How Genes Direct The Production Of Proteins- Exam III Flashcards
Cell achieve their specialized function based upon the expression of ______ and any subsequent _____ of the resulting proteins.
Specific genes; post-translational modifications
What is degraded quicker DNA or RNA? Why?
RNA because of nucleophilic attack of the ribose moiety
What degrades RNA very quickly?
Ribonuclease
In both prokaryotes and eukaryotes, you can have adjacent genes that get transcribed in:
Opposite directions
A segment of DNA that is transcribed into RNA and its associated transcriptional control regions
Gene
The transcriptional control regions of genes and RNA
Promotor regions
The type of RNA that is translated into proteins
Messenger RNA (mRNA)
The type of RNA that are important for the transfer of amino acids to the growing peptide chain.
Transfer RNA (tRNA)
What is the most abundant form of RNA?
Ribosomal RNA (rRNA)
Form of RNA that encodes ribosomal proteins
Ribosomal RNA (rRNA)
What form of RNA blocks the translation on specific mRNAs and thereby regulate gene expression?
microRNA (miRNA)
What form of RNA turns off gene expression by directing the selective degradation of mRNAs
Small interfering RNAs (siRNAs)
What form of RNA that process and chemically modify rRNAs
Small nucleolar RNAs (snoRNAs)
What form of RNAs modify snoRNAs and snRNAs?
Small cajal RNAs (scaRNAs)
Involved in telomere synthesis, X-chromosome interaction, and protein transport into the ER
Other non coding RNAs
Abundance of rRNA in the cell
~80%
abundance of tRNA in the cell:
~15%
Abundance of mRNA inside the cell:
3-5%
All RNAs have to be transcribed from a:
Gene in the genome
In eukaryotic organisms, most protein coding genes are transcribed by:
RNA polymerase II
When you see RNA polymerase II think:
Protein coding
Transcription always starts at a _____ point in the DNA and requires unwinding of the DNA to create the proper single-stranded template
Specific
Gene expression is regulated by numerous transcription factors that interact with ______ in DNA or proteins bound to these regions.
Promotor elements
The presence/absence of specific factors is an obligatory first step in the initiation of ______ binding.
RNA polymerase
An important sequence of the 5’ side (start site) of transcription
TATA Box
Transcription starts at what base:
Base 1
TATA box is rich in:
Thymidine and adenine residues
The TATA box will bind a very important transcription factor, (a dimer) called:
TBP & TFIID
The dimer that TATA box binds to is composed of:
TBP & TFIID
The TATA box localizes the dimer to position itself relative to the start site of transcription through the binding of the _____ to the TATA box
TBP
Once the TATA Box bind TBP what happens:
TFIID will bind and correctly position itself
Once the TBP and TFIID factors are positioned properly, _____ will come in and position itself.
TFIIB
The binding and positioning of TFIIB leads to the recruitment of:
A bunch of other factors
Once the TATA box has bound TBP and TBP allows for the correct positioning of TFIID, and TFIID allows for the correct positioning of TFIIB, and TFIIB recruits all the other important guys, this will allow for the:
Proper binding of RNA polymerase II
It’s important that RNA polymerase II positions itself:
Around the DNA molecule in the proper place
The RNA polymerase II should be bound on the DNA so that the start site of transcription occurs at:
Nucleotide 1
The TATA is located:
Left of the start site of transcription (-15 to -25 ) 5’ to the start site
Once the RNA polymerase II has bound there is a ____ that wraps around the DNA
CTD- (cytoplasmic tail domain)
A couple of _____ reactions occur on the cytoplasmic tail domain of the RNA polymerase II
Phosphorylation
The phosphorylation reactions on the CTD of the RNA polymerase II leads to:
The disassembly of a lot of the general transcription factors
When we have disassembly of most of the general transcription factors, caused by phosphorylation reactions on CTD, this allows for ____ activity and a _____ that is ready to go.
Helicase activity, and RNA polymerase ready to go
Inside the binding pocket or the RNA polymerase, what is functioning?
Helicase
The RNA polymerase is adding ______ to the growing RNA transcript through the uptake channel.
Ribonucleoside triphosphates
On the growing mRNA transcript, the 5’ _____ is connecting to the 3’ ____
5’ Phosphate to 3’ hydroxyl
RNA is not just a ____ molecule because it can fold back on itself and base pair
Linear molecule
Key transcription factor TFIID is made of:
TBP subunit + TAF subunit
The TBP subunit recognizes:
TATA box
the TAF subunit recognizes other ____ sequences near the transcription start point and regulates DNA-binding by_____.
DNA sequences; by TBP
TFIIB recognizes the _____ element in promoters
BRE
The TFIIB accurately positions:
RNA polymerase II
What element is important for accurately positioning the RNA polymerase at the transcriptional start site
BRE element
All of the RNA polymerases have a preference for the types of genes that they bind-
RNA Polymerase I:
RNA Polymerase II:
RNA Polymerase III:
RNA polymerase I- rRNA genes
RNA polymerase II- protein coding genes, snoRNA genes, miRNA genes, siRNAgenes and most snRNA genes
RNA polymerase III- tRNA genes
Processing events of mRNA include:
Capping, Splicing, Editing, Polyadenylation, Transport
Capping:
Guanasine cap added to 5’ end
In protein coding genes, poly-A tail added to the 3’ end
Polyadenylation
Transport of mRNA involves the movement out of the _____ and into the _____.
Nucleus ——> cytoplasm
Linear coding sequence is made of all of the _____ joined
Exons
In mRNA processing the 5’ and 3’ untranslated region gets:
Kept in the linear sequence
splicing occurs by a complex of RNA and protein molecules collectively known as the
Splicesome
The spliceosome is made up of:
SnRNAs in a complex with 7 protein subunits
The spliceosome made of the snRNAs in a complex with the 7 protein subunits come together and form a:
SNP
What are the snRNAs involve din splicing?
U1, U2, U4, U5 and U6
The snRNAs of the spliceosome provide proper:
Base pairing with the mRNA
Splicing will join the ___ end of exon 1 to the ____ end of exon 2 and the ____ end of exon 2 to the ______ end of exon 3
3’ end of exon 1 to 5’ end of exon 2 and the 3’ end of exon 2 to the 5’ end of exon 3
Splicing involves the formation of a ____ structure.
Lariat
In splicing, a particular ____ residue in the intron sequence that undergoes a nucleophilic attack at the junction between the intron and the exon.
Adenosine
What is more important for splicing, the sequence of nucleotides in the exon or intron? Why?
The sequences in the intron because this determines where the splicing will occur
We estimate about _____ proteins in the human proteome
~250,000
The tropomyosin gene can be spliced to form what types of mRNA based on the splicing resulting in different isoforms of the mRNA
Striated muscle mRNA
smooth muscle mRNA
Fibroblast mRNA (x2)
Brain mRNA
The 5’ cap and splicing of the primary mRNA transcript occur as soon as the ______ emerges from the RNA polymerase
HnRNA
The poly A tail added to the 3’ end occurs by a set of RNA-binding proteins and processing enzymes after it _____ from the RNA polymerase
Completely emerges
The mature mRNA means that the mRNA has been:
Spliced, capped and poly tail added
The mature mRNA gets transported from the nucleus to the _____ and to the ____ where protein synthesis can take place.
Cytoplasm and to the ER
Small non coding RNAs that are about 21-25 nucleotides long
MicroRNA (miRNA)
What type of RNA binds to the 3’UTR region of target mRNA to form an RNA-inducing silencing complex (RISC)
MiRNA
MiRNA bind to the 3’UTR of mRNA to form an:
RNA-inducing silencing complex (RISC)
The RISC (RNA-inducing silencing complex) formed by the miRNA :
Suppresses protein synthesis and or induces mRNA degredation
What suppresses protein synthesis or mRNA degradation?
RNA-inducing silencing complex (RISC)
Each miRNA can target ______ different mRNAs
Many
MicroRNA genes are transcribed by:
RNA polymerase II
These miRNAs are formed by: A miRNA gene gets transcribed through RNA polymerase II and they make an initial transcript that makes a hairpin double stranded molecule which is exported out of the nucleus and into the cytoplasm where a specific enzyme called ____ clips the bubble formed to create a mature miRNA that then binds to a bunch of proteins that make up a complex that up a ____ complex, and this complex binds to the mRNA at the 3’ untranslated region to form the ______.
Dicer; argonaute complex; RISC
3 bases code for:
A single amino acid
3 base sequence is known as a _____ in the mRNA
Codon
The genetic code is _____ for all organisms
Universal
Important features of the genetic code: (4)
- Commaless
- Degenerate
- 3rd base less specific
- 3 stop codons that do not code for amino acids
The commaless feature of the genetic code means that the code is read from beginning to end so the _____ is critical.
Reading frame
The degeneracy of the genetic code means:
More than one codon can make the same amino acid
The third base rule of the genetic code means:
The 3rd base is less specific than the first 2 (wobble position)
The 3 base genetic code allows for ____ possible codons.
64
AUG codes for:
Methionine
What are the 3 stop codons:
UAA UAG UGA
Roberts Syndrome severity can be as simple as ______ or as harsh as ______.
Craniofacial abnormality to lethal embryology
Roberts syndrome is a _____ mutation of ______
Homozygous mutation of ESCO2
ESCO2 in Roberts syndrome encodes for an:
Acetyltransferase
The ESCO2 in Roberts syndrome encodes acetyltransferase which is important for the formation of _____ that binds to chromosomes and creates cohesion between sister chromatids.
Cohesion complex
The changes in the level of ESCO2 result in changes in the level of :
Ribosomal gene transcription.
