1.2.9. Describe the basic structure of mononucleotides and the structures of DNA and RNA ; how complementary base pairing and hydrogen bonding between complementary strands are involved in the formation of the DNA double helix.

● Name two types of polynucleotides and briefly describe the role of each. What is the monomer of polynucleotides?

A polynucleotide is a polymer, or chain, of (repeating monomers) nucleotides ● Both DNA and RNA are polymers. The chemical structure of the simple monomer units making up these 2 molecules is very similar. The monomers of these polymers are called nucleotides or mononucleotides.

● How are the two strands of a DNA molecule held together?

The 2 strands of the double helix are held together by hydrogen bonds between the complementary base pairs. There are 10 of these pairs for each complete twist of the helix. The 2 strands are known as the 5' (5 prime) and 3' (3 prime) strand, named according to the number of the carbon atom in the pentose sugar to which the phosphate group is attached in the first nucleotide of the chain.

● Why is DNA described as antiparallel?

The two polynucleotide strands run 'antiparallel' to each other, with Nitrogenous Bases projecting inwards. The term 'antiparallel' means that the strands run in opposite directions, parallel to one another. The antiparallel strands twist in a complete DNA structure, forming a Double Helix.

● What bases are used in DNA? ● What bases are used in RNA?

○ There are 2 types of nitrogen containing bases found in nucleic acids. The purine bases have 2 nitrogen containing rings, while the pyrimidines have only one. These rings have the chemical property of being bases because of the nitrogen atoms they contain. Bases bonded together are termed 'paired', and are very specific as to which Base they will join to. These base pairings are termed Complementary Base Pairings. ● DNA contains combinations of 4 different bases with equal numbers of pyrimidines and purines. The purines are: Adenine (A) and guanine (G) The pyrimidines are: cytosine (C) and thymine (T). ● RNA contains combinations of 4 different bases with equal numbers of pyrimidines and purines. The purines are: Adenine (A) and guanine (G) The pyrimidines are: Cytosine (C) and uracil (U). ○ The reason that Purines will only bond with Pyrimidines is that Purines are larger molecules (composed of a double ring structure), so in order to ensure that the polynucleotide strands are equally spaced apart, the larger Bases must pair with the smaller bases. The root for the specific Complementary Base Pairings is the number of Hydrogen bonding sites available. Adenine and Thymine have two sites each, whereas Guanine and Cytosine have three sites each.

● What is a gene? ● What is a codon / triplet?

● A gene is a sequence of bases on a DNA molecule that codes for a sequence of amino acids in a polypeptide chain. ● Codon / triplet: every three bases is a triplet (also known as a codon) and each triplet codes for a specific amino acid. This is why the genetic code is a triplet code.

● Why is the genetic code described as: Universal? ● Why is the genetic code described as: Not overlapping? ● Why is the genetic code described as: Degenerate?

● All organisms in nature (from bacteria to humans) use exactly the same genetic code for each specific amino acid. ● This means that successive triplets are read in order. Each nucleotide is part of only one triplet codon. ● The genetic code is described as degenerate, or redundant, because a single amino acid may be coded for by more than one codon.

● Describe the structure of a mononucleotide. What charge does the phosphate group have? ● How are the sugar, the base and the phosphate group joined together?

● Each mononucleotide has 3 parts: ○ A 5 carbon or pentose sugar. The pentose sugar in RNA is ribose, and in DNA it is deoxyribose. Deoxyribose contains one oxygen atom fewer than ribose. ○ A nitrogen containing base ○ A phosphoric acid. A phosphate group (PO4 3-) is the third component. This phosphate group makes the mononucleotides, and hence the nucleic acids, acidic. ● The sugar, the base and the phosphate group joined together by condensation reactions (with the elimination of 2 water molecules) to form the nucleotide.

● What kind of reaction joins mononucleotides together to form the sugar phosphate backbone?

● Mononucleotides are linked together by condensation reactions to form polynucleotide strands (nucleic acids). The sugar of one nucleotide bonds to the phosphate group of the next nucleotide so polynucleotides always have a hydroxyl group at one end and a phosphate group at the other. The sugar and phosphate are joined by a phosphodiester bond formed by a condensation reaction.

● What is the difference between a RNA and a DNA mononucleotide. ● What is the difference between a RNA and a DNA polynucleotides.

● To form DNA, nucleotides containing the bases C, G, A and T join together. ● RNA is made up of long chains of nucleotides containing the bases C, G, A and U. ● RNA molecules form single polynucleotide strands which may be folded into complex shapes or remain as long thread-like molecules. ● A DNA molecule is made up of 2 polynucleotide strands (the polymers of nucleotides) twisted around each other. The sugars and phosphates form the backbone of the molecule. Pointing inwards are the bases. A purine always pairs with a pyrimidine: In DNA, adenine pairs with thymine and cytosine with guanine. This produces the DNA double helix.