Genetics Vocabulary

Flashcards of genetics vocabulary and concepts.

lacI

Encodes a negative regulator of Lac

LacI

A repressor that is inactivated by inducer

IPTG

A repressor that can't perform its role because IPTG is present and beta-galactosidase synthesis continues.

Structural Gene Mutation

A mutation in the structural gene that is not functional because it is not producing beta galactosidase.

Various activities of lacI

The actvities (DNA binding, inducer binding) are genetically separable

lac Oc mutations

A mutation in the lac O DNA sequence, such that lac repressor no longer recognizes site effectively leading to no more repression so lac production is constitutive.

lac I-

A mutation in DNA binding domain in LacI leads to not being able to recognize effectively lac O w/ high affinity get mutation which leads to constitutive synthesis of lac operon

lacI protein is a homotetramer

Each subunit associates w/ 3 other subunits; each subunit has DNA binding region and inducer binding region

IS mutation

Mutant repressor protein binds to the operator, preventing transcription; called super-repressor mutation

Constitutive transcription

Transcription due to mutation in lacOc or lacI- in DNA binding domain

lacP- mutation

No effective transcription due to lacP- mutation; lac promoter mutation in -10 or -35 box results in this

Binding of inducer

Binding of inducer reduces affinity for lacO through allosteric effects

Steric hindrance

Binding sites for LacI and RNA polymerase overlap: they cannot bind at the same time

lacO1

Contains an inverted repeat sequence that leads to binding of 2 of the subunits of lacO

lacO3

Two other subunits bind; further upstream of the promoter

cAMP

When CRP binds to cAMP it dimerizes, binds to the CRP-cAMP binding site, and recruits RNA poly

lytic; lysogenic

if Cro wins this cycle; if C1 wins this cycle

C1

Encodes a protein called lambda repressor and Cro encodes Cro

Q

A regulator of late genes; if this is transcribed and translated then you’ll have lysis

Lsyogeny

C1 expression

Lysis

Cro expression

C1

Expressed from promoter called PRM; only protein made by prophage and it represses

Cro

Expressed from promoter called Pr

Cro

Turns off C1, PR is active and transcribes Q, activator of late gene transcription

RecA

Has proteolytic activity

UV

This leads to cleavage of C1 by RecA

Growth Conditions

Under good conditions c1 is degraded and lysis is favored

Trp operon

An anabolic pathway, repressed by its end product: Trp

Leader sequence

Is transcribed and is imp in regulating transcription elongation on the RNA; at the beg of the transcription unit

Trp repressor

Binds operator under high trypotphan levels; it acts a corepressor, binds repressor, and see no transcription

L region

Open reading frame w/ start and stop codon

3-4 stem loop

a Rho-independent transcription terminator; this is a stem loop followed by stretch of UUs

Region 2 is unavailable to pair with 3, and 3 can pair with 4: production of stem-loop structure followed by UUUUU

Trp operon-tryptophan abundance

If no tryptophan available very few aminoacyl tryptophan tRNAs available so translation stalls on 1 and 2 and 3 will pair and then the transcription terminator can’t form and therefore transcription elongation proceeds through the operon

Trp operon-poor conditions

Euchromatin

Active chromatin

heterochromatin

Silent chromatin

cis-acting regulatory regions

DNA sequences in the vicinity of the structural portion of a gene that are required for gene

trans-acting regulatory proteins

Transcription factors, TATA binding proteins (TBP), general transcription factors (GFT)

Enhancers

activates transcription in cooperation with promoters bending DNA into loops

Trans-activation

Activate/represses the enhancer that it binds to; allows interaction w/ basal TF and the enzymes that modify histones

DNA binding domain

Recognizes a specific sequence in the enhancer; shared among TFs families and also w/ other chromatin binding proteins like histones

Dimerization

Protein-protein interaction domain; modulates activity by interaction w/ other TFs; act in pairs so need 2 molecules to form active complex

signal transduction

The pathways are events outside the cell that stimulate sequential events inside the cell that result in new gene expression patterns

Ig heavy-chain gene enhancer

Tissue-specific

histone gene promoters

Ubiquitous

Band shift assay

Something that binds DNA will be a bigger complex and moves more slower

DNA footprint protection assay

Area where protein is bound will cover the DNA and protect it from DNAse 1

Locus Control Regions

LCR is highly specialized enhancer that regulates the transcription of multiple related genes packaged in a complex

B-globin gene

Encode the beta-globin polypeptide, 2 copies of which join w/ 2 copies of alpha-globin to form hemoglobin

DNase I hypersensitive sites

These regions when open are sensitive to DNases and harbors an enhancer

Modified transgene w/ added LCR region

Tissue-specific transgene expression, genome integration site independent expression, copy-number dependent expression

Saccharomyces

when galactose is the only sugar available, wt yeast induce transcription of 4 enzyme-producing genes, GAL1, GAL2, GAL7, and GAL10

Upstream activator sequence

Enhancer element associated w/ each gene in this pathway

Gal4

A regulatory activator protein encoded by the GAL4 gene (not shown here)

Gal4 to Gal80

Blocks transactivation domain so no transcription

Gal80

When galactose is present, galactose and Gal3 encoded by the GAL3 gene (constitutively expressed) bind to this releases Gal4, freeing the DNA binding domain of Gal4 to recognized and bind to the UASG sites

Gal4 binding to UASG

Leads to formation of a multiprotein complex called the mediator

Eukaryotic repressors

Inhibits transcription through diff mechanism than those seen in bacteria

Mig1

The protein Mig1 is produced in the presence of glucose and binds a silencer sequence (“negative enhancer”) b/w UASG and the GAL1 promoter

insulator sequences

cis-acting sequences located b/w enhancers and promoters of genes that need to be protected from the action of enhancers

Genomic imprinting

Affects small # of mammalian genes and involves the expression of only one of the inherited alleles of a gene, depending on the parent from which it is inherited

Maternal chromosome

On the maternal chromosome, an enhancer drives expression of H19 and an insulator protein blocks IGF2 expression

Paternal chromosome

On paternal chromosome, methylation inactivates the ICR and blocks H19 expression; the enhancer drives IGF2 expression

Beckwith-Weidemann syndrome

Overgrowth- results when both the maternal and paternal inherited chromosomes display the characteristic expression patterns of the paternally inherited locus (IGF ON)

Russell-Silver syndrome

restricted growth- results if both chromosomes display the typical maternal expression pattern. (IGF OFF)

Heterochromatin

Highly condensed, usually inactive transcriptionally; dark stained regions of chromosomes

Euchromatin

Relaxed, usually active transcriptionally, lightly stained regions of chromosomes

Su (var) mutations

Mutations restrict heterochromatin spread or interfere w/ its formation; this suppresses mutant phenotype so more wt seen

E (var) mutations

Mutations enhance mt phenotypes by encouraging spread of heterochromatin

HMT

Histone methyl transferase

Some regulatory sequences

Regulatory sequences aren’t tightly bound by histones so that regulatory proteins can easily access the DNA sequences

Chromatin remodelers

Change the distribution or composition of histones

Chromatin modifiers

Can enzymatically modify histones by adding or removing acetyl or methyl groups to particular amino acid residues, most often on lysine of histones

Housekeeping genes

Have “open” promoters w/ a nucleosome-depleted region (NDR)

Covered promoters

Characterize genes whose transcription regulated; transcription blocked until nucleosomes displaced or removed from the promoter

Pioneer factors bind to DNA and open heterochromatin by recruiting chromatin modifier and remodeling complexes

Activation of transcription at closed promoters

DNase 1 hypersensitive sites

Regions that are free of nucleosomes (or have unstable nucleosomes) and therefore are accessible by DNase I

Chromatin remodeling

Modifications that reposition nucleosomes so as to open or close promoters and other regulatory sequences

Methylases and acetylases

Chemical group that is added to chromatin by writer enzymes

Demethylases and deacetylases

Chemical group that is removed from chromatin by eraser enzymes

Readers

Proteins that recognize modified histones

Histone code

Combo of histone modifications; no one mark is sufficient to determine expression/repression

HATs

Are recruited by activators and add acetyl groups to pos charged residues in the N-terminal histone tails; act as writers

HDACs

Are recruited by repressors; these act as erasers and acetyl groups are removed by

Histone methyltransferases (HMTs)=writers

Methyl groups are added to N-terminal histone tails by

Polycomb group (PcG) protein

Complexes repress target gene expression by recruiting protein complex that deacetylate (HDAC) methylate (HMT) histones (H3K27-hetrochrom)

Trithorax (Trx) protein

Complexes maintain active gene expression by recruitng protein complexes that acetylate (HAT) and demethylate (HDMT) histones; (H3K27-euchrom)

Epigenetic modifications

Alter chromatin structure, don’t alter DNA sequence, are transmissible during cell division, and they are reversible

long noncoding rNAs (IncRNAs)

Long RNAs that lack substantial open reading frames

RNA interference (RNAi)

Double stranded (dsRNA) silences gene expression transcriptionally or post- transcriptionally

Dicer

An RNAase III enzyme is required for this process in flies, worms, and mammals which cuts dsRNA into 21-25 bp siRNA or miRNA segments

CRISPR-cas

Acts as a defense mechanism against invading nucleic acids

Transposable genetic elements

Transmissible genetic elements that move within the genome by an enzyme-driven process transposition

DNA transposons

Transpose as DNA sequences and may be replicative or non-replicative

Retrotransposons

Are composed of DNA but transpose through an RNA intermediate

Transposase

The staggered cuts are made by this, produced by the transposable element

Insertion sequences

IS (800– 2000 bp of DNA) are simple transposable elements containing terminal inverted repeats (IR) surrounding a gene encoding transposase

Composite transposons

(10,000 bp in length) carry a transposase gene, two flanking IS elements, and one or more additional genes

Eukaryotic transposable elements

Eukaryotic transposable elements abundant and highly varied with two types: short sequences with inverted repeats and retrotransposons

Hybrid dysgenesis

Hybrid element is produced in which sterility occurs in F1 when lab strain females called M cytotype are mated to P- strain males