[CHEM200] Nucleic Acids (How Structure Conveys Information) Reviewer

ULBIS, CHRISTINE MARIE HONG (SEAT #36) 3BIOLOGY-6

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LEVEL OF STRUCTURE IN NUCLEIC ACIDS  Primary Structure – order of bases in polynucleotide sequence  Secondary Structure – it is the threedimensional conformation of the backbone  Tertiary Structure – the supercoiling of the molecule

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Two Principal Types of Nucleic Acids:  Deoxyribonucleic acid (DNA)  Ribonucleic acid (RNA) THE COVALENT STRUCTURE OF POLYNUCLEOTIDES Nucleotides – monomers of nucleic acids and consists of three parts:  Nitrogenous Bases – nitrogen-containing aromatic compounds that make up the coding portion of nucleic acids o Pyramidine – nitrogen-containing aromatic compounds that contain a sixmembered ring  Cytosine – found in both RNA and DNA  Thymine – substitutes uracil in DNA  Uracil – occurs only in RNA o Purine – nitrogen-containing aromatic compounds that contain a six-membered ring fused to a five-membered ring Adenine  Guanine  Adenine  Sugar  Phosphoric Acid Residue Nucleoside – a purine or pyramidine base bonded to a sugar (ribose or deoxyribose); differs from a nucleotide by lacking a phosphate group and a base o Ribonucleoside - a compound formed when a nucleobase forms a glycosidic bond with Dribose o Deoxyribonucleoside – compound formed when a nucleobase and B-D-deoxyribose form glycosidic bond  The glycosidic linkage is from the C-1’ carbon of the sugar to the N-1 nitrogen of pyramidines or to the N-9 nitrogen of purines.  When phosphoric acid is esterified to one of the hydroxyl groups of the sugar portion of a nucleoside, a nucleotide is formed.  A nucleotide is named for the parent nucleoside, with the suffix –monophosphate added.  The position of the phosphate ester is specified by the number of the carbon atom at the hydroxyl group to which it is esterified. Example: adenosine 3’-monophosphate Deoxycytidine 5’-monophosphate

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The linkage between monomers in nucleic acids involves formation of two ester bonds by phosphoric acid. The hydroxyl groups to which the phosphoric acid is esterified are those bonded to the 3’ and 5’ carbons on adjacent residues. The resulting repeated linkage is a 3’, 5’-phosphodiester bond. The nucleotide residues of nucleic acids are numbered from the 5’ end, which normally carries a phosphate group, to the 3’ end, which normally has a free hydroxyl group. 3’, 5’-phosphodiester bond – a covalent linkage in which phosphoric acid is esterified to the 3’ hydroxyl of one nucleoside and the 5’ hydroxyl of another nucleoside; forms the backbone of nucleic acids

THE STRUCTURE OF DNA Double Helix – two polynucleotide chains wrapped around each other; it is the fundamental structural motif of DNA  DNA consists of two polynucleotide chains wrapped around each other to form a helix.  Hydrogen bonds between bases on opposite chains determine the alignment of the helix, with the paired bases lying in planes perpendicular to the helix axis.  Sugar-phosphate backbone is outer part of helix.  The chains run in anti-parallel directions, one 3’ to 5’ and the other 5’ to 3’.  Base pairing is complementary meaning that adenine pairs with thymine and that guanine pairs with cytosine.  Because complementary base pairing occurs along the entire double-helix, the two chains are also referred to as complementary strands.  The outside diameter of the helix is 20 A (2 nm). The length of one complete turn of the helix along its axis is 34 A (3.4 nm) and contains 10 base pairs.  The atoms that make up the two polynucleotide chains of the double helix do not completely fill an imaginary cylinder; instead, they leave empty spaces known as grooves at which drugs or polypeptides bind to DNA.  Major Groove – the larger of the two empty spaces in an imaginary cylinder that encloses the DNA double helix  Minor Groove – the smaller of the two empty spaces in an imaginary cylinder that encloses the DNA double helix  At neural, physiological pH, each phosphate group of the backbone carries a negative charge.  Positively charged ions, such as Na+ and Mg2+, and polypeptides with positively charged side chains must be associated with DNA in order to neutralize the negative charges.

Conformations of Double Helix o B-DNA – most common form of the DNA double helix o A-DNA – form of DNA double helix characterized by having fewer residues per turn and major and minor grooves with dimensions that are more similar to each other than those of B-DNA  It has 11 base pairs for each turn of the helix.  Its base pairs are not perpendicular to the helix axis but lie at an angle of about 20o to the perpendicular. o Z-DNA – form of DNA that is left-handed helix, which occur naturally, most often when there is a sequence of alternating DNA  It is produced by flipping one side of the backbone 180o without having to break either the backbone or the hydrogen bonding of the complementary bases.  Name is from the zigzag look of phosphodiester backbone when viewed from the side. 

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The ring portions of the DNA bases are very hydrophobic and interact with each other via hydrophobic bonding (can der Waals interactions) of their pi-cloud electrons. This process is usually referred to as base stacking, and even single-stranded DNA tends to form structures in which the bases stack. Base stacking – interactions between bases are next to each other in a DNA chain In standard B-DNA, each base pair is rotated 32o with respect to the preceding one. This form is perfect for maximal base pairing, but it is not optimal for maximal overlap of the bases. In addition, the edges of the bases that are exposed to the minor groove must come in contact with water in this form. Many of the bases twist in a characteristic way, called propeller twist. In this form, the basepairing distances are less optimal, but the base stacking is more optimal, and water is eliminated from the minor-groove contacts with the bases.

Prokaryotic DNA Supercoiling  Prokaryotic DNA is circular and this DNA forms supercoils (extra twists–over and above those of the double helix–in closed circular DNA).  Negative Supercoils – circular DNA with fewer than the normal number of turns of the helix.  The strands are underwound and introduces a torsional stress that favors unwinding of the right-handed B-DNA double helix.  Positive Supercoils – circular DNA with more than the normal number of turns of the helix

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 They consist of overwound strands and overwinds right-handed B-DNA double helix Both form of supercoiling compact the DNA. Naturally occurring circular DNA is negatively supercoiled except during replication, when it becomes positively supercoiled. Enzymes that are involved in changing the supercoiled state of DNA are called topoisomerases. They relax supercoiling in closed circular DNA.  Class I Topoisomerases – cut the phosphodiester backbone of one strand of DNA, pass the other end through, and then reseal the backbone.  Class II Topoisomerases – cut both strands of DNA, pass some of the remaining DNA helix between the cut ends, and then reseal DNA gyrase is a bacterial topoisomerase that introduces negative supercoils into closed circular DNA.

Eukaryotic DNA Supercoiling  Eukaryotic DNA is complexed with a number of proteins, especially with basic proteins that have abundant positively charged side chains at physiological (neutral) pH.  Electrostatic attraction between the negatively charged phosphate groups on the DNA and the positively charged groups on the proteins favor the formation of complexes. The resulting material is called chromatin. Thus, topological changes induced by supercoiling must be accommodated by histone-protein component of chromatin. Chromatin – a complex of DNA and protein found in eukaryotic nuclei Histones - basic proteins found complexed to eukaryotic DNA  Five main types: H1, H2A, H2B, H3, and H4  All types contain large numbers of basic amino acid residues such as lysine and arginine.  The H1 protein is easy to remove from chromatin, but disassociating the other histones from the complex is more difficult.  In electron micrographs, the chromatin resembles beads on a string. o Nucleosome – the “bead” on a string; it is a globular structure in chromatin in which DNA is wrapped around an aggregate of histone molecule  The protein core is an octamer, which includes two molecules of each histone but H1.  The composition of the octamer is (H2A)2(H2B)2(H3)2(H4)2.

Space Regions – “string” portions and consist of DNA complexed to some H1 histone and nonhistone proteins As the DNA coils around the histones in the nucleosome, about 150 base pairs are in contact with the proteins; the spacer region is about 30 to 50 base pairs long. Histones can be modified by acetylation, methylation, phosphorylation, and ubiquitinylation.  Ubiquitin is a protein involved in the degradation of other proteins. Modifying histones changes their DNA and protein-binding characteristics, and how these changes affect transcription and replication is a subject of active research. o

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However, the stacking of the bases in the native conformation of DNA contributes the largest part of the stabilization energy. Energy must be added to a sample of DNA to break the hydrogen bonds and to disrupt the stacking interactions. This is usually carried out by heating the DNA in solution.

Melting – heat denaturation of DNA; this can be monitored experimentally by observing the absorption of UV light  The bases absorb light in the 260-nmwavelength region. Hyperchromicity – as the DNA is heated and the strands separate, the wavelength of absorption does not change, but the amount of light absorbed increases  This is based on the fact that the bases, which are stacked on top of one another in native DNA, becomes unstacked as the DNA is denatured.

DENATURATION OF DNA  Hydrogen bonds between the base pairs are an important factor in holding the double helix together.  The amount of stabilizing energy associated with the hydrogen bonds is not great, but the hydrogen bonds hold the two polynucleotide chains in the proper alignment. PRINCIPAL KINDS OF RNA AND THEIR STRUCTURES  A sequence of three bases in mRNA directs the  Various kunds of RNA participate in the incorporation of a particular amino acid into a synthesis of protens in a series of reactions growing protein chain. ultimately directed by the base sequence of the  In prokaryotes, there is no nuclear cell’s DNA. membrane, so mRNA can direct the  Six kinds of RNA: synthesis of proteins while it is still being transcribed  transfer RNA (tRNA)  Eukaryotic mRNA, on the other hand,  ribosomal RNA (rRNA) undergoes considerable processing. One  messenger RNA (mRNA) of the most important parts of the  small nuclear RNA (snRNA) process is splicing out intervening  micro RNA (miRNA) sequences (introns), so that the parts of  small interfering RNA (siRNA) the mRNA that will be expressed (exons)  The base sequences of all types of RNA are are contiguous to each other. determined by that of DNA.  Small nuclear RNAs are found only in the  The process by which the order of bases is nucleus of eukaryotic cells, and they are distinct passed from DNA to RNA is called from the other RNA types. They are involved in transcription. processing of initial mRNA transcription  Ribosomes, in which rRNA is associated with products to a mature form suitable for export proteins, are the sites for assembly of the from the nucleus to the cytoplasm for growing polypeptide chain in protein synthesis. translation.  Amino acids are brought to the assembly  Micro RNAs and small interfering RNAs are the site covalently bonded to tRNA as most recent discoveries. aminoacyl-tRNAs.  SiRNAs are the main players in RNA  The order of bases in mRNA specifies the interference (RNAi), a process that was first order of amino acids in the growing discovered in plants and later in mammals, protein; this process is called translation including humans. of the genetic message. RNA interference (RNAi) – process where Translation – the process of protein short synthesis in which the amino acid pieces of RNA affect gene expression sequence of the protein reflects the sequence of bases in the gene that codes for that protein Roles of Different Kinds of RNA RNA Type Size Function

Transfer RNA

Small

Transports amino acids to site of protein synthesis

Ribosomal RNA

Several kinds–variable in size

Combines with proteins to form ribosomes, the site of protein synthesis

Messenger RNA Small nuclear RNA Small RNA

interfering

Micro RNA

Directs amino acid sequence of proteins Variable Small

Processes initial mRNA to its mature form in eukaryotes

Small

Affects gene expression; used by scientists to knock out a gene being studied

Small

Affects gene development

expression;

important

in

growth

and