General metabolic reactions of amino acids ( Deamination and Transamination ) for the liberation of ammonia

Deamination : The removal of amino group (-NH2) from the amino acids as NH3 is called deamination. Deamination results in the liberation of ammonia for urea synthesis. Deamination may be either oxidative or non-oxidative. 

                               

(1) Oxidative deamination : Oxidative deamination is the liberation of free ammonia from the amino group (-NH2) of amino acids coupled with oxidation. This takes place mostly in liver and kidney. The purpose of oxidative deamination is to provide NH3 for urea synthesis and α- keto acids for a variety of reactions including energy generation. 

It is catalysed by one of three following  enzymes :

                                           

                                                   1. L-Amino acid oxidases

                                                   2. D-Amino acid oxidases 

                                                   3. Glutamate dehydrogenase

Deamination by L- Amino acid oxidase

  

Deamination by D-Amino acid oxidase

Deamination by glutamate dehydrogenase

          

                                                                

(2) Non-oxidative deamination : Non –oxidation deamination is the liberation of free ammonia from the amino acids without undergoing oxidation.

Transamination :

The transfer of an amino (-NH3) group from an amino acid to a keto acid is known as transamination. This process involves the interconversion of a pair of amino acids and a pair of keto acids, catalysed by a group of enzymes called transaminases of aminotransferase

Salient feature of transamination : 

(1) All transaminases require pysidoxal phosphate (PLP), a coenzymes derived from vitamin B6.

(2)Specific transaminases exist for each pair of amino and keto acids. However, only two namely, aspartate transminase and alanine transaminase make a signtificant contribution for transamination.

(3) There is no free NH3 liberated only the transfer of amino group.

(4) Transamination is reversible. 

(5) Transamination is very important for the redistribution of amino groups and production of non-essential amino acids as per the requirement of the cell.

(6) Transamination diverts the excess amino acids towards energy generation.

(7) The amino acids undergo transamination to finally concentrate nitrogen in glutamate. Glutamate is the only amino acid that undergoes oxidative deamination to a significant extent to liberate free NH3 for urea synthesis.

(8) All amino acids extent except lysine, threonine, praline and hydeoxyproline, participate in transmination.

(9) Transamination is not restricted to α-amino groups only. For instance, δ-amino group of ornothine is transaminated.

(10) Serum transminases are important for diagnostic and prognostic purposes.

Biochemistry and Biochemistry Books essential for gathering proper knowledge in various sector of biochemistry

Simply Biochemistry means the study of the chemistry of biological system (including structure, composition, and chemical reactions of substances in living systems).It is the seperate department of science in which Biology combines with  organic, inorganic, or physical chemistry. In this department  study how living things obtain energy from food, the chemical basis of heredity, and what fundamental changes occur in disease .

Biochemistry includes the study of molecular biology; physiology; immunochemistry; neurochemistry; Biotechnology; Bioinformatrics ; Virology and Bacteriology ; Nutrition and bioinorganic, bioorganic, and biophysical chemistry.

A true biochemist must have  knowledge  in some subjects to develop  :
        
                                              

• statistics, chemistry and biology
• cells and organs, and the role of genes and proteins in living things
• chemicals, poisons and molecules, and their effects on living things
• practical skills for performing experiments and operating scientific equipment
• skills in researching, as well as analysing and interpreting research results
• maths and computer skills

Various book of different sector of biochemistry is essential to gather knowledge. For biochemistry, some book name with writter and publishers are mention in below........

Biophysical Chemistry :
       
                          1.Physical Chemistry with Application in Biological systems
                                                      By Ramond Chang
                                                      Publisher : Macmillan publishers co.
                                                                      New York,USA.

                          2.Text Book of Physical chemistry
                                                      By S.Glasstone
                                                      Publisher : D.Van Nostrand Company
                                                                      New York , USA.

                          3.Elements of Physical Chemistry
                                                       By S. Glasstone and D. Lewis
                                                       Publisher : The Macmillan Press
                                                                        New York ,USA.
                     
                           4. Essential of Physical Chemistry***
                                                       By B.S. Bahl,G.D. Tuli and A. Bahl
                                                       Publisher : S. Chand  & Company Ltd.

                                                                                    New delhi, India.

Bioorganic Chemistry
                         5.Organic chemistry
                                          
                                                 By R.T. Morrison and R.N. Boyd
                                                  Publishers : Allyn and Bacon Inc.
                 
                        6. Organic Chemistry
                          
                                                 By I.L. Finar ( Vol.1 and Vol.2 )
                                                 Publishers : English Language Book
                                                 Society and Liongman Group Ltd.

                       7. Organic Chemistry
              
                                                 By H. Hart and R.D. Schuetz
                                                 Publisher : Houghton Miffir Company
   
                       8. Contemporary Organic Chemistry

                                                By A.L. Ternay
                                                W.B. Saunders Company


Biochemistry

                       9. Lehninger Principles of Biochemistry

                                                By David L.Nelson &

                                                     Michael M.Cox
                                                Publisher : W.H. Freeman and Company
                   
                       10. Biochemistry
                                              
                                               By Lubert Stryer
                                               Publisher : W.H. Freeman and Company

Introduction of Biochemistry (Basic biological content those must be known to study biochemistry)

1. History and Scope of Biochemistry  
2. Concept of life and living process
3. The cell and its evolution
4. Biomolecules : 

            (a)  Carbohydrates :                Definition,characteristics and biological functions

                                                           of carbohydrates,Classification and nomenclature

                                                           Optical properties,Ring structure of common

                                                           monosaccharides,proof of ring structure of
                                                           glucose,Mutation of glucose,General properties
                                                           and coloure test of reducing sugars,Important
                                                           derivatives of  monosaccharides Sugar acids.
                                                           

                         Disaccharides    :     Maltose,Lactose,Sucrose, Some other                                                                                 disaccharides Isolation of disaccharides

                                                         from natural source, structure and 

                                                         biological importance of disaccharides .
                         Polysaccharides :     Structural and storage polysaccharides,
                                                         Structures and functions of starch,Glycogen
                                                         and Cellulose .Other polysaccharides of
                                                         biological interests,structure and functions.

              (b) Lipids             :              Nomenclature,classsification,general reactions
                                                        of fats,fatty acids and sterols. Biological
                                                        functions of lipids or fat, different classes of
                                                        lipids , isolation of cholesterol and
                                                        phospholids from natural sources.
                       
              (c) Amino acids and peptides : Structural features ,optical activity
                                                               classifictions,physical properties of
                                                               amino acids and peptides.
           

              (d) Proteins                      : General introduction of proteins,

                                                        classification of  proteins based on

                                                        biological functions,shapeand structure.

                                                        Isolation and purification of protein,
                                                        different structure of proteins,sequence
                                                        determination of various proteins e.g.
                                                        Insuline,sequence homology of
                                                        homologous proteins,denaturation of 
                                                        proteins.
                          Fibrous proteins  :  Protein conformation,alpha-keratins,
                                                        X-ray analysis of keratin,planar peptide
                                                        bonds,alpha-helix,helix forming and
                                                        destabilizing amino acids,the insolubility of
                                                        alpha-keratins,beta-keratins,conformation
                                                        of alpha and beta-keratins,structure of
                                                        collagen and elastin. Filamentous proteins-
                                                        Actin,Mysin and Microtubules.

                         Globular proteins : Distinctive tertiary structure of myoglobin
                                                        and ribonuclease,renaturation of unfolded
                                                        and denatured ribonuclease, factors
                                                        maintaining the tertiary structure of globular
                                                        proteins,oxygen binding curve of
                                                        haemoglobin and myglobin,the cooperative
                                                        binding of oxygen  by haemoglobin ,
                                                        factors contributiung to oxygen saturation
                                                        curve of haemoglobin,sickle-cell anaemia and
                                                        its relation to haemoglobin.

                        Protein purification and characterisation :
                                                        Dialysis and ultrafiltration,density gradient
                                                        centrifugation,gel filtration,isoelectric 
                                                        precipitation , solvent fractionation,                                                                               salting-in and salting-out of proteins
                                                        electrophoresis,ion-exchange chromatography
                                                        selective absorption,affinity chromatography,
                                                        minimum molecular weight determination.
           
              (e) Nucleic acids      :         Occurrence, structure, composition and functions.            
                                               
                                             Questions related with this syllabus

CONTENT /SYLLABUS OF METABOLISM OF NITROGENOUS COMPOUND

1. Amino acid Metabolism : 

• Structure of 20 essential Amino acids   
• General reactions of amino acids
• Various enzymes involved in Amino acids metabolism
• Overview of amino acid catabolism in mammals
• Oxidative degradation of 20 amino acids to specialized products
• Pathways(summary) of Amino acid degradation
• Metabolic fate of Amino Groups
• Glucogenic and ketogenic amino acids
• Overview of Amino acids biosynthesis
• Regulation of amino acids biosynthesis
• Regulation of amino acids metabolism
• Metabolism of branch chain amino acids
• Propionate and methylmalonate metabolism
• Urea cycle and its link to TCA cycle
• Regulation of Urea cycle
• Nitrogen cycle and Nitrogen fixation  
• Folic acid and One-carbon metabolism
• Glutathion metabolism
• Metabolism of  Amonia : Formation ,Transport and storage,disposal,                Toxicity,Trapping and Elimination , Function.
• Glucose -Alanine cycle
• Enzyme cofactors in amino acid catabilosm       
• Molecules derived from Amino acids : Heme,Creatine and phosphocreatine ,   Glutathione, Plant substances(Auxin,Lignin,Cinnamate), Biological Amines (Dopamine,Norepinephrine, Epineprine, GABA, Serotonin,Histamine,Cimetidine, Spermine,Spermidine) , Nitric Oxide (NO). 

        Clinical correlations : Phenylketonuria, Alkaptanuria, Folic Acid deficiency,
                                          Hyperamonemia and Hepatic coma, Deficiencies of the
                                          Urea cycle enzymes.
2. Nucleotide Metabolism :

• Nucleotides and its metabolic function

• Enzymes involved in nucleotides metabolism

• Denovo and salvage pathway,

• Bioynthesis of purine and pyrimidine nucleotides, 

• Degradation of purine and pyrimidine nucleotides,

• Uric acid and gout, 

• Formation of deoxyribonucleotides, 

• PRPP  participating reaction ,

• Regulation of purine nucleotide biosynthesis by feedback inhibition,

• Regulation of pyrimidine biosynthesis by feedback inhibition,

• Inhibitors of purine synthesis 

• Biosynthesis of nucleotide coenzymes,

• Purine and pyrimidine cycle, 

• Heme metabolism, 

• Bilirubin metabolism and clinical significance,

 Clinical Correlations : Gout, Hyperuricemia, Lesch-Nyhan syndrome, Orotic aciduria,      

                                 Immunodeficiency diseases associated with purine metabolism.

3. Xenobiotics : Introduction of Xenobiotics,General properties of Xenobiotic metabolite,

                        Entry of Xenobiotics to body,    Role of liver in Xenobiotics metaboism,  

                        Cyt.b 450 ( properties, structure, role in  xenobiotic  metabolism ) ,

                        Methods of xenobiotics metabolism or reaction(Conjugation,Reduction,

                        Hydrolysis and oxidation) of xenobiotic metabolism .   

                                     Question Realated with this Syllabus.