Nucleic Acids and the RNA world

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1

metabolism

the ability to acquire particular molecules and use them in controlled chemical reactions that maintain conditions suitable for life and contribute to growth

2

nucleic acid

a polymer made up of monomers of nucleotides

3

nucleotides

molecules that make up nucleic acids; includes a phosphate group, bonded to a sugar molecule, bonded to a nitrogenous base

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ribonucleotide

a nucleotide with the sugar molecule ribose (where ribose has an -OH group bonded to the second carbon in the ring)

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deoxyribonucleotide

a nucleotide with the sugar molecule deoxyribose (where deoxyribose "lacking oxygen" has just an Hydrogen atom bonded to the second carbon in the ring)

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purines

a nitrogenous base on nucleotides; smaller than pyrimidines and include cytosine, uracil, and thymine

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pyrimidines

a nitrogenous base on nucleotides; larger than purines and include guanine and adenine

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purines and pyrimidines found in ribonucleotides

purines: adenine (A), guanine (G) and pyrimidines: cytosine (C), uracil (C)

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purines and pyrimidines found in deoxyribonucleotides

purine: adenine (A), guanine (G) and pyrimidines: cytosine (C), thymine (T)

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phosphodiester linkage, bond

a bond between the phosphate group of one nucleotide and the hydroxyl group (on the sugar) of another; joins the 5' carbon on the ribose of one nucleotide to the 3' carbon on the ribose of another; is formed in endergonic condensation reaction

11

ribonucleic acid (RNA)

polymer when the nucleotides involved contain the sugar ribose

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deoxyribonucleic acid (DNA)

polymer when the nucleotides involved contain the sugar deoxyribose

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directionality of nucleic acids

the sequence of bases found in an RNA or DNA strand in the 5' --> 3' direction (logical because bases are added at the 3' end of the growing molecule)

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polymerization of nucleic acids

occurs when phosphate groups are added to nucleotides, creating nucleotide triphosphates; raises free energy of nucleotide monomers and enables reaction

15

phosphorylated

when molecules have phosphate groups attached to it through polymerization

16

primary structure of DNA

a sugar-phosphate backbone, created by phosphodiester linkages, and a sequence of four nitrogenous bases extending from it... the sugar in the DNA's backbone is deoxyribose; contains information in the form of molecular code

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secondary structure of DNA

consists of two DNA strands running in opposite directions, with strands being held together by complimentary base pairing (G-C and A-T) and are twisted into a double helix

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what did Watson and Crick find out?

based on measurements made by Rosalind Franklin and Maurice Wilkins, they found that the pattern suggested the molecule was helical or spiral in nature; arrange two strands of DNA side by side and ran one strand in 5'-->3' and the other 3'-->5' to be antiparallel... inside the double helix. the bases lined up in a way that allowed hydrogen bonds to form between certain purines and pyrimidines and discovered complimentary base pairing

19

how is DNA stable?

deoxyribonucleotides lack a reactive 2' hydroxyl group and because their antiparallel DNA strands form a secondary structure called a double helix; the double helix is stabilized by hydrogen bonds that form between complementary purine & pyrimidine bases stacked on the inside of the spiral; this structural stability and regularity makes DNA ineffective at catalysis however

20

how does DNA form a template for its own synthesis?

if the hydrogen bonds between complementary base pairs are broken, the DNA helix can separate... each strand of DNA can serve as a template for the formation of a new strand as free nucleotides attach according to complementary base pairing... when the new strands polymerize to from sugar-phosphate backbone, second structure is restored

21

primary structure of RNA

a sugar-phosphate backbone, created by phosphodiester linkages, and a sequence of four nitrogenous bases extending from it... the sugar in the RNA's backbone is ribose; contains information in the form of molecular code

22

secondary structure of RNA

purine and pyrimidine bases (G-C and A-U) undergo hydrogen bonding with complementary bases on the same strand, rather than forming H bonds w/ complementary bases on a different stand; the key is when bases on one part of the strand fold over and align w/ ribonucleotides on another segment of the same strand, the two sugar-phosphate strands are antiparallel resulting in a stable double helix... if the section where the fold occurs includes a large # of unbonded bases, then a stem-and-loop structure called a hairpin forms

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tertiary and quarternary structures of RNA

can occur because RNA molecules fold in precise ways and many interact with each other

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functions of RNA

an "all-purpose" macromolecule that catalyzes chemical reactions (the way proteins do) and carries information (the way DNA does)