Chapter 13: Regulation of Gene Expression

Enhancer

A DNA sequence that increases the level of transcription of a gene that is located nearby on the same chromosome.

Carcinogen

A cancer causing substance in living tissue.

Corepressor

A corepressor is a substance that inhibits the expression of genes. In prokaryotes, corepressors are small molecules whereas in eukaryotes, corepressors are proteins.

Frameshift mutation

A frameshift mutation (also called a framing error or a reading frame shift) is a genetic mutation caused by indels (insertions or deletions) of a number of nucleotides in a DNA sequence that is not divisible by three.

Mutation

A gene mutation is a permanent alteration in the DNA sequence that makes up a gene, such that the sequence differs from what is found in most people. Mutations range in size; they can affect anywhere from a single DNA building block (base pair) to a large segment of a chromosome that includes multiple genes. Can be hereditary or acquired.

Oncogene

A gene that in certain circumstances can transform a cell into a tumor cell

miRNA

A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression.

Point mutation

A mutation affecting only one or very few nucleotides in a gene sequence.

Phosphatase

A phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol. Because a phosphatase enzyme catalyzes the hydrolysis of its substrate, it is a subcategory of hydrolases.

Promoter

A promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5' region of the sense strand).

Repressor

A protein in which its binding to the operator inhibits the transcription of one or more genes.

Proto-Oncogene

A proto-oncogene is a normal gene that could become an oncogene due to mutations or increased expression. Proto-oncogenes code for proteins that help to regulate cell growth and differentiation.

Regulator

A regulator gene, regulator, or regulatory gene is a gene involved in controlling the expression of one or more other genes. Regulatory sequences, which encode regulatory genes, are often 5' to the start site of transcription of the gene they regulate.

Exon

A segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence.

Intron

A segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.

snRNA

A small nuclear RNA (snRNA) is one of many small RNA species confined to the nucleus; several of the snRNAs are involved in splicing or other RNA processing reactions. Small cytoplasmic RNAs (scRNA) are present in the cytoplasm and (sometimes are also found in the nucleus).

Barr Body

A small, densely staining structure in the cell nuclei of female mammals, consisting of a condensed, inactive X chromosome. It is regarded as diagnostic of genetic femaleness.

Structural Genes

A structural gene is a gene that codes for any RNA or protein product other than a regulatory factor

Repressor

A substance that acts on an operon to inhibit messenger RNA synthesis.

Transcription Activatior

A transcriptional activator is a protein (transcription factor) that increases gene transcription of a gene or set of genes. Most activators are DNA-binding proteins that bind to enhancers or promoter-proximal elements.

Tumor supressor

A tumor suppressor gene, or antioncogene, is a gene that protects a cell from one step on the path to cancer. When this gene mutates to cause a loss or reduction in its function, the cell can progress to cancer, usually in combination with other genetic changes.

Acetylation

Acetylation is the process where an acetyl functional group is transferred from one molecule (in this case, Acetyl-Coenzyme A) to another. Deacetylation is simply the reverse reaction where an acetyl group is removed from a molecule.

Alternative mRNA Splicing

Alternative splicing, or differential splicing, is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.

Mutagen

An agent, such as radiation or a chemical substance, that causes genetic mutation.

Protease

An enzyme that breaks down proteins and peptides.

Kinase

An enzyme that catalyzes the transfer of a phosphate group from ATP to a specified molecule.

Inducer

An inducer is a molecule that regulates gene expression. An inducer can bind to protein repressors or activators. Inducers function by disabling repressors. The gene is expressed because an inducer binds to the repressor.

Operator

An operator is a segment of DNA to which a transcription factor binds to regulate gene expression by repressing it. The protein that does this is called a repressor. Repressors bind to operators to prevent transcription.

Histones

Any of a group of basic proteins found in chromatin.

sRNA

Bacterial small RNAs (sRNA) are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops.

CAP

CAP is a DNA binding protein involved with the transcription of several genes, including those that code for enzymes involved in the metabolism of certain sugars

Catabolic

Catabolic reactions usually release energy that is used to drive chemical reactions.

Chromatin remodeling complex

Chromatin remodeling is the rearrangement of chromatin from a condensed state to a transcriptionally accessible state, allowing transcription factors or other DNA binding proteins to access DNA and control gene expression.

Heterochromatin

Chromosome material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed.

Euchromatin

Chromosome material that does not stain strongly except during cell division. It represents the major genes and is involved in transcription.

Epigenetic Inheritance

Epigenetic inheritance is an unconventional finding. It goes against the idea that inheritance happens only through the DNA code that passes from parent to offspring. It means that a parent's experiences, in the form of epigenetic tags, can be passed down to future generations.

Methylation

Histone methylation is a process by which methyl groups are transferred to amino acids of histone proteins that make up nucleosomes, which the DNA double helix wraps around to form chromosomes.

Deletion

In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: Δ) is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is lost during DNA replication. Any number of nucleotides can be deleted, from a single base to an entire piece of chromosome.[1] The smallest single base deletion mutations are believed to occur by a single base flipping in the template DNA, followed by template DNA strand slippage, within the DNA polymerase active site.[2][3][4] Deletions can be caused by errors in chromosomal crossover during meiosis, which causes several serious genetic diseases.

Silencer

In genetics, a silencer is a DNA sequence capable of binding transcription regulation factors, called repressors. DNA contains genes and provides the template to produce messenger RNA (mRNA). That mRNA is then translated into proteins. When a repressor protein binds to the silencer region of DNA, RNA polymerase is prevented from transcribing the DNA sequence into RNA. With transcription blocked, the translation of RNA into proteins is impossible. Thus, silencers prevent genes from being expressed as proteins.

Insertion

In genetics, an insertion (also called an insertion mutation) is the addition of one or more nucleotide base pairs into a DNA sequence.

Negative Control

In negative control, the genes in the operon are expressed unless they are switched off by a repressor protein. Thus the operon will be turned on constitutively (the genes will be expressed) when the repressor in inactivated.

Repressible

In negative repressible operons, transcription of the operon normally takes place. Repressor proteins are produced by a regulator gene, but they are unable to bind to the operator in their normal conformation.

Positive Control

In positive control, the genes are expressed only when an active regulator protein, e.g. an activator, is present. Thus the operon will be turned off when the positive regulatory protein is absent or inactivated.

Trp Vs. Lac

In the lac operon, allolactose binds to the repressor protein, allowing gene transcription, while in the trp operon, tryptophan binds to the repressor protein effectively blocking gene transcription. In both situations, repression is that of RNA polymerase transcribing the genes in the operon.

Inducible

Inducible operons are an example of negative control of gene expression. Their default state is "off", meaning that binding of the active regulator protein to DNA, thereby blocking transcription initiation, is the default state.

Mediator Proteins

Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes

Proteasome

Proteasomes are protein complexes inside all eukaryotes and archaea, and in some bacteria. In eukaryotes, proteasomes are located in the nucleus and the cytoplasm. The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds.

RNA interference

RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules. Historically, it was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling.

siRNA

Small (or short) interfering RNA (siRNA) is the most commonly used RNA interference (RNAi) tool for inducing short-term silencing of protein coding genes. siRNA is a synthetic RNA duplex designed to specifically target a particular mRNA for degradation.

RISC

The RNA-induced silencing complex, or RISC, is a ribonucleoprotein complex involved in the RNA interference pathway. The pathway scans the cell for mRNA that are viral in nature or ones that have been transcribed from viral DNA and/or transposable elements in the genome.

Anabolic

The chemical reactions that synthesize molecules in metabolism. Anabolic reactions usually require energy. Anabolic reactions build new molecules and/or store energy.

Radiation

The emission of energy as electromagnetic waves or as moving subatomic particles, especially high-energy particles that cause ionization. Used to treat cancer.

Unpacking

The unpacking of DNA to access genes more easily.

Transcription Factors

Transcription factors are proteins involved in the process of converting, or transcribing, DNA into RNA. Transcription factors include a wide number of proteins, excluding RNA polymerase, that initiate and regulate the transcription of genes.

cAMP

cAMP is a second messenger important in many biological processes. cAMP is a derivative of adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway.

dsRNA

dsRNA forms the genetic material of some viruses (double-stranded RNA viruses). Double-stranded RNA such as viral RNA or siRNA can trigger RNA interference in eukaryotes, as well as interferon response in vertebrates.