BIOCHEMISTRY – EXAM 2 [complete questions and answers]GRADED A+

hapter 9 – Nucleic Acids: How Structure Conveys Information Levels of Structure in Nucleic Acids: - Primary structure – order of bases in the polynucleotide sequence (specifies genetic code) - Secondary structure – 3D ...

hapter 9 – Nucleic Acids: How Structure Conveys Information Levels of Structure in Nucleic Acids: - Primary structure – order of bases in the polynucleotide sequence (specifies genetic code) - Secondary structure – 3D conformation of the polynucleotide backbone - Tertiary structure – supercoiling of the molecule - Quaternary structure – interaction with other classes of macromolecules, such as proteins Nucleotides: purine of pyrimidine bases bonded to sugars, which are bonded to phosphate groups - Nucleic acid bases: nitrogen-containing aromatic compounds that make up the coding portion of nucleic acids o Pyrimidine bases: a six-membered ring, parent compounds of several nucleobases o Purine bases: six-membered ring fused to a five membered ring, parent compounds of adenine and guanine - Nucleoside: purine or pyrimidine base bonded to a sugar (ribose of deoxyribose), lacks a phosphate group - Formed when phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’ -OH or the 5’ -OH - Named for the parent nucleoside, with the suffix -monophosphate added - Polymerization of nucleotides produces nucleic acids o 3’, 5’ -phosphodiester bond: 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 Deoxyribonucleic Acid, DNA - Biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate o The 3’ -OH is joined to the 5’ -OH of the next by a phosphodiester bond - Nucleotide residues of nucleic acids are numbered from the 5’ end to the 3’ end - In one system of notation: single letters A, G, C, U and T represent the individual bases - Differs from RNA as the sugar is 2’-deoxyribose rather than ribose: letter d could be added to indicate a deoxyribonucleotide reside Structure of DNA - Primary structure – seq. of bases along pentose-phosphodiester backbone of a DNA molecule - Secondary structure – ordered arrangement of nucleic acid strands - Tertiary structure – 3D arrangement of all atoms of nucleic acid, referred to as supercoiling DNA Double Helix - Two polynucleotide chains wrapped around each other, fundamental structural motif of DNA, proposed by James Watson and Francis Crick in 1953, based on x-ray crystallography - Base pairing is complementary, and the major factor stabilizing the double helix is base pairing by hydrogen bonding between adenine-thymine (A-T) and guanine-cytosine (G-C) o A-T base pair has two hydrogen bonds, G-C has three hydrogen bonds - Consists of: Major groove: larger of two empty spaces in an imaginary cylinder that encloses the DNA double helix (minor groove: the smaller of two…^^) DNA Conformations: - B-DNA: considered the normal, physiological DNA form, right-handed helix, with an inner diameter of 11Å, 10 base pairs per turn of the helix - A-DNA: right handed helix but thicker than B-DNA, 11 base pairs per turn of the helix, not found in in vivo techniques - Z-DNA: left-handed double helix, may play a role in the regulation of gene expression, occurs in nature and usually consists of alternating purine-pyrimidine bases, produced by flipping one side of the backbone 180* without disturbing the backbone covalent bonds or hydrogen bonds Features of DNA: Base Stacking - Bases are hydrophobic and interact with each other via hydrophobic bonding - In standard B-DNA, each base is rotated 32* with respect to the preceding one: o perfect for maximal base pairing but not optimal for maximum overlap of bases o bases that are exposed to the minor groove must come in contact with water