Chapter 3 Structures and Functions of Nucleic Acids. Nucleic acid. A biopolymer composed of nucleotides linked in a linear sequential order through 3’,5’ phosphodiester bonds. Classification of nucleic acid. Ribonucleic acid (RNA) is composed of ribonucleotides .
Chapter 3Structures and Functions of Nucleic Acids
A biopolymer composed of nucleotides linked in a linear sequential order through 3’,5’ phosphodiester bonds
Section 1Chemical Components of Nucleic Acids
§ 1.1 Molecular Constituents
Nucleic acid can be hydrolyzed into nucleotides by nucleases. The hydrolyzed nucleic acid has equal quantity of base, pentose and phosphate.
Purine N-9 or pyrimidine N-1 is connected to pentose (or deoxypentose) C-1’ through a glycosidic bond.
A nucleoside (or deoxynucleoside) and a phosphoric acid are linked together through the 5’-phosphoester bond.
Composition of DNA and RNA
Multiple phosphate nucleotides
Cyclic ribonucleotide: 3’,5’-cAMP, 3’,5’-cGMP, used in signal transduction
Biologically active systems containing ribonucleotide: NAD+, NADP+, CoA-SH
Phosphoester bond formation
The -P atom of the triphosphate group of a dNTP attacks the C-3’ OH group of a nucleotide or an existing DNA chain, and forms a 3’-phosphoester bond.
Nucleic acid chain extension
A nucleic acid chain, having a phosphate group at 5’ end and a -OH group at 3’ end, can only be extended from the 3’ end.
Alternative phosphodiester bonds and pentoses constitute the 5’-3’ backbone of nucleic acids.
Section 2Structures and Functions of Nucleic Acids
The secondary structure is defined as the relative spatial position of all the atoms of nucleotide residues.
Historic X-ray diffraction picture
Building a milestone of life
James Watson and Francis Crick proposed a double helix model of DNA in 1953.
It symbolized the new era of modern biology.
Backbone and bases
The hydrophilic backbone is on the outside of the duplex, and the bases lie in the inner portion of the duplex.
Watson-Crick base pair
Watson-Crick base pair
Major and minor grooves
Small molecules like drugs bind in the minor groove, whereas particular protein motifs can interact with the major grooves.
Structural features of DNAs
Hoogsteen base pair
The third strand is using Hoogsteen H-bonds to pair with bases on the first strand.
G-quartet of DNA
Four strands are arranged in either parallel or antiparallel manner.
§2.3.a Supercoil structure
Circular DNAs in nature, in general, are negatively supercoiled.
§2.3.b Prokaryotic DNA
§2.3.c Eukaryotic DNA
Beads on a string
The total length of 46 human chromosomes is about 1.7 m, and becomes 200 nm long after 5 times condensation.
DNA is fundamental to individual life in terms of
Section 3Structures and Functions of RNA
Matured mRNA of eukaryote
tRNA serves as an amino acid carrier to transport AA for protein synthesis.
Reversed L-shape structure
Two key sites of tRNA
Codon and anticodon
The anticodon on tRNA pairs with the codon on mRNA.
Amino acid attachment
rRNA provides a proper place for protein synthesis.
Components of ribosomes
(E.coli)(Liver of mouse)
Smaller subunit 30s40s
rRNA 16s 1542 nucleotides 18s 1874 nucleotides
proteins 21 40% of total weight 33 50% of total weight
Larger subunit 50s60s
rRNA 23s 2940 nucleotides28s 4718 nucleotides
5s 120 nucleotides 5.85s 160nucleotides
proteins 31 30% of total weight49 35% of total weight
Ribosome of E. coli
Secondary structure of 18S rRNA
The secondary structure of rRNA has many loops and stems, which can bind ribosomal proteins to form an assembly for protein synthesis.
EM of polysomes
Section 4Physical and Chemical Properties of Nucleic Acids
§ 4.1 UV Absorption
Application of OD260
Transition of dsDNA to ssDNA
The absorbance at 260nm of a DNA solution increases when a dsDNA is melted into two single strands. The change is called hyperchromicity.
Melting curve of dsDNA
Melting curve shift
Tm of dsDNA depends on its average G+C content. The higher the G+C content, the higher the Tm.
Denaturation of DNA
Extremes in pH or
of DNA strands
Two separated complementary DNA strands can rejoin together to form a double helical form spontaneously when the temperature or pH returns to the biological range. This process is called renaturation or annealing.
Two dsDNA molecules from different species are completely denutured by heating. When mixed and slowly cooled, complementary DNA strands of each species will associate and anneal to form normal duplexes.
Target DNA detection
probe: …. TAGCTGAG …target: …. ATCGACTC …
probe: …. TAGCTGAG …non-target: …. ATCAGCTC …
Definition and classification
Nucleasesare enzymes that are able to hydrolyze phosphoester bonds and cleave DNA or RNA into fragments.
ExonucleasesThey can cleave terminal nucleotides either from 5’-end or from 3’-end, such as enzymes used in the DNA replication.Endonucleases They can cleave internally at either 3’ or 5’ side of a phosphate group, such as the restriction endonucleases used to construct the recombinant DNA.