structure & functions of macromolecules – Nucleic Acids: Study Notes (DLA)

What is the primary function of nucleic acids?

The primary function of nucleic acids is to store and transmit genetic (hereditary) information.

What are the two main types of nucleic acids?

The two main types of nucleic acids are RNA (ribonucleic acid) and DNA (deoxyribonucleic acid).

What are nucleotides?

Nucleotides are the monomeric building blocks of nucleic acid polymers.

What components make up a nucleotide?

A nucleotide consists of a heterocyclic nitrogenous base, a pentose sugar (ribose for RNA or deoxyribose for DNA), and a phosphate group.

What is a nucleoside?

A nucleoside is composed of a nitrogenous base and a sugar.

What is a nucleotide?

A nucleotide is composed of a nitrogenous base, a sugar, and a phosphate group.

What are nucleotides considered as?

Nucleotides can be considered nucleoside-mono phosphates, usually containing 5'-phosphates.

How is the base linked to the pentose in nucleotides?

The base is linked by a β-N-glycosidic bond to C-1' of the pentose and N-1 of pyrimidines and N-9 of purines.

How is the phosphate group attached to the pentose in nucleotides?

The phosphate group is attached to the C-5' of the pentose by an ester bond.

What are the two categories of nitrogenous bases in nucleic acids?

The bases found in RNA and DNA are categorized as purines and pyrimidines.

What are pyrimidines?

Pyrimidines are heterocyclic compounds containing nitrogen atoms at positions 1 and 3 of a 6-member ring, including thymine, cytosine, and uracil.

What are purines?

Purines are heterocyclic compounds consisting of a pyrimidine fused to a 5-member imidazole ring, including adenine and guanine.

What are the bases associated with a nucleotide found in RNA?

The bases associated with a nucleotide that are found in RNA are: adenine, guanine, cytosine, and uracil.

What are some rare modified bases found in transfer RNA (tRNA)?

The rare modified bases found within transfer RNA (tRNA) are: 4-thiouracil, dihydrouracil, and 6-mercaptopurine.

What are the bases associated with a nucleotide found in DNA?

The bases associated with a nucleotide found in DNA are: adenine, guanine, cytosine, and thymine.

What are common minor bases found in DNA?

In DNA, common minor bases are those modified by the addition of a methyl (-CH3) group, which play important roles in the regulation of gene transcription and mRNA translation.

What role do certain modifications of DNA bases play in eukaryotes and viral DNA?

In eukaryotes, modifications play important roles in the regulation of gene transcription and mRNA translation. In viral DNA, certain bases may be hydroxymethylated or glycosylated, affecting gene expression and protecting DNA from endonuclease digestion.

What are some minor bases found in modified DNA?

Minor bases include: 5-methyl-C, 5-hydroxymethyl-C, 6-methyl-A, 2-methyl-G, and 7-methyl-G.

What are ribonucleoside triphosphates and deoxyribonucleoside triphosphates?

Ribonucleoside triphosphates and deoxyribonucleoside triphosphates serve as precursors or substrates for the synthesis of RNA and DNA respectively.

How are DNA and RNA generated?

DNA and RNA are generated by the polymerization of nucleotides to form polynucleotides.

What type of bond links nucleotide monomers in RNA and DNA?

The link, in both RNA and DNA, between the nucleotide monomers is a 3', 5'-phosphodiester bond.

What defines the polarity of polynucleotide chains?

The polynucleotide chains have polarity: a 5' end defined by the presence of a phosphate group bound to the 5' carbon atom of the sugar, and a 3' end defined by the presence of a hydroxy (-OH) group bound to the 3' carbon atom of the sugar.

What is the primary structure of nucleic acids?

The primary structure refers to the sequence of nucleotides (bases) along the chain, listed from 5' to 3'. For example, 5' – AGGCTAAC – 3'.

What is the secondary structure of nucleic acids?

The secondary structure is the 3-dimensional structure of the backbone, such as the double helix of DNA.

What is the tertiary structure of nucleic acids?

The tertiary structure refers to the super-coiling of the secondary structure.

What is the quaternary structure of nucleic acids?

The quaternary structure involves the interaction of nucleic acids with proteins.

Who proposed the structure of the DNA molecule known as B-type DNA?

The structure of B-type DNA was proposed by James Watson and Francis Crick in 1953, based on X-ray diffraction patterns from Rosalind Franklin and Maurice Wilkins, and base ratios from Erwin Chargaff.

What are the main features of the DNA double helix?

The features of the DNA double helix include:

• a. Two complementary anti-parallel strands coiled (right handed) along a common axis.

• b. The chains are held together by hydrogen bonds: A-T and G-C pairs.

• c. Bases are on the inside with their planes being perpendicular to the helix axis.

• d. The sugar and phosphate groups are on the outside.

• e. The planes of the sugars are almost at right angles to those of the bases.

• f. The diameter of the helix is about 2.0 nm containing 10.4 base pairs per turn (3.4 nm).

• g. Stabilization of the helix is achieved by hydrogen bonds, stacking interactions (van der Waals forces) of the bases, hydrophobic effects, and charge effects.

• h. The helix contains a major groove and a minor groove which provide sites for DNA-protein binding.

What role do hydrogen bonds play in the DNA helix?

Hydrogen bonds between the complementary base pairs hold the DNA helix together. Their weakness allows the strands of DNA to separate during replication and transcription.

What is A-type DNA and when is it favored?

A-type DNA structure is favored when a DNA solution is dehydrated. Like B-DNA, A-DNA is a right-handed double helix with 11 base pairs (bp) per turn and a diameter of about 2.6 nm. The planes of the bases are not perpendicular, resulting in a deeper major groove and a shallower minor groove. A-type DNA has been observed in short DNA molecules, double-stranded RNA, and DNA/RNA hybrids, but it has not been observed in the cell.

What is Z-type DNA?

is characterized as a left-handed helix with 12 base pairs (bp) per turn. The backbone exhibits a zig-zag extended pattern. This structure is formed in sequences of alternating purines and pyrimidines, such as GC. Evidence suggests that Z-type DNA is present in both eukaryotes and prokaryotes and may play a role in recombination and regulation of gene expression.

What are RNA molecules and how are they synthesized?

RNA molecules are synthesized as single stranded ribonucleic acid polymers. Following synthesis, transfer RNA (tRNA) and ribosomal RNA (rRNA) fold and form intra-molecular hydrogen bonding resulting in regions of double stranded RNA.

What are the four different types of RNA?

The four different types of RNA are:

• mRNA (2% of total cellular RNA) – the message that directs the amino acid sequence of proteins.

• rRNA (82%) – a component of the structure of the ribosome.

• snRNA (less than 1%) – involved in mRNA splicing and gene regulation.

• tRNA (16%) – adaptor molecules that transport amino acids to the ribosomes.

What shape does tRNA typically adopt, and what does this shape result from?

In tRNA, the intra-chain complementary base pairing produces a clover leaf shape with stem-loop or hairpin turns. The 3’-end containing the sequence CCA is the point of attachment of the amino acid (at the terminal A residue).

What is the role of the anticodon sequence in tRNA?

An anticodon sequence (triplet) base pairs with a specific codon on the mRNA to facilitate polypeptide synthesis during translation.

What is DNA denaturation?

DNA denaturation is the breaking of hydrogen bonds and unstacking of the bases, resulting in the separation of strands. Denaturation in vitro can be accomplished by heating or exposure to alkali.

What is renaturation in the context of DNA?

Renaturation refers to the reassociation (annealing) of strands with slow cooling after denaturation. The rate of renaturation depends on the DNA concentration, time, and DNA complexity, with a rate that is inversely proportional to the complexity of the DNA.

What is the melting temperature (Tm) of DNA?

The melting temperature (Tm) is the temperature at which double-stranded DNA is half-denatured. The melting temperature increases with increasing GC content.

What is hybridization in molecular biology?

Hybridization is the formation of hybrid DNA molecules or DNA/RNA hybrids between single stranded molecules containing certain amounts of complementarity. The hybridization process is the foundation for a number of molecular biology reactions and analysis.

What are cyclic AMP and cyclic GMP?

Cyclic AMP (cAMP) and cyclic GMP (cGMP) are 3’, 5’- cyclic derivatives of AMP and GMP that are involved as second messengers in signal transduction from hormones to intracellular enzymes in eukaryotes. In prokaryotes, they are involved in intracellular signaling and gene expression.

What is the role of synthetic analogs of nucleosides and nucleotides in chemotherapy?

Synthetic analogs of bases, nucleosides, and nucleotides are used in chemotherapy to inhibit enzymes that function in nucleic acid synthesis, or to be incorporated into DNA, resulting in termination of DNA replication.

What are nucleoside analogs and how do they work?

Nucleoside analogs like Azidothymidine (AZT) and Didanosine (ddl) lack a free 3’ hydroxyl (-OH) group, have high affinity for the reverse transcriptase enzyme, and inhibit their activity. They are used in the treatment of retroviral infections such as HIV.

What is Acyclovir and what is its usage?

Acyclovir possesses an open chain structure in place of the pentose sugar ring structure. It is a potent inhibitor of viral DNA polymerase, causing termination of DNA replication and is used in the treatment of Herpes virus.

What is Tenofovir and how does it function?

Tenofovir is a nucleotide analog that possesses an open chain structure in place of the pentose sugar ring structure. It is a potent reverse transcriptase inhibitor and is used to treat HIV infection.

What are Arabinosides and their role in cancer treatment?

Cytosine arabinoside and adenosine arabinoside possess unusual planar structures that inhibit DNA polymerase activity and induce DNA damage by incorporating into DNA during replication. These drugs are used as anti-cancer drugs by selectively destroying rapidly dividing cancer cells.

What are cytidine analogs and their effect on DNA methylation?

Cytidine analogs like 5-aza-2’-deoxycytidine and 5-azacytidine disrupt DNA methylation by preventing DNA methyl-transferase enzymes from methylating cytosine at position 5. They are also direct inhibitors of DNA methyl-transferase enzymes and play a role in regulating gene transcription in eukaryotes.

What is 5-fluorouracil and how does it function as an anti-cancer agent?

5-fluorouracil is an anti-cancer agent that, in cells, is converted to FdUMP, which inhibits thymidylate kinase. This action inhibits the synthesis of thymine nucleotides that are required for DNA synthesis.

What is Azathioprine and how does it function in organ transplantation?

Azathioprine is metabolized to 6-mercaptopurine, which suppresses rejection during organ transplantation by inhibiting the immune response.

What is Allopurinol and how does it work in the treatment of gout?

Allopurinol is a treatment for gout that inhibits xanthine oxidase, thereby lowering the conversion of purine bases to uric acid end products. The purines are excreted as xanthine and hypoxanthine, which are more soluble than uric acid.

What is Adenosine (Adenocard) IV and its role in treating supraventricular tachycardia?

Adenosine (Adenocard) IV is used to treat supraventricular tachycardia by slowing the heart rate. It also plays a role in sleep regulation, with high levels corresponding to extended periods of wakefulness and low levels corresponding to periods of sleep.