Nucleic Acids, DNA Replication, Gene Expression, and Protein Structure

Vocabulary flashcards covering chapters 4.1-4.2, 15.1-15.3, 15.5, 16.1-16.4, 17.1-17.5, and 3.1-3.4 from Biological Science (8th Edition).

Nucleic Acid

A polymer composed of nucleotide monomers that stores and encodes biological information.

Nucleotide

The structural monomer of nucleic acids, consisting of a phosphate group, a 5-carbon sugar, and a nitrogenous base.

Purines

A class of double-ring nitrogenous bases containing nine atoms, which includes Adenine (A) and Guanine (G).

Pyrimidines

A class of single-ring nitrogenous bases containing six atoms, which includes Cytosine (C), Uracil (U), and Thymine (T).

Phosphodiester Linkage

The covalent bond that joins nucleotides together, formed between the 3' hydroxyl group of one sugar and the 5' phosphate group of another.

Semiconservative Replication

The mechanism of DNA replication in which parental strands separate and each serves as a template for a new daughter strand, producing two molecules with one old and one new strand.

Meselson-Stahl Experiment

An experiment using isotopic nitrogen labeling ($^{15}\text{N}$ and ${}^{14}\text{N}$) in E. coli that demonstrated DNA replication proceeds semiconservatively.

DNA Polymerase

An enzyme that catalyzes DNA synthesis by adding dNTPs exclusively to the 3' hydroxyl end of a growing DNA strand in the 5' to 3' direction.

DNA Helicase

An enzyme that breaks hydrogen bonds between complementary base pairs to open the DNA double helix during replication.

Single-Strand DNA-Binding Proteins (SSBPs)

Proteins that attach to separated single-stranded DNA to prevent the strands from re-annealing during replication.

Topoisomerase

An enzyme that cuts and rejoins the DNA double helix downstream of the replication fork to relieve twisting tension caused by unwinding.

Primase

A type of RNA polymerase that synthesizes a short RNA primer to provide a free 3' OH group for DNA polymerase to initiate strand synthesis.

Leading Strand

The newly synthesized DNA strand that is created continuously toward the replication fork in the 5' to 3' direction.

Lagging Strand

The newly synthesized DNA strand that is created discontinuously away from the replication fork as a series of Okazaki fragments.

Okazaki Fragments

Short segments of DNA synthesized on the lagging strand template during DNA replication.

DNA Ligase

An enzyme that joins Okazaki fragments into a continuous strand by catalyzing phosphodiester bond formation between adjacent fragments.

Nucleotide Excision Repair

A DNA repair mechanism that detects structural damage (such as thymine dimer kinks), nicks the damaged strand, removes the affected region, and replaces it using the undamaged strand as a template.

Xeroderma Pigmentosum (XP)

A rare autosomal recessive disorder in humans caused by mutations in nucleotide excision repair systems, leading to extreme sensitivity to UV light and elevated risk of skin cancer.

One-Gene, One-Enzyme Hypothesis

The principle proposed by Beadle and Tatum stating that each gene contains the instructions required to produce a single enzyme.

Central Dogma of Molecular Biology

The core framework describing the flow of genetic information in cells: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Proteins}$.

Transcription

The enzymatic process of copying information from a DNA template strand into a complementary RNA transcript.

Translation

The process of decoding information carried in mRNA to synthesize a polypeptide chain at a ribosome.

Genotype

The genetic constituent of an organism, defined by its specific sequence of DNA bases.

Phenotype

The physical and functional characteristics of an organism, which are a direct product of the proteins synthesized.

Codon

A triplet of nucleotides in mRNA that codes for a specific amino acid or signals translation start or stop.

Silent Mutation

A point mutation that alters a codon without changing the encoded amino acid, resulting in no change in phenotype.

Missense Mutation

A point mutation that changes a codon so that it specifies a different amino acid, altering the primary structure of the protein.

Nonsense Mutation

A point mutation that converts an amino-acid-specifying codon into an early stop codon, leading to truncated polypeptides.

Frameshift Mutation

A mutation caused by the addition or deletion of a nucleotide that shifts the mRNA reading frame, altering all subsequent codons.

Sigma Protein

A bacterial protein factor that binds to RNA polymerase core enzyme to form a holoenzyme and guides it to specific promoter sites.

Promoter

A sequence of DNA (such as the -10 and -35 boxes in bacteria) where RNA polymerase or holoenzyme binds to initiate transcription.

Introns

Noncoding regions of eukaryotic primary RNA transcripts that are removed during splicing.

Exons

Protein-coding regions of eukaryotic primary RNA transcripts that are retained and joined together in mature mRNA.

Spliceosome

A complex of small nuclear ribonucleoproteins (snRNPs) and proteins that executes pre-mRNA splicing inside the nucleus.

5' Cap

A modified guanine nucleotide added to the 5' end of eukaryotic pre-mRNA that facilitates ribosome binding and protects against degradation.

Poly(A) Tail

A stretch of 100 to 250 adenine nucleotides added to the 3' end of eukaryotic mRNA required for translation and stability.

Transfer RNA (tRNA)

An adapter RNA molecule containing an anticodon loop and a 3' CCA amino acid attachment site that delivers amino acids during translation.

Aminoacyl-tRNA Synthetase

An enzyme that catalyzes the ATP-dependent covalent attachment of a specific amino acid to its corresponding tRNA.

Wobble Hypothesis

The model proposing that flexible base pairing at the third position of an mRNA codon allows a single tRNA to recognize multiple codons.

A Site

The ribosomal acceptor site that accommodates an incoming charged aminoacyl tRNA.

P Site

The peptidyl site on a ribosome that holds the tRNA carrying the growing polypeptide chain.

E Site

The exit site on a ribosome from which uncharged tRNAs are ejected.

Shine-Dalgarno Sequence

The bacterial ribosome-binding site located upstream of the start codon that aligns mRNA with the small ribosomal subunit.

Release Factor

A protein that recognizes a stop codon in the A site and breaks the bond linking the tRNA in the P site to the polypeptide chain.

Peptide Bond

A covalent C-N bond formed between the carboxyl group of one amino acid and the amino group of another via a condensation reaction.

Primary Structure of Protein

The unique sequence of amino acid residues in a polypeptide chain joined by peptide bonds.

Secondary Structure of Protein

Local structural motifs, such as $\alpha$-helices and $\beta$-pleated sheets, formed by hydrogen bonding along the peptide backbone.

Tertiary Structure of Protein

The overall three-dimensional shape of a single polypeptide, stabilized by interactions among amino acid R-groups and the backbone.

Quaternary Structure of Protein

The functional structure resulting from the combination and interaction of two or more distinct polypeptide subunits.

Molecular Chaperones

Proteins, such as Heat shock protein 90 (Hsp90), that facilitate proper folding of polypeptides and block inappropriate protein aggregation.