Molecular Biology and Virology: Gene Expression, Epigenetics, ncRNAs, and Viruses

Vocabulary practice flashcards covering Gene Expression and Regulation (Chapter 15), Epigenetics and Chromatin Structure (Chapter 16), Non-coding RNAs and CRISPR-Cas (Chapter 17), and Viruses and HIV Biology (Chapter 18).

Gene Expression

The process by which the information within a gene is accessed, first to synthesize RNA and polypeptides, and eventually to affect the properties of cells and the phenotype of multicellular organisms.

Gene Regulation

The phenomenon in which the level of gene expression can vary under different conditions by being increased or decreased.

Transcription Factors

A category of proteins that influence the ability of RNA polymerase to transcribe DNA to RNA.

General Transcription Factors (GTFs)

Transcription factors required for the binding of RNA polymerase to the core promoter and progression to the elongation stage, necessary for any transcription to occur.

Regulatory Transcription Factors (RTFs)

Transcription factors in eukaryotic cells that regulate the rate of transcription of target genes by influencing RNA polymerase's ability to begin transcription of a particular gene.

Enhancer

A DNA region, usually $50$ to $1000\text{ bp}$ in length, that contains one or more regulatory elements where transcription factor binding increases the rate of transcription.

Up-Regulation

Genetic regulation that leads to an increase in gene expression, which can be $10$ to $1000\text{-fold}$.

Down-Regulation

Genetic regulation that leads to a decrease in gene expression.

Combinatorial Control

The phenomenon in which the combination of many factors determines the expression of any given gene.

Closed Conformation

A state of chromatin where DNA is tightly packed, rendering transcription difficult or impossible.

Open Conformation

A state of loosely packed chromatin that can be easily accessed by transcription factors and RNA polymerase, allowing transcription to occur.

ATP-Dependent Chromatin Remodeling

Dynamic changes in chromatin structure carried out by multi-protein machines that reposition and restructure nucleosomes during the life of a cell.

DNA Translocase

A catalytic ATPase subunit found in all ATP-dependent chromatin-remodeling complexes that moves along the DNA.

Histone Variants

Histone proteins encoded by genes that have accumulated mutations altering their amino acid sequences, which are incorporated into nucleosomes to create specialized chromatin regions.

Histone Code

The pattern of histone covalent modifications that acts like a language in specifying alterations in chromatin structure and providing binding sites for proteins.

Nucleosome-Free Region (NFR)

A region found at the beginning and end of many genes (at transcriptional start and termination sites) where nucleosomes are absent.

DNA Methylation

A process where an enzyme covalently attaches a methyl ($-\text{CH}_3$) group to a base in DNA, typically cytosine at its $5'$ carbon in eukaryotes.

CpG Island

A group of CG base sequences clustered near a promoter region of a gene, typically $1000$ to $2000$ nucleotides long, containing a high number of CpG sites connected by phosphodiester linkages.

Housekeeping Genes

Genes that code for proteins required in most cells of a multicellular organism, whose CpG islands characteristically remain unmethylated.

Tissue-Specific Genes

Highly regulated genes expressed only in a particular cell type, whose expression may be silenced in other tissues by the methylation of CpG islands.

De Novo Methylation

The enzymatic methylation of DNA that was previously unmethylated.

Maintenance Methylation

The methylation of hemimethylated DNA following DNA replication.

Steroid Receptors

A category of regulatory transcription factors that respond directly to the binding of a steroid hormone to affect gene transcription.

Glucocorticoid Response Elements (GREs)

Enhancer DNA sequences located near dozens of different genes that allow glucocorticoid hormones to activate multiple genes.

Epigenetics

The study of mechanisms that lead to changes in gene expression that can be passed from cell to cell and are reversible, but do not involve a change in the base sequence of DNA.

Euchromatin

Centrally located, transcriptionally active regions of chromatin that are not stained during interphase.

Heterochromatin

Highly compacted, transcriptionally repressed regions of chromatin that are stained throughout the cell cycle and localized along the periphery of the nuclear lamina.

Reader Domains

Protein domains that control protein binding to a nucleosome by recognizing specific posttranslational modifications (PTMs).

Writer Domains

Chromatin-modifying domains on proteins that catalyze the addition of posttranslational modifications (PTMs) to histones.

Eraser Domains

Chromatin-modifying domains on proteins that remove posttranslational modifications (PTMs) from histones.

Facultative Heterochromatin

A reversible, cell-type-specific form of heterochromatin characterized by discrete CpG island methylation and the presence of H3K9me3.

Lamina-Associated Domains (LADs)

Chromosomal regions associated with the nuclear lamina that organize chromosomes into chromatin territories and may be involved in gene expression.

Nucleation

The initial phase of heterochromatin formation occurring at a short chromosomal site bound by chromatin-modifying enzymes and chromatin-remodeling complexes.

Non-Coding RNAs (ncRNAs)

RNA molecules transcribed from genes that do not code for polypeptides, performing cellular functions by binding molecules such as DNA, RNA, and proteins.

Ribozyme

An RNA molecule that exhibits catalytic activity.

Decoy ncRNA

A non-coding RNA that recognizes and sequesters other ncRNAs (such as miRNAs) to prevent them from carrying out their inhibitory functions.

Long Non-Coding RNAs (lncRNAs)

Non-coding RNAs that are longer than $200$ nucleotides in length.

Small Regulatory RNAs

Short non-coding RNAs that are shorter than $200$ nucleotides in length, including microRNAs.

Protobiont

An aggregate of molecules and macromolecules that preceded living cells, possessing a boundary like a lipid bilayer that maintained a distinct internal chemical environment.

RNA World

A hypothesized period on Earth in which RNA molecules within protobionts performed information storage, self-replication, and catalytic activities without DNA or proteins.

CRISPR-Cas System

A prokaryotic defense system that protects against foreign invaders, such as bacteriophages, plasmids, and transposons, using ncRNAs and Cas protein complexes.

Spacers

Short, unique sequences derived from foreign DNA that are interspersed between clustered, regular palindromic repeats in the CRISPR locus.

Capsid

The protein coat enclosing a viral genome, composed of one or more types of protein subunits called capsomers.

Viral Envelope

A lipid bilayer derived from the host cell's plasma membrane and embedded with viral spike glycoproteins (peplomers) that encloses the capsid.

Bacteriophages

Viruses that infect bacteria, possessing complex capsids and specialized structures for anchoring and injecting viral nucleic acid.

Integrase

An enzyme that functions in the integration of viral DNA or a retrotransposon into a host chromosome.

Provirus

Viral DNA that has been integrated into the chromosomal DNA of a eukaryotic host cell.

Prophage

Phage DNA that has been integrated into a bacterial chromosome.

Lysogenic Cycle

A growth cycle in which a phage integrates its genetic material into the chromosome of the host bacterium as a prophage, remaining dormant without producing new phages.

Lytic Cycle

A viral reproductive cycle involving viral synthesis, assembly, and release that ultimately leads to the lysis and destruction of the host cell.

Episome

A genetic element, such as a plasmid or certain viral genomes, that can replicate independently of the chromosomal DNA or occasionally integrate into it.

Emerging Viruses

Viruses that have arisen recently and are more likely to cause infection than previous strains, such as new strains of influenza and HIV.

gag Gene

An HIV gene encoding a polyprotein that is cleaved into matrix protein, capsid protein, nucleocapsid protein, and p6 for viral assembly and capsid formation.

pol Gene

An HIV gene encoding a polyprotein that is cleaved into three enzymes: HIV protease, reverse transcriptase, and integrase.

env Gene

An HIV gene encoding a polyprotein that is cleaved into the envelope glycoproteins gp41 and gp120.