Introduction to Molecular Biology PDF

Introduction to Molecular biology  Bacteria Animals Plants humans  What are the common thing among:- Chairs Pencil Cupboard  Animals Bacteria Cell is the buliding unit P...

Introduction to Molecular biology  Bacteria Animals Plants humans  What are the common thing among:- Chairs Pencil Cupboard  Animals Bacteria Cell is the buliding unit Plants humans  Viruses are not cells but depend on cells for their replication  The nucleus is a membrane-enclosed structure that contains the chromosomes in eukaryotic cells. The nucleoid, in contrast, is the aggregated mass of DNA that constitutes the chromosome of cells of Bacteria and Archaea Introduction to molecular biology Why do we study molecular biology ??? 1. Because it is required to get the degree  2. To understand the basic behavior of cells (growth, division, specialization and interaction in terms of molecules 3. Medical applications: Identifying of disease-causing genes, sequencing of human genomes, gene therapy 4. Industrial applications: biotechnology products, production of enzymes and protein, bioremediation, Food industry (xanthan), insulin production 5. Agricultural processes: growth hormons, cell and tissue cultures 6. Animal production: dolly, silk worms 7. Forensic applications: crimes, fathership  Introduction to molecular biology HISTORY The term „molecular biology“ was introduced in 1938 by Warren Weaver from the Rockefeller foundation DNA was first described in 1869 by F. Miescher Watson and Crick offered a model for the structure of DNA and ist replication (DNA is the basis of heredity) Shortly, thereafter, RNA was discovered as an intermediate in protein synthesis  Introduction to molecular biology Plant animal Cell chromo Nucleuous somes bacteria Or nucleoid humans genes Genes are the functional unit of genetic information Central dogma of molecular biology  Introduction to molecular biology - Typical cells contain 104-105 different kinds of molecules half Small molecules (inorganic ions and organic compounds) Polymers moleculaer weight :- < several hundreds 104-1012 Proteins Polysaccharides Nucleic acids  Water and macromolecules The bacterial cell is about 70% water, with over one-half of the dry portion being made up of protein and one-quarter being made up of nucleic acids.  PROTEINS Proteins are polymers of monomers called amino acids.  Hydrogen, an amino functional group (–NH2), and a carboxylic acid functional group (–COOH) are a part of each amino acid  The fourth bond (R bond) can be one of 21 common side groups, which may be ionic, polar, or nonpolar. It is the heterogeneity of these side groups that defines the properties of a peptide or protein. Introduction to molecular biology Amino acids Acidic R Basic R Neutral R Hydrophilic Hydrophobic  Through a dehydration synthesis reaction, amino acids can bond covalently by forming a peptide bond between the amino and carboxylic acid groups. Introduction to molecular biology α-carboxyl group α -carbon α-amino group R-group Methyl, sulfydrl, another methyl, a string a methyls, rings of carbons, and several other organic groups Noninformational Molecules Polysaccharides Introduction to molecular biology  The relatively simple structure of the polysaccharides and their derivatives makes them the most abundant natural polymer on Earth and allows them to be used for metabolism, as a component of information transfer molecules, and for cellular structure.  Glycosidic bonds combine monomeric units (monosaccharides) into polymers (polysaccharides), all with a carbon-water (carbohydrate) chemical composition approaching (CH2O)n.  The two different orientations of the glycosidic bonds that link sugar residues impart different properties to the resultant molecules. Polysaccharides can also contain other molecules such as proteins or lipids, forming complex polysaccharides. Introduction to molecular biology Molecular biology Phosphodiester bond  Introduction to molecular biology - Polysaccharides are polymers of sugars (Glucose) - Complex compounds due to the formation of covalent bonds - one sugar unit can be joined by more than two other sugars forming branched Macromolecules -They can be too big and macroscopic - The cell wall of many bacteria and plant cells are single gigantic polysaccharide molecules Informational Molecules Nucleic Acids  The nucleic acids deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are macromolecules composed of monomers called nucleotides. Therefore, DNA and RNA are polynucleotides. Without a phosphate, a base bonded to its sugar is referred to as a nucleoside. Molecular biology Polynucleotide consisting of nucleotides Nucleotide Cyclic five-C Nitrogenous Phosphate sugars base group Ribose deoxyribose H2PO4  Molecular biology Nitrogenous bases Pyrimidines Purines Cytosine Thymine Uracil Adenine Guanine C T U A G Molecular biology  It is the primary structure, or order, of pyrimidine and purine bases connected by the phosphodiester bond that gives nucleic acids their information-storing capacity.  Both RNA and DNA are informational macromolecules. RNA can fold into various configurations to obtain secondary structure. Molecular biology N-glycosylic bond Nucleotide (mono, di and poly) Molecular biology Molecular biology Are nucleic acids negatively or positively charged? And why?? Answer: They are negatively charged due to the presence of the phosphate group Nitrogenous base + Sugar Nucleoside Nitrogenous base + Sugar + phosphate Nucleotide Phosphate Nucleoside + Nucleotide  In all cells, DNA exists as two polynucleotide strands whose base sequences are complementary. The complementarity of DNA arises from the specific pairing of the purine and pyrimidine bases: Adenine always pairs with thymine, and guanine always pairs with cytosine. DNA Structure: The Double Helix DNA is a double-stranded molecule that forms a helical configuration and is measured in terms of numbers of base pairs Complementary due to the specific pairing between purines and pyrimidines and form double helix The two strands in the double helix are antiparallel, but inverted repeats allow for the formation of secondary structure.  Size of a DNA molecule Can be expressed by the number of thousands of nucleotide bases 1000 nucleotide=1 kilobase (1 kbp) E-coli has about 4640 kb of DNA in its chromosome 1 Megabase pair (1Mbp)=million of base pairs  Size of a DNA molecule each base pair takes up 0.34 nanometers (nm) in length Each turn of the helix contains ca. 10 bp How many turns and how long is a 1 Kbp DNA fragment ?? 100 turns and 0.34 µm Inverted repeats, secondary structure and stem loops  Widespread in RNA produced from DANN This secondary structure is critical for the functioning of transfer RNA and ribosomal RNA Inverted repeats in DNA are binding sites for DNA-binding proteins Molecular biology Why macromolecules have a three-dimensional structure ??? ANSWER: Because they mainly contain weak (noncovalent) interactions? Molecular biology Strong and weak chemical bonds + Covalent bonds O + 2H ------------------------ H2O Six electrons in Single electron the outermost shell  Molecular biology The Random coil The three dimensional configuration of free rotating chains of polypeptides And polynucleotides is called random coiling Intrastrand interaction vs Interstrand interaction 1. Hydrogen bonds C C=O…..H-N C-OH……O=C N-H…..N C Molecular biology RNA Intrastrand hydrogen bonding in RNA result in folding of the RNA Introduction to molecular biology DNA Interstrand hydrogen bonging in DNA result in double stranded molecules  2. The hydrophobic interactions The interaction between two molecules (or portions of molecules) that are somewhat insoluable in water Example: the nitrogenous bases in nucleic acids are planar organic rings carrying localized weak charges Hydrophobic interactions among nitrogenous bases result in BASE STACKING Molecular biology 3. Ionic bonds Result from Attraction or repulsion of unlike and like charges, respectively Example: Amino acids: aspartic and glutamic acids which are negatively charged interact with lysine, histidine and arginine which are positively charged Ionic bonds are the strongest among the noncovalent interactions It is destroyed by extremes of pH and high concentrations of salts  Molecular biology Van der Waals Attraction - Very weak forces exist among all molecules and result from circulation of electrons -The attaction forces dependent on 1/r6 where r is the distance between their nuclei - Can be easily overcome by thermal motion - The two molecules can bind to one another by van der Waal forces if their shape are complementary - Example is the binding of substrates to enzyme Molecular biology  DNA Denaturation The strands of a double-helical DNA molecule can be denatured by heat and allowed to reassociate following cooling