Gene Expression and Regulation Flashcards
Inhibitors to know!!!
process by which an enzyme system converts the genetic information in dsDNA into an RNA strand with a complementary base sequence
trancription
RNA synthesis does not require
a primer
mRNA in eukaryotes is synthesized by
RNA polymerase II
two or more upstream activating sequences
rho-independent terminators:
have a self-complementary region that forms a hairpin
have a conserved string of three A residues that are transcribed into U residues near the 3′ end of the hairpin
an array of proteins that work with Pol II form the active transcription complex
transcription factors
those required at every Pol II promoter
general transcription factors
Transcription factors are: (specificity)
tissue specific
gene specific
Enhancer Sequences
- may be long distances upstream or downstream of the start site
- must be on the same strand as the gene
- can be found within introns
- can affect transcription regardless of its orientation
Transcription Factor 3A protein has the motif
Zinc finger protein motif
= responsible for the synthesis of a transcript called pre-ribosomal RNA (or pre-rRNA)
RNA polymerase I (Pol I)
pre-rRNA contains the precursor for the 18S, 5.8S, and 28S rRNAs
RNA polymerase II needs to have
TATA box binding protein and TFIID to transcribe
In Eukaryotes, the TATA box is necessary but not sufficient for strong promoter activity. Additional elements are located between -40 and -110
Termination of transcription in eukaryotes requires a
poly-a-addition signal (AAUAAA)
Processes and Possible Regulation
nucleotidal transferase
does not require a template
Always present in constant amounts regardless of the metabolic state of the organism
Constitutive enzymes
Usually found in low amounts and can increase when their substrates are present
induced enzymes
Enzymes are not synthesized if not needed
Enzyme repression
Describes the complete regulatory unit of a set of cluster genes; it includes adjacent structural genes that code for related enzymes or associated proteins and control element
operon
genes for products that are required at all times and are expressed continuously
examples: enzymes of central metabolic pathways
cellular concentrations of the proteins encoded vary
housekeeping genes
= expression of a gene at approximately constant levels
constitutive gene expression
The RNA polymerase-promoter interaction strongly influences the rate of
transcription initiation
The lac Operon is subject to ________ regulation
negative
lactose (lac) operon includes the genes for:
- β-galactosidase (Z)
- galactoside permease (Y)
- thiogalactoside transacetylase (A) = modifies toxic galactosides to facilitate their removal
the lac operon is repressed in the absence of lactose
repression is not absolute
an inducer of the lac operon
allolactose, an isomer of lactose
binding of allolactose to the Lac repressor causes a conformational change and dissociation
results in expression of lac operon genes
phosphodiesterase cleaves
cAMP in the presense of glucose
process in which a particular exon may or may not be incorporated into the mature mRNA transcript
alternative splicing
occurs in > 95% of human genes
REQUIREMENTS FOR RNA BIOSYNTHESIS
- A double-stranded (ds) DNA template
- DNA-dependent RNA polymerases
- 4 nucleoside triphosphates
- Mg++ for optimal activity
- Transcription occurs in the 5’à3’ direction
- Only 1 strand of the DNA molecule serves as the template in a given region
NO PRIMER NEEDED UNLIKE DNA SYNTHESIS
Prokaryotic Subunits of RNA Polymerase from E. coli
- Subunit # Role
- α 2 Binds regulatory sequences
- β 1 Forms phosphodiester bonds
- β’ 1 Binds DNA template
- w (omega)1 conformation maintenance & recruitment of the b’ subunit
- σ70 1 Recognizes promoter & initiates synthesis
- The core enzyme is composed of all the subunits except the sigma subunit.
- The holoenzyme is composed of all the subunits, including the sigma subunit.
Eukaryotic RNA Polymerases
Initiation begins with the recognition of the _______ by the _______component of _______
TATA box; TATA box binding protein (TBP); TFIID
Differences between transcription in eukaryotes and prokaryotes
- One type of RNA polymerase in prokaryotes and three in eukaryotes
- Prokaryotes make POLYCISTRONIC mRNA and eukaryotes make MONOCISTRONIC mRNA.
- Prokaryotic mRNA undergoes very little modifications while eukaryotic mRNA undergoes multiple modifications.
- This is because mRNA from prokaryotes can be co-transcriptionally translated while eukaryotic mRNA cannot and need modification to increase molecular stability as well as protect against degradation.
The base sequence of an intron begins with _______ and the exon ends with _______.
GU; AG
Important internal site located 20 to 50 nucleotides upstream of the 3’ splice site in introns
branch site
Amino acids are activated and attached to their corresponding tRNA by
aminoacyl-tRNA synthetase
Formation of aminoacyl-transfer RNAs ( tRNAs)
- An amino acid first reacts with adenosine triphosphate (ATP), forming an activated amino acid (aminoacyl-adenosine monophosphate [AMP]) and pyrophosphate, which is cleaved to two inorganic phosphates (Pi).
- The aminoacyl-AMP then forms an ester with the 20-or30-hydroxyl of a tRNA specific for that amino acid, producing an aminoacyl-tRNA and AMP.
- Once an amino acid is attached to a tRNA, insertion of the amino acid into a growing polypeptide chain depends on the codon–anticodon interaction
Steps of Translation
- Initiation: Involves the assembly of an active ribosomal complex
- Elongation & Translocation: New amino acids are brought to the ribosome according to the codon sequence and translocated to a growing polypeptide chain
- Termination: At certain “stop” codons, translation is ended.
- Release : The newly formed polypeptide is released
Note that translation occurs from the amino terminal to the carboxy terminal and mRNA is read in the 5’ to 3’ direction
40s ribosomal subunit associates with eIF3 to physically block 40s & 60s subunit association
anti-association factor
