Molecular Biology: Nucleic Acid Structures, DNA Replication, Gene Expression, and Mutations

Vocabulary practice flashcards covering nucleic acid structures, DNA replication mechanisms and enzymes, transcription, translation machinery, the genetic code, and mutation types based on lecture notes and diagrams.

Nucleotide

The monomer subunit of nucleic acids, consisting of one, two, or three phosphate groups, a five-carbon monosaccharide (ribose or deoxyribose), and a nitrogenous base that makes each nucleotide unique.

Phosphodiester bond

The covalent bond that connects nucleotides within a strand of DNA or RNA by linking the phosphate group of one nucleotide to the hydroxyl ($-\text{OH}$) group of another.

Antiparallel

The orientation of two strands in a double-stranded nucleic acid molecule running in opposite directions, where the phosphate group end ($5'$) of one strand aligns with the hydroxyl group end ($3'$) of the complementary strand.

Complementary strands

Nucleic acid strands arranged antiparallel to each other whose opposing nitrogenous bases specifically pair via hydrogen bonding ($A$ with $T$ or $U$, and $C$ with $G$).

Base pairing hydrogen bonds

Specific noncovalent interactions between nitrogenous bases in a double helix where adenine and thymine form two hydrogen bonds, and cytosine and guanine form three hydrogen bonds.

Genome

All the genetic information (DNA) present in a cell of an organism.

Chromosome

A single DNA molecule containing many genes; typically circular and not wrapped around proteins in prokaryotes, but linear, multiple in number, and wrapped around proteins in eukaryotes.

Origin of replication (ORI)

A specific sequence of DNA where proteins required to initiate DNA replication attach; prokaryotic chromosomes possess a single ORI, while eukaryotic chromosomes possess multiple ORIs.

Replication fork

The Y-shaped region where the double-stranded DNA helix opens up on one side of a replication bubble during replication.

DNA helicase

The enzyme that unwinds and separates the two strands of the DNA double helix during replication.

DNA polymerase

An enzyme that synthesizes new DNA strands in the phosphate-to-hydroxyl direction, requiring a template DNA strand and an RNA primer, with the ability to proofread and correct mismatched nucleotides.

RNA primer

A short piece of RNA (typically around 10 nucleotides long) synthesized by a specific enzyme that provides the necessary starting point for DNA polymerase to begin forming a new strand.

DNA ligase

An enzyme that links discontinuous fragments of a newly synthesized DNA strand together by forming covalent phosphodiester bonds.

Gene

A specific sequence of DNA that contains the information needed to make a functional product, such as a polypeptide (protein) or a functional RNA.

Promoter

A specific sequence of DNA that indicates the start of a gene and serves as the binding site where RNA polymerase interacts to initiate transcription.

Terminator

A specific sequence of DNA marking the end of a gene that signals RNA polymerase to stop transcribing.

Template strand

The single strand of DNA that RNA polymerase reads to synthesize a complementary RNA molecule during transcription.

Coding strand

The strand of DNA in a gene whose nucleotide sequence matches the resulting mRNA sequence (with T's in the DNA matching U's in the RNA) because both are complementary to the template strand.

RNA polymerase

An enzyme that unwinds the DNA helix and synthesizes an RNA strand complementary to the DNA template strand in the phosphate group end to hydroxyl group end direction.

Epigenetic tags

Chemical functional groups attached to DNA nucleotides or the proteins DNA is wrapped around that regulate gene expression by making DNA accessible or inaccessible to RNA polymerase.

RNA splicing

The post-transcriptional process in eukaryotic cells where non-coding RNA pieces (introns) not required for translation are removed, and coding segments (exons) are joined together.

Alternative splicing

A mechanism in eukaryotic cells where a single pre-mRNA can be spliced in different patterns to generate different mature mRNAs, allowing one gene to produce multiple protein variants.

Codon

A contiguous, non-overlapping grouping of three nucleotides in an mRNA that specifies a single amino acid or signals the start or stop of translation.

Unambiguous (genetic code)

The feature of the genetic code stating that each individual codon specifies exactly one type of amino acid.

Redundant (genetic code)

The feature of the genetic code where multiple different codons can specify the same amino acid, reducing the likelihood that sequence changes alter the resulting protein.

Start codon

The specific codon ($\text{AUG}$) that marks where translation begins and determines the reading frame of codons, while also specifying the amino acid methionine (Met).

Stop codon

One of three specific codons ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$) that mark the end of translation and do not specify any amino acid or correspond to any tRNA.

Transfer RNA (tRNA)

A functional adaptor RNA molecule with a folded structure that carries a specific amino acid covalently attached at one end and an anticodon complementary to an mRNA codon at the other.

Anticodon

A specific sequence of three nucleotides on a tRNA that interacts with a complementary mRNA codon via hydrogen bonds during translation.

Ribosome

A complex composed of ribosomal RNAs (rRNAs) and proteins that positions mRNAs and tRNAs and catalyzes the formation of covalent peptide bonds between amino acids.

Ribozyme

An RNA molecule that has catalytic activity and functions as an enzyme, such as the rRNA within a ribosome that forms peptide bonds during translation.

Mutation

A permanent, random change in the DNA sequence of an organism's genome that serves as a primary source of genetic diversity for evolution.

Substitution mutation

A mutation that changes a single base pair in a DNA sequence, altering at most one codon in the transcribed mRNA.

Silent mutation

A substitution mutation that changes a codon to another codon specifying the exact same amino acid, leaving the amino acid sequence unchanged.

Missense mutation

A substitution mutation that alters a codon to specify a different amino acid without altering the overall number of amino acids in the polypeptide.

Nonsense mutation

A substitution mutation that alters a codon that normally specifies an amino acid into a premature stop codon, causing early termination of translation.

Frameshift mutation

A mutation caused by the insertion or deletion of one or two nucleotides in a protein-coding region, altering the triplet reading frame of all subsequent codons and typically changing polypeptide length and function.