Nucleic Acids Part 1

Vocabulary practice flashcards covering nucleic acid structures, chemical nomenclature of nitrogenous bases, DNA replication enzymes, levels of nucleic acid structure, RNA types, and prokaryotic transcription mechanisms based on the lecture notes.

Nucleic Acid

A polymer composed of nucleotide monomers found in the cell nucleus that is acidic in nature and functions to store, transmit, and express genetic information.

Nucleotide

The monomeric building block of nucleic acids, consisting of three components: a pentose sugar, a phosphate group ($\text{PO}_4^{3-}$), and a heterocyclic nitrogenous base.

Ribose vs. 2-Deoxyribose

Pentose sugars distinguished by carbon-$2'$ ($\text{C-2'}$): ribose (in RNA) contains a hydroxyl group ($-\text{OH}$) at $\text{C-2'}$, whereas 2-deoxyribose (in DNA) has only a hydrogen atom ($-\text{H}$) at $\text{C-2'}$.

Pyrimidines

A class of smaller, single-ring nitrogenous heterocyclic bases found in nucleic acids, comprising cytosine, thymine (in DNA), and uracil (in RNA).

Purines

A class of larger, bicyclic (double-ring) nitrogenous heterocyclic bases found in nucleic acids, comprising adenine and guanine.

Thymine (T)

A pyrimidine base with ketone groups at $\text{C-2}$ and $\text{C-4}$ and a methyl group at $\text{C-5}$, systematically named 5-methyl-1H-pyrimidine-2,4-dione.

Cytosine (C)

A pyrimidine base featuring an amino group at $\text{C-4}$ and a ketone group at $\text{C-2}$, systematically named 4-amino-1H-pyrimidine-2-one.

Uracil (U)

A pyrimidine base present in RNA possessing two ketone groups at $\text{C-2}$ and $\text{C-4}$ (dioxo) and lacking a methyl group, systematically named 1H-pyrimidine-2,4-dione.

Adenine (A)

A purine base featuring an amino group at $\text{C-6}$, known as a 6-aminopurine derivative with the IUPAC name 7H-purin-6-amine.

Guanine (G)

A purine base bearing an amino group at $\text{C-2}$ and a ketone group at $\text{C-6}$, systematically named 2-amino-1,7-dihydropurin-6-one.

Hydrogen Phosphate Ion ($\text{HPO}_4^{2-}$)

The fully dissociated form of phosphoric acid ($\text{H}_3\text{PO}_4$) that exists under cellular pH conditions and constitutes the phosphate component of nucleotides.

Nucleoside

A compound formed by a condensation reaction between a pentose sugar and a nitrogenous base via an N\text{-\beta-glycosidic linkage} between $\text{C-1'}$ of the sugar and $\text{N-9}$ of a purine or $\text{N-1}$ of a pyrimidine, releasing one water molecule.

Phosphodiester Bond

The covalent linkage connecting the sugar of one nucleotide to the phosphate group of another, establishing the alternating sugar-phosphate backbone of nucleic acids.

Primary Structure of Nucleic Acids

The linear sequence of nucleotides linked together by phosphodiester bonds in a polynucleotide chain, read in the $5' \rightarrow 3'$ direction.

Secondary Structure of Nucleic Acids

The spatial arrangement formed by complementary base pairing held together by hydrogen bonds, creating a double helix in DNA or single-stranded folded motifs in RNA.

Tertiary Structure of Nucleic Acids

The three-dimensional folding of a nucleic acid strand stabilized by hydrogen bonds, ionic bonds, base stacking, and hydrophobic interactions (e.g., the 3D folded conformation of tRNA).

Quaternary Structure of Nucleic Acids

The macromolecular assembly of multiple nucleic acid molecules and/or proteins into a functional complex, exemplified by the ribosome composed of large and small subunits of rRNA and proteins.

Chargaff's Base-Pairing Rules

The principle stating that in double-stranded DNA, the percentage of adenine equals thymine ($\%A = \%T$) and the percentage of cytosine equals guanine ($\%C = \%G$), such as in humans where DNA contains $30\%$ adenine, $30\%$ thymine, $20\%$ guanine, and $20\%$ cytosine.

Semiconservative Replication

The mechanism of DNA synthesis in which each daughter double helix contains one original intact template strand and one newly synthesized strand.

Helicase

The replication enzyme that unwinds and separates double-stranded DNA into single strands by cleaving the hydrogen bonds between complementary base pairs.

DNA Polymerase III

The primary enzyme responsible for continuous DNA synthesis on the leading strand in the $5' \rightarrow 3'$ direction and the elongation of Okazaki fragments.

Okazaki Fragments

Short, discontinuously synthesized DNA fragments produced on the lagging strand during DNA replication because synthesis moves away from the replication fork.

DNA Polymerase I

The enzyme that removes short RNA primers from the newly synthesized DNA strand and replaces them with DNA nucleotides.

DNA Ligase

The enzyme that covalently seals nicks in the sugar-phosphate backbone by joining adjacent Okazaki fragments on the lagging strand.

Chromosome

A thread-like nuclear structure composed of $15\%$ DNA by mass and $85\%$ protein by mass (predominantly histones and other structural proteins) that packages genetic information.

Histone

A structural protein that serves as a spool around which the DNA double helix winds to organize and package genetic material into nucleosomes.

Nucleosome

The fundamental packaging unit of chromatin, composed of a core of 8 histone proteins wrapped by coiled DNA.

Chromatin

A higher-order cellular structure formed by numerous nucleosomes further coiled and folded into fibers.

Gene

A segment of DNA base sequence (typically 1,000 to 3,500 nucleotide units long in humans) containing the instructions for producing a specific hnRNA/mRNA molecule or protein.

Genome

The complete complement of genetic material (total DNA) contained within the chromosomes of an organism, encompassing approximately 20,000 to 25,000 genes in humans.

Heterogeneous Nuclear RNA (hnRNA)

The primary, unprocessed RNA transcript synthesized directly from the DNA template in the nucleus, which undergoes splicing, capping, and poly-A tail addition before becoming mature mRNA.

Messenger RNA (mRNA)

The processed RNA transcript that carries genetic instructions for protein synthesis from nuclear DNA out to cytoplasmic ribosomes.

Small Nuclear RNA (snRNA)

A specialized RNA of about 100 to 200 nucleotides that associates with proteins to form the spliceosome and assists in splicing introns from hnRNA.

Ribosomal RNA (rRNA)

The enzymatic and structural RNA molecule that associates with proteins to build ribosomes, the cellular machines where protein synthesis takes place.

Transfer RNA (tRNA)

The smallest RNA species (75 to 90 nucleotides) adopting a cloverleaf/hairpin structure that contains an anticodon region and delivers specific amino acids to ribosomes during translation.

Transcription

The phase of protein synthesis where DNA directs the enzymatic synthesis of complementary RNA molecules via initiation, elongation, and termination stages.

Translation

The phase of protein synthesis where the codon sequence of mRNA is decoded by ribosomes and tRNAs in the cytoplasm to assemble an amino acid chain.

Promoter

A specific DNA regulatory sequence recognized by RNA polymerase to initiate transcription, locate the start point, and begin unwinding the DNA helix.

Template (Antisense) Strand

The single strand of DNA oriented in the $3' \rightarrow 5'$ direction that serves as the guide for RNA polymerase to assemble a complementary RNA transcript in the $5' \rightarrow 3'$ direction.

Rho-Dependent Termination

A prokaryotic transcription termination mechanism where the Rho protein factor binds the rut site on the transcript, moves in the $5' \rightarrow 3'$ direction via ATP hydrolysis, and unwinds the RNA–DNA hybrid to release the transcript.

Hairpin Loop (RNA)

A stable secondary structure formed when a single-stranded RNA folds back onto itself through complementary base pairing between GC-rich inverted repeats.

Rho-Independent Termination

An intrinsic prokaryotic transcription termination mechanism triggered by the transcription of a GC-rich inverted repeat that folds into a hairpin loop, followed by a string of weak A–U bonds causing RNA polymerase to pause and release the transcript.