1 Nucleic Acid Chemistry Growth and Development Block Professor Nikhat Ahmed Siddiqui,PhD

2 U.S. Department of Energy Human Genome Program,

Objectives Name the different types of Bases and sugars present in Nucleic Acid Define Nucleoside, nucleotide, DNA and RNA. Name the structural component of each one. Define Nuclear DNA, name its different forms and describe the structure of its B-form. Define nucleosome, describe its structure and list the different stages of chromatin condensation till chromosome. Describe the general structure of RNA and name its different types with the function of each type. 3

4 The Genome The genome of an organism is the totality of genetic information and is encoded in the DNA (or, for some viruses, RNA). The genome of an organism is the totality of genetic information and is encoded in the DNA (or, for some viruses, RNA). commons.wikimedia.org/wiki/Image:Genome.jpg commons.wikimedia.org/wiki/Image:Genome.jpg

5 DNA and RNA are long chain polymers of small compound called nucleotides. DNA and RNA are long chain polymers of small compound called nucleotides. Each nucleotide is composed of a base; sugar (ribose in RNA or deoxyribose in DNA) and a phosphate group. Each nucleotide is composed of a base; sugar (ribose in RNA or deoxyribose in DNA) and a phosphate group. The phosphate joins the sugars in a DNA or RNA chain through their 5` and 3` hydroxyl group by phosphodiester bonds. The phosphate joins the sugars in a DNA or RNA chain through their 5` and 3` hydroxyl group by phosphodiester bonds. General Structure of Nucleic Acid

Nitrogenous Bases

7 Pentose Sugar ‘Ribose ’

Nucleosides Purine /pyrimidine base linked to sugar residue is called Nucleoside eg: Adenosine,Guanosine, Cytidine,Thymidine,Uridine Linked to D-ribose as in RNA Linked to D-2-deoxyribose as in DNA Linkage in Purine or Pyrimidine Nucleosides β-N-Glycosidic linkage. The attachment of the C1 of the pentose sugar to N9 of purine or N1 of pyrimidine makes a Nucleoside The attachment of the C1 of the pentose sugar to N9 of purine or N1 of pyrimidine makes a Nucleoside

Nucleotides It is a nucleoside to which a phosphate group is attached to the sugar molecule. The nucleotides are Nucleoside-P i.e. Base + sugar + phosphate Nucleotides present in DNA: dAMP deoxyadenylate, dGMP,dCMP,dTMP Nucleotides present in RNA: AMP adenylic Acid,GMP,CMP,UMP

10 James Watson and Francis Crick worked out the three-dimensional structure of DNA, based on work by Rosalind Franklin James Watson and Francis Crick worked out the three-dimensional structure of DNA, based on work by Rosalind Franklin DNA is a double-stranded helix Figure 10.3A, B

11 Deoxyribonucleic Acid (DNA) Deoxyribonucleic Acid (DNA), the genetic material of all cellular organisms and most viruses, the gigantic molecule which is used to encode genetic information for all life on Earth. Deoxyribonucleic Acid (DNA), the genetic material of all cellular organisms and most viruses, the gigantic molecule which is used to encode genetic information for all life on Earth.

A Polymer of Deoxyribonucleotides Double –Stranded Individual deoxynucleoside triphosphates are coupled by Phosphodiester bonds. ESTERIFICATION - LINK 3’ CARBON of one RIBOSE with 5’ C of another - TERMINAL ENDS : 5’ AND 3’ A “DOUBLE HELICAL” STRUCTURE - Common Axis for both HELICES “- HANDEDNESS” OF HELICES - ANTIPARALLEL RELATIONSHIP BETWEEN 2 DNA STRANDS Structure of DNA PERIPHERY OF DNA: SUGAR-PHOSPHATE CHAIN TRIPHOSPHATES ARE COUPLED BY PHOSPHODIESTER CORE OF DNA BASES ARE STACKED IN PARALLEL FASHION CHARGAFF’S RULES The ratio ofPyrimidine to purine is~1 A = T G = C COMPLEMENTARY” BASE PAIRING between two strands of DNA

DNA contains only four types of nucleotides, which are the building blocks of nucleic acids. Each nucleotide in DNA is made of: a five carbon sugar a phosphate group and one of four possible nitrogen bases Deoxyribose. DNA Structure

14 Orders of DNA Structure 1.Primary: Linear sequence of deoxyribonucleotide units 2.Secondary: Double Stranded Helix 3.Tertiary: double helix wrapped around Histone Octamer toform a Nucleosome 4.Higher Orders: Formationof 30nm Fibers (chromatin),Chromosomes Chromosomal DNA is Packaged and organized at several levels Eukaryotic genes: DNA molecules complexed with other proteins especially basic proteins called histones, to form a substance known as chromatin. A human cell contains about 2 meters of DNA. So it is tightly packed

FORCES THAT STABILIZE NUCLEIC ACID STRUCTURES SUGAR-PHOSPHATE CHAIN CONFORMATIONS BASE PAIRING BASE-STACKING,HYDROPHOBIC IONIC INTERACTIONS

16 A always pairs with T, and G with C

17 Hydrogen bonds between bases hold the strands together: A and T, C and G Hydrogen bonds between bases hold the strands together: A and T, C and G Figure 10.3D Ribbon modelPartial chemical structureComputer model Hydrogen bond

STRUCTURE OF THE DOUBLE HELIX THREE MAJOR FORMS B-DNA B-DNA A-DNA A-DNA Z-DNA Z-DNA B-DNA IS BIOLOGICALLY THE MOST COMMON RIGHT-HANDED RIGHT-HANDED DIAMETER 20 Angstrom (A) DIAMETER 20 Angstrom (A) COMPLEMENTARY BASE-PAIRING (WATSON-CRICK) COMPLEMENTARY BASE-PAIRING (WATSON-CRICK) A-T A-T G-C G-C 10 base pair per turn repeating every 3.4nm EACH BASE PAIR HAS ~ THE SAME WIDTH A FROM C1’ TO C1’ A FROM C1’ TO C1’ A-T AND G-C PAIRS ARE INTERCHANGEABLE “PSEUDO-DYAD” AXIS OF SYMMETRY

19 DNA Forms

MAJOR AND MINOR GROOVES MINOR MINOR EXPOSES EDGE FROM WHICH C1’ ATOMS EXTEND EXPOSES EDGE FROM WHICH C1’ ATOMS EXTEND MAJOR MAJOR EXPOSES OPPOSITE EDGE OF BASE PAIR EXPOSES OPPOSITE EDGE OF BASE PAIR THE PATTERN OF H-BOND POSSIBILITIES IS MORE SPECIFIC AND MORE DISCRIMINATING IN THE MAJOR GROOVE THE PATTERN OF H-BOND POSSIBILITIES IS MORE SPECIFIC AND MORE DISCRIMINATING IN THE MAJOR GROOVE

GEOMETRY OF B-DNA IDEAL B-DNA HAS 10 BASE PAIRS PER TURN BASE THICKNESS AROMATIC RINGS WITH 3.4 A P ITCH = 10 X 3.4 = 34 A PER COMPLETE TURN Diameter is 2.37 nm AXIS PASSES THROUGH MIDDLE OF EACH BP MINOR GROOVE IS NARROW MAJOR GROOVE IS WIDE

STRUCTURAL VARIANTS OF DNA DEPEND UPON: SOLVENT COMPOSITION SOLVENT COMPOSITION - WATER - WATER - IONS - IONS BASE COMPOSITION BASE COMPOSITION

Nuclear DNA Nuclear DNA is bound to basic proteins called Histones. DNA present in every nucleated cell and carries the genetic information.

24 Thread like structure. Thread like structure. Located in the cell nucleus. Located in the cell nucleus. The storage place for all genetic information. The storage place for all genetic information. The number of chromosomes varies from one species to another. The number of chromosomes varies from one species to another. The Chromosome

25 Chromosomal DNA is Packaged and organized at several levels Chromosomal DNA is Packaged and organized at several levels Eukaryotic genes: DNA molecules complexed with other proteins especially basic proteins called histones, to form a substance known as chromatin. A human cell contains about 2 meters of DNA. So it is tightly packed. Eukaryotic genes: DNA molecules complexed with other proteins especially basic proteins called histones, to form a substance known as chromatin. A human cell contains about 2 meters of DNA. So it is tightly packed. 1. Nucleosomes: 10 nm chromatin fibril 2. The 30nm fibril composed of nucleosomes. 3. Higher ordered structures: a) Loop domains b) SMC Proteins and control of higher order domains. -mitotic chromosome condensation,SMC proteins and condensin -mitotic chromosome condensation,SMC proteins and condensin Structural Maintenance of chromosomes

26 Chromatin Structure (Nucleosomes) Chromatin Structure (Nucleosomes) Eukaryotic chromatin is folded in several ways. The first order of folding involves structures called nucleosomes, which have a core of histones, around which the DNA winds ( four pairs of histones H2A, H2B,H3 and H4 in a wedge shaped disc, around it wrapped a stretch of 147 bp of DNA). Eukaryotic chromatin is folded in several ways. The first order of folding involves structures called nucleosomes, which have a core of histones, around which the DNA winds ( four pairs of histones H2A, H2B,H3 and H4 in a wedge shaped disc, around it wrapped a stretch of 147 bp of DNA). Nucleosomes are linked by DNA linker wrapped around H1. Nucleosomes are linked by DNA linker wrapped around H1. Nucleosomes are the basic unit of eukaryotic chromosome structure “Beads on a string “ 10 nm Chromatin fibril

27 The DNA in eucaryotes is tightly bound to an equal mass of histones, which form a repeating array of DNA-protein particles called nucleosomes. The nucleosome is composed of an octameric core of histone proteins around which the DNA double helix is wrapped. Nucleosomes are usually packed together (with the aid of histone H1 molecules) into quasi-regular arrays to form a 30-nm fiber. Despite the high degree of compaction in chromatin, its structure must be highly dynamic to allow the cell access to the DNA

30 nm Chromatin fibril 28

THE TOPOLOGY OF DNA “SUPERCOILING” : DNA’S “TERTIARY STRUCTURE L = “LINKING NUMBER” L = “LINKING NUMBER” A TOPOLOGIC INVARIANT A TOPOLOGIC INVARIANT THE # OF TIMES ONE DNA STRAND WINDS AROUND THE OTHER L = T + W T IS THE “TWIST THE # OF COMPLETE REVOLUTIONS THAT ONE DNA STRAND MAKES AROUND THE DUPLEX AXIS W IS THE “WRITHE” THE # OF TIMES THE DUPLEX AXIS TURNS AROUND THE SUPERHELICAL AXIS

DNA TOPOLOGY THE TOPOLOGICAL PROPERTIES OF DNA HELP US THE TOPOLOGICAL PROPERTIES OF DNA HELP US TO EXPLAIN DNA COMPACTING IN THE NUCLEUS DNA COMPACTING IN THE NUCLEUS UNWINDING OF DNA AT THE REPLICATION FORK UNWINDING OF DNA AT THE REPLICATION FORK FORMATION AND MAINTENANCE OF THE FORMATION AND MAINTENANCE OF THE TRANSCRIPTION BUBBLE TRANSCRIPTION BUBBLE MANAGING THE SUPERCOILING IN THE ADVANCING TRANSCRIPTION BUBBLE MANAGING THE SUPERCOILING IN THE ADVANCING TRANSCRIPTION BUBBLE

31 Function of The DNA Deoxyribonucleic Acid (DNA), the gigantic molecule which is used to encode genetic information for all life on Earth. Deoxyribonucleic Acid (DNA), the gigantic molecule which is used to encode genetic information for all life on Earth. The chemical basis of hereditary and genetic variation are related to DNA. The chemical basis of hereditary and genetic variation are related to DNA. DNA directs the synthesis of RNA which in turn directs protein synthesis. DNA directs the synthesis of RNA which in turn directs protein synthesis.

The nucleotides within RNA contain the base uracil instead of thymine Each nucleotide in RNA contains: a five carbon sugar (ribose) In the 2’ position, a Hydroxyl group (Not present in the 2’ position in Deoxyribose) a phosphate group a nitrogenous base (all the same ones as DNA, except the Pyrimidine thymine is replaced with uracil.) Uracil is a pyrimidine, as you can see from the structure RNA

Differences with DNA

34 The RNA Three major classes of RNA: messenger (mRNA), transfer (tRNA) and ribosomal (rRNA). Minor classes of RNA include small nuclear RNA ; small nucleolar RNA;……….. Three major classes of RNA: messenger (mRNA), transfer (tRNA) and ribosomal (rRNA). Minor classes of RNA include small nuclear RNA ; small nucleolar RNA;………..

35 The RNA - The concentration of purine and pyrimidine bases do not necessarily equal one another in RNA because RNA is single stranded. However, the single strand of RNA is capable of folding back on itself like a hairpin and acquiring double strand structure.

36 RNA is also a nucleic acid RNA is also a nucleic acid different sugar different sugar U instead of T U instead of T Single strand, usually Single strand, usually Figure 10.2C, D Phosphate group Nitrogenous base (A, G, C, or U) Uracil (U) Sugar (ribose)

37 Messenger RNA mRNA molecules represent transcripts of structural genes that encode all the information necessary for the synthesis of a single type polypeptide of protein. mRNA molecules represent transcripts of structural genes that encode all the information necessary for the synthesis of a single type polypeptide of protein. mRNA; intermediate carrier of genetic information; deliver genetic information to the cytoplasm where protein synthesis take place. mRNA; intermediate carrier of genetic information; deliver genetic information to the cytoplasm where protein synthesis take place. The mRNA also contains regions that are not translated: in eukaryotes this includes the 5' untranslated region, 3' untranslated region, 5' capand poly-A tail. The mRNA also contains regions that are not translated: in eukaryotes this includes the 5' untranslated region, 3' untranslated region, 5' capand poly-A tail.

38 Transfer RNA(tRNA) All tRNAs share a common secondary structure represented by a cloverleaf. They have four-paired stems defining three stem loops (the D loop, anticodon loop, and T loop) and the acceptor stem to which amino acids are added in the charging step. All tRNAs share a common secondary structure represented by a cloverleaf. They have four-paired stems defining three stem loops (the D loop, anticodon loop, and T loop) and the acceptor stem to which amino acids are added in the charging step. RNA molecules that carry amino acids to the growing polypeptide. RNA molecules that carry amino acids to the growing polypeptide. a. Function 1) Carries amino acids to mRNA at the ribosome 2) tRNA molecules are specific to the amino acid they carry; therefore, there are 20 tRNA molecules

39 Ribosomal RNA (rRNA) Ribosomal RNA (rRNA) is the central component of the ribosome, the function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by providing peptidyl transferase activity. Ribosomal RNA (rRNA) is the central component of the ribosome, the function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by providing peptidyl transferase activity. a. Important structural component of ribosome b. Ribosome - composed of one large and one small subunit; location for protein synthesis in cells a. Important structural component of ribosome b. Ribosome - composed of one large and one small subunit; location for protein synthesis in cells

40 Thank You