Topic 7-1 Flashcards
under the microscope, DNA molecules undergoing transcription exhibit:
Christmas-tree-like structures
what are the RNA subunits?
rNTPs (ribonucleoside triphosphates)
what are the DNA subunits?
dNTPs (deoxyribonucleoside triphosphates)
what is the difference between RNA sugars and DNA sugars?
RNA has a hydroxyl group on the 2’ carbon
why is RNA more unstable than DNA?
bc of the 2’OH
what is the difference between RNA bases and DNA bases?
RNA contains uracil, adn DNA contains thymine
true or false: RNA has no secondary structure
false. RNA is single stranded but can contain many types of secondary structure
a flexible secondary shape can allow some RNA to act as:
ribozymes/ catalytic RNA
what are the four main functions of ribozymes?
1) cut/edit out own sequence
2) connect RNA olecules together
3) replicate other RNA
4) catalyze peptide bond formation b/w a.a.
there are many classes of RNA, what are the four that we focus on in this class?
- ribosomal RNA (rRNA)
- messenger RNA (mRNA)
- transfer RNA (tRNA)
- CRISPR RNA (crRNA)
what is transcription?
the synthesis of an RNA molecule from a DNA template
what are the three major components required for RNA transcription?
- a DNA template
- ribonucleotide triphosphates
- the transcription apparatus (proteins necessary for catalysing the synthesis of RNA)
unlike replication, transcription is _________ in what DNA sequences are transcribed
highly selective
during transcription, RNA molecules are synthesized in the _______ direction, and is both _______ and _______ to the DNA template strand
5’ –> 3’, complementary, antiparallel
a stretch of DNA encoding RNA molecule and sequences necessary for transcription (promoter, RNA coding region, terminator)
transcriptional unit
- contains sequences that the transcriptional apparatus recognize and bind
- dictates which DNA strand is the template strand and transcription start site
these are characteristics of the:
promoter
- contains sequences that signal to end transcription
- usually part of the RNA coding sequence and resulting transcript
these are characteristics of the:
terminator
the first nucleotide transcribed is numbered ____ and numbering ___ downstream. nucleotides upstream of the start site are numbered ___
+1, increases, negative
RNA polymerase and array of accessory proteins
transcriptional apparatus
a large multimeric enzyme (contains several polypeptide chains)
RNA polymerase
the core enzyme of RNA polymerase contains these five subunits:
- alpha (2)
- beta
- beta prime
- omega
what is the function of the core enzyme of RNA polymerase?
catalyzes addition of rNTPs, thus elongation of RNA molecule
different accessory proteins regulate:
special transcriptional functions
what are the three main transcriptional stages?
1) initiation
2) elongation
3) termination
transcriptional appratus that assembles on promoter and begins RNA synthesis
initiation
what are the four main steps of initiation?
1) promoter recognition/ binding
2) formation of transcription bubble
3) creation of first bonds between rNTPs
4) escape of transcriptional apparatus from promoter
critical step for regulating selective gene expression (when and how frequent)
promoter recognition and binding
the promoter sequence encodes three key pieces of information:
- where to start
- which is the template strand
- which direction to move
set of most commonly encountered nucleotides among sequences with considerable similarity or consensus. similar location w/ respect to start site
consensus sequence
most bacterial promoters have two:
consenseus sequences
the pribnow (TATAAT) box
located -10 bp upstream of the start site
TTGACA promoter
located -35 bp upstream of the start site
a bacterial accessory protein that binds to the core RNA polymerase (forming the holoenzyme)
sigma factor
stabilizes polymerase binding to proper promoter start sites ensuring initiation of gene transcription
sigma factor
true or false: the signma factor is required only for promoter binding and initiation and detaches after a few RNA nucleotides have been added
true
the holoenzyme changes structure leading to tighter binding and unwinding of DNA to form the:
transcription bubble (nucleotides -12 to +2)
as subsequent rNTPs are added to the RNA molecule, ______ are cleaved in the rxn
two phosphates
polymerase changes shape again such that it “lets loose” of consenses sequences in promoter and is free to:
move and transcribe downstream
what are the three main processes involved in elongation?
- unwinding DNA at downstream edge of bubble
- adding nucleotides to RNA molecule
- rewinding DNA at upstream edge
DNA _______ ahead of bubble, negative _______ behind bubble
supercoiling, supercoiling
likely relieve supercoiling
topoisomerases
a “pause” in transcription caused by backbacking, where:
polymerase slides backward along the DNA template
transcriptional pausing is important for:
proofreading
what are the three main steps of termination?
1) RNA polmerase stops RNA synthesis
2) RNA molecule is released from polymerase and dissociates from DNA
3) polymerase detaches from DNA
what are the two major types of termination mechanisms?
rho-dependent and rho-independent
genes with the rho-dependent terminator have two features:
- RNA sequence where rho binds, called the Rut (rho utilization) site
- terminator sequence causes polymerase to pause (allows rho to advance towards transcription site)
the rho protein has ________ activitiy that unwinds the RNA:DNA hybrid thus terminating transcription
helicase
genes with the rho-independent terminator have two features:
- inverted repeats - two sections of terminator have complementary (inverted strands)
- string of ‘A’s in the DNA template follows last inverted repreat (string of ‘U’s in RNA)
in rho-independent termination, the string of uracil causes polymerase to pause, allowing ________ to form
the inverted repeat hairpin
