Nucleic Acid

Mary K. Campbell
Shawn O. Farrell cengage.com/chemistry/campbell Chapter Nine
Nucleic Acids: How Structure
Conveys Information

Paul D. Adams • University of Arkansas

Nucleic Acids
• Nucleic acid: a biopolymer containing three types of monomer units
• a base derived from purine or pyrimidine (nucleobases)
• a monosaccharide, either D-ribose or 2-deoxy-D-ribose
• phosphoric acid
• RNA (Ribonucleic Acid)
• DNA (Deoxyribonucleic Acid)

Nucleic Acids
• 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
• 3°structure: supercoiling
• 4°structure: interaction between DNA and proteins Pyrimidine/Purine Bases
• The structures of pyrimidine and purine are shown here for comparison

Other Bases
• Less common bases can occur • Principally but not exclusively, in transfer
RNAs

Nucleosides
• Nucleoside: a compound that consists of D-ribose or 2-deoxy-D-ribose covalently bonded to a nucleobase by a -N-glycosidic bond
• Lacks phosphate group

Nucleotides
• Nucleotide: 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
• Name based on parent nucleoside with a suffix
“monophosphate”
• Polymerization leads to nucleic acids. Linkage is repeated (3’,5’phosphodiester bond)
• (Biochemical Connections p.
232)

Glycosidic Linkage
• Glycosidic bond: between Base and Sugar
- C-1of the sugar binds to the N-1 of pyrimidine or to the N-9 of purines

DNA - 1° Structure
• Deoxyribonucleic acids, DNA: 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 • 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,U and T)

DNA differs from RNA
Sugar is 2’-deoxyribose, not ribose. • Sometimes “d” used to designate “deoxy”
• Writing a DNA strand
– an abbreviated notation
– even more abbreviated notations d(GACAT) pdApdCpdGpdT pdACGT

DNA - 2° Structure
• Secondary structure: the ordered arrangement of nucleic acid strands
• the double helix model of
DNA 2°structure was proposed by James
Watson and Francis
Crick in 1953
• 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
• structure based on X-Ray crystallography DNA Secondary Structure
• DNA consists of two polynucleotide chains wrapped around each other to form a helix
• Bases point toward inside and the sugar-phosphate backbone is the outer part of the helix
• The chains run in antiparallel directions, one 3’ to 5’ and one 5’ to 3’

DNA Secondary structure

• The length of one complete turn of the helix along its axis is 34 Ao (3.4 nm) and consists ten base pairs
• The atoms that make up the two polynucleotide chains of the double helix do not completely fill an imaginary cylinder around the double helix; they leave empty spaces known as grooves
• major groove and minor groove, sites for drugs or proteins bind to DNA

DNA Secondary Structure
• At pH 7.0, phosphodiester back bone is negative charged • Interacts with basic histone proteins (which have a protonated amino) by electrostatic interaction

T-A Base Pairing
• Base pairing is complimentary

• 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

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

Nucleic acids
• Chemical experiments showed that : moles of T = moles of A moles of G = moles of C
C can’t pair with A (only one H bond, weak) T can’t pair with G (only one H bond, weak)
Because of the ring structures, only these combination fit into helix

Other Forms of DNA
• B-DNA

• considered the physiological form
• a right-handed helix, 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

Comparison of A,B, and Z forms of DNA
• Both A and B-DNA are right-handed helices
• Z-DNA is left handed
• Z-DNA occurs in nature, usually consists of alternating purinepyrimidine bases
• Methylated cytosine found also in Z-DNA

Other Features of DNA
• Base stacking
• bases are hydrophobic and interact by hydrophobic interactions • in standard B-DNA, each base rotated by 32° compared to the next and, while this is perfect for maximum base pairing, it is not optimal for maximum overlap of bases; in addition, bases exposed to the minor groove come in contact with water
• many bases adopt a propeller-twist in which base pairing distances are less optimal but base stacking is more optimal and water is eliminated from minor groove contacts

Propeller Twists
• Bases that are exposed to minor groove contact with water
• They twist in a “propeller twist” fashion
• Results in:
• less optimal base pair distance
• More optimal base pair stacking (eliminates presence of water molecules) 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 DNA - 3° Structure
• Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling
• 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.
• Topoisomerases
• 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: a bacterial topoisomerase

Super DNA Coiled Topology
• Prokaryotic DNA is circular. It can form supercoils.
• Double helix can be considered to a 2-stranded, right handed coiled rope
• Can undergo positive/negative supercoiling

Chromatin
• The structure of chromatin

• Each “Bead” is a nucleosome • Nucleosome consists of:
DNA wrapped around histone core
• Recent research has shown that structure and spacing of nucleosomes is important in chromatin function. Supercoiling in Eukaryotic DNA
• 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: DNA molecules wound around particles of histones in a beadlike structure
• Topological changes induced by supercoiling accommodated by histone-protein component of chromatin. Denaturation of DNA
• Denaturation: disruption of 2° structure • most commonly by heat denaturation (melting)
• as strands separate, absorbance at 260 nm increases
• increase is called hyperchromicity
• midpoint of transition (melting) curve = Tm
• the higher the % G-C, the higher the Tm
• renaturation is possible on slow cooling Denaturation of DNA
• Double helix unwinds when DNA is denatured
• Can be re-formed with slow cooling and annealing

Principal Kinds of RNA
• RNA
• consist of long, unbranched chains of 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 (it is 2-deoxy-D-ribose in DNA)
• the pyrimidine bases are uracil and cytosine (they are thymine and cytosine in DNA)
• in general, RNA is single stranded (DNA is double stranded) Information Transfer in Cells
• Information encoded in the nucleotide sequence of DNA is transcribed through
RNA synthesis
• Sequence then dictated by DNA sequence • Central dogma of biology RNA
• RNA molecules are classified according to their structure and function

tRNA
• 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

rRNA
• Ribosomal RNA, rRNA: a ribonucleic acid found in ribosomes, the site of protein synthesis
• only a few types of rRNA exist in cells
• ribosomes consist of 60 to 65% rRNA and 35 to 40% protein • in both prokaryotes and eukaryotes, ribosomes consist of two subunits, one larger than the other
• analyzed by analytical ultracentrifugation
• particles characterized by sedimentation coefficients, expressed in Svedberg units (S)

mRNA
• Messenger RNA, mRNA: a ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteins
• present in cells in relatively small amounts and very short-lived • single stranded
• biosynthesis is directed by information encoded on
DNA
• a complementary strand of mRNA is synthesized along one strand of an unwound DNA, starting from the 3’ end

snRNA
• Small nuclear RNA (snRNA) is a recently discovered RNA
• Found in nucleus of eukaryotes
• Small (100-200 nucleotides long)

• Forms complexes with protein and form small nuclear ribonucleoprotein particles (snRNPs)
• snRNPs help with processing of initial mRNA transcribed from DNA

The Structure of the Prokaryotic Ribosome