What is the 'Double sieve' proofreading?
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A mechanism that results in 1 error in 40,000 reactions.
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What is the 'Double sieve' proofreading?
A mechanism that results in 1 error in 40,000 reactions.
What is the structure of tRNA?
tRNA is a single-stranded molecule that folds into a cloverleaf shape.
How many high-energy bonds are used from one ATP?
Two.
What is the activity of rRNA in the large ribosomal subunit?
Peptidyl transferase, which is a ribozyme.
What is the genetic code?
The set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins.
How many eukaryotic RNA polymerases are there?
Three.
What type of reaction is involved in peptide bond formation?
Condensation reaction, which releases H2O.
What is the term used to describe the redundancy in the genetic code for amino acids?
Degeneracy or redundancy.
What are the active sites of ribosomes responsible for?
Catalyzing the formation of peptide bonds between amino acids during protein synthesis.
How are the names of amino acids commonly abbreviated?
In two common ways.
What are the names of the three eukaryotic RNA polymerases?
RNA polymerase I, RNA polymerase II, and RNA polymerase III.
what help RNA polymerase get started?
two types of transcription factors.
What are the names of basal Transcription Factors (bTSF)?
TFIIB, TFIID, TFIIH
What is the difference between mRNA sequence and coding strand sequence?
mRNA sequence uses U instead of T.
What is the process of converting genes into RNA called?
Transcription.
In prokaryotes, where does transcription occur?
In the cytoplasm.
What do Basal/General Transcription Factors bind to?
The core promoter. TATA box
What are the components of each gene?
A segment encoding the RNA to be transcribed and regulatory sequences binding protein factors.
What is eukaryotic transcription?
The process of transcribing DNA into RNA in eukaryotic cells.
What happens when a new tRNA binds in the A site during elongation?
Peptidyl transferase makes a peptide bond.
How are some genes transcribed from DNA?
Using one DNA strand as a template.
How does the N terminus of a protein correspond to the mRNA sequence?
It corresponds to the 5’ end of mRNA.
What is the base pairing between tRNA anticodon loop and mRNA codon?
Complementary, antiparallel binding.
What is an operator in DNA?
A negative regulatory element where repressor proteins bind and block the ability of RNA Polymerase to interact with the promoter.
What is the function of Basal/General Transcription Factors in relation to RNA polymerase?
They help position RNA polymerase properly at the start site.
What is the enzyme responsible for prokaryotic transcription?
RNA polymerase.
What is the role of eukaryotic release factor (eRF) in termination?
It binds the stop codon in the A site.
Where does eukaryotic transcription occur?
In the nucleus of eukaryotic cells.
What is an operon?
A cluster of genes with related functions, regulated so that all the genes in the cluster are turned on and off together.
What is the function of regulatory sequences in a gene?
They bind protein factors that control and participate in the process of transcription.
What causes the shift of two tRNAs to the E and P sites during elongation?
Conformational changes in the large ribosomal subunit.
What is the most abundant type of RNA in rapidly growing mammalian cells?
rRNA (ribosomal RNA).
What do Basal/General Transcription Factors help to create in the DNA?
A transcription bubble by separating DNA strands.
Do both strands of DNA in a chromosome encode for genes?
Yes, both strands encode for genes.
What is the enzyme responsible for eukaryotic transcription?
RNA polymerase.
What is the anticodon for methionyl-tRNA?
CAU.
What happens when a repressor is present at the operator?
Transcription is blocked (RNA polymerase cannot bind promoter).
How does the C terminus of a protein correspond to the mRNA sequence?
It corresponds to the 3’ end of mRNA.
What is the upstream sequence in a gene?
DNA or RNA located towards the 5’ end from the reference point.
What are the various types of RNAs that genes encode?
mRNA, tRNA, rRNA.
What is the role of peptidyl transferase in termination?
It adds H2O to the C-terminus to release the protein in a reaction that hydrolyzes GTP.
What is the result of coordinate control of genes with related function?
It often produces polycistronic mRNA.
What is the function of Aminoacyl - tRNA synthetases?
They have self-checking functions to prevent incorrectly paired aminoacyl tRNAs from forming.
How much does the mRNA move through the ribosome during elongation?
Exactly 3 nucleotides.
What is the first step of translation initiation in bacteria?
Binding of a 30S ribosomal subunit to initiation factors IF1 and IF3.
Are Basal/General Transcription Factors regulated in response to the environment?
No, they are not regulated in response to the environment.
What percentage of the total RNA in rapidly growing mammalian cells is tRNA?
15 percent.
What is a gene?
A segment of DNA that contains all the information necessary for the synthesis of a polypeptide or RNA product.
Where is the downstream sequence located in a gene?
Towards the 3’ end from the reference point.
What is the role of transcription factors in eukaryotic transcription?
They help RNA polymerase bind to the promoter region of the DNA.
Is a given RNA product derived from both strands of DNA?
No, it is only derived from one of the two strands.
What happens if an incorrectly paired product is released by an aminoacyl tRNA synthetase?
There is no mechanism during translation to detect the error, and the incorrect amino acid will be introduced into some protein.
What happens when a repressor is absent at the operator?
Transcription can occur (RNA polymerase can bind promoter).
What is required for the translocation step during elongation?
Elongation factor - 2.
What is the mRNA codon for methionine?
AUG.
know the RNA sequence from the template DNA strand.
Reverse transcription.
How are the structural genes of an operon transcribed?
As one long polycistronic mRNA.
What are consensus sites in transcription?
They are the binding sites of a given transcription factor, which may vary slightly on different genes.
What type of RNA constitutes only a small portion of the total RNA in rapidly growing mammalian cells?
mRNA (messenger RNA).
What does a gene contain?
All the information necessary for the synthesis of a polypeptide or RNA product.
What is the mechanism by which Diphtheria Toxin and Pseudomonas Exotoxin A inhibit translation?
They inhibit eukaryotic elongation factor - 2 (eEF2) through ADP-ribosylation.
What will happen if an abnormal aminoacyl tRNA (ala - tRNA ser) encounters a serine codon?
Alanine will be incorporated into the protein.
What joins the complex after the 30S ribosomal subunit and initiation factors IF1 and IF3?
mRNA, the initiator N-formylmethionyl (fMet) tRNA, and IF2 (bound to GTP).
What does transcription produce that is complementary to one strand of DNA?
RNA.
What is the role of TATA Binding Protein (TBP) in transcription?
It binds directly to the TATA box and is part of TFIID.
What happens during translation of the polycistronic mRNA?
Different start and stop codons lead to a number of distinct proteins being produced.
What is the arrangement of multiple clustered enhancer modules interspersed with silencer and insulator elements called?
Eukaryotic gene regulatory elements.
How does the binding affinity of a transcription factor change based on DNA sequence?
The binding affinity is higher if the DNA sequence conforms well to the consensus.
What is the target of Shiga Toxins in the ribosome?
The 28S rRNA in the 60S large subunit of the ribosome.
What is the structure of a protein-coding gene?
Intron-exon structure.
What happens after IF1 and IF3 are released in translation initiation in bacteria?
A 50S subunit binds to the complex, and IF2 is released.
How many nucleotides long is each codon?
Three nucleotides.
What happens upon completion of the initiator complex in transcription?
It causes a conformational change, and TBP kinks DNA to help separate the strands.
What is the function of enhancers in gene transcription?
Enhancers increase the rate of transcription from a gene.
What are the Proximal Regulatory Sequences in eukaryotic gene structure?
Approximately 250bp sequence upstream of the gene that contains primary regulatory elements.
What is the consequence of Shiga Toxins targeting the 28S rRNA?
It causes inhibition of elongation factor (EF1a)-dependent aminoacyl-tRNA binding and subsequent peptide elongation, resulting in cell death.
Where can the eukaryotic gene regulatory elements be located in relation to the composite core promoter?
10 to 50 kilobases either upstream or downstream.
What happens to genes with 'better' binding sites for a transcription factor?
They will bind that transcription factor more readily than others when amounts are limiting.
What are the two ends of a DNA strand called?
3' and 5'.
What is the function of silencers in gene transcription?
Silencers decrease the rate of transcription from a gene.
What is the role of TFIIH in transcription?
It is the last to bind the initiation complex, has helicase activity to unwind DNA, and kinase activity to signal the beginning of transcription.
How many codons are there in total?
64 codons.
What is the Promoter in eukaryotic gene structure?
A stretch of DNA upstream to gene coding sequence that contains binding sites for regulatory proteins such as transcription factors and RNA polymerase.
What do the bacterial toxins do to the 28S rRNA in the 60S subunit?
They clip an adenine residue from the 28S rRNA.
What are the components of a composite core promoter?
TATA box (TATA), initiator sequences (INRs), and downstream promoter elements (DPEs).
What is the function of enhancer-promoter chromosomal looping?
It allows distal enhancer elements to physically interact with and activate gene promoters.
What are the components of the basic eukaryotic gene structure?
Upstream and downstream regulatory sequences, 5’ and 3’ Untranslated Regions (UTR), exons, and introns.
What type of proteins bind to enhancers?
Activators.
What is the function of tRNAs in protein synthesis?
They carry amino acids to the ribosome.
What is the role of TFIIB in transcription initiation?
It plays a critical role in the assembly of the RNA polymerase II preinitiation complex, stabilizes the TBP complex, and recruits RNA polymerase II and other transcription factors.
Why do transcription and translation occur simultaneously in prokaryotes?
Because prokaryotes do not have a nucleus to separate DNA from other cellular components.
What do the proximal promoter elements include?
A variety of regulatory elements (RE).
What happens when the RNA polymerase encounters a termination signal in prokaryotic transcription?
Transcription stops.
What is the Core in eukaryotic gene structure?
The minimal sequence required to properly initiate transcription, including the transcription start site (or INR) and TATA box.
What is the role of CTCF and cohesin in enhancer-promoter chromosomal looping?
They mediate the looping process.
What does the 'Start codon' (AUG) encode for in eukaryotes?
Methionine.
What enzyme transcribes DNA into RNA?
RNA polymerase.
What type of proteins bind to silencers?
Repressors.
What is the function of ribosomes in protein synthesis?
They are the site of protein synthesis.
What is the function of exons in eukaryotic gene structure?
Exons encode RNA that will remain with the mature mRNA.
What do transcriptional activators (TSFs) bind in the regulatory regions of genes?
Enhancer elements.
What are the two mechanisms of transcription termination in bacterial cells?
Rho-independent termination and Rho-dependent termination.
What happens once newly synthesized RNA exits the RNA polymerase complex in prokaryotes?
Ribosomes bind and translation occurs.
How do enhancer-promoter interactions affect gene promoters?
They increase the binding of transcription factors, chromatin modifiers, and the Mediator complex to recruit RNA polymerase II (RNAPII).
What is the TATA box in eukaryotic gene structure?
A binding sequence for general transcription factors and RNA polymerase (preinitiation complex).
What is the function of some proximal promoter elements?
Modulating transcription in response to cell signaling.
How does RNA polymerase add ribonucleotides to the RNA chain?
One-by-one, using an exposed DNA strand as a template.
What is the template strand in DNA replication?
The strand used to make a complementary RNA copy.
What does the 'Start codon' (AUG) encode for in prokaryotes?
Formylmethionine (fMet).
Where can enhancers and silencers be located in relation to the transcription start site of the gene?
They can be located thousands of base pairs away or closer to the transcription start site.
What is the function of introns in eukaryotic gene structure?
Introns encode RNA that will be spliced out and will not be part of the mature mRNA.
What is the preferred DNA sequence that each transcriptional activator (TSF) binds?
Consensus binding site.
What is the result of multiple ribosomes binding to a single mRNA molecule in prokaryotes?
Formation of polyribosomes, which dramatically increase the level of translation.
What is the Wobble Hypothesis?
It refers to nontraditional base-pairing between the 5′-nucleotide of the anticodon with the 3′-nucleotide of the codon.
How does Rho-independent termination stop transcription?
It relies on the formation of a secondary structure in the newly transcribed RNA to dislodge the RNA polymerase from the DNA template.
What are the characteristics of enhancers?
Elevated DNA sequence conservation, open chromatin, transcription factor binding motifs, characteristic histone modifications, DNA hypomethylation, and bidirectional transcription to generate enhancer RNAs (eRNAs).
How do enhancer sequences affect gene transcription?
Enhancer sequences can be positioned in both forward or reversed sequence orientations and still affect gene transcription.
What is the coding strand in DNA replication?
The non-template strand that has the same sequence as the RNA transcript.
What is the resulting structure of the RNA transcript?
Single-stranded and complementary to the template strand.
How many codons specify for stop codons?
Three codons (UAA, UAG, UGA).
How do transcriptional activators (TSFs) regulate transcription?
In response to environmental signals.
Why does the 5’ base of the tRNA anticodon undergo more movement?
Because it is not as spatially defined as the other two bases.
What does the electron microscopy image show in prokaryotes?
Simultaneous transcription and translation.
What is required for Rho-dependent termination in prokaryotic transcription?
The action of the rho protein.
What do transcriptional activators (TSFs) facilitate the formation of?
Basal initiation complex.
What is the function of the core polymerase in transcription?
To read and translocate down the DNA molecule and synthesize RNA.
What does UTR stand for in molecular biology?
Untranslated Region.
What happens to the DNA behind the polymerase as it moves along the template?
It rewinds.
What does the movement of the 5’ base of the tRNA anticodon allow?
It allows the formation of non-standard base-pairs.
What is the function of enhancer/silencer elements in gene expression?
They regulate the transcription of genes.
How does the rho protein cause transcription to stop in Rho-dependent termination?
It moves along the newly transcribed RNA, catching up with the RNA polymerase when it pauses at the termination site, and causing the polymerase to leave the DNA template.
What is the role of the σ subunit in transcription?
It is weakly bound to the core polymerase and is required for promoter recognition at the transcriptional start.
What is the convention for indicating the name of the amino acid codon that the tRNA anticodon recognizes?
By using a superscript.
How long is the region of hybrid DNA/RNA helix that forms transiently?
Approximately nine nucleotides in length.
What is the initial step of prokaryotic transcription?
The binding of the holoenzyme to the untranscribed DNA promoter.
How many tRNA species are needed to correspond to 61 codons according to the Wobble Hypothesis?
It is not necessary to have 61 tRNA species.
What is the initiation codon for translation in both prokaryotic and eukaryotic cells?
Methionine (fMet for prokaryotes), usually encoded by AUG.
What is the process of 'charging' tRNAs also known as?
Activation of tRNAs.
How many functionally different σ factors are there and what is their role?
There are several functionally different σ factors, each directing the core polymerase to different classes of promoters under different conditions, such as starvation or changing nutrient sources.
How are tRNA molecules specific for alanine codons identified?
As tRNA Ala.
In which direction does RNA polymerase read the Template Strand?
3' to 5'.
What are the two consensus sequences recognized by the holoenzyme σ factor in prokaryotic transcription?
What does the RNA polymerase holoenzyme bind to?
The promoter.
How many tRNA are found per cell to code for 20 amino acids?
30-34 tRNA.
How are initiation codons identified in prokaryotic and eukaryotic cells?
The signals that identify initiation codons are different in prokaryotic and eukaryotic cells.
How many proteins are required for initiation in eukaryotes?
At least 11 proteins, designated eIFs (eukaryotic initiation factors).
What is the function of Aminoacyl tRNA synthetases?
They create a high-energy bond between the correct amino acid and the tRNA.
What happens to the σ factor once transcription is initiated?
The σ factor disassociates from the core polymerase.
In which direction is the RNA produced by RNA polymerase?
5' to 3'.
Where is the -35 Sequence located in relation to the transcriptional start site?
Centered about 35 bases upstream of the transcriptional start site (+1).
What is a tRNA called once the amino acid is attached to it?
Aminoacyl tRNA.
What results in an open promoter complex and initiation of transcription?
Local DNA unwinding.
What is the function of the 5’ UTR in eukaryotic mRNA?
Controlling the translation of mRNA to protein and regulating the binding of ribosomes to mRNA for translation.
What is the initiator methionyl tRNA bound to?
eIF2.
What precedes the initiation codons in bacterial mRNAs? what then happens?
A Shine-Dalgarno sequence that aligns the mRNA on the ribosome. they initiate translation at the 5’ end of an mRNA and at the internal initiation sites of polycistronic mRNAs.
How many enzymes are there in the family of Aminoacyl tRNA synthetases?
20 enzymes.
Which strand is displaced and not read by the polymerase?
The Coding Strand.
What are the components of the prokaryote RNA Polymerase core polymerase?
One ω subunit, two α subunits, one β subunit, and one β’ subunit.
What is the term for an alanyl tRNA specific for alanine codons?
alanyl tRNA Ala.
What does RNA polymerase produce?
A complementary RNA to the template strand.
Where is the Pribnow Box located in relation to the transcriptional start site?
Centered at about 10 bases upstream of the transcriptional start site.
Where does the 5’ UTR start and end?
It starts at the transcriptional start site and extends to 1bp before the AUG sequence of the gene.
In which direction does the RNA polymerase move along the DNA template during elongation?
3’ to 5’.
What is the process of elongation in prokaryotes similar to in eukaryotes?
Elongation in prokaryotes is similar to elongation in eukaryotes.
What is the location of DNA in prokaryotes?
DNA is found in the cytoplasm.
Which protein brings the mRNA to the initiation complex in eukaryotes?
eIF4E.
How do eukaryotic mRNAs get recognized for translation initiation?
Eukaryotic mRNAs are recognized by the 7-methylguanosine cap at the 5′ terminus.
What is the starting codon for the genetic code?
The first AUG.
What is the holoenzyme composed of?
The holoenzyme is composed of the core polymerase and the σ subunit.
What is the role of Aminoacyl tRNA synthetases in the accuracy of translation?
They are largely responsible for the accuracy of translation.
In what form is the tRNA said to be when it has an amino acid attached to it?
Charged form.
What is the template for RNA formation during transcription?
Template strand.
What is another name for the 5’ UTR?
Leader sequence.
What is released as the RNA polymerase moves along the DNA template during elongation?
The σ subunit.
What is the equivalent of EF-Tu (G protein) in eukaryotes?
eEF1α.
Where is DNA confined in eukaryotes?
DNA is confined to the nucleus and mitochondria.
What do ribosomes do after recognizing the 7-methylguanosine cap in eukaryotic mRNAs?
The ribosomes then scan downstream until they encounter the initiation codon.
How many nucleotides does the genetic code 'read' at a time?
3 nucleotides at a time.
What has to be recycled in eukaryotic initiation, serving as a regulation point?
eIF-2-GTP.
How does Aminoacyl tRNA synthetases create a high-energy bond between the correct amino acid and the tRNA?
It uses 2 high-energy bonds from one ATP.
What is the function of the 3’ UTR in eukaryotic mRNA?
Containing regulatory sequences that affect translation from the mRNA, important for mRNA stability, and encoding the transcriptional termination sequence.
What is another name for the template strand?
Antisense strand.
What is a characteristic of RNA polymerase in terms of primer requirement?
It does not require a primer.
What is the equivalent of EF-Ts GTP exchange factor in eukaryotes?
eEF1βγ.
How are genes expressed in prokaryotes?
Genes are expressed polycistronic and clustered to form functional groups called operons.
What type of tRNA is involved in eukaryotic initiation and what is it charged with?
Special initiator tRNA charged with methionine.
What is the condition for reaching a stop codon in the genetic code?
An 'in-frame' stop codon.
What sequence does the 3’ UTR follow immediately after?
The stop codon of the ORF (Open Reading Frame).
What is the coding strand's role in transcription?
It is part of the gene but is not directly involved in transcription.
What is the consequence of RNA polymerase lacking proofreading activity?
It results in a high rate of errors.
What is the equivalent of EF-G in eukaryotes?
eEF2.
How are genes expressed in eukaryotes?
Genes are expressed monocistronic.
What does 'wobble' refer to in the genetic code?
The binding between tRNA and the mRNA codon.
What is involved in the recognition of the 5’ Cap and poly A tail in eukaryotic initiation?
eIFs.
What is another name for the coding strand?
Sense strand.
What encodes a large 45S rRNA precursor in eukaryotic cells?
A single gene.
What is the requirement for mRNA processing in eukaryotes?
mRNA must be processed for nuclear export (mRNA has a 5’ methyl-cap and 3’ poly-A tail).
What is the role of messenger RNA (mRNA) during translation?
It acts as a working copy of the gene with codons for each amino acid transcribed from DNA to mRNA.
What does it mean for the genetic code to be 'universal'?
It is conserved throughout evolution.
What sources of energy are used in eukaryotic initiation?
Energy from ATP and GTP.
