Nucleic Acids: How Structure Conveys Information Chapter 9.
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Transcript of Nucleic Acids: How Structure Conveys Information Chapter 9.
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Nucleic Acids: How Structure Conveys Information
Chapter 9
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Levels of structure in Nucleic Acids
Primary – Order of bases in polynucleotide sequence
Secondary – Three-dimensional conformation of the backbone
Tertiary – Supercoiling of molecule Quaternary - Interaction between DNA and
proteins
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What are nucleotides? Monomers of Nucleic acids – Nucleotides Consists of nitrogenous base, sugar and
phosphoric acid residue Covalently bonded
RNA (Ribonucleic Acid)
DNA (Deoxyribonucleic Acid)
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Pyrimidine and Purine Bases
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Other Bases
Less common bases/Unusual bases
Principally but not exclusively, in transfer RNAs
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What are Nucleosides? Nucleoside:Nucleoside: a compound that consists of D-ribose or 2-
deoxy-D-ribose covalently bonded to a nucleobase by a β-N-glycosidic bond
Lacks phosphate group
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Nucleotides A nucleoside in which a
molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’-OH or the 5’-OH
Polymerization leads to nucleic acids. Linkage is repeated (3’,5’-phosphodiester bond)
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DNA - 1° Structure
Deoxyribonucleic acids :Deoxyribonucleic acids : a biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate the 3’-OH of one 2-deoxy-D-ribose is joined
to the 5’-OH of the next 2-deoxy-D-ribose by a phosphodiester bond
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DNA - 1° Structure
“d” used to designate “deoxy”
Primary 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
A,G,C, and T
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Secondary structure of DNA
Double helix: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
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How is the base pairing of DNA complementary? 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
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How is the base pairing of DNA complementary?
G-C base pair comprised of 3 hydrogen bonds
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Are there other possible conformations of double helix DNA? A-DNAA-DNA
a right-handed helix, but thicker than B-DNA
11 base pairs per turn of the helix
has not been found in vivo
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Are there other possible conformations of double helix DNA?
B-DNAB-DNA considered the
physiological form
a right-handed helix
10 base pairs per turn (34Å) of the helix
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Are there other possible conformations of double helix DNA? Z-DNAZ-DNA
• a left-handed double helix
• may play a role in gene expression
• Alternating purine and pyrimidine sequences
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Z-form is derivative of B-form
Produced by flipping one side of the backbone 180˚ without disturbing the backbone covalent bonds or hydrogen bonds
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Differences between three forms
Both A and B-DNA are right-handed helices
• Z-DNA is left handed
• Z-DNA occurs in nature, usually consists of alternating purine-pyrimidine bases
• Methylated cytosine found also in Z-DNA
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Tertiary structure of DNATertiary structure of DNA
Tertiary structure:Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling
Circular DNA:Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by phosphodiester bonds
Supercoiling- Further coiling and twisting of DNA helix
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What are Topoisomerases?
Enzymes that can change supercoiled state of DNA – TopoIsomerases
Class I and Class II
DNA gyrase
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How does prokaryotic DNA supercoil into its tertiary structure?
Class I: cut the phosphodiester backbone of one strand, pass the end through, and reseal
Class II: cut both strands, pass some of the remaining DNA helix between the cut strands, and reseal
DNA gyrase introduces negative supercoils into DNA
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Super DNA Coiled Topology Double helix can be considered to a 2-
stranded, right handed coiled rope Can undergo positive/negative supercoiling
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How does eukaryotic DNA supercoil into its tertiary structure? Histone:Histone: a protein, particularly rich in the basic amino acids
Lys and Arg; found associated with eukaryotic DNA five main types: H1, H2A, H2B, H3, H4
Chromatin:Chromatin: DNA molecules wound around particles of histones in a beadlike structure
Topological changes induced by supercoiling accommodated
by histone-protein component of chromatin.
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Chromatin
• Each “Bead” is a nucleosome
• Nucleosome consists of: DNA wrapped around histone core
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Denaturation of DNA
Denaturation:Denaturation: disruption of 2° structure most commonly by heat denaturation
(melting) absorbance at 260 nm Hyperchromicity midpoint of transition (melting)
curve = Tm
the higher the % G-C, the higher the Tm
renaturation is possible on slow cooling
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Denaturation and Renaturation of DNA Double helix unwinds when DNA is denatured Can be re-formed with slow cooling and
annealing
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Principal Kinds of RNA
Six kinds of RNA – messenger RNA (mRNA) transfer RNA (tRNA) ribosomal RNA (rRNA) small nuclear RNA (snRNA) micro RNA (miRNA) small interfering (siRNA)
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Structure of RNA
RNA nucleotides joined by phosphodiester bonds
between the 3’-OH of one pentose and the 5’-OH of the next
the pentose unit is D-ribose the pyrimidine bases are uracil and cytosine RNA is single stranded
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Central dogma theory
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RNA molecules are classified according to their structure and function
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Transfer RNA-tRNA
the smallest kind of the three RNAs
a single-stranded polynucleotide chain between 73-94 nucleotide residues
carries an amino acid at its 3’ end
intramolecular hydrogen bonding occurs in tRNA
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Ribosomal RNA- rRNARibosomal RNA- rRNA Only a few types of rRNA exist in cells
ribosomes consist of 60 to 65% rRNA and 35 to 40% protein
prokaryotes and eukaryotes - ribosomes consist of two subunits
analyzed by analytical ultracentrifugation - sedimentation coefficients - expressed in Svedberg units (S)
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Messenger RNA - mRNAMessenger RNA - mRNA
A ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteinsPresent in cells in small amounts (5-10 %)Very short-lived
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Small nuclear RNA (snRNA)
Found in nucleus of eukaryotes
Small (100-200 nucleotides long)
Forms complexes with protein - small nuclear ribonucleoprotein particles (snRNPs)
snRNPs help with processing of initial mRNA transcribed from DNA
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Small interfering RNA (siRNA)
Used in RNA interference Eliminate expression of an undesirable gene
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