BIOL_SCI 201: Gene Regulation & Molecular Biology

Exam 4

transcription

making RNA from DNA

translation

making protein from mRNA

transcription factor

protein that regulates gene transcription by binding DNA

general transcription factor

required for all genes transcribed by RNA polymerase II (eukaryotes)

mediator

acts as molecular bridge between transcription factors - especially activators bound to enhancers - and RNA polymerase II, helping to initiate and regulate transcription (eukaryotes)

master regulator

key transcription factor controlling cell identity (eukaryotes)

activator

enhances transcription

repressor

inhibits transcription

DNA binding domain

region of protein that binds DNA

activation domain

part of a transcription factor that typically binds with Mediator to promote transcription (eukaryotes)

repression

reduction or inhibition of gene expression

expression

process of producing RNA or protein from a gene

gene

segment of DNA encoding a functional product, usually a protein

regulatory sequence

DNA elements controlling gene expression like enhancers and promoters

promoter

DNA region where RNA polymerase binds to initiate transcription

core promoter

essential region (TATA box in eukaryotes and -35/-10 in prokaryotes) for transcription start

proximal promoter

near core region where transcription factors bind upstream of core promoter

enhancer

distant DNA sequence several thousands base pairs from core promoter that boosts transcription (eukaryotes)

consensus logo

visual showing conserved nucleotide residues that a specific regulatory factor likes to bind with

operon (P)

group of genes transcribed together from 1 promoter region (lac, trp operons)

operator (P)

DNA site where repressors bind to block transcription

LacI (lac operon component)

repressor protein blocking transcription

LacO (lac operon component)

DNA site bound by LacI

Trp repressor

binds operator in presence of tryptophan to inhibit transcription

epigenetics (E)

heritable gene expression changes without DNA sequence alteration

chromatin structure

arrangement of DNA and histones affecting gene accessibility

condense (chromatin structure)

tightly packed, transcriptionally inactive

decondense (chromatin structure)

loosely packed, transcriptionally active

heterochromatin (chromatin structure)

tightly packed, transcriptionally inactive regions of chromatin

euchromatin (chromatin structure)

loosely packed, transcriptionally active regions of chromatin

histone acetylation

covalent attachment of acetyl group to lysine on histone tail, neutralizes positive charge on the lysine to promote euchromatin

histone methylation

covalent attachment of methyl group to amino acids on histone tail, activates or represses depending on site

DNA methylation

typically represses gene expression

HAT (histone acetyltransferase)

enzyme that acetylates/activates histones

HDAC (histone deacetylase)

enzyme that removes acetyl groups to repress gene expression

chromatin remodeling factor

alters nucleosome positioning to control DNA accessibility

differentiation

process by which cells become specialized

totipotent

can form all cell types

pluripotent

can become any cell of the body but cannot form an entire organism

multipotent

can become multiple cell types within a lineage

unipotent

can become one specific cell type

RNAi

mechanism using small RNAs to silence gene expression

miRNA (microRNA)

endogenous (internally produced) small RNA that suppresses gene expression post-transcriptionally

siRNA (small interfering RNA)

short double-stranded RNA used to knock down genes

RISC (RNA-induced silencing complex)

uses miRNA/siRNA to degrade or inhibit mRNA

degradation

breakdown of RNA/proteins

cleavage

specific cutting of RNA or protein molecules

promoter reporter

reporter gene like GFP under control of specific promoter

GFP

green fluorescent protein used as visual marker for gene expression

fusion protein

hybrid protein made by combining sequences from 2 different genes

overexpress

artificially increasing gene expression

knockdown

partial suppression of gene expression

knockout

complete inactivation of a gene

RNA-Seq

high-thorough sequencing of RNA to analyze expression levels

sequence reads

DNA sequences generated by sequencing; reads are aligned to a genome and number of reads corresponds to amount of expression detected for that region of the genome (can be used to determine amount of mRNA produced or the proportion of isoforms depending on specific introns having more or less reads)

RT-qPCR

technique to quantify RNA by reverse transcription followed by PCR

in situ hybridization

detects RNA/DNA in tissues using labeled probes

CRISPR-Cas9

tool for targeted DNA editing using guide RNA and Cas9 nuclease

disrupt

interfere with gene function - often via mutation or delection

NHEJ (non-homologous end joining)

error-prone DNA repair mechanism for double helix breaks

HDR (homology-directed repair)

precise repair for double helix breaks using homologous template

homologous recombination

genetic exchange between similar DNA sequences typically used to knockout a gene by replacing the coding sequence with a selectable marker

plasmid/vector

DNA molecule used to transfer genes into cells

mutation

any change in the DNA sequence that could result in change to a protein and its function

loss of function mutation

mutation of the gene results in the loss of activity of resulting protein (protein no longer functions correctly)

indels

insertions or deletions of DNA bases

replace coding sequence

substituting a gene’s coding region with another for reporting or selection

construct

specifically designed piece of DNA used in genetic engineering to introduce specific changes into a target gene within the genome

G418

antibiotic selecting cells expressing NeoR

ganciclovir

drug killing cells with tkHSV gene

NeoR

gene conferring resistance to G418

tkHSV

gene rendering cells sensitive to ganciclovir

select/selection

choosing cells that have undergone desired genetic changes

isolate

extract or separate specific cells or molecules

target

gene, RNA, protein being studied or modified

upregulation

increased gene expression

downregulation

decreased gene expression

transiently

temporarily expressed or active

permanent

long-term or irreversible change

globally

refers to changes that affect a large number of genes across the genome rather than being limited to a specific gene