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Stanford CS 374 - Basic Molecular Biology

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2 NucleotidesFigure 1Figure 2Figure 4Figure 54 DNA, RNA and protein metabolismFigure 67 Central Dogma of Molecular BiologyFigure 78 Computer Scientist vs BiologistsBasic Molecular Biology CS374 Fall 2004 Lecture 2, 9/30/04Lecturer: Omkar Deshpande Scribe: Maria Teresa Gil LucientesBasic Molecular BiologyReferences:1. David L. Nelson, Michael M. Cox “Lehninger Principles of Biochemistry”, Worth Publishers, Third Edition, 2000.2. Slides from Omkar Deshpande’s lecture http://ai.stanford.edu/~serafim/CS374_2004/Presentations/CS374_2004_Lecture2_BioBackground.ppt3. Some definitions have been taken from: http://www.wordiq.com/1 MotivationThis lecture explains some basic molecular biology concepts we need to know, in order to understandbetter the next lectures of the quarter. In addition to this basic terminology, the lecture introduces somefundamental ideas in the metabolism of DNA, RNA and proteins. Finally, the Central Dogma of theMolecular Biology as well as some differences between Computer Scientists and Biologists are discussed.2 NucleotidesNucleotides have an important role in cellular metabolism and are the constituents of nucleic acids:deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleotides have three different components:(1) a nitrogenous (nitrogen-containing) organic base, (2) a pentose or carbon sugar, and (3) a phosphate,see figure 1.Figure 1The nitrogenous bases are derivates of two parent compounds, pyrimidine and purine. Both DNA andRNA contain two major purine bases, adenine (A) and guanine (G), and two major pyrimidines. In bothDNA and RNA one of the pyrimidines is cytosine (C), but the second major pyrimidine is thymine (T) inDNA and uracil (U) in RNA, figure 2.1Basic Molecular Biology CS374 Fall 2004 Lecture 2, 9/30/04Lecturer: Omkar Deshpande Scribe: Maria Teresa Gil LucientesFigure 23 Nucleic AcidsA nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotidesthat contains genetic information. The most common nucleic acids are deoxyrribonucleic acid (DNA) andribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses.The successive nucleotides of both DNA and RNA are covalently linked through what is calledphosphodiester linkage, forming a polynucleotide strand. Thus, the covalent backbones of nucleic acidsconsist of alternating phosphate and pentose residues, and the nitrogenous bases may be regarded as sidegroups joined to the backbone at regular intervals.3.1 DNADeoxyribonucleic acid (DNA) is a nucleic acid which carries genetic instructions for the biologicaldevelopment of all cellular forms of life and many viruses. DNA is sometimes referred to as the moleculeof heredity as it is inherited and used to propagate traits. During reproduction, it is replicated andtransmitted to offspring.The 3D molecular structure of the DNA is a double helix (Figure 3): two polynucleotide strands cometogether through complementary pairing of the bases, which occurs by hydrogen bonding (Figure 4). Eachbase forms hydrogen bonds readily to only one other -- A to T and C to G -- so that the identity of the baseon one strand dictates what base must face it on the opposing strand. Thus, the entire nucleotide sequenceof each strand is complementary to that of the other.2Basic Molecular Biology CS374 Fall 2004 Lecture 2, 9/30/04Lecturer: Omkar Deshpande Scribe: Maria Teresa Gil LucientesBecause pairing causes the nucleotide bases to face the helical axis, the sugar and phosphate groups of thenucleotides run along the outside, and the two chains they form are sometimes called the "backbones" ofthe helix. In fact, it is chemical bonds between the phosphates and the sugars that link one nucleotide to thenext in the DNA strand.Figure 3 Figure 4The asymmetric shape and linkage of nucleotides means that a DNA strand always has a discernibledirectionality. Because of this directionality, close inspection of a double helix reveals that nucleotides areheading one way along one strand (the "ascending strand"), and the other way along the other strand (the"descending strand"). This arrangement of the strands is called antiparallel.As a result of their antiparallel arrangement and the sequence-reading preferences of enzymes, even if bothstrands carried identical instead of complementary sequences, cells could properly translate only one ofthem. Molecular biologists call a sequence sense if it is translated or translatable, and they call itscomplement antisense. It follows then, somewhat paradoxically, that the template for transcription is theantisense strand (from below to above). The resulting transcript is an RNA replica of the sense strand andis itself sense (from above to below).3.2 RNA Ribonucleic acid (RNA) is a nucleic acid consisting of a string of covalently-bound nucleotides. It isbiochemically distinguished from DNA by the presence of an additional hydroxyl group, attached to eachpentose ring; as well as by the use of uracil, instead of thymine. RNA transmits genetic information fromDNA (via transcription) into proteins (by translation).3Basic Molecular Biology CS374 Fall 2004 Lecture 2, 9/30/04Lecturer: Omkar Deshpande Scribe: Maria Teresa Gil LucientesStructurally, RNA is indistinguishable from DNA except for the critical presence (noted above) of anadditional hydroxyl group attached to the pentose ring in the 2' position. This additional group gives themolecule far greater catalytic versatility and allows it to perform reactions that DNA is incapable ofperforming.Other major difference between RNA and DNA is that RNA is almost exclusively found in the single-stranded form (an exception being the genetic material of some kinds of viruses). RNA molecules oftenfold into more complex structures by making use of complementary internal sequences.There are several types of RNA. The most important are:- Messenger RNA (mRNA) is transcribed directly from a gene's DNA and is used to encodeproteins.- Transfer RNA (tRNA) is RNA that transfers a specific amino acid to a growing polypeptide chainat the ribosomal site of protein synthesis during translation.- Ribosomal RNA (rRNA) is the primary constituent of ribosomes. Ribosomes are the protein-manufacturing organelles of cells and exist in the


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Stanford CS 374 - Basic Molecular Biology

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