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NUCLEIC ACIDS. OBJECTIVES. Identify/ recognize nucleic acid Components in nucleic acid – monosaccharide, nucleobases, phosphoric acid Differentiate - between 2 types of nucleic acids, DNA and RNA - between nucleotide and nucleoside

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    2. OBJECTIVES • Identify/ recognize nucleic acid • Components in nucleic acid – monosaccharide, nucleobases, phosphoric acid • Differentiate - between 2 types of nucleic acids, DNA and RNA - between nucleotide and nucleoside • Definition – nucleotide, nucleoside, DNA and RNA

    3. Nucleic Acids • Nucleic acid: a biopolymer containing three types of monomer units • a nitrogenous base (nucleobases), either purine or pyrimidine • a monosaccharide (aldopentose), either D-ribose or 2-deoxy-D-ribose • phosphoric acid/phospharyl group • Two types - RNA (Ribonucleic Acid) - DNA (Deoxyribonucleic Acid)

    4. Nucleobases Nonpolar • Heterocylic compounds containing C, H, N, and O • Purine and pyrimidine methyl 1 ring structure (C) (T) (U) 2 ring structure (A) (G)

    5. Monosaccharide/sugar Polar Only  anomer present in nucleic acid • 2 type of aldopentoses found - Ribose (RNA) - 2-deoxyribose (DNA) • Deoxyribose, derivative of ribose – lacks an oxygen atom at C2

    6. Nucleosides • Nucleoside: a compound that consists of D-ribose or 2-deoxy-D-ribose (monosaccharide) covalently bonded to a nucleobase by a -N-glycosidic bond • Covalent linkage forms between N9 of purines or N1 of pyrimidines to C1 (anomeric carbon of ribose or 2-deoxyribose) Lack phosphate group Pyrimidine Purine

    7. Nucleotides • Nucleotide: a nucleoside in which a molecule of phosphoric acid/phosphoryl group is esterified with an -OH of the monosaccharide, at the 5’-OH • As constituents of cofactors, Coenzyme A (CoA), flavin adenine dinucleotide (FAD) & nicotinamide adenine dinucleotides (NAD) Nucleobase, aldopentose sugar and phosphoryl group Phosphoric acid - polar

    8. 5’ = attach to C5 of pentose SUGAR?

    9. NOMENCLATURE of Nucleotide Based on the nucleoside, plus the phosphate group

    10. Nucleotide Sequence • Gene: Sequence of nucleotides that encodes a polypeptide, eventually forming a functional protein • Gene: a discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (RNA in some viruses) • The nucleotide sequence is depending on the bases (nucleobases) present

    11. Nucleic Acid: Biopolymer, nucleotide as monomer DNA RNA 1. Bases = ATGC 2. Aldopentose = Ribose 3. Phosphoryl group 1. Bases = AUGC 2. Aldopentose = Deoxyribose 3. Phosphoryl group Nucleoside Naming of nucleotide: if Base adenine  Deoxyadenosine 5’ monophosphate Naming of nucleotide: if Base adenine Adenosine 5’monophosphate

    12. Nucleic Acid - DNA and RNA • DNA stands for deoxyribonucleic acid. It is the genetic code molecule for most organisms. • RNA stands for ribonucleic acid. RNA molecules are involved in converting the genetic information in DNA into proteins. In retroviruses, RNA is the genetic material. NUCLEIC ACIDS ARE POLYMERS OF NUCLEOTIDES

    13. Nucleic Acids • DNA or RNA • consist of a chain of nucleotides joined together by phosphodiester bonds • DNA = material of inheritance, carrier of genetic information • RNA = DNA code is transcribed into RNA which in turn is translated into the corresponding protein transcription translation DNA RNA protein

    14. Polynucleotide = DNA and RNA DNA Hydrolysis – break bond Condensation – form bond • DNA and RNA are polymers whose monomer units are nucleotides = polynucleotides • Deoxyribonucleic acids, DNA: a biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphoryl group • the 3’-OH of one nucleotide is joined to the 5’ P of the next nucleotide by a phosphodiester bond 3’ 5’ -phosphodiester bond

    15. DNA structure • Levels of structure • 1° structure: the order of bases on the polynucleotide sequence; the order of bases specifies the genetic code • 2° structure: the three-dimensional conformation of the polynucleotide backbone = double helix structure • 3° structure: supercoiling • 4° structure: interaction between DNA and proteins

    16. DNA - 1° Structure • Primary Structure:the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule • base sequence is read from the 5’ end to the 3’ end • System of notation single letter (A,G,C and T) 5’ – G G C A T T G C G C - 3’ Pg 237, Campbell and Farrel. READ! On the right 3’ 5’ -phosphodiester bond

    17. 5’-end guanine thymine cytosine 3’-5’ link 3’-end Segment of DNA Chain • 5’ end – phosphate group is free • 3’end – 3’ OH in deoxyribose is free

    18. DNA - 2° Structure • Secondary structure: the ordered arrangement of nucleic acid strands • Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strandsare coiled in a right-handed manner about the same axis • The chains run antiparallel and are held together by hydrogen bonding between complementary base pairs: A=T, G=C. DNA double helix

    19. DNA structural elements OH P • 2 right-handed, helical, polynucleotide chains, coiled around a common axis to form a double helix • 2 characteristic: Major groove and minor groove – binding site for drug or polypeptide • 2 strands run in opposite direction (antiparallel)-3’,5’-phosphodiester bridges run in opposite direction • 1 base (purine) from single strand link to 1 base (pyrimidine) from other stand (complimentary) • Bases are perpendicular to helix axis • Polarity and non-polarity regions • Aqueous environment – polar, charged, covalent backbone deoxyribose and phosphate groups outside of the helix • Hydrophobic purine and pyrimidine bases avoid water by turning towards the inside of the structure

    20. Groovy DNA DNA-protein interaction

    21. T-A Base Pairing • Base pairing is complementary: A=T, GC • A major factor stabilizing the double helix is base pairing by hydrogen bonding between T-A and between C-G • T-A base pair comprised of 2hydrogen bonds Complementary base pairing

    22. G-C Base Pair • G-C base pair comprised of 3 hydrogen bonds • G-C base pair comprised of 3 hydrogen bonds

    23. Forms of DNA • B-DNA • considered the physiological form • a right-handed helix, inside diameter 11Å • 10 base pairs per turn (34Å) of the helix • A-DNA • a right-handed helix, but thicker than B-DNA • 11 base pairs per turn of the helix • has not been found in vivo • Z-DNA • a left-handed double helix • may play a role in gene expression • Z-DNA occurs in nature, usually consists of alternating purine-pyrimidine bases • Methylated cytosine found also in Z-DNA

    24. Structural features of A-, B-, and Z- DNA Type A-DNA B-DNA Z-DNA Helical senses right handed right handed left handed Diameter (Å) ~26 ~20 ~18 Base pairs/turn 11 10 12 Major groove narrow/deep wide/deep Flat Minor groove wide/shallow narrow/deep narrow/deep Pg 294, Concepts in Biochemistry. 3/e 2006 John Wiley & Sons 20 Å

    25. DNA - 3° Structure • Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling • Supercoiling- Further coiling and twisting of DNA helix.

    26. DNA • DNA can forms tertiary structure by twist into complex arrangement – supercoil • Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each strand (2 polynucleotide chains) are joined by phosphodiester bonds • Can be found in microorganisms (bacteriophages, bacteria) • Circular twisted into supercoiled DNA - 3° Structure • Supercoil - results of extra twisting in the linear duplex form

    27. DNA • Circular DNA: In microorganisms (bacteriophages, bacteria) • Circular twisted into supercoiled DNA - 3° Structure • In eukaryotes, the 3° structure involves histone (protein)- Chromatin: DNA molecules wound around particles of histones in a beadlike structure

    28. PROPERTIES OF SUPERCOIL • Supercoiled is less stable than the relaxed form • Compact hence it more easily stored in the cell • Play a regulatory role in DNA replication

    29. Bacteriophage : DNA – threadlike structure

    30. Super DNA Coiled Topology • Double helix can be considered to a 2-stranded, right handed coiled rope • Can undergo positive/negative supercoiling Counterclockwise clockwise

    31. DNA - 4° Structure • Four stranded form of DNA (quadruplex DNA) • Role in regulating and stabilizing telomeres and in regulation of gene expression • Small molecules such as porphyrins and anthraquinones present, to stabilize the structure G-quadruplex