Amino Acids & their role in Proteins  (esp., enzymes)
   Proteins - the penultimate molecules ?
           
 structurally complex
   
          functionally sophisticated
             most abundant molecule in cells
                                                  15% of cells dry mass
            
long repeats of individual monomers...
                           Amino Acids

Helicase



                                                           

 

 

 

 

 

 

reading pages  41-44

                                  R 
                     
H2N -  C  - COOH
                                 
H

    20 common amino acids - mcb 2.14 p42  ( a, b, and c )*
      lys-arg-his-asp-glu-ala-val-leu-ile-pro-phe-met-trp-gly-cys-ser-thr-tyr
  
    k -  r -  h -  d -  e -  a -  v -   l -  i -  p  -  f  -  m -  w - g  - c -  s  - t  - y

    

 

 

 

 

     

 

why only these 20 ?    
 
all are a-amino acids      &      most the L-stereoisomer...     
       a = N-C-COOH    βN-C-C-COOH    γN-C-C-C-COOH
 2 stereo-isomers (enantiomers = mirror images)
      
levo-rotatory (left)    &     dextro-rotatory (right)
      
mostly L-amino acids occur in living cell proteins 
 calcite mineral*
                                                  thus, an evolutionary anomaly...

  

 but, there are some
unusual aas that play structurally important roles
          4-hydroxy proline         occurs in plant cell wall proteins
          5-hydroxy lysine           occurs in fibrous proteins as collagen
          N-methyl lysine            occurs in myosin contractile proteins
          γ-carboxy glutamate    occurs in prothrombin
  
            Amino Acids...   structures & chemical properties of AAs [m.w.king]

 

 

 

 

 

  

   
     1st amino acid discovered was  asparagine   (1806 in asparagus)
     last amino acid described was  
threonine     (1938)
   STRUCTURE* - amino acids have a carboxyl group (- COOH) & 
   
                           amino group (-NH2) ...bound to an asymmetric carbon
                   

   20 ubiquitous aa's have 4 groups on a-C  in a tetrahedron shape 

     Charge of Amino Acids -     an ACID molecule that tends to release a H+ (-COO-
                                             & a BASE with a group that readily combines with a H+ (NH3+)
      Zwitterion  -  an ampholyte*  molecules holds equal # of opposite charges, as an amino acid
                                are neutral;             [amphoteric -
can react as either an acid  or base
          Isoelectric Point  -  pH where no net charge in molecule
          pK  -  pH where groups are 50% ionized & 50% non-ionized

 

 

 

 

 

classes of amino acids...     [classified by chemistry of R-Groups]      

polar

charged
  ACIDIC... negatively charged   ASP & GLU
     R group with 2nd
COOH that ionizes above pH 7.0     
  BASIC... positively charged     LYS, ARG, HIS        mcb 2.14*
    
R group with 2nd amide that protonates below pH 7.0

  POLAR UNCHARGED...      SER, THR, ASN, GLN, TYR,
     are soluble in water, i.e., hydrophilic                          mcb 2.14*
    NON-POLAR... (aliphatic)    ALA, VAL, ILE, LEU, PHE, TRP
     contain only hydrocarbons R groups = hydrophobicity mcb 2.14*
  AROMATIC & SPECIAL          PHE,TRP,TYR,GLY,PRO,CYS
     contain R groups with ring structures  &  others        mcb 2.14*

 

 

 

 
Peptide Bond...
       

formed by condensation reaction* between 
amino of one aa...     &    carboxyl of another aa ...     mcb 3.3 - a tripeptide
*
 

substituted amide covalent bond  =   dipeptide 
has partial double bond character -
      shorter & stronger than C-C
      longer, yet weaker than C=C
      no free rotation (group in same plane, but TRANS)
      results is zig-zag planar molecule  

              representative views of:    peptide bonds*    &     a polypeptide*
 

 

 

 

 

 
  
There are only 3 known ways to make a peptide bond...

1. chemical abiotic synthesis in the laboratory...  PPTI

2.  genetic engineering cloning mechanisms...   humulin

3.  biologically, in cells...   (@ rate of 25aa/sec in prokaryotic cells)


  Some common peptide terminology:

        dipeptide,   tripeptide,   oligopeptide,   polypeptide

            protein - polymer of a-L-amino acids joined by peptide bonds
 
  
ways of depicting proteins:  mcb 3.8*     whale myoglobin  - ecb 2/e panel 4.2 pg 132-133

 

 

 

 

 

 

 

 

 examples of naturally occurring small oligopeptides[many are vertebrate hormones]

 Nutra Sweet    -  a dipeptide* (2aa) of  L-aspartyl-phenylalanyl-methyl ester... aspartame
 insulin             - two polypeptides...    controls carbohydrate metabolism
                                        1. alpha chain of 30 aas   &   2. beta chain of 21 aa
 glucagon          - pancreatic hormone 29 aa...    opposes insulin action
 corticotropin  - 39aa - anterior pituitary hormone...  stimulates adrenal cortex
 oxytocin         - 9aa - hormone of posterior pituitary...  stimulates uterine contractions
 bradykinin      - 9aa hormone acts on smooth muscle... vasodilatation/inflammation
 angiotensin     - octapeptide (derived from angiotensinogen by kidney enzyme renin) 
                        - increases blood pressure   ACE  Inhibitors block AT & lower bp. [sport]
 thyrotropin relasing factor  (TSH) -  3 aas [Glu-His-Pro] of hypothalmus...
                       -
stimulates thyroid to release thyroid hormone
 enkephalins     - either of two penta-peptides with opiate & analgesic activity, occurs
                                   naturally in brain & have marked affinity for opiate  receptors
            - compare with endorphins