nucleic acids: how structure conveys information chapter 9
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Nucleic Acids: How Structure Conveys Information
Chapter 9
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
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)
Pyrimidine and Purine Bases
Other Bases
Less common bases/Unusual bases
Principally but not exclusively, in transfer RNAs
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
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)
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
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
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
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
How is the base pairing of DNA complementary?
G-C base pair comprised of 3 hydrogen bonds
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
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
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
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
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
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
What are Topoisomerases?
Enzymes that can change supercoiled state of DNA – TopoIsomerases
Class I and Class II
DNA gyrase
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
Super DNA Coiled Topology Double helix can be considered to a 2-
stranded, right handed coiled rope Can undergo positive/negative supercoiling
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.
Chromatin
• Each “Bead” is a nucleosome
• Nucleosome consists of: DNA wrapped around histone core
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
Denaturation and Renaturation of DNA Double helix unwinds when DNA is denatured Can be re-formed with slow cooling and
annealing
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)
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
Central dogma theory
RNA molecules are classified according to their structure and function
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
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)
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
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
Small interfering RNA (siRNA)
Used in RNA interference Eliminate expression of an undesirable gene
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