Unit3 Flashcards
core enzyme
The portion of RNA polymerase that catalyzes RNA synthesis.
holoenzyme
The complete RNA polymerase enzyme, consisting of the core enzyme and a sigma factor.
sigma factor
A protein that helps RNA polymerase recognize the promoter sequence and initiate transcription.
transcription factor
A protein that binds to DNA and regulates gene expression.
terminator
A DNA sequence that signals the end of transcription.
promoter
A DNA sequence that signals the start of transcription.
What components are necessary for transcription to end?
A terminator sequence in the DNA and specific RNA sequences that form a hairpin structure.
inducible
A gene or operon whose expression is increased in response to a specific stimulus.
open reading frame (ORF)
A sequence of DNA or RNA that can be translated into a protein.
monocistronic
Describing mRNA that encodes a single protein.
polycistronic
Describing mRNA that encodes multiple proteins.
operon operator
A DNA sequence within the operon that binds to a repressor protein, inhibiting transcription.
repressor
A protein that binds to an operator sequence, inhibiting transcription.
inducer
A molecule that binds to a repressor protein, causing it to release from the operator and allowing transcription to proceed.
constitutive gene expression
The continuous expression of a gene or operon.
beta-galactosidase
An enzyme that breaks down lactose into glucose and galactose.
permease
A protein that transports lactose into the cell.
transacetylase
An enzyme involved in the metabolism of lactose.
operator
A DNA sequence within the operon that binds to a repressor protein, inhibiting transcription.
cAMP
Cyclic adenosine monophosphate, a second messenger molecule that activates the CAP protein.
CAP site
A DNA sequence within the promoter region of the lac operon that binds to the CAP-cAMP complex, enhancing transcription.
How does the presence of glucose regulate the lac operon?
Glucose inhibits the production of cAMP, which reduces the activity of the CAP-cAMP complex. This leads to decreased transcription of the lac operon.
trp attenuation
A regulatory mechanism in bacteria that controls the expression of genes involved in tryptophan biosynthesis. It involves premature termination of transcription.
attenuator
A DNA sequence within the leader region of an operon that can form alternative stem-loop structures, affecting transcription termination.
tryptophan
An amino acid that serves as a corepressor in the trp operon.
repressor
A protein that binds to an operator sequence, inhibiting transcription.
2:3 stem loop forms
A stem-loop structure that forms in the leader mRNA when tryptophan levels are high, leading to transcription termination.
poly U
A stretch of uracil nucleotides in the leader mRNA that follows the 2:3 stem loop, contributing to the stability of the termination structure.
What dictates which stem loops form?
The availability of tryptophan-charged tRNAs and the rate of ribosome movement along the leader mRNA.
trp-charged tRNAs
When tryptophan levels are high, there are more trp-charged tRNAs available, which allows the ribosome to move quickly through the leader region, promoting the formation of the 2:3 stem loop and transcription termination.
RNA polymerase
The enzyme that synthesizes RNA from a DNA template.
reporter assay
An experimental technique used to study gene expression by linking a regulatory sequence of interest to a reporter gene, whose product is easily detectable.
transfection
The introduction of foreign genetic material into a cell.
cDNA
Complementary DNA, a DNA copy of mRNA.
in vitro
Experiments performed outside of a living organism, often in a test tube or petri dish.
in vivo
Experiments performed within a living organism.
transcriptional regulation
The control of gene expression at the level of transcription.
reporter gene
A gene encoding a protein product that is easily detectable, often used in reporter assays.
eukaryotic
Organisms whose cells contain a nucleus and other membrane-bound organelles.
prokaryotic
Organisms whose cells lack a nucleus and other membrane-bound organelles.
RNA polymerase
An enzyme that synthesizes RNA molecules from a DNA template.
gene
A segment of DNA that encodes a specific protein or RNA molecule.
nucleus
A membrane-bound organelle in eukaryotic cells that contains the genetic material.
mRNA
Messenger RNA, a type of RNA that carries genetic information from DNA to ribosomes for protein synthesis.
cytoplasm
The fluid-filled region of a cell that surrounds the nucleus and contains organelles.
nucleosomes
Basic units of chromatin, consisting of DNA wrapped around histone proteins.
chromatin
The complex of DNA and proteins that makes up chromosomes.
RNA polymerase II
The main RNA polymerase responsible for transcribing protein-coding genes in eukaryotes.
tRNA
Transfer RNA, a type of RNA that carries amino acids to the ribosome for protein synthesis.
sigma factor
A protein that binds to RNA polymerase and helps it recognize promoter sequences in bacteria.
holoenzyme
A complex of proteins, including RNA polymerase and sigma factor, that initiates transcription in bacteria.
transcription factors
Proteins that bind to DNA and regulate the rate of transcription.
5’ capping
The addition of a modified guanine nucleotide to the 5’ end of mRNA.
3’ poly-A tail addition
The addition of a string of adenine nucleotides to the 3’ end of mRNA.
splicing
The removal of introns and the joining of exons in pre-mRNA.
alternative splicing
A process that allows different protein isoforms to be produced from a single gene.
regulatory region
A DNA sequence that controls the expression of a gene.
promoter
A DNA sequence that signals the start of transcription.
enhancer
A DNA sequence that can increase the rate of transcription.
operator
A DNA sequence that can bind to a repressor protein, inhibiting transcription.
bacteria
Single-celled prokaryotic organisms.
protein
A large molecule composed of amino acids.
luciferase
An enzyme that produces light.
luminometer
A device used to measure luminescence.
green fluorescent protein
A protein that emits green light when exposed to blue light.
beta-galactosidase
An enzyme that breaks down lactose.
ribosomes
Cellular structures responsible for protein synthesis.
tRNA
Transfer RNA, a type of RNA that carries amino acids to the ribosome for protein synthesis.
translational control
The regulation of gene expression at the level of translation.
Northern blot
A technique used to detect specific RNA molecules.
in situ hybridization
A technique used to detect specific RNA or DNA sequences in cells or tissues.
transfection
The introduction of foreign genetic material into a cell.
basal transcription
The minimum level of transcription required for gene expression.
core promoter
The DNA sequence that is directly recognized by RNA polymerase II.
TATA box
A DNA sequence found in many eukaryotic promoters.
initiator sequence
A DNA sequence that can function as a core promoter element in the absence of a TATA box.
primer extension
A technique used to determine the transcription start site of a gene.
RNA polymerase II basal transcription complex
A complex of proteins that assembles at the core promoter and initiates transcription.
general transcription factors
Proteins that bind to the core promoter and help RNA polymerase II initiate transcription.
primer extension assay
A technique used to determine the transcription start site of a gene.
TATA-Binding Protein (TBP)
A protein that binds to the TATA box and recruits other transcription factors.
pyrimidine
A nitrogenous base, such as cytosine or thymine, that contains a single ring.
downstream promoter element
A DNA sequence located downstream of the core promoter that can influence transcription.
reverse transcriptase
An enzyme that synthesizes DNA from an RNA template.
helicase
An enzyme that unwinds DNA.
kinase
An enzyme that adds phosphate groups to proteins.
TFIID
A general transcription factor that contains TBP.
TFIIA
A general transcription factor that stabilizes the binding of TFIID to DNA.
TFIIB
A general transcription factor that recruits RNA polymerase II to the promoter.
TFIIF
A general transcription factor that helps RNA polymerase II bind to the promoter and initiate transcription.
TFIIE
A general transcription factor that helps recruit TFIIH to the promoter.
TFIIH
A general transcription factor that unwinds DNA and phosphorylates RNA polymerase II.
RNA polymerase II C-terminal domain (CTD)
A domain on RNA polymerase II that is phosphorylated during transcription initiation and elongation.
amino acid
The building blocks of proteins.
helix-turn-helix
A common DNA-binding motif found in many transcription factors.
zinc fingers
A DNA-binding motif that uses zinc ions to coordinate protein structure.
leucine zippers
A DNA-binding motif that uses leucine residues to form a dimerization interface.
helix-loop-helix
A DNA-binding motif that uses two alpha helices separated by a loop.
peptide chain
A chain of amino acids linked together by peptide bonds.
holotrimer
A protein complex composed of three subunits.
DNA binding domain
A protein domain that recognizes and binds to specific DNA sequences.
Enhancer
A regulatory DNA sequence that can be located far from the gene it regulates and can increase gene expression.
Activation domain
A protein domain that interacts with other proteins (e.g., co-activators) to stimulate transcription.
Regulatory promoter
A promoter that contains binding sites for transcription factors that regulate gene expression.
Activator
A transcription factor that binds to an enhancer or regulatory promoter to increase gene expression.
Co-activator
A protein that interacts with an activator to enhance its ability to stimulate transcription.
Mediator complex
A large protein complex that bridges the interaction between transcription factors and RNA polymerase II, facilitating the initiation of transcription.
Promoter deletions
A technique used to identify the core promoter elements by progressively deleting regions of the promoter and measuring the effect on gene expression.
Linker scanning mutagenesis
A technique used to identify regulatory elements within a DNA sequence by systematically replacing short stretches of DNA with a linker sequence and measuring the effect on gene expression.
Heterochromatin
Tightly packed form of chromatin that is transcriptionally inactive.
Euchromatin
Loosely packed form of chromatin that is transcriptionally active.
Chromatin Remodeling
Process of altering chromatin structure to regulate gene expression.
Nucleosome Modification
Chemical modifications of histones within nucleosomes to affect gene expression.
Acetylation
Addition of an acetyl group to a histone, typically leading to increased gene expression.
Methylation
Addition of a methyl group to a histone or DNA, typically leading to decreased gene expression.
Epigenetics
Study of heritable changes in gene expression that do not involve changes to the underlying DNA sequence.
Fusion Protein
Protein created by combining two or more genes or protein fragments.
Yeast-Two Hybrid Assay
Technique used to identify protein-protein interactions.
Hyperacetylation
Increased level of acetylation on histones, associated with increased gene expression.
Hypoacetylation
Decreased level of acetylation on histones, associated with decreased gene expression.
Chimeric Proteins
Proteins composed of parts from different sources, often used in research and biotechnology.
RNA Splicing
Process of removing introns from pre-mRNA and joining exons together to form mature mRNA.
Alternative Splicing
Process of producing different mRNA transcripts from a single gene by splicing exons in different combinations.
Oligo(dT) Column
Column chromatography technique used to isolate mRNA from a mixture of nucleic acids.
Capping
Addition of a modified guanine nucleotide to the 5’ end of pre-mRNA to protect it from degradation and enhance translation efficiency.
Polyadenylation
Addition of a poly(A) tail to the 3’ end of pre-mRNA to protect it from degradation and enhance translation efficiency.
mRNA Processing
Series of modifications made to pre-mRNA to produce mature mRNA, including capping, polyadenylation, and splicing.
Spliceosome
A large complex of proteins and RNA molecules that removes introns from pre-mRNA.
Self-splicing
The ability of some RNA molecules to catalyze their own splicing without the need for additional proteins.
Transesterification
A chemical reaction that involves the exchange of an ester group between two molecules. In splicing, it involves the breaking and forming of phosphodiester bonds.
Branchpoint
A specific nucleotide sequence within an intron that is essential for the splicing reaction.
snRNA (small nuclear RNA)
A class of small RNA molecules that form part of the spliceosome and play a crucial role in splicing.
snRNP (small nuclear ribonucleoprotein)
A complex of snRNA and proteins that functions as a unit in the spliceosome.
Intron lariat
A loop-shaped structure formed during splicing, containing the excised intron.
U6
A specific snRNA that plays a critical role in catalysis during splicing.
U2
A specific snRNA that recognizes the branchpoint sequence and helps to form the spliceosome.
U1
A specific snRNA that recognizes the 5’ splice site of an intron.
U5
A specific snRNA that interacts with both the 5’ and 3’ splice sites, bringing them together for splicing.
UTR (Untranslated Region)
A region of mRNA that is transcribed but not translated into protein. UTRs can influence mRNA stability, localization, and translation efficiency.
Polyadenylation signal
A specific sequence of nucleotides in mRNA that signals the addition of a poly(A) tail.
Polyadenylation site
The site in the mRNA where the poly(A) tail is added.
RNA interference (RNAi)
A biological process in which RNA molecules inhibit gene expression by targeting mRNA for degradation or translational repression.
miRNA (microRNA)
A small non-coding RNA molecule that regulates gene expression by binding to the 3’ UTR of target mRNAs.
shRNA (short hairpin RNA)
An artificial RNA molecule with a hairpin structure that can be processed by cellular machinery to produce siRNA.
siRNA (small interfering RNA)
A small double-stranded RNA molecule that triggers RNA interference by targeting specific mRNA sequences for degradation.
Guide strand
The strand of siRNA or miRNA that directs the RNA-induced silencing complex (RISC) to the target mRNA.
DICER
An enzyme that cleaves double-stranded RNA into small interfering RNA (siRNA) or microRNA (miRNA).
R2D2
A protein that assists DICER in processing double-stranded RNA.
Argonaute
A protein that is a key component of the RNA-induced silencing complex (RISC).
RISC (RNA-induced silencing complex)
A protein complex that binds to siRNA or miRNA and cleaves target mRNA or represses translation.
Transfer RNA (tRNA)
A type of RNA molecule that transfers amino acids to the ribosome during protein synthesis. It has a specific anticodon that recognizes a codon on mRNA.
Ribosomal RNA (rRNA)
A type of RNA molecule that forms the structural and catalytic core of the ribosome, the cellular machinery responsible for protein synthesis.
Peptidyl transferase
An enzymatic activity of the ribosome that catalyzes the formation of peptide bonds between amino acids during protein synthesis. 1
Charged tRNA
A tRNA molecule that is covalently linked to an amino acid.
RNA processing
A series of modifications that RNA molecules undergo after transcription to produce mature, functional RNA molecules.
Codon
A sequence of three nucleotides in mRNA that codes for a specific amino acid or a stop signal.
Anticodon
A sequence of three nucleotides in tRNA that is complementary to a codon in mRNA.
pre-rRNA
A precursor RNA molecule that is processed to form mature ribosomal RNA.
snoRNA (small nucleolar RNA)
A small RNA molecule that guides the modification of other RNAs, such as rRNA and tRNA.
snoRNP (small nucleolar ribonucleoprotein)
A complex of snoRNA and proteins that carries out RNA modification.
Ribozyme
An RNA molecule that can catalyze chemical reactions, such as peptide bond formation in the ribosome.
