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NUCLEIC ACIDS

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Title: Nucleic acids Author: compaq Last modified by: User Created Date: 3/21/2007 8:48:12 AM Document presentation format: On-screen Show Company – PowerPoint PPT presentation

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Title: NUCLEIC ACIDS


1
NUCLEIC ACIDS
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 5monophosphate
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
DNA
Polynucleotide DNA and RNA
  • 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

Hydrolysis break bond Condensation form 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
Segment of DNA Chain
  • 5 end phosphate group is free
  • 3end 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 strands are 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 AT, GC.

DNA double helix
19
DNA structural elements
  • 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

OH
P
20
Groovy DNA
DNA-protein interaction
21
T-A Base Pairing
  • Base pairing is complementary AT, 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 2 hydrogen 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 wi
de/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
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