Quiz ch4-5 Flashcards by Maggie McDowell

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

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The two types of transcription termination in bacteria that we discussed can be either “dependent” or “independent” of what protein?

Rho protein

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What three letters are used to describe the sites in the large ribosomal subunit where tRNAs can occupy?

APE

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What enzymatic activity converts GTP to GDP

GTPase

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What type of enzyme replaces GDP with GTP following GTPase activity

GTF

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Which step of transcription is most often regulated in bacteria

initiation

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Which step of transcription is most often regulated in human cells

initiation

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Which step of translation is most often regulated in human cells?

initiation

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How many “waves” of gene expression occur during T7 bacteriophage infections?

3 early, intermated, late

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What polymerase transcribes T7 class I genes?

host polymerase

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What polymerase transcribes T7 class III genes?

T7 polymerase

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What word describes circular nucleic acids that are linked together like links of a chain

Catanaded

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What happens to telomerase sequence each time a human chromosome is copied

they get shorter

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How many replication forks are found on a bacterial chromosome that is in the middle of being replicated.

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Replication bubbles form at what genetic element

origin of replication

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Does the leading or lagging strand of DNA have need for many Okazaki fragments.

lagging strand

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What issue downstream of the replication fork is resolved by DNA gyrase( a topoisomerase)

supercoiling

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What is the purpose of a DNA polymerase’s optional activity of 3’–>5’ DNA exonuclease activity?

to correct an error

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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

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Which direction does a polymerase typically travel, 3’–>5’ or 5’–>3’?

5’-3’

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Which genetic elements are removed from human pre-mRNAs during processing, introns or exons?

introns

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Besides splicing, what two other steps occur during RNA processing in human cells?

5 prime cap and poly- A tail

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Cells have different types of RNA endonucleases. What is the substrate for RNaseH?

Any RNA/DNA duplex

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What step of transcription does lambda phage protein, Cro, regulate

initation

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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?

What regulatory protein needs to be expressed before the lambda phage head and tail structural proteins are expressed?

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

15. 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

What IUPAC single-letter code represents either A,C,G, or T

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

Quiz ch4-5 Flashcards

(82 cards)