L2 Readings Flashcards
can cells synthesize a large number of protein from from a single gene? how long does it take and why?
how about the efficiency of protein production
yes
many RNA copies can be made from the same gene and every RNA copy makes the same protein molecules.
- the almost immediate separation of the RNA strand from the DNA as it synthesized means that many RNA copies can be made from the same gene in
a short time, with the synthesis of additional RNA molecules being started before the previous RNA molecules are completed
importantly henes can be transcribed and translated at different efficiencies, making lots of one protein and little of another
what is different between RNA and DNA structure
DNA is a double helix
RNA is single stranded and thus can fold up into a particular 3D shape through repulsion and attraction of base pairs – this helps the RNA form precise structural and catalytic functions
how does transcription go
Similar to the process of DNA replication.
- Transcription begins with the opening and unwinding of a small portion of the DNA double helix to expose the bases on each DNA strand.
- One of the two strands of the DNA double helix then acts as a template for the synthesis of an RNA molecule.
- As in DNA replication, the nucleotide sequence of the RNA chain is determined by the complementary base-pairing between incoming nucleotides (ATGC –> AUGC)
- The incoming ribonucleotide is covalently linked to the growing RNA chain in an enzymatically catalyzed reaction.
- The RNA chain’s nucleotide sequence is exactly complementary to the strand of DNA used as the template
how does transcription differ from DNA replication
- RNA strand is not h-bonded to the DNA template strand
–> Instead just behind the region where the nucleotides form the RNA chain is displaced and the DNA helix reforms thus single stranded - RNA is copied from a limited region of the DNA thus is much shorter (DNA 250 mill nucleotide pairs long, RNA not more than a few thousands if that)
- RNA polymerase performs transcription - links the nucleotides together using phosphodiester bonds to form a linear chain
how does RNA polymerase move along the DNA
- moves in a stepwise fashion along the DNA
- unwinding the dna helix just ahead of its active site for polymerization to expose a new region of the template strand for complementary base-pairing.
- In this way, the growing RNA chain is extended by one nucleotide at a time in the 5′-to-3′ direction
- The substrates are ribonucleoside triphosphates (ATP, CTP, UTP, and GTP); as in DNA replication, the hydrolysis of high-energy bonds provides the energy needed to drive the reaction forward
how is RNA polymerase different from DNA polymerase (3)
- it catalyzes the linkage between ribonucleotides instead of deoxyribonucleotides
- RNA polymerase can start and RNA chain without a primer unlike DNA polymerase in replication (this is thought to be the case because transcription does not need to be as accurate as DNA replication – does not include genetic information and thus less consequences)
- Unlike DNA polymerases, which make their products in segments that are later stitched together, RNA polymerases are processive; that is, the same RNA polymerase that begins an RNA molecule must finish it without dissociating from the DNA template
can rna polymerase edit its polypeptide chain if the incorrect ribonucleotide is added?
yes
the polymerase can back up, and the active site of the enzyme can perform an excision reaction that resembles the reverse of the polymerization reaction, except that a water molecule replaces the pyrophosphate and a nucleoside monophosphate is released.
what are non-coding RNAs
RNAs that do not code for a protein – RNA that does not get translated into a protein – RNA molecule itself is the final product
what are transcription units and how do they differ in eukaryotes and prokaryotes
- Each transcribed segment of DNA is called a transcription unit.
- In eukaryotes, a transcription unit typically carries the information of just one gene, and thus codes for either a single RNA molecule or a single protein (unless spliced to produce different mRNAs and thus related proteins)
- In bacteria, a set of adjacent genes is often transcribed as a unit; the resulting mRNA molecule thus carries the information for producing several distinct proteins.
what does the sigma factor subunit do with the bacterial RNA polymerase core enzyme?
it associates with the enzyme and assist it in reading the signals in the DNA that tell it where to begin transcribing
what is another name for the sigma factor and the core enzyme for RNA? where does this complex tightly bind and why? after the sigma factor binds what happens – what is it called? then what happens to the strength of the complex bindment?
the RNA polymerase holoenzyme
this complex together tightly adheres to the DNA promoter (sequence of nucleotides indicating the starting point of RNA synthesis) because the sigma factor binds with special edges in this region on the DNA double helix.
after the sigma factor binds to the unpaired bases on one of the strands of the double helix (not the template strand), a short stretch of nucleotides (around 10 nucleotides) on each strand is open. this open region is called the transcription bubble, and is stabilized by the bound sigma factor.
afterwards, the complex only weakly adheres to the DNA and slides along one base pair for every nucleotide added, allowing mRNA to be synthesized by the template DNA strand and polymerase.
what is the scrunching method for RNA synthesis
The first 10 or so nucleotides of RNA are synthesized using a “scrunching” mechanism, in which RNA polymerase remains bound to the promoter and pulls the upstream DNA into its active site, thereby expanding the transcription bubble.
this creates stress so short rna molecules are released periodically to relive stress and force the polymerase to repeat the process of transcription –> abortive initiation
Eventually this process of abortive initiation is overcome, and the stress generated by scrunching helps the core enzyme to break free of its interactions with the promoter DNA and discard the σ factor
when does rna elongation stop? what happens when it stops and how does transcription start over again?
- when it reaches the terminator signal (2nd overall signal)
- here the polymerase halts and releases both the newly made RNA molecule and the DNA template
- The free polymerase core enzyme then reassociates with a free σ factor to form a holoenzyme that can begin the process of transcription again
what direction is RNA synthesized by the polymerase
5’ to 3’ position
why are promoter sequences asymetric
Ensures that RNA polymerase can bind in only one orientation. Because the polymerase can synthesize RNA only in the 5′-to-3′ direction, the promoter orientation specifies the strand to be used as a template
