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.     

                       














      

Metabolism of biomolecules in various living organisms

Definition : Metabolism is the sum total chemical reactions occuring in the living system to sustain life.The word metabolism can also use to reffer all chemical reactions occuring within living system including  digestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories.

Metabolism is broadly divided into two categories :

1. Catabolism : The degradative or breakdown process of  organic molecules to simpler ones, with a release of energy.

2. Anabolism : The biosynthetic processes in which  energy  is used to construct complex components of cells such as proteins and nucleic acids from simple precursors.

The chemical reactions of metabolism are organized in a metabolic pathway that constitutes a series of enzymatic reaction to produce specific products. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy and will not occur by themselves, by coupling them to spontaneous reactions that release energy.Enzymes act as catalysts and allow these reactions to proceed quickly and efficiently. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells. The term metabolite is applied to a substrate or an intermediate or a product in metabolic reaction.

The metabolism of an organism determines which substances it will find nutritious and which it will find poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The speed of metabolism, the metabolic rate, also influences how much food an organism will require.

A striking feature of metabolism is the similarity of the basic metabolic pathways between even vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all organisms, being found in species as diverse as the unicellular bacteria ''Escherichia coli'' and huge multicellular organisms like elephants. These striking similarities in metabolism are probably due to  their early appearance in evolutionary history and being retained because of their high efficiency of different pathways.

Catabolism and Anabolism

Types of metabolic reactions

Metabolism of Carbohydrates

Metabolism of Lipids

Metabolism of Amino Acids

Metabolism of Nucleotides

Metabolism of Minerals

Membrane Proteins

Definition : Proteins that are firmly anchored in the plasma membrane via interactions between its hydrophobic domains and the membrane phospholipids.Also known as intrinsic protein .They include most membrane associated enzymes, antigenic proteins, transport proteins and drug hormone and lectin receptor.

Some membrane proteins are bound only to the membrane surface, whereas others have one region buried within the membrane and domains on one or both sides of it. Protein domains on the extracellular membrane surface are generally involved in cell-cell signaling or interactions. Domains within the membrane, particularly those that form channels and pores, move molecules across the membrane. Domains lying along the cytosolic face of the membrane have a wide range of functions, from anchoring cytoskeletal proteins to the membrane to triggering intracellular signaling pathways.  

Figure :  Transmembrane proteins within lipid bilayer membrane

There are about a thousand receptors in the human genome.These are membrane proteins that bind to chemicals (e.g., drugs) outside of the cell, and this binding process causes a chemical response on the inside of cells.  For example, morphine binds to the mu-opioid receptor in the membranes of brain cells, and the interiors of the cells respond by reducing nerve transmission.

Ion-channels are membrane proteins that allow transport of chemical species into and out of cells.  Nerve transmission, for example, is caused by a difference in ionic strengths across the membrane and this is mediated by ion channels.

Classification of membrane proteins :

Membrane proteins are classified based on the basis of removal of the protein from the membrane .

       

                               1. Integral (intrinsic) Proteins .

                               2. Peripheral (extrinsic) protens.


1. Integral poteins : Integral proteins are very firmly associated with the membrane removal only by agents that interfere with the hydrophobic interactions, such as detergents, organic solvents.

Integral proteins contain sequences rich in hydrophobic hydrocarbons of the lipids , thereby stabilizing the protein-lipid complex.Many integral membrane proteins are glycoproteins.

They act as  transport channels, linkers, receptors, enzymes, structural membrane-anchoring domains, proteins involved in accumulation and transduction of energy, and proteins responsible for cell adhesion. 

2. Peripheral proteins : Peripheral proteins are located on the membrane surface . They associate with the membrane through electrostatic interactions and hydrogen bonding with the hydrophilic domains of integral proteins and with the polar head groups of membrane lipids . Peripheral proteins localized to the cytosolic face of the plasma membrane include the cytoskeletal proteins spectrin and actin in erythrocytes.

They are released by treatment with salt solutions of different ionic strength , extremes of PH; a commonly used  agent is carbonate at high PH. Many peripheral proteins are enzymes and are typical water soluble proteins.

They serve regulators of membrane-bound  enzymes or may limit the mobility of integral proteins by tethering them to intracellular structures.

The peripheral proteins are subclassified on the basis of their mode of attachment to a membrane .

a. Proteolipids : Proteolipids are hydrophobic lipoproteins soluble in chloform and methanol but insoluble in water .They are presents in many membrane but particularly in myelin.

b. Lipophilin : Lipophilin a major lipoprotein of  brain myelin, contains over 65% hydrophobic amino acids and covalently bound fatty acids.

Functions of membrane proteins : Membrane proteins have a variety of functions including ;

1. Membrane proteins act as mediators of transmembrane movement of charged and uncharged molecules.

2. As receptors for the binding hormones and growth factors .

3. Serve as connection between the cells internal and external environments .

4. Act as enzymes involved in transduction of signals.

 5. Some integral membrane proteins have a structural role to maintain the shape of the cell.

6. Transport proteins play an important role in the maintenence of concentrations of ions of cells .These transport proteins come in two forms : Carrier proteins and Channel proteins.

7. They control cell adhesion to form tissues, they dictate development of plants and animals, and they control important metabolic processes, including salt balance, energy production and transmission, and photosynthesis.  In short, they are important in across medicine and agriculture.

Fluid Mosaic Model OR Lipid Bilayer Structure of Cell Membrane

Fluid mosaic model : A model that describes the structure of cell membranes . This model conceived by S.J.Singer and G.L.Nicolson in 1972 to describe the structural features of biological membrane . In this model a flexible layer made of lipid molecules is interspersed with large protein molecules that act as channels through which other molecules enter and leave the cell.

The plasma membrane of cells has two layers (a bilayer) of phospholipids. Each phospholipids molecules has a polar head and nonpolar tail. In lipid bilayer  the non polar regions of the phospholipids in each layer face the core of the bilayer ,because nonpolar tail is hydrophobic and their polar head (hydrophilic) groups face outward interacting with the aqeous phase on either side.

                                   Figure : Fluid Mosaic Model of cell Membrane

Proteins are embedded in this bilayer sheet held by hydrophobic interactions between the membrane lipids and hydrophobic domains exposed on both sides, giving the membrane the look of a mosaic .The fatty acyl chains in the interrior of the membrane form a fluid hydrophobic region and integral proteins float in this sea of lipid and  the carbohydrate moieties attached to some proteins .

The membrane is assymmetric due to the irregular distribution of proteins .The lipid and protein units in membrane form an appearence of mosaic or a ceramic tile unlike a fixed mosaic of ceramic tile and mortar is free to change constantly. The membrane mosaic is fluid because most of the interactions among its components are noncovalent ,leaving individual lipid and protein molecules free to move literally in the plane of the membrane.

Peptides

Peptides are chains of amino acids  in which two or more amino acids are joined by a characristics bond termed as a peptide bond.When two amino acids are covalently joined through a substituted amide linkage , termed a peptide bond, to yield a dipeptide. Such a linkage is formed by a removal of the elements of water from the α-carboxylic group of one amino acid and the α- amino group of another . The peptide bond between two amino acids  are formed by a condensation reaction.

Three amino acids can be joined by two peptide bonds to form a tripeptide ; similarly amino acids can be linked to form tetrapeptides, pentapeptides, and so forth. When few amino acids are joined in this fasion , the structure is called an oligopeptide.When many amino acods are joined, the product is called a polypeptide. Proteins are also a polymer of amino acids. Although the terms protein and polypeptide are sometimes used interchangeably, molecules reffered to as polypeptides generally have molecular weights below 10000 and those  called proteins have higher molecular weights.The number of amino acids is less than about 50 these molecules are named peptides while larger sequences are referred to as proteins.

In a peptide , the amino acid residue at the end with free α- amino group is the amino-terminal(N-terminal) residue : the residue at the other end, which has a free carboxyl group, is the carboxy terminal (C-terminal) residue .

                                                          
                                                              Peptide Bond

                                                            Peptides

Peptide classes  : Depending on synthesis of  peptides are classified into some major classes including

Milk peptide : This type of peptide are produced by enzymatic breakdown of milk protein  or  by the proteinases formed by lactobacilli during the fermentation of milk . Several milk peptide show antihypertensive effects in animal and in clincal studies.

Ribosomal peptide : Ribosomal peptides are synthesized by translation of mRNA.They are often subjected to proteolysis to generate the mature form. These act as hormones and  signaling molecules.

Nonribosomal Peptides : These peptides are assembled by enzymes that are specific to each peptide, rather than by the ribosome. The most common non-ribosomal peptide is glutathione, which is a component of the antioxidant defenses of most aerobic organisms.

Peptone : Peptones are derived from animal milk or meat digested by proteolytic digestion.Peptone is used in nutrient media for growing bacteria and fung.

Biologically active peptides and polypeptides 

Peptides  are present in every living cell and possess a variety of biochemical activities.Naturally occuring peptides range in length from two to many thousands of amino acids residues. Even the smallest peptides can have biologically important effects. Many small peptides exert their effects at very low concentrations. A number of vertebrate hormones are small peptides include oxytocin(nine amino acid residue) ,which is secreted by the posterior pituitary and stimulates uterine contractions ; brddykinin (nine residues) ,which inhibits inflammation of tissues ; and thyrotropine realising factor (three residues), which formed in the hypothalamus and stimulates the release of another hormone ,thyrotropin ,from the anterior pituitary gland. Some toxic mushrooms poisons such as amanitin, are also small peptides, as are many antibiotics .

Slightly larger are small polypeptides and oligopeptides such as the pancreatic hormone insulin which contains two plypeptide chains onehaving 30 amino acids residues and the other 21.Glucagon ,another pancreatic hormone,has 29 residues; it opposes the action of insulin.Corticotropin is a 39 residue hormone of the anterior pituitary gland that stimulates the adrenal cortex.

Synthesis of peptides :

Peptides are synthesized by coupling the carboxyl group or C-terminus of one amino acid to the amino group or N-terminus of another. There are two strategies for peptide synthesis: liquid-phase peptide synthesis and solid-phase peptide synthesis (SPPS).

                                          Figure : Solid -phase peptide synthesis




Peptides in Molecular Biology  :

Peptides have recently received prominence in molecular biology for several reasons. The  peptides allow the creation of peptide antibodies in animals without the need to purify the protein of interest.This involves synthesizing antigenic peptides of sections of the protein of interest.

Another reason is that peptides have become instrumental in mass spectrometry, allowing the identification of proteins of interest based on peptide masses and sequence. In this case the peptides are most often generated by in-gel digestion after electrophoretic separation of the proteins.

Peptides have recently been used in the study of protein structure and function. For example, synthetic peptides can be used as probes to see where protein-peptide interactions occur.

Inhibitory peptides are also used in clinical research to examine the effects of peptides on the inhibition of cancer proteins and other diseases.