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  Estructura de Proteínas  


En la naturaleza encontramos a las proteínas en arreglos conformacionales específicos según su secuencia y el medio donde se encuentre la proteína, a esto se le llama estructura nativa la cual se puede dividir para su estudio en:

Estructura primaria

Estructura secundaria

Estructura terciaria

Estructura cuaternaria

Enzymes  catalytic activity    A ------> B
Transport Proteins bind & carry ligand molecules (hemoglobins)
Storage Proteins ovalbumin (egg), ferretin (iron), casein (milk)
Contractile Proteins can contract, change shape (actin & myosins) and
make up elements of cytoskeleton & muscles
Structural Proteins provide support... collagen fibers of tendons (wounds),
elastin of ligaments, keratin of hair & feathers,
fibroin of silk & spider webs
Defensive Proteins provide protection:  antibodies (IgG),    fibrinogen,
thrombin,  and  snake venoms (digestive enzymes)
Regulatory Proteins regulate metabolic processes: includes hormones,
transcription factors & enhancers
  nomeclature         protein nomenclature is based on solubility

      table 1*

        Concept Activity - 5.4 - Protein Functions


 Structure and Properties of Proteins 
  PROTEINS - are  POLYMERs  of AMINO ACIDS with biological reactivity 
made of alpha - amino acids (commonly 20)
in humans only 11 of 20 amino acids can be synthesized; 9 others (essential aa's) must be eaten. [HIS, ILE, LEU, LYS, MET, PHE, THR, TRP, & VAL]
    STRUCTURE of Amino Acids               fig of alpha amino acid*
aa's contain 2 functional groups: a carboxyl group (-COOH)  &   an amino group (-NH2) & each of these functional groups are often ionized* at physiological pH    
    ZWITTERION... 2 functional groups of opposite charges in same molecule (as in aa's)
                     What is charge of glycine at pH 3.0 ?        at pH 9.0 ?      (ans*)
Essential Nonessential
Isoleucine Alanine
Leucine Arginine*
Lysine Aspartate
Methionine Cysteine*
Phenylalanine Glutamate
Threonine Glutamine*
Tryptophan Glycine*
Valine Proline*
Histidine Serine*
Tyrosine* Asparagine*
Selenocysteine** Pyrrolysine**

(*) Essential only in certain cases.[1][2]

(**) Truly unclassified. Added to sustain the 22 Numbers of Essential Amino Acids.

Amino acid's are CLASSED by TYPE via chemical properties of R or Side groups...

Polar Charged
negatively charged amino acids - ASP & GLU
R group with a 2nd COOH that ionizes* above pH 7.0    
Polar Charged
positively charged amino acids - LYS, ARG, HIS
R group with a 2nd amide* that protonates below pH 7.0    figure*
   POLAR      UNCHARGED includes SER, THR, TYR, ASN, GLN    (cys)                   
are soluble in water, i.e., hydrophilic  (attract H-bonds)                figure*
contain hydroxyl or amino functional groups    
includes GLY, ALA, VAL, LEU, ILE, PRO                                  figure*
all contain only hydrocarbons R groups   =   hydrophobic like lipid
AROMATIC (hydrophobic non-polars)    PHE & TRP     (TYR)    &    MET,  CYS
all contain R groups with    ring structures*         or       Sulfur*   
peptide bond COVALENT LINK between carboxyl end (COOH) of aa-1
&   amino end (NH2) of aa-2   =   Peptide Bond

peptide bond

forms a dipeptide*   or eventually a polypeptide*        (figure)
linked by a condensation reaction (removes water = dehydration)
link between carboxyl -OH of one aa & amine -H of another
      it's intermediate in length & strength between C-C  &  C=C
      peptide bond is shorter & stronger than C-C
      longer, but weaker, than  C=C, but acts like one, thus there is
              no free rotation (attached group in same plane)   figure*
non-protein ex:  capsaicin (chili peppers active ingredient)  

                                                      Concept Activity - 5.4 - Protein Structure



 FRACTIONATION - Procedures for Isolation & Purification of "new" protein...
  Crude Homogenates  "grind & find"        [ mortar/pestle, blenders & homognizers
homogenize cells      grinderssonicators,  &  barocycler-(bbi) ]
  Differential Centrifugation  subcell fractionation* in a centrifuge developed by G.Palade     
speeds to 250,000xg --> [supernatant & pellet fractions]
  Sumanas, Inc. cell fractionation animation* listen at home
  Column Chromatography - separates proteins from others via flow thru media in a glass column

    gel filtration

    concept figure 1* [exclusion chromatography]    
Sephadex - porous carbohydrate polymer beads*
retard small MW proteins &
pass large MW proteins
figure 2*   based on SIZE   gel filtration methodology

                        ion exchange

 protein is retarded by binding to ionic charge
on column's media  (anionic or cation)     figure*


 polymeric beads with special ligands* which
bind specific proteins, but not other proteins    end 7


Gel Electrophoresis    - passage of protein mixture through a porous gel via an 
electrical charge that results in  separation of blood proteins by size & charge*
      PAGE   polyacrylamide gel electrophoresis PAGE*       [gel chambers]
proteomics - protein fingerprints can indicate evolutionary relations


(sodium dodecyl sulphate)- separates proteins via mass (MW)
1 SDS molecules binds equal to # peptide bonds    
Fig1* & Fig2*     animation of SDS*view @ home  & procedures
         Identification & 
 colorimetric reaction [Biuret & Bradford] where amount of
color produced is proportional to amount protein present 
a Standard*Curve* ]      advertisement


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