Molecular Biology I BIO316 Lecture 1 PDF

Molecular Biology I BIO316 Lecture 1 The molecular nature of the Genetic Material Prepared by Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics ...

Molecular Biology I BIO316 Lecture 1 The molecular nature of the Genetic Material Prepared by Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli  The chemical nature of Nucleic acids Associate Professor of Biochemistry and Molecular Genetics  Nucleotides: Building Blocks of Nucleic Acids  The structural components of DNA and RNA are very similar.  DNA is a nucleic acid, and nucleotides are the building blocks of all nucleic acid molecules.  These structural units consist of three essential components:  Nitrogenous base.  Pentose sugar (5-carbon sugar).  Phosphate group.  There are two kinds of nitrogenous bases:  The nine-member double-ring purines.  The three pyrimidines  The six-member single-ring pyrimidines. are cytosine, thymine,  Two types of purines and three types of and uracil, abbreviated pyrimidines are commonly found in nucleic acids. C, T, and U.  The two purines are adenine and guanine, abbreviated A and G.  Dr. Rami Elshazli  The chemical nature of Nucleic acids Associate Professor of Biochemistry and Molecular Genetics  Nucleotides: Building Blocks of Nucleic Acids  Both DNA and RNA contain A, C, and G, but only DNA contains the base T and only RNA contains the base U.  The pentose sugars found in nucleic acids give them their names.  Ribonucleic acids (RNA) contain ribose, while deoxyribonucleic acids (DNA) contain deoxyribose.  Each carbon atom is distinguished by a number with a prime sign (e.g., C-1ʹ, C-2ʹ).  The absence of a hydroxyl group at the C-2ʹ position distinguishes DNA from RNA.  Nucleoside: If a molecule is composed of a purine or pyrimidine base and a ribose or deoxyribose sugar, the chemical unit is called a nucleoside.  Nucleotide: If a phosphate group is added to the nucleoside, the molecule is called a nucleotide.  Dr. Rami Elshazli  Nature of Genetic material Associate Professor of Biochemistry and Molecular Genetics  DNA consists of four chemically similar nucleotides.  Protein contains 20 different amino acids that are much more chemically diverse than nucleotides.  Nucleotides contain phosphorus, but proteins do not, and some amino acids contain sulfur, but DNA does not.  DNA structure  The DNA molecule consisted of three main components:  5-carbon Ribose sugar.  Phosphate (PO4) group.  Nitrogen-containing (nitrogenous) base.  The base may be a purine (adenine, A, or guanine, G), a two-ringed structure; or a pyrimidine (thymine, T, or cytosine, C), a single-ringed structure.  RNA contains the pyrimidine uracil (U) in place of thymine.  Dr. Rami Elshazli  DNA structure Associate Professor of Biochemistry and Molecular Genetics  The nitrogenous base may be:  Two-ringed structure purine: [adenine (A) or guanine (G)].  Single-ringed structure pyrimidine [thymine (T) or cytosine (C)].  RNA contains the pyrimidine uracil (U) in place of thymine.  The ribose sugars found in nucleic acids consist of a five membered ring with four carbon atoms and an oxygen atom.  The carbon atoms are numbered 1′ to  The phosphate group is attached to the 5′, proceeding clockwise from the 5′ carbon atom of the sugar, and the oxygen atom. base is attached to the 1′ carbon atom.  In addition, a free hydroxyl (– OH) group  The symbol ( ′ ) is pronounced as prime. is attached to the 3′ carbon atom.  Dr. Rami Elshazli  DNA structure Associate Professor of Biochemistry and Molecular Genetics  The nucleotide monomers linked together through dehydration reaction involving the 5′ phosphate of one nucleotide with the 3′ hydroxyl of another nucleotide.  This linkage is called a phosphodiester bond because the phosphate group is now linked to the two sugars by means of a pair of ester bonds.  Many thousands of nucleotides can join via these linkages to form long nucleic acid polymers.  Linear strands of DNA or RNA, almost always have a free 5′ phosphate group at one end and a free 3′ hydroxyl group at the other.  The sequence of bases is usually written in the 5′-to-3′ direction.  Dr. Rami Elshazli  Chargaff’s rules Associate Professor of Biochemistry and Molecular Genetics  Erwin Chargaff showed that the nucleotide composition of DNA molecules varied in complex ways.  This strongly suggested that DNA was not a simple repeating polymer.  Chargaff observed an important underlying regularity in the ratios of the bases found in native DNA.  The amount of adenine present in DNA always equals the amount of thymine, and the amount of guanine always equals the amount of cytosine.  Two important findings from this work are often called Chargaff’s rules:  The proportion of A always equals that of T, and the proportion of G always equals that of C.  A = T and G = C.  The ratio of G–C to A–T varies with different species.  Dr. Rami Elshazli  X-ray diffraction patterns of DNA Associate Professor of Biochemistry and Molecular Genetics  The technique of X-ray diffraction provided more information about the possible structure of DNA.  In X-ray diffraction, crystals of a molecule are bombarded with a beam of X-rays.  The rays are diffracted, by the molecules they encounter, and the diffraction pattern is recorded on photographic film to yield information about the three-dimensional structure of a molecule.  British researcher Maurice Wilkins succeeded in obtaining the first crude diffraction information on DNA in 1950.  These X-ray photos suggested that the DNA molecule has the shape of a helix.  British chemist Rosalind Franklin continued this work, perfecting the technique to obtain clearer “pictures” of the oriented DNA fibers.  These images confirmed that DNA was a helix, and indicating a diameter of about 2 nm and a complete helical turn every 3.4 nm.  Dr. Rami Elshazli  Watson–Crick model Associate Professor of Biochemistry and Molecular Genetics  Watson and Crick identified the form of the DNA bases.  The structural forms have unique different hydrogen- bonding possibilities.  American chemist James Watson and English molecular biologist Francis Crick worked out a likely structure for the DNA molecule.  The key to their model was that each DNA molecule is made up of two chains of nucleotides that are intertwined—the double helix.  Dr. Rami Elshazli  The phosphodiester backbone Associate Professor of Biochemistry and Molecular Genetics  The two strands of the double helix are made up of long polymers of nucleotides.  Each strand is made up of repeating sugar and phosphate units joined by phosphodiester bonds.  These phosphodiester bonds will be called the backbone of the molecule.  The two strands of the backbone are then wrapped about a common axis forming a double helix.  Dr. Rami Elshazli  Complementarity of bases Associate Professor of Biochemistry and Molecular Genetics  Watson and Crick proposed that the two strands were held together by formation of hydrogen bonds between bases on opposite strands.  These bonds would result in specific base-pairs:  Adenine (A) can form two hydrogen bonds with thymine (T).  Guanine (G) can form three hydrogen bonds with cytosine (C).  This configuration also pairs a two-ringed purine with a single-ringed pyrimidine, so that the diameter of each base-pair is the same.  This pattern of base-pairing is referring as complementary.  This always pairs a purine with a pyrimidine, keeping the diameter of the double helix constant.  If the sequence of one strand is ATGC, then the complementary strand sequence must be TACG.  Dr. Rami Elshazli  Complementarity of bases Associate Professor of Biochemistry and Molecular Genetics  In a double helix, adenine forms two hydrogen bonds with thymine, but it will not form hydrogen bonds properly with cytosine.  Similarly, guanine forms three hydrogen bonds with cytosine, but it will not form hydrogen bonds properly with thymine.  Because of this base-pairing, adenine and thymine always occur in the same proportions in any DNA molecule, as do guanine and cytosine.  Dr. Rami Elshazli  Antiparallel configuration Associate Professor of Biochemistry and Molecular Genetics  A single phosphodiester strand has an inherent polarity, meaning that one end terminates in a 3′ OH and the other end terminates in a 5′ PO4.  Strands are referred to having either a 5′-to-3′ or a 3′-to-5′ polarity.  Double-stranded DNA always has the antiparallel configuration, with one strand running 5′ to 3′ and the other running 3′ to 5′.  This antiparallel nature also has important implications for DNA replication.  Dr. Rami Elshazli  The Watson–Crick DNA molecule Associate Professor of Biochemistry and Molecular Genetics  Watson and Crick published their analysis of DNA structure in 1953.  This model has the following major features:  Two long polynucleotide chains are coiled around a central axis, forming a double helix.  The two chains are antiparallel; their C-5′-to-3′ orientations run in opposite directions.  The bases of both chains are flat structures lying perpendicular to the axis.  The nitrogenous bases of opposite chains are paired with hydrogen bonds.  Each complete turn of the helix is 34 Å (3.4 nm) long; thus, each turn of the helix is the length of a series of 10 base pairs.  A larger major groove alternating with a smaller minor groove winds along the length of the molecule.  The double helix has a diameter of 20 Å (2.0 nm).  Dr. Rami Elshazli  The Watson–Crick DNA molecule Associate Professor of Biochemistry and Molecular Genetics  In the Watson and Crick model, a DNA molecule consists of two phosphodiester strands wrapped about a common helical axis.  The bases extending to interior of the helix.  The sequence of bases on the two strands are complementary, so they form base-pairs that hold the strands together.  Each strand is also polar, with a 5′ and a 3′ end, and they are oriented in the opposite (antiparallel) direction.  Dr. Rami Elshazli  RNA structure Associate Professor of Biochemistry and Molecular Genetics  The structure of RNA molecules resembles DNA, with several important exceptions.  The sugar ribose replaces deoxyribose, and the nitrogenous base uracil replaces thymine.  Another important difference is that most RNA is single stranded.  Three major classes of cellular RNA molecules function during the expression of genetic information:  Ribosomal RNA (rRNA).  Messenger RNA (mRNA).  Transfer RNA (tRNA).  Because uracil replaces thymine in RNA, uracil is complementary to adenine during transcription and during RNA base pairing.  Dr. Rami Elshazli Comparison between DNA & RNA Associate Professor of Biochemistry and Molecular Genetics DNA RNA Shape Double strand helix Single strand helix Site Nucleus & Mitochondria Cytoplasm Synthesis By replication By transcription Significance  Formation of DNA by replication  Biosynthesis of proteins through translation  Formation of RNA by transcription Sugar Deoxyribose Ribose Types One Three (mRNA/tRNA/rRNA) Bases Adenine A, Guanine G, Cytosine C & Thymine T Adenine A, Guanine G, Cytosine C & Uracil U  Dr. Rami Elshazli Lecture summary Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics