Molecular Biology PDF

1 Molecular Biology Dr. Youssef M.M. Mohammed Associate Professor of Mycology  Course contents Macromolecules Viral replication Structure and function DNA, RNA, protein Genetic material Vira...

1 Molecular Biology Dr. Youssef M.M. Mohammed Associate Professor of Mycology  Course contents Macromolecules Viral replication Structure and function DNA, RNA, protein Genetic material Viral genome Prokaryotic genome Genetic information Eukaryotic genome Genome Chromsome Flow of genetic information Operon – Replication of DNA, RNA Gene Codon – Gene expression – Transcription Cell division » RNA maturation – Translation In prokaryotes » Posttranslational modifications In eukaryotes – Regulation  Biological Macromolecules Biomolecules Polymers Monomers Condensation Hydrolysis (macromolecules) (sub-units) Polysaccharides Simple sugars Lipids Fatty acids Proteins Amino acids Nucleic acids Nucleotides  Biological Macromolecules Nucleic acids DNA, RNA Informational Carry transfer express genetics information Proteins Bio-Polymers Non-Informational Polysaccharides, Lipids Complex Biological Macromolecules  Amino acids Zwitterion (inner salt or dipolar ion) Basic structure α-amino acids β-amino acids  Amino acids Building blocks of proteins Contain carbon, hydrogen, nitrogen, oxygen, sulfur ≈ 500 amino acids are known Only 20 amino acids appear in genetic code Behave as zwitterions in solution  Amino acids α-amino acids: Both amino and carboxyl groups attached to α-carbon β-amino acids: Amino and carboxyl groups attached to different carbons β-Amino acids not found in ribosomally synthesized proteins even though they are present in cells Each amino acid has R group attached to α-carbon R group determines chemical characteristics Amino acids classified according to R group Classification of amino acids Non-polar e.g. Alanine Neutral Polar e.g. Serine Amino Acids Basic (+ve) e.g. Lysine Charged (Polar) Acidic (-ve) e.g. Aspartic acid  Amino acids and their Abbreviations Amino Acids Three Letter Code Single Letter Code Glycine GLY G Phenylalanine PHE F Alanine ALA A Tyrosine TYR Y Valine VAL V Tryptophane TRP W Leucine LEU L Histidine HIS H IsoLeucine ILE I Lysine LYS K Threonine THR T Argenine ARG R Serine SER S Aspartate ASP D Methionine MET M Glutamate GLU E Cystein CYS C Asparagine ASN N Proline PRO P Glutamine GLN Q  Protein Large biomolecules (macromolecules) Made up of one or more long polypeptide chains Polypeptide chain is linear chain of amino acid Proteins differ in their sequence of amino acids Sequence of amino acid defined by nucleotide sequence Amino acids (20) link together in different combinations Amino acids bonded together by peptide bonds Protein folding into 3D structure that decides its activity  Protein Formation of peptide ponds  Protein mRNA 5ʹ 3ʹ end end Protein N C terminal terminal Translation of mRNA into protein  Protein structure Primary structure Sequence of amino acids in polypeptide chain Polypeptide chain has two ends; carboxyl terminus (C-terminus) and amino terminus (N-terminus) Amino acids linked by peptide bonds between α- carboxyl and α-amino groups Polypeptides have ≈100-1500 amino acids  Protein structure Secondary structure Highly regular local sub-structures on actual polypeptide backbone chain Two main types of secondary structure, α-helix and β-sheets Defined by patterns of hydrogen bonds between main-chain peptide groups  Protein structure Tertiary structure Three-dimensional structure created by single polypeptide chain α-helices and β-sheets folded into compact globular structure driven by non-specific hydrophobic interactions It may include one or several domains  Protein structure Quaternary structure Three-dimensional structure consisting of aggregation of two or more polypeptide chains that operate as single functional unit (multimer) Stabilized by same non-covalent interactions and disulfide bonds as in tertiary structure Multimers are complexes of two or more polypeptides » Dimer contains two subunits » Trimer contains three subunits » Tetramer contains four subunits » Pentamer contains five subunits Protein structure  Primary structure (amino acid sequence) Folding Folding OR α-Helix β-Sheet Secondary structure Folding Quaternary structure Tertiary structure  Protein structure Proteins of related functions often have similar amino acid sequences Protein secondary and tertiary structures are dictated by primary structurs Alteration of amino acids (due to mutations) in the active sites is very drastic Amino acid sequence of protein determines its structure Similar sequences fold into similar structures Structure of protein determines its function Similar protein structures perform similar functions Function prediction is matter of detecting similarity Sequence Structure Function  Protein Domains Semi-independent structural and functional units within single polypeptide chain Similar domains can found in proteins with different functions Small proteins often composed of single domain, while most large proteins consist of multiple domains Domains can work independently or cooperate with neighbour domains Different arrangements of domains create proteins of different functions Detection of protein domains pivotal for – Classification – Function and structure prediction – Protein design Typically consisting of 40 to 700 amino acids  Protein Motifs Short conserved sequence pattern associated with distinct structural site performing particular function Typically between 10 to 20 amino acids long Found in various locations within protein and can repeated multiple times Structural motifs – Short segments of protein 3D structure or amino acid sequence – Spatially close but not necessarily adjacent in sequence – May be conserved in large number of different proteins – Their role may be structural or functional  Protein function Proteins have a wide variety of functions Enzymes Signal receptor Transport Storage Structural proteins Nutritional proteins Immune proteins (antibody) Regulatory proteins