Molecular Structure of DNA PDF

Molecular Structure of DNA History of DNA By the end of nineteenth century it has been recognized that chromosomes are the carriers of the inherited information. The genetic information of all living organisms is stored in deoxyribonucleic acid (DNA) of the chromosomes (except the...

Molecular Structure of DNA History of DNA By the end of nineteenth century it has been recognized that chromosomes are the carriers of the inherited information. The genetic information of all living organisms is stored in deoxyribonucleic acid (DNA) of the chromosomes (except the RNA) viruses. DNA molecule is the most complex macromolecule of the cell. DNA from a single human cell extends in a single thread for almost 2 meters long!!!....It contains information equal to a library of about 1,000 books). Watson and Crick model of DNA (1953): Watson and Crick used the information of Franklin's X- ray photo of DNA and proposed their famous model of the structure of DNA molecule. According to their model, the DNA molecule is represented by a ladder –like structure.the side chains (backbone) of this ladder are made up of the pentose sugar (deoxyribose) and phosphate.The nitrogen bases held the two strands together through hydrogen bonds forming the cross-rungs of the ladder. DNA was made of 2 long stands that wind together to form double helix.  Molecular Structure of DNA The each DNA strand is made up of repeating units called nucleotides. Each DNA nucleotide is formed of three structures: 1- A Five- carbon Pentose sugar (deoxyribose ). 2- Phosphate group. 3- Nitrogenous base. DNA nucleotide Nucleotide subunits are linked by the formation of a phosphodiester bond between carbon atom number 3 of the sugar molecule of one nucleotide and the carbon atom number 5 of the sugar molecule of the next nucleotide with the phosphate group in between. The nitrogenous bases are linked to carbon atom number one of sugar molecules by glycosidic bonds. -2-  Molecular Structure of DNA The orientation of the two strands is antiparallel (i.e their 5 '→3 ' direction are opposite).This mean that the two ends of the chain are not the same.The chain has a 5 ' carbon (with a phosphate group on it ) at one end and a 3'carbon (with a hydroxyl group on it ) at the other end.This make the two strands of the helix run in opposite directions , one strand runs in the direction 5'→3' and the other strand runs in the direction 3 '→5'. The double helix of DNA has constant width (20 ˚A) which represents the diameter of the molecule this width is suitable to be occupied by be either (C) and (G) Joined by three hydrogen bonds or (A) and (T) joined by two hydrogen bonds (obligatory). This mean that, DNA had specific base-pairing between the nitrogen bases. The space is not suitable to be filled by two purines because the combination of them would be wider.At the same time the space between the two strands is not suitable to be occupied by two pyrimidines, this is because their width together would be narrower. The opposite combination ( cytosine with adenine and guanine with thymine) do not lead to favorable hydrogen bonding. Each strand is formed of chain of nucleotides arranged in a specific way called the “Complementary Rule” -3-  Molecular Structure of DNA Since the base pairing is specific, once the sequence of bases in one strand is known, the sequence of the other strand is also known. Thus, if one strand has the sequence 5' ACTAGAC 3' the other strand must have the following complementary sequence 3' TGATCTG 5'. Watson and Crick model of DNA (1953) -4- Molecular Structure of DNA -5-  Molecular Structure of DNA Nitrogenous base: There are two types of nitrogenous bases: Purines pyrimidines Includes guanine (G) and adenine (A) cytosine (C) and thymine (T) composed of five –membered ring fused a six membered ring to the six-membered ring glycosidic Carbon atom number 1 of Carbon number 1 of the linkage the sugar binds to sugar binds to nitrogen formed between nitrogen number 9 of the number 3 of the base purine base. Structural formula -6-  Molecular Structure of DNA Chargaff `s rules : In the same DNA molecule:- 1-number of purines = number of pyrimidines. 2-amount of adenine = amount of thymine. 3-amount of guanine= amount of cytosine. 5- So, A+G / T+C=1(purines/ pyrimidines)=1 6-the base ratio A+T / C+G varies widely among organisms, but always constant for any species (species specific). Base pairing -7-  Molecular Structure of DNA Genetic Diversity… Different arrangements of nucleotides in a nucleic acid (DNA) provides the key to DIVERSITY among living organisms. -8-  Molecular Structure of DNA Note: A nucleotide consists of a nucleoside and one phosphate group. A nucleoside consists of pentose sugar molecule and one nitrogenous base (A,T,G or C). -9-  Molecular Structure of DNA DNA Replication All living organisms possessing DNA as their genetic material ( prokaryotes or eukaryotes ) must duplicate their DNA before every cell division. DNA replication is the process of DNA synthesis where by a parent DNA molecule is faithfully copied giving rise to two identical daughter molecules. DNA replication occurs at polymerization rates of about 500 nucleotides per second in bacteria and about 50 nucleotides per second in mammals. DNA replication is a complex process achieved by means of a multienzyme complex called the replication apparatus or ( replisome ).  Semi-conservative Model: Watson and Crick showed that the two strands of the parental DNA molecule separate and each functions as a template for synthesis of a new complementary strand.. Because each of the two daughter molecules containing one old and one new strand , the process of DNA replication is said to be (semi-conservative). - 01 -  Molecular Structure of DNA Fig.A Fig.B - 00 -  Molecular Structure of DNA Replicons: Replication does not occur all at once, it occurs within small units of DNA duplex called (replicons). It always has an origin at which replication starts and then proceeds. Not all replicons replicate at the same time. Some replicate early and some replicate later. Replicons fuse as replication proceeds. The steps of DNA replication (semi-conservative model): 1-Initiation: 1-Begins at a specific DNA sequence called an origin of replication (initiation point ). 2- Unwinding and separation of the two DNA strands of the double helix by DNA-helicase enzyme. 3- The two separated strands are prevented from rewinding by binding with helix- destabilizing proteins (single strand DNA binding proteins (SSB), these proteins are able to bind to the single – stranded DNA without covering the bases so that they are still readable by DNA polymerase). Binding of helix-destabilizing protein to the separated DNA strands resulted in the formation of two replication forks (y-shaped). 4- The replication process thus initiates, and the replication forks proceed in two opposite directions along the DNA molecule. - 02 -  Molecular Structure of DNA ❷ Primer Synthesis: 1-The synthesis of a new, complementary strand of DNA using the existing strand as a template is brought about by enzymes known as DNA polymerases. In addition to replication they also play an important role in DNA repair and recombination. 2- DNA polymerases cannot start DNA synthesis independently, and require 3' hydroxyl group to start the addition of complementary nucleotides. This is provided by an enzyme called DNA primase which synthesizes a short stretch of RNA onto the existing DNA strands. This short segment is called a primer, and comprises 9-12 nucleotides. Once the primers are formed on both the strands, DNA polymerases can extend these primers into new DNA strands. ❸ Leading Strand Synthesis DNA polymerases can add new nucleotides only to the 3' end of an existing strand, and hence can synthesize DNA in 5' → 3' direction only. But the DNA strands run in opposite directions, and hence the synthesis of DNA on one strand can occur continuously. This is known as the leading strand.. Here, DNA polymerase III (DNA pol III) recognizes the 3' OH - 03 -  Molecular Structure of DNA end of the RNA primer, and adds new complementary nucleotides. As the replication fork progresses, new nucleotides are added in a continuous manner, thus generating the new strand. ❹ Lagging Strand Synthesis: On the opposite strand, DNA is synthesized in a discontinuous manner by generating a series small fragments of new DNA in the 5' → 3' direction. These fragments are called Okazaki fragments, which are later joined to form a continuous chain of nucleotides. This strand is known as the lagging strand since the process of DNA synthesis on this strand proceeds at a lower rate. Here, the primase adds primers at several places along the unwound strand. DNA pol III extends the primer by adding new nucleotides. - 04 -  Molecular Structure of DNA ❺ Primer Removal Although new DNA strands have been synthesized the RNA primers present on the newly formed strands need to be replaced by DNA. This activity is performed by the enzyme DNA polymerase I (DNA pol I). ❻ Ligation: After primer removal is completed the lagging strand still contains gaps or nicks between the adjacent Okazaki fragments. The enzyme ligase identifies and seals these nicks by creating a phosphodiester bond between the 5' phosphate and 3' hydroxyl groups of adjacent fragments. ❼ Termination This replication machinery halts at specific termination sites which comprise a unique nucleotide sequence. This sequence is - 05 -  Molecular Structure of DNA identified by specialized proteins called tus which bind onto these sites, thus physically blocking the path of helicase. When helicase encounters the tus protein it falls off along with the nearby single- strand binding proteins Two Summary: 1-Newly synthesized strands:- a-leading strand: - Is formed continuously toward replication fork (its template 5'→3'). - Is formed more rapidly than lagging strand. b- lagging strand: -Is formed discontinuously as a short fragments (Okazaki fragments) away from replication fork ( its template 3'→5'). - formed discontinuously due to: a- it grow in direction away from replication fork. b- DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3' end of a DNA strand. The fragments link together by DNA-ligase. 2- DNA –helicase: Unwinds and separates DNA double helix at origin of replication. - 06 -  Molecular Structure of DNA 3- Destabilizing proteins : Prevent reformation of DNA double helix by attaching the separated DNA strands at the replication forks. 4-. DNA – polymerase: Add nucleotides to 3’ end of RNA -primer -enzyme of replication, - move in 5’ → 3’ directions - works at replication fork - uses energy by breaking down nucleoside triphosphate. 5- DNA –ligase: links Okazaki – DNA fragments of lagging strand by the formation of phosphodiester bonds. 6-. RNA –primer: Is formed of 9-12 RNA nucleotides, provides a 3’ end to which DNA polymerase can add nucleotide at beginning of DNA replication Later degraded & replaced with DNA –nucleotide. - 07 -