Cell and Molecular Biology - Exam 2 Master Set

_____ are nucleotide bases that float around in solution to be used when copying the DNA template

dNTPs

_____ is the DNA-dependent RNA polymerase that adds the RNA primer to the template strand

Primase

____ binds to the primase and synthesizes the reverse complement of the parent strand in the ___—→___. It can also act as an ______ for proofreading in the ___—→___ direction. It works on the leading strand.

DNApol3, 5’, 3’, exonuclease, 3’, 5’

The ______ strand moves towards the replication fork and the ______ strand moves away from the replication fork.

leading, lagging

The lagging strand is built in ______. They are eventually joined together after _____ removes each RNA primer at the beginning of each fragment, and then ______ connects the gaps.

Okazaki fragments, DNApol1, DNA ligase

______ removes RNA primers and replaces them with the correct nucleotides.

DNApol1

DNApol1 can do all that DNApol3 can, but in a ______ pace. And it can ______, which DNApol3 cannot do.

slower, remove primers

_______ fills in the gap left after DNApol1 removes the primer. It adds the final ________

DNA ligase, phosphodiester bond

______ are “overhangs” of DNA that allow for docking.

Telomeres

______ contains an RNA sequence that binds to the overhand, and lengthens the parent strand so that DNApoly3 can “dock” and add the end of the chromosome to prevent shortening of the lagging strand.

Telomerases

a biological state where damaged cells permanently stop dividing

cell senescence

_________ recognize errors in the DNA and excise that region so that DNA polymerase and ligase can fill the gap

Repair endonucleases

Telomerase binds to the ____ end of the _____ strand, so that that strand can be extended

3’, parent

_______ uses one strand of a sister chromosome as a template for one strand of the broken chromosome, then that strand acts as a template for its complement so that the double-stranded break can be repaired.

Homologous recombination

_______ uses DNA ligase to rejoin the two broken ends, when the double-stranded break is not missing any DNA sequences.

Nonhomologous end joining

In CRISPR editing, _____ is the endonuclease that recognizes ____ so that it can excise the _____.

Cas9, PAM, protospacer

_____ means using drugs that have already been screened and approved by the FDA for other indications

Repurposing

EC₅₀ is the _____ from a drug, and you usually want it to be ___

effective concentration to give a 50% response, low

Remdesivir is an _____ inhibitor

RdRp

____ carries out information copied from DNA in the form of a series of codons

mRNA

____ “deciphers” the mRNA codons by delivering a specific amino acid for its associated codon

tRNA

_____ associates with a set of proteins to form ribosomes, acting as enzymes

rRNA

Gene

the entire nucleic acid sequence that encodes for the gene product

Genes do not always have to be polypeptides. DNA regions can encode for _____ molecules, which are also considered genes.

non-coding RNA

____ make up ___% of the DNA, and they are the part of the DNA code that gets ____

exons, 1, expressed

_____ make up ___% of the gene, and they are the part of the DNA code that gets _______

Introns, 24, spliced out of the final sequence

______ DNA makes up ____% of the gene, and it is the DNA that _____

Extragenic, 75, lies between genes

Bacteria have a _____ strand and a ____ strand.

template, coding

In bacteria, the upstream direction is the ____ direction on the _____ strand. Because transcription happens in the 5’—>3’ direction, it is ahead of where it starts.

5’, coding

Bacteria have a _____ where RNApolymerase binds to

promoter

Bacteria have _______ for conservation

consensus sequences

In bacteria, RNApol binds to the ____ on the ____ strand, then adds _____ one by one until 9 have been added, so that elongation can then occur

promoter, template, NTPs

In Bacteria, RNApol ____ DNA, adds ____, then ____ the DNA all while moving in the __—> __ direction on the template strand to elongate in the RNA in the 5’—>3’ direction

unwinds, NTPs, rewinds, 3’, 5’

In Bacteria, the terminator is in the ______ of the transcript, and it forms a ____ loop that is _____

secondary structure, hairpin, self-complementary

There are 3 types of RNA polymerases in Eukaryotes. What does RNApol2 do?

Synthesizes pre-mRNA

In eukaryotes, the start point is marked by the ______, which is downstream of the _____ which marks the gene. Together, they make up the ______

Initiator sequence, TATA box, core promoter

In Eurkaryotes, a ______ bids to the TATA box before RNApol2 is able to. One such of these is _____ which binds to the TATA box

basal transcription factor, TFIID

In eukaryotes, the ______ is the complex made from TFIID and multiple other _____ that bind to it, all while being bound to the TATA box.

pre-initiation complex, transcription factors

in Eukaryotes, Pre-mRNA is modified into mRNA by the addition of a ____ and a ______, and edited by ______.

5’ cap, poly(A) tail, splicing

The purpose of the 5’ cap is to

flag for nuclear export, protect against degradation, binding sit for the ribosome

The 5’ cap is added via a _____ that ONLY associated with RNApol2

capping enzyme

______ is the process by which the poly(A) tail is added. It occurs when ____ finds AAUAAA which is the _____ that marks the end of the “important stuff”

Polyadenylation, PAP, poly(A) signal

The purpose of the poly(A) tail is to ____, coated with _____ to protect from deadenylases. But when the mRNA is “done” performing its function, ______ promotes rapid degradation.

protect against degradation, PABPs, de-adenylation

During splicing, _____ are taken OUT of the final sequence, and ____ are left

introns, exons

_______ allows a single gene to produce multiple variants by splicing different parts of it, depending on what it wants to express

alternative splicing

Splicing introns occurs at _____ which specify the beginning and end of introns

splice sites

Splicing is catalyzed by the ______ which is composed of proteins and _____

spliceosome, snRNPs

Remdesivir is a ______ (looks like RdRp substrate), and it is a ____ (has phosphate “protecting groups” that allows it to cross the plasma membrane)

nucleotide analog, prodrug

____ are small proteins released by cells that act as chemical messengers to to regulate immune response and inflammation.

Cytokines

_____ is when the body releases an excessive amount of cytokines, that lead to widespread inflammation

Cytokine storm

The ____ refers to the whole collection of genes and regulatory sequences that are regulated together under by one piece of mRNA

operon

_____ is mRNA that codes for more than one polypeptide, and is only found in prokaryotes.

Polycistronic mRNA

An operon consists of both _____ genes (code for the enzymes/proteins of interest) and _____ genes (express regulatory proteins for the gene)

structural, regulatory

The _____ is a sequence located between the core promotor and the first structural gene, where proteins can bind to either inhibit or promote transcription.

operator

_____ bind the operator to inhibit the operon. This is an example of _____ control of transcription because it turns transcription off.

Repressors, negative

In the lac operon, _____ binds to the operator to _____ it and _____ gene transcription.

allolactase, release, promote

In the lac operon, the ___ is the protein that enhaces gene promotion, and it is activated by ____

CAP, cAMP

In the lac operon, what level of transcription would you get with no lactose and no glucose present?

no transcription

In the lac operon, what level of transcription would you get with no lactose, but with glucose present?

no transcription

In the lac operon, what level of transcription would you get with lactose and no glucose present?

High transcription

In the lac operon, what level of transcription would you get with lactose and glucose present?

Partial transcription

In the lac operon, glucose pathways are _____, meaning if glucose is present, it will turn down other pathways of catabolism

constitutively expressed

The trp operon is an example of ________ because when there is enough of it in the environment, it will activate the repressor so that it can bind to the operator and block transcription.

end product repression

_____ are regions near the promoter that regulatory proteins bind to.

cis-acting elements

______ are regulatory genes that bind to regulatory sites on the DNA to regulate transcription

trans-acting elements

______ are an example of ____-acting proteins because they bind to ____-acting elements

transcription factors, trans, cis

Under the umbrella of cis-acting elements, ____ control elements are <100bp upstread or downstream of the operator, and ____ control elements are further than 100bp upstream or downstream from the operator.

proximal, distal

Distal control elements can exist as both _____ or ______.

enhancers, repressors