DNA L1 G 2 Molecular Biology Lecture Notes PDF

Molecular biology Assist.pro; MUSTAFA ADNAN ALNOORI Lect (1) The three-domain system is a biological classification introduced by Carl Woese. in 1990 that divides cellular life forms into archaea , bacteria , and eukaryote domains ,The key difference from earlier classifications is...

Molecular biology Assist.pro; MUSTAFA ADNAN ALNOORI Lect (1) The three-domain system is a biological classification introduced by Carl Woese. in 1990 that divides cellular life forms into archaea , bacteria , and eukaryote domains ,The key difference from earlier classifications is the splitting of archaea from bacteria. JAMES WATSON AND FRANCIS CRICK PUBLISHED A PAPER ON THE STRUCTURE OF DNA WHICH BEGAN A NEW ERA IN ITS UNDERSTANDING RACE TO DETERMINE 3D STRUCTURE AMONG THE SCIENTISTS WORKING ON THE PROBLEM WERE LINUS PAULING, MAURICE WILKINS AND ROSALIND FRANKLIN Most importantly, x-ray diffraction studies of DNA fibers performed by Rosalind Franklin and Maurice Wilkins showed that DNA molecules are helical and exhibit two periodicities repeating along the length of the fiber  a primary repeat of 3.4 Å  a secondary repeat of 34 Å. DNA is a two-stranded molecule that appears twisted, giving it a unique shape referred to as the double helix Each of the two strands is a long sequence of nucleotides or individual units made of: a phosphate molecule a sugar molecule called deoxyribose, containing five carbons a nitrogen-containing region phosphate molecule a sugar molecule (deoxyribose) There are four types of nitrogen-containing regions called bases: adenine (A) guanine (G)  Cytosine(C) Thymine(DAN only)(T) Uracil (RNA only)(U) Nucleosides A nucleoside is one of the four DNA bases covalently attached to the C1' position of a sugar. The sugar in deoxynucleosides is 2'-deoxyribose. The sugar in ribonucleosides is ribose. Nucleosides differ from nucleotides in that they lack phosphate groups. The four different nucleosides of DNA are deoxyadenosine (dA), deoxyguanosine (dG), deoxycytosine (dC), and deoxythymidine (dT, or T). In dA and dG, there is an "N-glycoside" bond between the sugar C1' and N9 of the purine. Nucleotides A nucleotide is a nucleoside with one or more phosphate groups covalently attached to the 3'- and/or 5'-hydroxyl group(s). DNA Backbone The DNA backbone is a polymer with an alternating sugar-phosphate sequence. The deoxyribose sugars are joined at both the 3'- hydroxyl and 5'-hydroxyl groups to phosphate groups in ester links, also known as "phosphodiester" bonds. Not only do the hydrogen bonds hold the chains together, they also are very specific in which bases are connected by the hydrogen bonds. Adenine (A) forms two hydrogen bonds only with thymine (T). Guanidine (G) forms three hydrogen bonds only with cytosine (C) In the double-stranded DNA, the two strands run in opposite directions and the bases pair up such that A always pairs with T and G always pairs with C. The A-T base-pair has 2 hydrogen bonds and the G-C base-pair has 3 hydrogen bonds. The G-C interaction is therefore stronger (by about 30%) than A-T, and A-T rich regions of DNA are more prone to thermal fluctuations. Double-helical Strand Complementarity The two antiparallel chains of double-helical DNA are not identical in either base sequence or composition. Instead, they are complementary to one another. Wherever adenine occurs in one chain, thymine occurs in the other. Similarly, guanine occurs opposite cytosine in the two chains The backbone of polynucleotides are highly charged (1 unit negative charge for each phosphate group; 2 negative charges per base-pair). If there is no salt in the surrounding medium, there is a strong repulsion between the two strands and they will fall apart. Therefore counter-ions are essential for the double-helical structure. Counter-ions shield the charges on the sugar- phosphate backbone. They may also contribute to an attractive interaction from fluctuating counter-ions around the backbone, similar to the Van der Waals interactions for fluctuating induced dipoles.  Watson-Crick Model for the Structure of Double-helical DNA (II) The most common DNA structure in solution is the B-DNA. Under conditions of applied force or twists in the DNA, or under low hydration conditions, it can adopt several helical conformations, referred to as the A-DNA, Z-DNA.  A-DNA B-DNA Z-DNA Right-handed helix Right-handed Left-handed Short and broad Long and thin Longer and thinner There is evidence for some short tracts of Z-DNA in bacterial and eukaryotic cells. These Z-DNA tracts may play a role (as yet unidentified) in regulating the expression of some genes or in genetic recombination. RNA structures RNA molecules are also polynucleotides with a sugar- phosphate backbone and four kinds of bases. The main differences between RNA and DNA are: RNA molecules are single-stranded. The sugar in RNA is a ribose sugar (as opposed to deoxy- ribose) and has an –OH at the 2' C position highlighted in red in the figure below (DNA sugars have –H at that position) Thymine in DNA is replaced by Uracil in RNA. T has a methyl (-CH3) group instead of the H atom shown in red in U. What are the three types of RNA? Messenger RNA (mRNA) copies portions of genetic code, a process called transcription , and transports these copies to ribosomes, which are the cellular factories that facilitate the production of proteins from this code. Transfer RNA (tRNA) is responsible for bringing amino acids, basic protein building blocks, to these ribosomes, in response to the coded instructions introduced by the mRNA. This protein-building process is called translation. Finally, Ribosomal RNA (rRNA) is a component of the ribosome factory itself without which protein production would not occur. Messenger RNA Transfer RNA Ribosomal RNA (mRNA) (tRNA) (rRNA) Comparison DNA RNA Function DNA replicates and stores genetic RNA converts the genetic information. information contained within DNA to a format used to build proteins Structure DNA consists of two strands, arranged RNA only has one strand, but like in a double helix. These strands are DNA, is made up of nucleotides. made up of subunits called RNA strands are shorter than DNA nucleotides. strands. RNA sometimes forms a secondary double helix structure, Sugar deoxyribose ribose Base Pairs Adenine and Thymine (A-T) Adenine and Uracil (A-U) Cytosine and Guanine (C-G) Cytosine and Guanine (C-G) Comparison DNA RNA Location DNA is found in the nucleus, RNA forms in the nucleolus, and with a small amount in mitochondria. then moves to specialized regions of the cytoplasm Reactivity DNA is a more stable molecule than not stable in alkaline conditions. RNA, it is more easily subject to attack by enzymes. Ultraviolet (UV) Sensitive to damage more resistant to damage Sensitivity