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Introduction to Biochemistry, Cell and Molecular Biology II Losiana Nayak Indian Statistical Institute http://www.isical.ac.in/~losiana_t/ Molecular Biology A field of science concerned with studying the chemical structures and processes of biological phenomena at the molecular level. A branch of biology dealing with the ultimate physicochemical organization of living matter and especially with the molecular basis of inheritance and protein synthesis. Ref: http://www.britannica.com/ Cell: structural unit of life A cell can be distinguished into a outer membrane, central nucleus and cytoplasm. Cell membrane nucleus cytoplasm Typical structure of a cell Robert Hooke, an English scientist, first described cells in 1665. Cell theory consists of three basic points: 1. All living things are made of cells. 2. The cell is the smallest living thing that can perform all the functions of life. 3. All cells must come from preexisting cells. An animal Cell Plant cells are different from animal cells. They contain the green photosynthetic pigment chloroplast. Growth The answer is cell division, which is of two types 1. 2. Mitosis [Somatic division] Meiosis [Genetic division/ Reductional division] Functions of a cell? Genetic control Energy house Support Storage Packaging Transport Central Dogma of molecular biology Information Only Goes One Way The central dogma states that once “information” has passed into protein it cannot get out again. The transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein, may be possible, but transfer from protein to protein, or from protein to nucleic acid, is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein. Francis Crick, 1958 T Packaging G A C C GA DNA Histone octomer T C A G T G T C A Histone proteins T A G C B DNA Helix C G T A 2 nm T Packaging G A C C GA DNA Histone octomer T C A G T G T C A Histone proteins T A G C B DNA Helix C G T A 2 nm T Packaging G A C C GA DNA 11 nm T C A G T G T C A Histone octomer Histone proteins T A C B DNA Helix C G T Nucleosome G A 2 nm Packaging DNA Histone H1 A G T C A T A G C C G T A Packaging DNA Histone H1 A G T C A T A G C C G T A Packaging DNA “Beads on a string” A G T C A 11 nm 30 nm T A G C C G Tight helical fiber Looped 200 nm Domains A T Protein scaffold Packaging DNA Nucleosomes 11 nm 30 nm T G Tight helical fiber Metaphase Chromosome 700 nm 200 nm Looped Domains C A 2 nm B DNA Helix Protein scaffold A “Simple” Eukaryotic Gene Transcription Start Site 3’ Untranslated Region 5’ Untranslated Region Introns 5’ Exon 1 Int. 1 Promoter/ Control Region Exon 2 3’ Int. 2 Exon 3 Exons RNA Transcript Terminator Sequence Eukaryotic Gene Expression Cytoplasm DNA Packaging Nuclear pores Transcription Transportation Modification RNA Nucleus G AAAAAA Export e som bo Ri RNA Processing mRNA G Degradation Degradation etc. AAAAAA Translation Stages of Transcription 1. 2. 3. Transcription can be logically divided into three distinct stages: Initiation Elongation Termination Transcription Initiation Proteins called transcription factors bind to the promoter region of a gene If the appropriate transcription factors are present, RNA polymerase binds to form an initiation complex RNA polymerase melts the DNA at the transcription start site Polymerization of RNA begins Coding (sense) strand 5’ 3’ 3’ 5’ Template (antisense) strand Transcription Coding (sense) strand 5’ 3’ 3’ 5’ RNA Pol. 5’ RNA Template (antisense) strand Transcription Coding (sense) strand 5’ 3’ 3’ 5’ Template (antisense) strand 5’ RNA Pol. Transcription Termination There are two types of termination: Rho dependent requires a protein called Rho, that binds to and slides along the RNA transcript. The terminator sequence slows down the elongation complex, Rho catches up and knocks it off the DNA Rho independent termination depends on both slowing down the elongation complex, and an AT rich region that destabilizes the elongation complex Termination (Rho Independent) RNA Pol. RNA Pol. RNA 5’ RNA Pol. 5’ RNA 5’ Terminator Termination (Rho Dependent) Terminator RNA Pol. RNA 5’ ρ Help, rho hit me! ρ 5’ 5’ RNA RNA Pol. RNA Pol. ρ Products of Transcription Transcription produces three major RNA products: 1.Ribosomal RNA (rRNA) - Several rRNAs are vital constituents of ribosomes 2.Transfer RNA (tRNA) - The molecule that physically couples nucleic acid codons with specific amino acids 3.Messenger RNA (mRNA) - The nucleic acid messenger that carries encoded information from genes on DNA to the protein manufacturing ribosomes Requirements for Translation Ribosomes - rRNA and Protiens mRNA - Nucleotides tRNA Aminoacyl-tRNA Synthetase, L Amino Acids ATP - For energy Ribosome Structure Peptidyl-tRNA binding site Aminoacyl-tRNA binding site P Exit site A E Large subunit 5’ GAG...C-AGGAGG-NNNNNNNNNN-AUG---NNN---NNN---NNN---NNN--mRNA Small subunit 3’ Translation - Initiation fMet Large subunit E P A UAC 5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA Small mRNA subunit 3’ Translation - Elongation Polypeptide Arg Met Phe Leu Ser Aminoacyl tRNA Gly Ribosome E P A UCU CCA 5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA mRNA 3’ Translation - Elongation Polypeptide Met Phe Leu Ser Gly Arg Aminoacyl tRNA Ribosome E P A CCA UCU 5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA mRNA 3’ Translation - Elongation Polypeptide Met Phe Leu Ser Gly Arg Ribosome E P A CCA UCU 5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA mRNA 3’ Translation - Elongation Polypeptide Met Phe Leu Ala Ser Gly Aminoacyl tRNA Arg Ribosome E P A CGA CCA UCU 5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA mRNA 3’ Translation - Elongation Polypeptide Met Phe Leu Ser Gly Arg CA C Ribosome E Ala P A UCU CGA 5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA mRNA 3’ Translation - Termination Met Phe Leu Ser Gly Polypeptide Arg Ala Ribosome Val E P A CGA CGA GCA...TAAAAAA STOP 5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT mRNA 3’ Translation - Termination Met Phe Leu Ser Gly Polypeptide Arg Ala CG Val CG A P A E A 5’GAG...CU-AUG--UUC--CUU--AGU--GGU--AGA--GCU--GUA--UGA-AT GCA...TAAAAAA 3’ mRNA STOP Transcription And Translation In Prokaryotes 5’ 3’ 3’ 5’ RNA Pol. Ribosome mRNA 5’ Ribosome AN OVERVIEW OF METABOLISM CARBOHYDRATE METABOLISM LIPID METABOLISM PROTEIN METABOILSM ENERGY METABOLISM WHAT IS METABOLISM? A Continuous gradual process of biological systems that includes both building and breaking of macronutrients for the purpose of growth, reproduction and senescence. WHAT IT INCLUDES? METABOLISM ANABOLISM CATABOLISM GENESIS LYSIS FATS POLYSACCHARIDES PROTEINS Fatty acids Glucose Aminoacids Glycerol Other Sugers CO A Acetyl Co A ATP ADP e O2 OXIDATIVE PHOSPHORYLATION CITRIC ACID CYCLE 2CO2 Signal transduction pathway? Signal means any communication that encodes a message Signal Transduction involves conversion of a signal from extracellular environment to functional changes within the cell A Signal transduction pathway is a series of steps that enable signal transmission through physical barriers like cell membrane, organelle membrane and nuclear membrane General process of a STP Extracellular signal is present outside a cell: typically a hormone, neurotransmitter or growth factor Signal binds to a receptor causing a change in receptor conformation, thus transmitting a signal to the interior of the cell The signal precipitates many enzyme catalyzed protein interactions, ultimately causing changes in the cell’s functions (ex. glucose uptake, cell division, transcription) Reference Biochemistry by Lubert Stryer Cell and Molecular Biology by De Roberties and De Roberties Some Slides are taken from Timothy G. Standish, Ph. D.