Molecular Biology: Transcription, Translation, and DNA Replication

Vocabulary practice flashcards covering transcript contents on mRNA processing, ribosome structure, translation, and DNA replication mechanisms in prokaryotes and eukaryotes.

Introns

Un-translated intervening sequences that interrupt the coding sequence (Exons) in the primary transcript of mRNA, ranging from $50$ to $90\, \%$ of the total primary transcript.

Splicing

The process discovered by Phillip Sharp and Richard J. Roberts involving the excision of introns and joining of exons to form a finished mRNA.

Spliceosome

A large and complex molecular machine in the nucleus of eukaryotes composed of five small nuclear RNAs ($snRNA$) and associated protein factors.

snRNP (snurps)

An RNA-protein complex formed when small nuclear RNAs ($snRNA$) are combined with protein factors.

Polypyrimidine tract (PPT)

A variable length of polypyrimidines at the $3'$ splice site that recruits factors to the $3'$ splice site and the branch point sequence ($BPS$).

Branch point sequence (BPS)

A sequence containing the conserved Adenosine required for the first step of splicing.

Lariat

The lasso-shaped structure formed when the $2'$ hydroxyl of Adenine attacks the phosphodiester linkage of the first exon during splicing.

U1 snRNP

The spliceosome component that base pairs with the $5'$ splice site of precursor RNA to initiate splicing assembly.

Complex A

The complex formed when $U2\, snRNP$ is recruited to the branch point during spliceosome assembly.

Ribosome

Abundant cellular organelles consisting of more than $50$ different proteins and RNA molecules; they make up about $80\, \%$ of total cellular RNA.

Svedberg (S) unit

A measure of how rapidly an object sediments in a centrifugal field, used to define the sizes of ribosomes and their RNA components.

Bacterial Ribosome (70S)

Composed of a large subunit ($50S$) and a small subunit ($30S$).

Eukaryotic Ribosome (80S)

Composed of a large subunit ($60S$) and a small subunit ($40S$).

Nucleolus

An organelle in the eukaryotic nucleus that transcribes and modifies ribosomal RNA ($rRNA$) and integrates ribosomal proteins to form immature ribosomes.

Nucleolar organizing regions (NORs)

Specific genetic loci composed of tandem repeats of $rDNA$ found on several chromosomes where nucleoli form.

Transfer RNA (tRNA)

An adaptor molecule $73$ to $94$ nucleotides in length that serves as the physical link between mRNA codons and amino acids.

Anticodon

A unit of three nucleotides in tRNA that forms base pairs with a codon in mRNA during protein biosynthesis.

Aminoacyl-tRNA synthetases

Enzymes that catalyze the covalent attachment of a specific amino acid to the $3'$ end of a tRNA.

Acceptor stem

A 7-base pair stem in tRNA that contains the $CCA$ $3'$ terminal group used to attach an amino acid.

Wobble base pairing

A phenomenon where some anticodons can pair with more than one codon because the third-position base pairing is flexible.

Genetic Code

A triplet code where each amino acid is encoded by a sequence of three consecutive nucleotides called a codon.

Degenerate code

The property of the genetic code having $64$ codons but only $20$ amino acids, meaning some amino acids are specified by synonymous codons.

Initiation codon

The codon ($AUG$) that sets the reading frame for translation.

Termination codons

Codons such as $UAA$, $UAG$, and $UGA$ that signal the end of a protein and do not encode amino acids.

Isoaccepting tRNAs

Different tRNAs that accept the same amino acid but have different anticodons.

Shine-Dalgarno sequence

A consensus sequence in bacterial mRNA complementary to the $3'$ end of $16S\, rRNA$ that positions the ribosome over the initiation codon.

Kozak sequence

The consensus sequence ($5'-ACCAUGG-3'$) that facilitates start codon identification in eukaryotic cells.

A, P, and E sites

The three ribosome sites occupied by tRNAs: aminoacyl (A), peptidyl (P), and exit (E).

Peptidyl transferase

The catalytic property of $rRNA$ in the large ribosomal subunit that acts as a ribozyme to form peptide bonds.

Semiconservative replication

The biological process donde each strand of the original DNA molecule serves as a template for the production of its counterpart.

Replicon

An individual unit of replication containing a replication origin.

Theta replication

A type of replication common in circular DNA (like $E.\, coli$) that generates a structure resembling the Greek letter $\theta$.

Replication fork

The point of unwinding where two single nucleotide strands separate from the double-stranded DNA helix.

Leading strand

The new DNA strand that undergoes continuous replication in the $5' \rightarrow 3'$ direction.

Lagging strand

The newly made DNA strand that undergoes discontinuous replication in short bursts.

Okazaki fragments

Short lengths of DNA produced by discontinuous synthesis on the lagging strand, named after Reiji Okazaki.

DNA helicase

An enzyme that breaks the hydrogen bonds between DNA bases to unwind the double helix.

Single-strand-binding (SSB) proteins

Proteins that stabilize single-stranded DNA and prevent it from reannealing during replication.

DNA gyrase

A topoisomerase that relieves strain (torque) ahead of the replication fork as DNA unwinds.

DNA polymerase III

The main workhorse of bacterial replication that synthesizes DNA in the $5' \rightarrow 3'$ direction and has $3' \rightarrow 5'$ exonuclease activity for proofreading.

DNA polymerase I

The enzyme in bacterial replication responsible for removing RNA primers and replacing them with DNA.

DNA ligase

The enzyme that seals nicks in the sugar-phosphate backbone by forming phosphodiester bonds without adding new nucleotides.

Tus protein

A protein in $E.\, coli$ that binds to termination sequences to block helicase and stall the replication fork.

Telomerase

The enzyme responsible for replicating chromosome ends (telomeres) by providing an RNA template for repeat sequence synthesis.