Chapter 10 - Expression of Genetic Information Flashcards
RNA Polymerase
transcribes DNA into RNA
Which polymerase requires a primer with a free 3’-OH group to initiate chain elongation?
DNA polymerase
Pribnow Box (prokaryotic)
TATAAT (-10 region) and TTGACA (-35 region)
Hogness Box (eukaryotic)
TATA box (-25 region) and CAAT box (-75 region) upstream from the +1 site; the CAAT box may or may not be present
What are some general stop signals?
GC-rich region followed by an AT-rich region on the DNA template
What is unique about the terminator sequence of E. coli?
to end protein synthesis, there is a base-paired hairpin sequence on the newly synthesized RNA strand
Base-Paired Hairpin Sequence
region of RNA sequence that’s rich in G and C, then a sequence of four or more U residues (poly-U tail)
Rho-independent termination
once hairpin pairing occurs, RNA polymerase pauses; uracil and adenine that are still annealed to each other (RNA-DNA hybrid) are unstable and RNA chain will dissociate from RNA polymerase and DNA duplex
Rho-dependent termination
involves rho protein, a hexameric protein of 46 kd subunits and has ATPase activity to allow it to specifically bind newly synthesized single-stranded RNA and pull itself towards the replication bubble where it will dislodge RNA polymerase from the DNA template
RNA Polymerase I
transcribe rRNA
RNA polymerase II
transcribes mRNA
RNA polymerase III
transcribes tRNA
RNA polymerase holoenzyme
four subunits alpha2, Beta, Beta’, and sigma
What is the accuracy of replication and transcription?
DNA polymerase enzymes edit and there are repair enzymes; roughly 10^10 bases will be replicated before an error is made that is not caught. RNA polymerase does not edit and do not have repair systems, so errors occur one in every 10^4 or 10^5 transcribed bases
What inhibits RNA polymerase?
actinomycin D (binds to double stranded DNA and prevents RNA polymerase from using it as a template for transcription)
Enhancer Sequences
typically far away from promoter region, can be up or downstream, can even be within gene itself
What is the purpose of 5’ capping of RNA?`
protects 5’ end from degradation and enhances stability of RNA molecule
What is the purpose of 3’ polyadenylation of RNA?
250 adenine residues from ATP are added to the free 3’ end of the RNA polymer to form poly-A tail to protect from nucleases and phosphatases
Shine-Dalgarno Sequence
about 10 nucleotides upstream from initiating codon is this purine-rich sequence of bases; responsible fro binding mRNA to the 16s subunit
What is required to make a protein?
20 aminoacyl-tRNAs, each attached to correct tRNA, mRNA that contains codons that specify protein sequence desired, ribosomes, initiation factors, elongation and termination factors, and GTP as an energy source
Puromycin
binds at the A-site and acts as an analog of an aminoacyl-tRNA, thus preventing other aminoacyl-tRNAs from entering the A-site
Helicase
catalyze unwinding
How can proofreading via 3’ –> 5’ exonuclease activity occur?
DNA polymerase I and III have 3’–>5’ exonuclease activity
DNA Ligase
catalyze the formation of a phosphodiester bond between 3’ hydroxyl at one end of replaced DNA strand and 5’-phosphate of previously synthesized DNA strand
Mutagens
external agents that can cause mutations and also increase the possibility of mutations occurring
Base Analog Mutagen
can easily substitute for a naturally occurring base in DNA like 5-bromouracil replacing thymine
Chemical Mutagen
Nitrous acid (HNO2) can cause deamination of cytosine to uracil: a transition mutation occurs
Ultraviolet (UV) Radiation Mutagens
if two pyrimidine residues like thymine are adjacent to each other, energy in UV radiation (about 260 nm) can link them together; thymine dimers inhibit DNA replication
Restriction Enzymes (Restriction Endonucleases)
recognize specific sequences in DNA polymers and cleave that DNA at those sites
