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Chapters 7 and 8

What is the "central dogma"?

Genetic information flows from DNA to RNA to protein.

Which base is not present in RNA?

T

In RNA, which base pairs with the base A?

U

An RNA molecule can fold into complex three-dimensional shapes because:

it is a single-stranded.

All of the RNA in a cell is made by what process?

Transcription

What determines the nucleotide sequence of an RNA strand?

Complementary base pairing with the DNA template during transcription

RNA polymerases join nucleotides through what kind of bond?

Phosphodiester

An RNA chain elongates in what direction?

5' to 3'

What energy drives the transcription reaction forward?

The hydrolysis of high-energy bonds of ribonucleoside triphosphates during elongation

True or False: RNA polymerases can start an RNA chain without a primer.

True

How does the error rate of RNA polymerase compare to the error rate of DNA polymerase (1 error in 10^7 nucleotides)?

Much greater.

True or False: Some genes do not encode proteins, but instead encode functional RNA.

True

To begin transcription, RNA polymerase recognizes nucleotide sequences in what region of DNA?

Promoter region

At which site on the DNA of a gene does RNA polymerase release its newly made RNA?

Terminator

What is the name of the subunit of bacterial RNA polymerase that recognizes the promoter of a gene?

Sigma factor

In eucaryotes, what must assemble at a promoter before RNA polymerase can transcribe a gene?

General transcription factors

The assembly of general transcription factors to a eucaryotic promoter begins at what site in a promoter?

The TATA box

How are bacterial mRNA transcription and translation separated spatially temporally?

Bacterial mRNAs are transcribed and translated simultaneously.

How are eucaryotic mRNA transcription and translation separated spatially and temporally?

Eucaryotic mRNAs are translated after they are exported from the nucleus.

What increases the stability of eucaryotic mRNA?

A 5'-end cap and a poly-A tail.

True or False: In bacteria, most protein-coding genes lack introns.

True

Introns are removed by what process?

RNA splicing in the nucleus

In eucaryotes, which parts of a gene are transcribed into RNA?

Introns and exons

True or False: Unlike the coding sequence of an exon, most of the nucleotide sequence of an intron is unimportant.

True

What structure is responsible for selecting and transporting only properly processed eucaryotic mRNAs into the cytoplasm?

The nuclear pore complex

True or False: In a eucaryotic mRNA, the poly-A tail promotes degradation of the molecule.

False

True or False: The evolution of introns is still a topic of debate.

True

True or False: Each nucleotide in an mRNA encodes one amino acid in a protein.

False

How many nucleotides are necessary to specify a single amino acid?

3

In principle, how many reading frames in RNA can potentially be translated into proteins?

3

True or False: Some codons code for more than one amino acid.

False

Amino acids are attached to their tRNA molecules by:

aminoacyl-tRNA synthetase

An RNA message is decoded by:

Ribosomes.

Within the ribosome, the formation of peptide bonds is catalyzed by:

An RNA molecule in the large ribosomal subunit.

What is the term for an RNA molecule that possesses catalytic activity?

Ribozyme

At which end of an mRNA molecule do ribosomal subunits first bind?

The 5' end

The translation of an mRNA begins at the start codon which is what set of base pairs?

AUG

In eucaryotes, the initiator tRNA always carries which amino acid?

Methionine

Which part of a protein is synthesized by a ribosome first?

The N-terminus

At what site does the charged initiator tRNA first bind on the ribosome?

P site

At what site do all charged tRNAs (with the exception of the initiator tRNA) first bind on the ribosome?

A site

True or False: Stop codons are not recognized by a tRNA

False

What is a polyribosome?

A cluster of ribosomes translating the same mRNA, but positioned at different sites along the mRNA

How do proteases act?

By hydrolyzing peptide bonds between amino acids in a protein

Where in a cell are most damaged proteins broken down?

Cytosol

Proteasomes act primarily on proteins that have been marked for destruction by the covalent attachment of which small protein?

Ubiquitin

Which type of molecule has the potential to perform the catalytic action of reproducing itself?

RNA

Which biochemical reaction is catalyzed by a ribozyme?

Peptide bond formation in protein synthesis

Which sugar cannot be readily made from formaldehyde in experiments simulating conditions on primitive Earth?

Deoxyribose

True or False: Liver cells and kidney cells in the same organism contain different genes.

False

A typical differentiated human cell will express how many of its approximately 25,000 genes?

From 5,000 to 15,000 genes.

True or False: A cell can change the expression of its genes in response to external signals.

True

True or False: Different cell types that respond to the same hormone usually turn on the same sets of genes.

False

Although all of the steps involved in expressing a gene can in principle be regulated, for most genes the most important point of control is:

Transcription initiation.

A gene regulatory protein usually binds to which groove in the DNA double helix?

Major groove

When a gene regulatory protein binds to DNA, its most important interactions occur with which parts of the DNA?

Base pairs

True or False: When a gene regulatory protein binds to DNA, it typically disrupts the hydrogen bonding between base pairs.

False

What is the initiation site in a gene?

The part of a promoter where transcription actually begins

In bacteria, when transcription regulators bind to regulatory DNA sequences close to where RNA polymerase binds, they do what?

Activate or repress transcription of the gene depending upon where they are located relative to the promoter.

What is the definition of an operon?

A set of genes (found in bacteria but not eucaryotes) that is transcribed into a single mRNA

What is the expression of the repressor protein of the tryptophan operon?

The gene for the tryptophan repressor is expressed constitutively.

In the bacterial cell, the tryptophan operon encodes the genes needed to synthesize tryptophan. When the concentration of tryptophan inside the cell is high what happens to tryptophan repressor?

It activates tryptophan repressor which shuts down the tryptophan operon.

Describe the lac operon in E. coli when lactose, but not glucose, is present in the culture medium.

CAP, but not the lac repressor, is bound to the lac operon's regulatory DNA, and the lac operon is expressed.

Describe the lac operon in E. coli when both lactose and glucose are present in the culture medium.

Neither CAP nor the lac repressor is bound to the lac operon's regulatory DNA, and the lac operon is not expressed.

In eucaryotes, where do transcription regulators bind?

Either upstream or downstream from a gene

True or False: Eucaryotic gene activator proteins stimulate transcription initiation by recruiting a DNA polymerase to the promoter.

False

True or False: The general transcription factors that assemble at a eucaryotic promoter are different, depending on the specific gene being transcribed by polymerase II.

False

How many different gene regulatory proteins work together to control a typical human gene?

Dozens

True or False: Even though control of eucaryotic gene expression is combinatorial, the effect of a single gene regulatory protein can still be decisive in switching any particular gene on or off.

True

True or False: Differentiated cells in multicellular organisms require hormonal input to 'remember' what type of cell they should be.

False

True or False: A single transcription regulator, if expressed in the appropriate precursor cell, can trigger the formation of a specialized cell type or even an entire organ.

True

What cell type, when fully differentiated does NOT divide to form new cells?

Neurons

What is an example of epigenetic inheritance?

The inheritance of methylation patters in DNA, the inheritance of patterns of chromosome condensation, or the inheritance of a regulatory protein that activates its own transcription.

What factors are involved in post-transcriptional control?

Riboswitches, microRNA, and RNA interference

What is a riboswitch?

An mRNA that can regulate its own transcription and translation

In bacteria, if a protein binds to the ribosomal binding site on an mRNA, what is the consequence?

The small ribosomal subunit will not be able to bind to the mRNA, and translation will be inhibited.

What is the ultimate fate of an mRNA that is targeted by a microRNA (miRNA) based on their complementary nucleotide sequences?

The mRNA will be destroyed by a nuclease.

What type of molecule triggers RNA interference (RNAi)?

Foreign, double-stranded RNA

Which form of post-transcriptional control is being exploited by scientists to inactivate genes of interest?

RNA interference

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