[Week 01] MONDAY - Class Intro., Central Dogma, Nucleic Acids.pdf
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Department
Biological Sciences
Course
BIO SCI 99
Professor
Brian Sato
Semester
Spring

Description
[Week 01] 03/31/14 MONDAY - Class Intro., Central Dogma, Nucleic Acids pgs. 47-50 The Central Dogma: Information Flow from DNA to RNA to Proteins 1: Turning point in understanding how info. flows in bio. sys. Watson & Crick's determination of DNA structure a) Their model of DNA structure: • reasoned from data collected by other scientists • consisted of 2 strands of DNA wound about one another in a spiral, double helix. - each strand composed of • a long string of the 4 nucleotides containing the bases: adenine (A) guanine (G) cytosine (C) thymine (T) - Nucleotides in one strand pair with those in the other. • A - T • G - C - the strands are said to be complementary b/c the sequence of one strand contains info. about the sequence of the other strand. b) Watson & Crick realized the DNA could logically be replicated by separating the 2 strands & using each as a template to synthesize a new, complementary strand 2: Genetics could be described in chemical terms with the discovery of the DNA structure. a) DNA & Proteins are linear polymer Idea is that sequence of nucleotides in DNA ˠ sequence of amino acids in protein, but... DNA is in the nucleus Proteins are synthesized in cytoplasm 㱤 need intermediate to shuttle info. between the 2 locations intermediate = RNA 3: Crick proposed: biological info. flows in the direction of DNA ˠ RNA ˠ Proteins DNA acts as a template for its own synthesis (DNA ˠ DNA) The Central Dogma of Information Flow: DNA ˠ RNA ˠ Protein The info. to replicate DNA is inherent in its structure (curved arrow). Info. flows from DNA to RNA by transcription. Info. flows from RNA to protein by translation. In some instances info. can flow backwards from RNA to DNA (reverse transcription). No evidence exists for info. flow from protein to nucleic acid. a) ex. of exceptions to the central dogma: • certain enzymes can synthesize DNA from RNA • some viruses use RNA as a template to make more RNA 4: RNA is widely accepted to be the molecule that mediates the transfer of info. from DNA in the nucleus to the site of protein synthesis in the cytoplasm. 3 different types of RNA req. for the process Ribosomal RNA: 1: Ribosomes • Particles in the cytoplasm where protein synthesis occurs. • Are large structures composed of both protein and RNA. • Consists of a large subunit and small subunit. 2: Ribosomal RNA (rRNA) • The RNA component in ribosomes Messenger RNA (mRNA): 1: Why rRNA is not the carrier of information from DNA to protein: • rRNA is an integral part of the ribosomes which makes specific proteins. • The nucleotide composition of rRNA is pretty much the same in different organisms where as the nucleotide composition of chromosomal DNA varies greatly from organism to organism. 2: Messenger RNA (mRNA) a template used by ribosomes (protein-synthesizing factories) to direct the construction of the protein sequence. • Only needed short-term ˠ to instruct the synthesis of proteins. 3: RNA Polymerase: • Enzyme that carries out RNA synthesis by the process of transcription. 4: Transcription: • The process of making single-stranded RNA copies of a DNA strand • RNA polymerase Synthesizes RNA by reading one strand of the duplex DNA, paring RNA bases to the bases in the DNA strand, to synthesized a single-stranded RNA molecule that has a sequence directed by the DNA sequence. The Process of Transcription: RNA polymerase opens the DNA duplex and uses one strand as a template for RNA synthesis. The Polymerase matches incoming nucleotides to the DNA template strand by base pairing and joins them together to form an RNA chain. As RNA polymerase advances along the template strand, the two DNA strands reassociate behind it to re-form to double helix. When the gene has been completely transcribed, the polymerase dissociates from DNA, releasing the completed RNA transcript. Transfer RNA: 1: How is the sequence of nucleotides in mRNA converted to a sequence of amino acids in proteins? DNA & RNA each consist of only 4 nucleotides Proteins have 20 different amino acids. ˠ assumption: the existence of a code that uses combination of nucleotides to specify amino acids. ˠ Combination of 3 nucleotides yields 64 permutations (more than enough to specify a code for 20 amino acids) 2: Transfer RNA (tRNA) • a small RNA to which amino acids could attach. • The adaptor between nucleic acid and protein. 3: How the DNA sequence could be converted to an amino acid sequence: • 3 bases in the tRNA form base pairs with a triplet sequence in the mRNA • When 2 amino acid-linked tRNAs alight side by side on the mRNA by base-pairing to adjacent triplets, the amino acids attached to the tRNA can be joined together. • cont. process over the length of an mRNA strand, amino acids carried to the mRNA by tRNAs become connected together in a linear order specified by the mRNA sequence. - occurs at the mRNA-tRNA complexes thread through the ribosome. 4: Translation: The overall process of protein synthesis, involving 3 different types of RNA molecules. The Process of Translation: The ribosome, composed of a large and small "subunit" (each consisting of many proteins and several rRNAs) ˠ mediates protein synthesis in cells. ˠ associated with both mRNA and tRNAs as it synthesizes polypeptide chains. Ribosome has 2 major sites for binding tRNA molecules, the P site and the A site. 2 tRNAs form base pairs with their respective, adjacent matching triplets on the mRNA: • the tRNA in the P site carries the growing polypeptides chain • the tRNA in the A site carries an amino acid (AA). The ribosome catalyzes the transfer of the polypeptide attached to the P-site tRNA to the amino acid on the A-site tRNA. Ribosome then shifts relative to mRNA so that the A-site tRNA, now holding the polypeptide, moves into the P site (and the tRNA previously at the P site departs) The next tRNA carrying an amino acid then binds to the vacant A site to cont. extending the polypeptide chain. 5: All RNAs (whether they code for proteins or not) are transcribed from DNA genes. 6: The end products of tRNA and rRNA genes are the RNA molecule itself. 7: Functional RNAs: ex: tRNA & rRNA • fold into specific 3D shapes and constitute about 95% of the RNA in the cell. 8: The increase discover of functional RNAs ˠ support idea that: many processes in early life forms were performed by RNA rather than proteins, & RNA cont. to be of central importance to cellular function today. pgs. 62-64 3.1 Chemical Building Blocks of Nucleic Acids and Proteins Nucleic Acids are Long Chains of Nucleotides 1: Deoxyribonucleic acid (DNA) & Ribonucleic acid (RNA) Store & transmit genetic info, in part by coding for proteins. • Some RNA molecules function catalytically / structurally w/in large, multimolecular complexes. • both RNA & DNA are composed of building blocks (monomers) called Nucleotides - are linked together in long, unbranched chains 2: Components of a nucleotides molecules: a: a nitrogenous base b: A 5 carbon (pentose) sugar ring c: a phosphate group 3: nucleoside: A sugar and base w/o the phosphate group 4: Deoxyribonucleotides: the nucleotides that make up DNA polymers • named for the type of pentose sugar found in DNA: deoxyribose • The phosphate group and sugar remain the same but, each deoxyribonucleotide contains 1 of 4 bases: • adenine (A) • cytosine (C) • guanine (G) • thymine (T) Each type of base establishes the ID of the individual deoxyribonucleotides Thus, info in DNA is written in a 4-letter alphabet. 5: Ribonucleotides: • Chemically very similar to DNA • Long unbranched polymer of nucleotides, containing the same pentose and a phosphate group, and 1 of 4 diff. nitrogenous bases. Distinctions between DNA & RNA: • Ribose has one more hydroxyl (-OH) group on the sugar ring than does deoxyribose • The assortment of nitrogenous bases found in RNA - Ribonucleotides contain 3 of the same bases found in DNA: • Adenine (A) • Cytosine (C) • Guanine (G) - instead of thymine (T), the 4th base in RNA is uracil (U) Uracil (U) is structurally identical to thymine except for the absence of the methyl (-CH ) group. KEY CONVENTION: DNA and RNA are defined by the type of sugar in the polynucleotide backbone (deoxyribose or ribose), not by the presence of thymine / uracil. pgs. 175-181 DNA & RNA STRUCTURE 1: DNA was discovered in the 19th century Francis Crick's first Drawing of DNA 2: [1953] James Watson & Francis Crick @ Structure Cambridge University ˠ used X-ray diffraction 2 base-paired strands of DNA form a helical data obtained by Rosalind Franklin to deduce structure in which the DNA's simple and beautiful double-helical structure. phosphate and sugar groups are on the outside and the - Gave rise to modern Molecular Biology bases are on the inside. 3: [19th cent.] RNA was 1st isolated from the nuclei The helix twists in a right- of cells. handed direction. • RNA is chemically distinct from DNA - contains a different kind of sugar in its nucleotide building blocks - were found to be components of ribosomes (the complexes that carry out protein synthesis) - mRNA were known to be intermediates, carrying genetic info. from genes to ribosomes. - tRNA ID as adaptor molecules that translate the info. in mRNA into a specific sequence of amino acids. - RNA comprise the genomes of certain viruses & some have the ability to work as catalysts
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