged
at PH > pI , The molecule is negatively charged |
|
|
Zwitterion
|
Total negative charge= total positive charge
|
|
|
Isoelectric point
|
pH=pI
|
|
|
pI
|
the pH at which the aa or protein is in zwiterion form
=pKa COOH = pKa NH3/ 2 pI of protein Determined experimentally by determining the pH at which the protein does not move in the electric field |
|
|
Primary structure
|
The aa sequence
|
|
|
Secondary structure
|
Local folding of the polypeptide backbone into regular patterns alpha helix and beta sheet.
|
|
|
Tertiary structure
|
3-D folding of protein stabilized by interactions b/ distant parts of the sequence
|
|
|
Quaternary structure
|
The interactions b/w different polypeptides into oligoneric structures stabilized by non-covalent bonds only. Not all proteins have this structure.
|
|
|
Noncovalent interactions
|
Hydropgobic bonds
H-bonds Ionic bonds Van der waal forces |
|
|
Hydrophobic interactions
|
Primarily entropy driven. H20 molecules surrounding hydrophobic molecule and restricted to an “ordoned” config (don’t like)
-folding of hydrophobic molecules into interior protein increases entropy of system and is thermodynamically favored. |
|
|
H-bond
|
Electrostatic interactions b/ w hydrogen atom covalently bound to an electronegative atom and a second electronegative atom lone pair of non-bonded electrons.
|
|
|
Ionic bonds
|
Also called electrostatic interactions or salt linkages.
Important for stabilization of protein Help mediate binding or charged ligands and substrate Most charged groups are on the surface of the protein where they are stabilized by hydrogen bonding and polar interations with water. |
|
|
Vander waals
|
Weak bonds interactions mediated by fluctuation electrical changes.
Each atom has a characterisitic “size” ore vander walls radius-atom are attracted to each other until the distance b/w them equals the sum of their vander waals radii Also includes repulsion forces- if two atoms get two close they repeal each other very strongly. |
|
|
Chaperone protein
|
Reversibly binds hydrophobic regions of nascent proteins prior to complete folding.
Help unfold misfold segments Prevents aggregation or other inappropriate interactions with other proteins Helps proteins to attain their most functional, compact formation. |
|
|
Globular protein
|
Spheroidal, fairly high water solubility, function as catalysts, transporters, and regulators of metabolic pathways.
|
|
|
Fibrous protein
|
Usually contain large amount of secondary structure, low solubility in water. Typically play structural roles.
|
|
|
Collegen
|
Most abundant protein
All of the collagen types have regions where there is a tripeptides Gly-Pro-Y and Gly-X-Hyp repeated in tandem several hundred times Contains unique aa-hydroxyproline and allysine |
|
|
Elastin
|
Abundant ligament, lungs, aterial, walls, and skin
Slastin molecules are formed from relatively loose and unstructured polypetide chains that are covalently linked into a rubber like elastin meshwork Aloows tissue to stretch without tearing Conatins the derived aa allysine which form unique cross-linked structures. |
|
|
Solubilty
|
Salting out
|
|
|
Ionic change
|
Ion exchange chromatography
Electrophoresis Isoelectric focusing |
|
|
Polarity
|
Hydrophobic interactions
Chromatography |
|
|
Size (MW)
|
SDS-page
Ultra centrifugation Gel filtration chrom |
|
|
Binding affinity
|
Affinity chrom
|
|
|
Salting out
|
Commonly used purification procedure
Different proteins precipitate at different salt con PH adjusted to control solubility-proteins are least soluble at their pI Varying pH and salt concentration allows for different presciptiation Most common salt used is (NH4)2SO4 |
|
|
Isoelectrical focusing
|
Gel filtration by pI
|
|
|
Ion exchange chrom
|
Cation (positive charge on resin)- exchanging resins binds- charged proteins
Anion exchanging resin_ binds positively charged. Change pH and salt concentration to either facilitate or retard binding of the protein to the resin |
|
|
Gel electrophorsis
|
separation by electric field
SDS page SDS polyacrylamide gel electrophoresis A negatively charge detergents SDS binds protein, # SDS molecules is proportional to the # aa, and the now uniformly negatively charged protein (anion) are separated by there mw |
|
|
Edmans reaction
|
The polypeptide chain-reacted w/ phenylisothiocyanate which reacts w/ the amino terminus (NH2) end and cleaves it off in sequential order.
Repeated until polypeptide sequence is determined |
