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34 Cards in this Set

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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