Nucleotides and Nucleic Acids Flashcards

Flashcards reviewing key concepts from a lecture on nucleotides, nucleic acids, DNA, and RNA.

Nucleotides

The monomer units or building blocks of nucleic acids (DNA and RNA).

Components of a nucleotide

a nitrogenous base, a pentose sugar, and a phosphate group.

Nucleoside

A molecule without the phosphate group in a nucleotide.

Parent compounds of nitrogenous bases

Pyrimidine and Purine

Purine bases

Adenine and Guanine

Pyrimidine bases

Cytosine, Uracil, and Thymine

Nucleotide Bonding

The base of a nucleotide is joined covalently (at N-1 of pyrimidines and N-9 of purines) in an N-β-glycosyl bond to C-1 of the pentose, and the phosphate is esterified to C-5 of the pentose.

Anti conformation

Places H8 over the sugar in purines.

Syn conformation

Places the atom away from the sugar & the bulk of the bicyclic purine over the sugar.

Anti conformation preference

Adenine nucleotides favor this conformation.

Syn conformation preference

Guanine nucleotides prefer this conformation due to the favorable interaction between 2-NH2 group & the 5’-phosphate group stabilizing the syn conformation.

Pyrimidines conformation

The H6 atom is above the pentose ring in the anti conformation and the larger O2 atom is above the sugar in the syn conformation.

UV light absorption of purines vs pyrimidines

Purine compounds absorb light more strongly than pyrimidine compounds.

Nucleotides

The monomer units or building blocks of nucleic acids

Examples of phosphoryl group donors

ATP or GTP

Regulatory nucleotides that act as second messengers

cAMP and cGMP

Two major purine bases in both DNA and RNA

Adenine (A) and guanine (G)

Pyrimidine base common to both DNA and RNA

Cytosine (C)

Second major pyrimidine in DNA and RNA

Thymine (T) in DNA and uracil (U) in RNA

Pentose sugar in DNA

2-deoxy-D-ribose

Pentose sugar in RNA

D-ribose

Long sequences that contain the genetic information in DNA

A, T, C, G

Most common minor bases in DNA

Methylated forms of the major bases

Phosphodiester bond

When the 5-phosphate group of one nucleotide unit is joined to the 3-hydroxyl group of the next nucleotide, creating a phosphodiester linkage.

Oligo-nucleotides

Nucleic acids containing 50 or fewer nucleotides.

Nucleic acid backbone

The covalent backbones of nucleic acids consist of alternating phosphate and pentose residues, and the nitrogenous bases may be regarded as side groups joined to the backbone at regular intervals.

5' and 3' ends

The 5’ end lacks a nucleotide at the 5’ position and the 3’ end lacks a nucleotide at the 3’ position.

Watson and Crick base pairing rules

A bonds specifically to T (or U) and G bonds to C.

Hydrophobic stacking interactions

One of two important modes of interaction between bases in nucleic acids where two or more bases are positioned with the planes of their rings parallel (like a stack of coins).

Primary structure of a nucleic acid

Its covalent structure and nucleotide sequence.

Secondary structure of a nucleic acid

Any regular, stable structure taken up by some or all of the nucleotides in a nucleic acid.

Tertiary structure of nucleic acids

The complex folding of large chromosomes within eukaryotic chromatin and bacterial nucleoids.

Structure of DNA

Two helical chains wound around the same axis to form a right-handed double helix.

Chargaff's rules for base composition

They vary from one species to another, specimens isolated from different tissues of the same species have the same base composition, and do not change with an organism’s age, nutritional state, or changing environment. Also, the number of adenosine residues is equal to the number of thymidine residues (A=T), and the number of guanosine residues is equal to the number of cytidine residues (G=C).

Most stable structure for a random-sequence DNA molecule under physiological conditions

B-DNA

A-form DNA

Right-handed double helix, wider than B-DNA, with 11 base pairs per helical turn. Favored in solutions relatively devoid of water.

Z-form DNA

Left-handed helix with 12 base pairs per helical turn, appearing more slender and elongated.

Superhelical form of circular DNA

Underwinding or overwinding the double helix.

Direction of superhelix in underwound DNA

Right handed

Direction of superhelix in overwound DNA

Left handed

Topological domain

A DNA segment contained in a manner that restrains rotation of the double helix.

Nucleoids

Compacted structures of bacterial chromosomes.

Proteins that interact with bacterial DNA to form nucleoids

HU and H-NS proteins

Loosely packed chromatin

Euchromatin, the transcriptionally active form of DNA.

Highly condensed, inactive form of DNA.

Heterochromatin

Denaturation or melting of DNA

Separation and unwinding of DNA strands.

Effect of G-C content on DNA denaturation

Molecules that contain a greater proportion of G-C pairs require higher temperatures to denature because the three hydrogen bonds in G-C pairs make these base pairs more stable than A-T pairs, which have only two hydrogen bonds.

Differences between RNA and DNA

RNA contains ribose rather than deoxyribose of DNA, usually exists as a single strand, and contains uracil instead of thymine.

Secondary structures in RNA formed by base pairing between distant complementary segments

Stem-loops and hairpins

mRNA (messenger RNA)

transfer of genetic information from DNA to protein synthesizing machinery

rRNA (ribosome RNA)

have structural roles and contribute to the formation and function of ribosomes (the organelle machinery for protein synthesis)

tRNA (transfer RNA)

serve as adapters for the translation of the information in the sequence of nucleotides of the mRNA into specific amino acids.

Ribozymes

have intrinsic catalytic properties

Small nuclear RNA (snRNA)

play pivotal roles in RNA processing

mRNA capping and tailing

The 5’-terminal of mRNA is ‘capped’ by a 7-methylguanosine triphosphate whichis involved in the recognition of mRNA by the translating machinery and prevents the mRNA from attack by 5’-exonucleases. The 3′-hydroxyl terminal, has an attached polymer of adenylate residues 20–250 nucleotides in length to maintain the intracellular stability of the specific mRNA.

tRNA amino acid attachment

The tRNA-appropriate amino acid is attached to the 3′-OH group of the A moiety of the acceptor arm. The D, TψC, and extra arms help define a specific tRNA.

Ribosome

a cytoplasmic nucleoprotein structure that acts as the machinery for the synthesis of proteins from the mRNA templates

rRNA function

play key roles in the binding of mRNA to ribosomes and its translation.

Nucleases

Enzymes capable of degrading nucleic acids

Exonuclease

Exonuclease act in one direction (3′ → 5′ or 5′ → 3′) only