Exam 3 Study Guide: Gene Structure, Molecular Genetics, and Epigenetics

Vocabulary practice flashcards covering gene structure, DNA synthesis, mutation and repair, transcription, translation, eukaryotic gene regulation, and epigenetics.

One gene–one enzyme hypothesis

The historical hypothesis formulated by Beadle and Tatum- each individual gene codes for the production of a single specific enzyme.

One gene–one polypeptide hypothesis

The revised concept that each gene encodes a specific polypeptide chain, reflecting that not all proteins are enzymes and some proteins consist of multiple distinct polypeptides.

Alternative RNA splicing

A eukaryotic post-transcriptional process in which different combinations of exons are joined or omitted, allowing a single gene to produce multiple mature mRNA and protein products.

Promoter

A regulatory DNA region located upstream of the transcribed region that serves as the binding site to assemble transcription machinery and start transcription.

Exons

Regions of a eukaryotic gene's transcript that are retained in the mature mRNA after splicing, which can include both protein-coding sequence and untranslated regions ($\text{UTRs}$).

Introns

Non-coding sequences within a eukaryotic primary RNA transcript that are removed by the spliceosome before translation.

Bacterial transformation

The phenomenon discovered by Griffith in which hereditary material taken up from one bacterial strain causes a permanent, inheritable change in another bacterial strain.

Avery–MacLeod–McCarty experiment

An experiment showing that treating heat-killed bacterial extracts with DNA-destroying enzymes stopped bacterial transformation, demonstrating that DNA carries hereditary information.

Hershey–Chase experiment

A study using bacteriophages with phosphorus-32 labeled DNA and sulfur-35 labeled proteins, demonstrating that viral DNA enters host cells while protein remains outside.

Phosphodiester bond

A covalent bond linking adjacent nucleotides together by joining the sugar of one nucleotide to the phosphate group of the next, forming the backbone of nucleic acid strands.

Antiparallel structure

The structural arrangement of double-stranded DNA where two complementary strands run in opposite orientations, one in the $5'$ to $3'$ direction and the other in the $3'$ to $5'$ direction.

Semiconservative replication

The mechanism of DNA duplication where the original strands separate and each serves as a template, producing daughter double helices composed of one original strand and one newly synthesized strand.

Helicase

The enzyme responsible for unwinding the double helix and separating parental DNA strands at the replication fork.

Single-strand binding proteins

Proteins that bind to exposed single strands of DNA at the replication fork to stabilize them and prevent them from premature re-annealing.

Topoisomerase

An enzyme that relieves torsional strain and prevents excessive supercoiling ahead of the advancing replication fork.

Primase

An RNA polymerase that synthesizes short RNA primers to provide a free $3'$ hydroxyl group required by DNA polymerase to begin synthesis.

Okazaki fragments

Short segments of DNA synthesized discontinuously along the lagging strand during DNA replication.

DNA ligase

An enzyme that joins adjacent fragments of newly synthesized DNA by sealing breaks and nicks in the phosphodiester backbone.

Somatic mutation

A mutation occurring in a non-germline body cell that may be passed to daughter cells within an individual via mitosis, but is not transmitted to offspring.

Germline mutation

A mutation occurring in reproductive cells that give rise to gametes, enabling the mutation to be transmitted to offspring through sexual reproduction.

Transition

A base substitution mutation involving the exchange of a purine for another purine (A for G, or G for A) or a pyrimidine for another pyrimidine (C for T, or T for C).

Transversion

A base substitution mutation involving the interchange between a purine and a pyrimidine base (such as purine to pyrimidine or pyrimidine to purine).

Synonymous substitution

A nucleotide substitution in a protein-coding region that changes a codon without changing the encoded amino acid, preserving the original polypeptide sequence.

Missense substitution

A base substitution mutation that changes a codon so that it encodes a different amino acid than the original sequence.

Nonsense substitution

A mutation that changes an amino-acid-specifying codon into a premature stop codon, causing early translation termination and a shortened polypeptide.

Frameshift mutation

An insertion or deletion of nucleotides within a coding sequence that is not a multiple of three, altering the downstream triplet reading frame during translation.

Trinucleotide repeat expansion

A mutation characterized by an increase in the number of three-nucleotide repeated units, which can cause anticipation and increase disease severity.

Senescence

A long-term state of persistent cell-cycle arrest in response to DNA damage, preventing damaged cells from continuing division without triggering apoptosis.

Sigma factor

A bacterial protein that binds to core RNA polymerase to form the holoenzyme, enabling sequence-specific recognition and binding of promoter regions.

5′ cap

A modified structure added to the $5'$ end of eukaryotic pre-mRNA that functions in transcript protection, nuclear export, and translation initiation.

Poly-A tail

A run of adenine nucleotides added to the cleaved $3'$ end of eukaryotic pre-mRNA that enhances mRNA stability and promotes efficient translation.

Aminoacyl-tRNA synthetase

An enzyme responsible for correctly matching and covalently attaching an appropriate amino acid to its cognate tRNA molecule.

A site (aminoacyl site)

The ribosomal binding pocket where incoming charged aminoacyl-tRNAs correctly match codons during translation elongation.

P site (peptidyl site)

The ribosomal site that holds the tRNA attached to the growing polypeptide chain, and where the initiator tRNA binds during initiation.

E site (exit site)

The ribosomal pocket from which uncharged tRNAs are released after transferring their polypeptide chain.

Histone acetylation

A chromatin modification typically associated with loosened chromatin packaging and increased transcription accessibility.

Core promoter

A DNA region positioned near the transcription start site ($+1$) where general transcription factors and RNA polymerase II assemble to initiate transcription.

Enhancers

Regulatory DNA sequences that bind activator proteins to increase transcription, often functioning from a distance via DNA looping.

Silencers

Regulatory DNA sequences that bind repressor proteins to decrease gene transcription.

Epigenome

The chemical marks on DNA and associated proteins, such as DNA methylation and histone modifications, that regulate gene expression without altering the underlying DNA sequence.

DNA methylation

The chemical addition of methyl groups to DNA bases, often occurring at promoters to repress transcription by altering protein binding and chromatin structure.

DNMT3

A DNA methyltransferase enzyme that establishes DNA methylation marks; down-regulation of its activity in honeybee larvae promotes queen-like development.

Viable yellow agouti mice

A mammalian model where maternal exposure to BPA reduces regulatory element methylation to increase agouti expression and produce yellow coats, an effect counteracted by methyl-donor supplements.