Topic 2B Flashcards
ribosome
a complex structure of RNA and protein, bound to the cytosolic face of the RER in the cytoplasm, on which proteins are synthesized
what experiment demonstrated support for the hypothesis of an RNA intermediary that carries genetic info from DNA to ribosomes?
Brenner, Jacob, Meselson; T2 to infect E. Coli cells by hacking cellular machinery to produce viral proteins. Even though T2 NA never associated with bacterial ribosomes, the infected cells produce a burst of RNA shortly after infection and before viral proteins are made
what are three difference between DNA and RNA?
RNA has a ribose sugar (reactive hydroxyl group attached), uracil base replaces thymine in RNA, 5’ end is triphosphate, not monophosphate (DNA)
RNA transcript
the RNA sequence synthesized from a DNA template, complementary to template except has U instead of T
RNA polymerase
the enzyme that carries out polymerization of ribonucleoside triphosphates from a DNA template to produce an RNA transcript
nontemplate strand
the untranscribed partner of the template strand of DNA used in transcription
the RNA transcript and the DNA template strand are:
antiparallel
promoter
a regulatory region where RNA polymerase and associated proteins bind to the DNA duplex
TATA box
a DNA sequence present in many promoters in eukaryotes and archaeons that serves as a protein-binding site (promoter) for a key general transcription factor; 5’-TATAAA-3’
RNA polymerase moves along the TEMPLATE STRAND from:
3’ to 5’ direction, opposite to direction of synthesis of RNA transcript
terminator
a DNA sequence at which transcription stops and the transcript is released
different genes in the same double-stranded DNA can be transcribed from opposite strands, what determines which strand is transcribed?
the position of the promoter
housekeeping gene
a gene that is transcribed continually because its product is needed at all times and in all cells
most genes are transcribed…when?
only at certain times, under certain conditions, or in certain cell types
for genes that have regulated transcription, what does the regulation of transcription usually depend on?
whether the RNA polymerase and associated proteins are able to bind with the promoter
sigma factor
a protein that associates with RNA polymerase that facilitates its binding to specific promoters
in bacteria, promoter recognition is mediated by:
one protein-sigma factor
in eukaryotes, promoter recognition requires:
the combined action of at least six proteins-general transcription factors (bound at promoter), at least one type of transcriptional activator protein (bound at enhancer)
general transcription factors
a set of proteins that bind to the promoter of a gene whose combined action is necessary for transcription
transcriptional activator protein
a protein that binds to a sequence in DNA (enhancer) to enable transcription to begin
enhancer
a specific DNA sequence necessary for transcription
transcriptional activator proteins help control:
when and in which cells transcription of a gene will occur, is also essential for allowing transcription of any eukaryotic gene to begin
mediator complex
a complex of proteins that interacts with the Pol II complex and allows transcription to begin
recruitment of the mediator complex and RNA polymerase requires:
DNA to loop around to bring factors into close proximity, allowing transcription to proceed
Pol II
the RNA polymerase complex responsible for transcription of protein-coding genes (eukaryotes)
initiation
the stage of translation in which methionine is established as the first amino acid in the new polypeptide chain
elongation
the process in protein translation in which successive amino acids are added one by one to the growing polypeptide chain
describe the RNA-DNA duplex
a bubble where DNA duplex strands are separated and RNA transcript is paired with template strand
the incoming ribonucleoside triphosphate is accepted by RNA polymerase only if:
it undergoes proper base pairing with the base in the template DNA strand (i.e. is complementary)
the energy released when the phosphate bond is broken is used to:
drive other chemical reactions (ex. attach incoming nucleotides to the 3’ end of chain)
the two phosphates of the incoming ribonucleotide are released as:
pyrophosphate
cleavage of the pyrophosphate molecule makes the polymerization reaction:
irreversible
what does transcription require?
template DNA, a supply of ribonucleoside triphosphates, RNA polymerase, a large multi-protein complex in which transcription occurs
primary transcript
the initial RNA transcript that comes off the template DNA strand
messenger RNA (mRNA)
the RNA molecule that combines with a ribosome to direct protein synthesis; it carries the genetic “message” from the DNA to the ribosome
what is the relation between the primary transcript and mRNA in prokaryotes?
the primary transcript is the mRNA
what can transcription and translation occur at once? (i.e. why can primary transcript also act as mRNA?)
because there is no nuclear envelope to spatially separate transcription and translation; the two processes are coupled (connected in space and time)
in prokaryotes, the protein-coding genes often contain:
the genetic information for the synthesis of two or more different proteins
polycistronic mRNA
a single molecule of messenger RNA that is formed by the transcription of a group of functionally related genes located next to one another along bacterial DNA; codes for multiple proteins
what acts as a barrier between transcription and translation in eukaryotes?
the nuclear envelope; allows for RNA processing to occur
RNA processing
chemical modification that converts the primary transcript into finished mRNA, enabling the RNA molecule to be transported to the cytoplasm and recognized by the translational machinery
5’ cap
the modification of the 5’ end of the primary transcript by the addition of a special nucleotide attached in an unusual chemical linkage
what does the 5’cap bond link?
triphosphate bridge between the 5’ carbons of both ribose sugars
why is the 5’ cap essential for translation in eukaryotes?
the ribosome recognizes mRNA by its 5’ cap, requires it to bind to ribosome
polyadenylation
the addition of a long string of consecutive A-bearing ribonucleotides to the 3’ end of the primary transcript
poly (A) tail
the nucleotides added to the 3’ end of the primary transcript by polyadenylation
5’ cap and poly(A) tail help to:
stabilize RNA transcript, protect the two ends of the transcript
exon
a sequence that is left intact in mRNA after RNA splicing (regions of protein-coding sequence)
intron
a sequence that is excised from the primary transcript and degraded during RNA splicing (non-coding regions)
RNA splicing
the process of intron removal from the primary transcript
spliceosome
a complex of RNA and protein that catalyzes RNA splicing
RNA processing consists of which three principal types of chemical modification?
- addition of 5’ cap
- polyadenylation
- RNA splicing
lariat
a loop and tail of RNA formed after RNA splicing
outline the mechanism of RNA splicing:
spliceosome brings a specific sequence within intron into close proximity with 5’ end of intron (5’ splice site), cuts RNA and cleaved end forms a loop (lariat), cleaved 5’ end attacks 3’ splice site, cleaving bond that holds lariat and attaching ends of exons
alternative splicing
a process in which primary transcripts from the same gene can be spliced in different ways to yield different mRNAs and therefore different protein products
what does the presence of multiple introns allow?
alternative splicing
not all primary transcripts are processed into RNA, these transcripts are produced by:
RNA polymerases other than Pol II, allows them to undergo different types of RNA processing
ribosomal RNA (rRNA)
noncoding RNA found in all ribosomes that aid in translation
transfer RNA (tRNA)
noncoding RNA that carries individual amino acids for use in translation
nucleolus
a distinct, dense, non-membrane-bound spherical structure within the nucleus that contains the genes and transcripts for ribosomal RNA
where are the genes and transcripts for ribosomal RNA concentrated in eukaryotes?
in the nucleolus
small nuclear RNA (snRNA)
noncoding RNA found in eukaryotes and involved in splicing, polyadenylation, and other processes in the body
what are two types of regulatory RNA transcripts?
miRNA and siRNA
microRNA (miRNA)
small, regulatory RNA molecules that can cleave or destabilize RNA or inhibit its translation
small interfering RNA (siRNA)
a type of small double-stranded regulatory RNA that becomes part of a complex able to cleave and destroy single-stranded RNA with a complementary sequence
what are the most abundant type of RNA transcripts in mammalian cells and why?
rRNA and tRNA, because they are needed in large amounts to synthesize the proteins encoded in mRNA
