Biology Chapter 18

Genomic Imprinting

a phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent

Differential Gene Expression

the expression of different sets of genes by cells with the same genome (a typical human cell probably expresses about 20% of its genes at any given time)

Allosteric Protein

a protein with two alternative shapes, active an inactive, the protein becomes active only when a molecule binds to it

DNA Methylation

addition of methyl group to DNA (usually to Cytosine), associated with decreased transcription (permanent deactivation)

Proximal Control Elements

control elements located close to the promoter

Distal Control Elements

control elements located far from the promoter

Cyclic AMP

(cAMP) cyclic adenosine monophosphate, accumulates when glucose is scarce, a ring-shaped molecule made from ATP that is a regulator of some bacterial operons [binds to catabolite activator protein (CAP)]

miRNA

(microRNA) about 20 nucleotides long, a small, single-stranded RNA molecule, generated from a hairpin structure on a precursor RNA transcribed from a particular gene, it associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence, up to 1/3 of all human genes may be regulated by miRNAs

Degradation of mRNA

(regulated by the 3' end UTR) mRNA breakdown begins with the enzymatic shortening of the poly-A tail, this helps trigger the action of enzymes that removes the 5' cap, once the cap is removed nuclease enzymes rapidly chew up the mRNA

Enhancers and Transcription Activators

1) activator proteins bind to distal control elements grouped as an enhancer in the DNA, this enhancer has three binding sites, 2) a DNA-bending protein brings the bound activators closer to the promoter, general transcription factors, mediator proteins, and RNA polymerase are nearby, 3) the activators bind to certain mediator proteins and general transcription factors, helping them form an active transcription initiation complex on the promoter

Positive Regulation of the Lac Operon by CAP

RNA polymerase has high affinity for the lac promoter only when catabolite activator protein (CAP) is bound to a DNA site at the upstream end of the promoter, CAP attaches to its DNA site only when associated with cyclic AMP (cAMP), whose concentration in the cell rises when the glucose concentration falls, thus, when glucose is present, even if lactose also is available, the cell preferentially catabolizes glucose and makes very little of the lactose-utilizing enzymes

Regulatory Gene

a gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes

Proteasomes

a giant protein complex that recognizes and destroys proteins tagged for elimination by the small protein ubiquitin

Activators in Prokaryotes

a protein that binds to DNA and stimulates gene transcription, activators bind in or near the promoter

Repressor in Prokaryotes

a protein that inhibits gene transcription, they bind to the DNA in or near the promoter (block the attachment of RNA polymerase to the promoter)

Repressor in Eukaryotes

a protein that inhibits gene transcription, they may bind to control elements within enhancers, to activators, or to other proteins in a way that blocks activators from binding to DNA

Enhancer

a segment of eukaryotic DNA containing multiple control elements, usually located far from the gene whose transcription it regulates

Control Element

a segment of noncoding DNA that helps regulate transcription of a gene by binding a transcription factor, multiple control elements are present in a eukaryotic gene's enhancer

Corepressor

a small molecule that binds to a bacterial repressor protein and changes its shape, allowing it to switch an operon off

Promoter

a specific nucleotide sequence in DNA that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place

Inducer

a specific small molecule that binds to a bacterial repressor protein and changes its shape so that it cannot bind to an operator, thus switching an operator on (inactivates the repressor)

Alternative RNA Splicing

a type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns

Operon

a unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway

Positive Gene Regulation

an activator interacts with the RNA polymerase in the promoter region to initiate transcription (example lac operon)

Lactose Present / Glucose Scarce

cAMP level high: abundant lac mRNA synthesized, if glucose is scarce, the high level of cAMP activates catabolite activator protein (CAP), and the lac operon produces large amounts of mRNA coding for the enzymes in the lactose pathway

Lactose Present / Glucose Present

cAMP level low: little lac mRNA synthesized, when glucose is present, cAMP is scarce, and catabolite activator protein (CAP) is unable to stimulate transcription

Protein Processing

cleavage, addition of chemical groups, transportation to target destinations

Operator

in bacterial DNA, a sequence of nucleotides near the start of an operon to which an active repressor can attach (binding is reversible), the binding of the repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon

3' end Untranslated Region

nucleotide sequence that affects how long an mRNA remains intact

Lactose Absent (Inducible Operon)

repressor active, operon off, the lac repressor is innately active, and in the absence of lactose it switches off the operon by binding to the operator

Tryptophan Absent (Repressible Operon)

repressor inactive, operon on, RNA polymerase attaches to the DNA at the promoter and transcribes the operon's genes

Lactose Present (Inducible Operon)

repressor inactive, operon on, allolactose, an isomer of lactose, derepresses the operon by inactivating the repressor, in this way the enzymes for lactose utilization are induced

Histones

set of basic positively charged proteins, bind and organize DNA into nucleosomes, involved in regulation of gene expression, added to DNA to make chromatin

Chromatin Structure and Activators/Repressors

some activators recruit proteins that acetylate histones near the promoters of specific genes (promoting transcription), some repressors recruit proteins that deacetylate histones (leading to reduced transcription)

Enhancers and Transcription Repressors

some repressors bind directly to control element DNA, blocking activator binding, or in some cases, turning off transcription even when activators are bound, other repressors block the binding of activators to proteins that allow the activators to bind to DNA

Histone Methylation

the addition of methyl groups (-CH3) to histone tails, promotes condensation of the chromatin (discourages transcription)

Histone Acetylation

the attachment of acetyl groups (-COCH3) to certain amino acids of histone proteins, the chromatin becomes less compact, and the DNA is accessible for transcription

Nucleosome

the basic, bead-like unit of DNA packing in eukaryotes, consisting of a segment of DNA wound around a protein core composed of two copies of each of four types of histone

Inducible Enzymes

their synthesis is induced by a chemical signal (allolactose for lac operon), function in catabolic pathways

Repressible Operon

transcription is usually on, but can be inhibited (repressed) when a specific small molecule binds allosterically to a regulatory protein (example tryptophan)

Inducible Operon

usually off, but can be stimulated (induced) when a specific small molecule interacts with a regulatory protein (example lac operon)

Initiation of Translation and Gene Regulation

the initiation of translation of the mRNAs can be blocked by regulatory proteins binding to specific sequences or structures within the untranslated region at the 5' end of the mRNA (preventing the attachment of ribosomes), another method is having stored mRNAs lack poly-A tails of sufficient lenght to allow translation initiation, another method is the activation/inactivation of one or more of the protein factors required to initiate translation, some plants and algae store mRNAs during periods of darkness; light then triggers the reactivation of the translational apparatus

Negative Gene Regulation

the operons are switched off by the active form of the repressor protein (examples lac operon and trp operon)

Combinatorial Control of Gene Activation

12 control element sequences available, the combination of control elements in the enhancer regulate gene expression by allowing cell-type specific transcription (availability of activator proteins)

Epigenic Inheritance

inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome

Tryptophan Present (Repressible Operon)

repressor active, operon off, as tryptophan accumulates, it inhibits its own production by activating the repressor protein, which binds to the operator, blocking transcription