Quiz ch4-5 Flashcards
Transcription begins at a nucleotide said to be at position +1. What is the number given to the nucleotide immediately upstream of the nucleotide at position +1?
-1
- The two types of transcription termination in bacteria that we discussed can be either “dependent” or “independent” of what protein?
Rho protein
What three letters are used to describe the sites in the large ribosomal subunit where tRNAs can occupy?
APE
What enzymatic activity converts GTP to GDP
GTPase
What type of enzyme replaces GDP with GTP following GTPase activity
GTF
Which step of transcription is most often regulated in bacteria
initiation
Which step of transcription is most often regulated in human cells
initiation
Which step of translation is most often regulated in human cells?
initiation
How many “waves” of gene expression occur during T7 bacteriophage infections?
3 early, intermated, late
What polymerase transcribes T7 class I genes?
host polymerase
What polymerase transcribes T7 class III genes?
T7 polymerase
What word describes circular nucleic acids that are linked together like links of a chain
Catanaded
What happens to telomerase sequence each time a human chromosome is copied
they get shorter
How many replication forks are found on a bacterial chromosome that is in the middle of being replicated.
2
Replication bubbles form at what genetic element
origin of replication
Does the leading or lagging strand of DNA have need for many Okazaki fragments.
lagging strand
What issue downstream of the replication fork is resolved by DNA gyrase( a topoisomerase)
supercoiling
What is the purpose of a DNA polymerase’s optional activity of 3’–>5’ DNA exonuclease activity?
to correct an error
What is the purpose of a DNA polymerase’s optional activity of 5’–>3” RNA exonuclease activity?
to remove RNA laid down by primase during replication
Which direction does a polymerase typically travel, 3’–>5’ or 5’–>3’?
5’-3’
Which genetic elements are removed from human pre-mRNAs during processing, introns or exons?
introns
Besides splicing, what two other steps occur during RNA processing in human cells?
5 prime cap and poly- A tail
Cells have different types of RNA endonucleases. What is the substrate for RNaseH?
Any RNA/DNA duplex
What step of transcription does lambda phage protein, Cro, regulate
initation
What step of transcription does lambda phage protein, N, regulate?
termination
What step of transcription does lambda phage protein, Q, regulate?
termination
Genetic elements known as “morons” are expressed by a lysogen
True
name an example of toxic protein encoded by a moron
Cholera or Shiga
What regulatory protein needs to be expressed before the Q protein is expressed by lambda phage?
N
What regulatory protein needs to be expressed before the lambda phage head and tail structural proteins are expressed?
Q
What regulatory protein needs to be expressed at high levels before all the promoters in the lambda phage genomic control region are silenced
Cro
Which DNA-binding protein gets “ diluted” as the number of DNA binding sites for this protein increases due to lambda genome replication
DnaA
What pairs of nucleotides are found in equal abundance according to a publication by Erwin Chargaff?
A=T C=G
While Chargaff’s rulle applies to most DNA genomes, what is different about phi X 174 bacteriophage’s genome to make it break the rule
single strand nucleic acid
How can the genome of phi X174 have fewer nucleotides than three times the number of amino acids it encodes?
overlapping genes
Draw the central dogma of biology and then add to steps of gene expression for M13 phage.
ssDNA <> dsDNA > RNA > Protein
What type of nucleic acid does the MS2 coat protein bind
ssRNA
RdRp needs to be packaged into the capsid of which types of RNA viruses?
+/- ssRNA and dsRNA
Pseudoknots are RNA secondary structure that cause ribosomal frameshifts. Do They typically cause a -1 or +1 shift
-1
Are the genome and anti-genome exit sites of the Qbeta RdRp close together of far apart
far apart
What are the three protein components of the elF4F complex
eIF4E, eIF4G, eIF4A
Which component of the eIF4F complex interacts with the cap?
eIF4E
Which component of the eIF4F complex interacts with PABP
eIF4E
Where do polioviruses “hide” their dsRNA replicative intermediate forms?
Viral Replication center
Why do polioviruses hide their dsRNA replicative intermediate forms
avoid immune infection
What is poly(I:C)
long dsRNA
Which RIG-I like receptor recognizes poly(I:C)
MDA5
Which RIG-I like receptor is a dominant negative?
LGB2
Of the three virion proteins that make up the outer capsid structure, which VP(s) if found in copies around the 5-fold axes of symmetry
VP1
Why is the 2200 amino acid-long polyprotein encoded by the poliovirus genome not found during a natural poliovirus infection
because it it cleaved into smaller functional proteins.
Poliovirus VP) accumulate during the chase phase of a pulse-chase experiment. Since newly-translated proteins are not getting radiolabeled during the chase phase, what can we conclude about the origin of the “new” VP0
It is a cleavage product
The 5’ cap structure is not found on the (+) SSRNA poliovirus genome, in the absence of the ability of eIF4E to start the “dog pile: on the cap, what component/feature of the genome are translation initiation factors recruited to
internal ribosome entry site
- The 5’ cap structure is not found on the (+)ssRNA norovirus genome. In the absence of the ability of eIF4E to start the “dog pile” on the cap, what component/feature of the genome are translation initiation factors recruited to?
Viral protein genome link
Picornavirus RdRp is able to add a nucleotide to viral protein genome-linked (VPg). What amino acid functional group of VPg is uridylated?
hydroxyl group
In order to pause translation, what does the signal recognition particle recognize?
signal peptide
What is the name of the pores within the rough ER that the paused ribosomes dock at before resuming translation?
translocons
What post-translation modification commonly occurs in the lumen of the ER
glycosylation
How do transport vesicles get transported from the ER to the Golgi
Motor proteins along cytoskeletal filaments
Name a cellular organelle that has two phospholipid membrane bilayers
nucleus
What secondary protein structure is common in transmembrane domains
alpha-helix
Contrast the cellular location of polyprotein translation during poliovirus infections and HCV infections
poliovirus- cytoplasm and HCV- ER membrane
What molecule recognizes a stop codon when suppression of termination occurs
tRNA but it does not completely match
What two RNA features result in a -1 ribosomal frameshift during translation of togavirus structural proteins
pseudoknot and slippery sequence
What molecule recognizes stop codons in classical translation termination
release factor
If a cathepsin protease cleaves the spike protein of a coronavirus, does virus entry into the cytoplasm occur at the plasma membrane or from within an endosome?
from within an endosome.
In laboratory-based tissue culture experiments, hydroxychloroquine can be used to prevent acidification of endosomes. How can this antagonize coronavirus replication cycle?
Hydroxychloroquine can prevent acidification of endosomes, which is necessary for the activation of some coronavirus entry mechanisms, thus antagonizing the replication cycle.
When the 43S pre-initiation complex is recruited by the eIF4F complex to the 5’ end of mRNAs, what is the new number/name of the combination of proteins and RNAs?
48S
Which molecule in the translation scanning complex interacts with the start codon?
initiator tRNA
Which RNA structure found in the togavirus genome interacts with ES6
3’ untranslated region
What post-translational modification causes the normally-active version of GTP-associated eIF2 to become inactive
phosphorylation
Describe a situation where coronavirus accessory proteins are not required for successful viral replication
conditions where the host response is insufficient
name one of the promoters that was cloned into a luciferase reporter gen in the “Activation and evasion of type I interferon responses by SARS-CoV” paper.
IFN-beta promoter
Which three transcription factor families need to be activated and bound to the IFNbeta promoter in order for transcription to be robust
IRF, NF-kB, and AP-1
What are the three transcription factors found in the ISGF3 transcription activation complex?
STAT1, STAT2, and IRF9
In order for the coronavirus RdRp complex to “jump” from one plave in the genome, what two genetic features need to be present
complementary sequence and polymerase template-switching mechanism
Was Marilyn Kozak interested in transcription or translation initiations
translation initiation
What IUPAC single letter code represents either A or G
R
What IUPAC single-letter code represents either A,C,G, or T
W
Roughly how many times longer are corona virus genomes compared to the other ssRNA viral genomes
3 time longer
How many benyvirus genome segments are packaged per virus particle
two
How many segments make up a complete benycirus genome
4 segments
If you mutated a protein-coding sequence so that it encoded as aspartic acid residue instead of an alanine, what would be the change in R-chain chemical property
nonpolar to negative charge
