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Signals and Systems in Biology All cells come from pre-existing cell - Rudolf Vircow A cell is the basic building unit of life A cell is a self replicating body capable of its own sustenance and maintenance. Mitocondria and Chloroplast – The kitchen of the cell. Nucleus – Contains information for replication i.e. the genetic material. A typical prokaryotic cell A typical plant cell bowserscience.wikispaces.com A typical mammalian cell Figure 1-30 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) Figure 1-21 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) Biological Viruses – Lie at the borderline between living and non-living Tobacco Mosaic Virus A bacteriophage (bacteria eater) Human Immunodeficiency Virus (HIV) Figure 2-17 Molecular Biology of the Cell (© Garland Science 2008) Genetic Material : DNA or De-oxy ribonucleic acid Figure 1-2a Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) There are four types of bases Adenine (A) Thymine (T) Guanine (G) Cytosine (C) The phosphate rich back bone of DNA makes it electro-negative, hence having affinity for positive charged molecules (eg. proteins). Figure 1-2b Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) Chemical structure of a single strand of DNA Figure 2-28 Molecular Biology of the Cell (© Garland Science 2008) Adenine always pairs with Thymine via 2 hydrogen bonds. Guanine always pairs with Cytosine via 3 hydrogen bonds. Figure 1-2c Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) DNA exists in a helix – proposed and proved by Watson, Crick and Franklin Helix imparts effective packaging of the genetic material inside the miniscule cell. Figure 1-2d,e Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) A typical .fna file downloadable from NCBI Figure 4-7 Molecular Biology of the Cell (© Garland Science 2008) Human Chromosomes Figure 4-10 Molecular Biology of the Cell (© Garland Science 2008) Life began in a RNA world because RNA can act as genetic material as well as an enzyme (ribozymes) Figure 6-98 Molecular Biology of the Cell (© Garland Science 2008) RNA – Ribonucleic acid Figure 6-4a Molecular Biology of the Cell (© Garland Science 2008) In RNA thymine is replaced by uracil base. Uracil base pairs with Adenine via 2 H-bonds Figure 6-4b Molecular Biology of the Cell (© Garland Science 2008) Chemical structure of RNA Figure 6-4c Molecular Biology of the Cell (© Garland Science 2008) Table 6-1 Molecular Biology of the Cell (© Garland Science 2008) mRNA : messenger RNA Figure 6-22a Molecular Biology of the Cell (© Garland Science 2008) rRNA : ribosomal RNA The RNA which is bound with ribosomes in the cell cytoplasm. It is usually a co-translation product. internal.champaignschools.org tRNA- Transfer RNA Figure 6-52a Molecular Biology of the Cell (© Garland Science 2008) Proteins Amino acids are the building blocks of proteins. There are twenty amino acids. Essential amino acids are those that cannot be synthesized by the organism de novo. For humans they are Phe, Val, Thr, Trp, Ile, Leu, Met, Lys and His. Figure 3-2 Molecular Biology of the Cell (© Garland Science 2008) Amino acids are the basic units of proteins The ‘H’ is replaced by various groups to generate other 19 amino acids. All the amino acids carry both positive and negative charges, hence they are termed as Zwitter ions. Bond between two amino acids is known as a peptide bond Proteins are also termed as polypeptides. In biological systems synthesis of proteins happens in N terminus→C terminus direction. http://www.ucl.ac.uk/~sjjgsca/ProteinStructure.html Four levels of protein structure αHelix β-Pleated sheets Ramachandran Plot Torsion in Phi and Psi angles can occur only in some permissable limits i.e only certain combinations of these two angles are possible. These limits were first mapped by G.N. Ramachandran in the 1960s. Figure 3-3a Molecular Biology of the Cell (© Garland Science 2008) Ramachandran Plot Figure 3-3b Molecular Biology of the Cell (© Garland Science 2008) Broadly proteins can be classified into four categories Central Dogma in Molecular Biology Some viruses were discovered to have RNA as genetic material and among them few replicate forming a DNA intermediate (Reverse Transcription). Figure 6-2 Molecular Biology of the Cell (© Garland Science 2008) The transfer of information from DNA to protein A nascent RNA is highly unstable. Post-transcriptional modifications confers stability to the RNA. Figure 3-15 Molecular Biology of the Cell (© Garland Science 2008) Transport of a modified RNA from nucleus to cytoplasm Figure 6-40 Molecular Biology of the Cell (© Garland Science 2008) Gene coding and non-coding region Figure 1-45 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) Following codons code for corresponding amino acids. This code is followed in every living organism on earth without ANY exception. The genetic code is degenerate: 64 codons code for 20 amino acids. Figure 6-50 Molecular Biology of the Cell (© Garland Science 2008) Wobble hypothesis : Rules of base pairing are relaxed at the third position Wobble rule makes the genetic code degenerate i.e. many codons code for a single amino acid. Figure 6-53 Molecular Biology of the Cell (© Garland Science 2008) Open Reading Frame (ORF)- Part of reading frame with no stop codon Figure 6-51 Molecular Biology of the Cell (© Garland Science 2008) Translation Figure 6-66 (part 1 of 4) Molecular Biology of the Cell (© Garland Science 2008) Translation Figure 6-66 Molecular Biology of the Cell (© Garland Science 2008) Termination of Translation Figure 6-74 (part 2 of 3) Molecular Biology of the Cell (© Garland Science 2008) Folding of proteins occur co-translationally Figure 6-84 Molecular Biology of the Cell (© Garland Science 2008) Biologically active protein is made after post-translational modifications of a polypeptide. Figure 6-82 Molecular Biology of the Cell (© Garland Science 2008) Flow of information from DNA to proteins To ensure the faithful decoding of information from DNA to proteins, there are several levels of regulation both at transcription and translational level. Figure 6-97 Molecular Biology of the Cell (© Garland Science 2008) Replication of DNA Figure 1-2 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) DNA replication is semi-conservative – Meselson and Stahl, 1958 Figure 1-3 Molecular Biology of the Cell, Fifth Edition (© Garland Science 2008) Process of replication of DNA is not identical on both the strands. Figure 5-21 Molecular Biology of the Cell (© Garland Science 2008) DNA replication initiates on a oligonucleotide called primer Figure 5-3 Molecular Biology of the Cell (© Garland Science 2008) Figure 5-26 Molecular Biology of the Cell (© Garland Science 2008) Mechanisms to ensure fidelity in replication Figure 5-48 Molecular Biology of the Cell (© Garland Science 2008) Table 4-1 Molecular Biology of the Cell (© Garland Science 2008)