Bio ch 15 &16

When a ribosome first assembles on the mRNA, the initiator tRNA occupies the A site while the P and E sites are empty.

False

In most cases, these promoters are located near the 3' end of the gene rather than near the 5' end.

None

Deleting a single base from an mRNA molecule usually alters one codon only.

False

Double-stranded RNA is processed by Drosha nuclease to produce a number of siRNAs.

False

In order to recognize and bind to the correct regulatory sequence, a regulatory protein must unwind and separate the 2 strands of the DNA double helix.

False

The helix-turn-helix motif has one helix that fits into the major groove of DNA and another helix that fits into the minor groove

False

You and a group of scientists are mapping out gene regulation in a new species. Based on what is currently known about control of gene expression, the control point to begin your study at would be

Initiation of transcription.

Which of the following statements about triplet repeat expansions are true? Check all that apply.

Triplet repeat expansions were first observed in humans A triplet repeat expansion increases the number of times that a 3-base-pair sequence is repeated in the DNA

There is only one start codon.

True

One or a few base pairs are gained.

Addition

Chromatin is present in ________ cells only

Eukaryote

Activators are regulatory proteins that bind to the promoter and act to stimulate the initiation of transcription.

False

An addition or deletion that alters the codons downstream from the mutation

Frameshift mutation

Suppose a mutation changes the amino acid that an aminoacyl-tRNA synthetase enzyme recognizes without changing the tRNA molecule that it recognizes. How is this likely to affect the process of protein synthesis? Check all that apply.

It will alter the sequence of amino acids in the polypeptide chains It will affect the synthesis of most or all of the proteins produced by the cell

_____________ acts to cleave target mRNAs or inhabit the translation or target mRNAs present in the cytoplasm of eukaryotes

Micro RNA

Regulatory proteins control transcription initiation by modulating the ability of DNA polymerase to bind to the promoter.

False

Regulatory proteins locate the correct binding site on DNA by accessing the sugars along the major groove

False

Repressors are regulatory proteins that bind to the promoter and act to prevent or decrease the initiation of transcription.

False

Ribosomes are composed of tRNA and protein.

False

Small RNAs can regulate gene expression by selective degradation of mRNA, inhibition of translation, or alteration of ribosome structure.

False

The coding region of the lac operon is transcribed when the CAP-cAMP complex is bound to the CAP binding site and the lac repressor is bound to the operator.

False

The genetic code is read in groups of 4 bases.

False

The lac operon is positively regulated by the lac repressor.

False

The most common DNA-binding motif is the beta-pleated sheet

False

There are 66 possible codons.

False

When lactose is absent, the lac repressor binds to the promoter and blocks transcription of the genes that code for proteins needed to metabolize lactose.

False

While endogenous siRNAs tend to repress genes different from their origin, miRNAs tend to repress the genes they were derived from.

False

These promoters contain a "core promoter" that can be composed of a number of different elements including a TATA box.

RNA polymerase II promoters

The best summary of gene splicing mechanisms are that

it offers gene plasticity to most eukaryotes. they allow one coding sequence to be expressed differently according to each cell type. it adds yet another layer to gene regulation.

Mature miRNA is loaded into a RISC, which can act to either cleave target tRNAs or to inhibit transcription of DNA.

False

Elongation

A charged tRNA with a complementary anticodon to the codon in the A site enters and binds. The tRNA in the E site is ejected. A peptide bond forms between the amino group of the amino acid attached to the A site tRNA and the carboxyl group of the growing polypeptide chain.

Processing of mRNA transcripts occurs in prokaryotes only

False

DNA is used as a template to make a complementary strand of DNA.

DNA Replication

When explaining to a science class the way that transcription factors can bind to DNA sites far away from the promoter and still cause transcription, you conclude that

DNA looping must bring the transcription factors close to the promoter.

The best description of how regulatory proteins recognize and bind to the correct sequences without unwinding the DNA double helix is

DNA-binding domains can recognize the chemical groups that protrude from the base-pairs into the major groove.

One or a few base pairs are lost.

Deletion

When observing the reactions within eukaryotic transcription you find there is a greater energy expenditure and several more enzymes and transcription factors than within prokaryotic transcription. The best explanation for this is that

In eukaryotes, DNA is complexed with chromatin and transcription elements can be located far away from the transcription start site.

You are studying a biochemical pathway in the mold Neurospora where enzyme 1 converts the initial substrate into intermediate substrate A; enzyme 2 converts intermediate substrate A into intermediate substrate B; enzyme 3 converts intermediate substrate B into intermediate substrate C; and enzyme 4 converts intermediate substrate C into the end product, an amino acid that is essential for growth. You isolate a mutant that is unable to grow on minimal media. Which data would provide the strongest support for the hypothesis that this mutation occurred in the gene that codes for enzyme 2?

The mold can grow on minimal medium plus intermediate substrate B, but not on minimal medium plus intermediate substrate A.

When working in your lab a colleague brings to you his observation of the insertion of a DNA-binding motif into the major groove. What would best describe the active source of this insertion?

The regulatory proteins are responsible for these motifs.

You are studying a eukaryotic gene that codes for the alpha-subunit in hemoglobin. What is the most likely result if base substitutions occur in the first nucleotide at the 5' end of an intron and also in the last nucleotide at the 3' end?

There will be no change in the polypeptide coded by this gene because introns are not expressed.

Termination

A release factor breaks the covalent bond that links the polypeptide chain to the P site tRNA. A release factor enters the A site of the ribosome. The mRNA, tRNA and 2 ribosomal subunits dissociate from each other.

Initiation

A tRNA molecule charged with its amino acid joins its first AUG codon in the mRNA strand. The small ribosomal subunit binds to mRNA. The large ribosomal subunit bind to the small ribosomal subunit.

Alteration of the nucleotide sequence in SRP RNA would most likely affect

Docking of ribosomes to the RER.

The coding region is located __________ from its promoter

Downstream

A study of the effects of damaging toxins on cells and tissue identifies ubiquitin as a key molecule. Why would you be interested in studying ubiquitin?

Proteins are marked for destruction if there is any damage on it.

You have designed a drug that stops the functions of proteasomes. What interactive structure will it also affect and why?

Proteins as proteasomes cleave this target.

These promoters are specific for each species, so cross-species comparisons do not yield any similarities.

RNA polymerase I promoters

In most cases, these promoters are internal to the gene itself rather than near the 5' end.

RNA polymerase III promoters

RNA is used as a template to make a complementary strand of DNA.

Reverse Transcription

_________ combines with protein to form the 2 ribosomal subunits

Ribosomal RNA

DNA is used as a template to make a complementary strand of RNA.

Transcription

When the CAP-cAMP complex binds to the CAP binding site, this bends the DNA which blocks binding of RNA polymerase to the promoter.

False

Changes a codon for one amino acid into a different codon for the same amino acid.

Silent mutation

One or a few base pairs are replaced by different base pairs

Substitution

As a cell biologist you are always trying to explain mechanisms of gene expression. The most accurate description of how RNA polymerase II functions would be

TFIID binds to TATA box on the DNA. TFIIB and TFIIA then bind. TFIIF bound to RNA Pol-II then attaches followed by TFIIE, TFIIH and TFIIJ this completes the initiation complex for making mRNA

___________ transports amino acids to the ribosomes for use in protein synthesis

Transfer RNA

RNA is used as a template to make a polypeptide.

Translation

This type of mutation causes Huntington's disease and has only been observed in humans and mice.

Triplet repeat expansion

A peptide bond forms between the amino acid attached to a tRNA in the A site and the growing polypeptide attached to a tRNA in the P site.

True

A single primary transcript can be spliced into different mature mRNAs by the inclusion of different exons, a process called alternative splicing

True

Binding of a regulatory protein to DNA either inhibits transcription by getting in the way of RNA polymerase or stimulates transcription by favoring the binding of RNA polymerase to the promoter.

True

CAP alone does not bind to DNA, but binding of cAMP to CAP alters its conformation so that it can bind to DNA.

True

DNA binding motifs generally contain a helical segment, called the recognition helix that fits snugly into the major groove of the DNA molecule

True

No more than 2 tRNA molecules are bound to a ribosome at any given time.

True

The principle of colinearity of genes and proteins does not apply to eukaryotes because

most eukaryotic genes contain introns.

The correct order of gene expression control mechanisms in eukaryotes is

transcription initiation, transcription elongation, transcription termination, post-transcriptional processing, nuclear export.

Some small RNAs regulate gene expression at the transcriptional level by mediating the formation of heterochromatin.

True

The DNA double-helix contains a major groove and a minor groove

True

The codons do not overlap each other.

True

The final processed form of mRNA is called the mature mRNA

True

The genetic code includes specific start and stop codons.

True

The genetic code is the same in almost all living organisms.

True

The poly-A tail appears to play a role in the stability of mRNAs by protecting them from degradation

True

Uncharged tRNA molecules in the E site are ejected from the ribosome.

True

When lactose is present, the lac repressor cannot bind to the operator; therefore, RNA polymerase can transcribe the genes that code for proteins needed to metabolize lactose.

True

Before the mRNA is processed, it is called the primary transcript

True

The lac operon consists of a coding region, which contains 3 genes that code for proteins needed to metabolize lactose, and a regulatory region, which regulates transcription of the coding region.

True

The presence of glucose blocks induction of the lac operon.

True

Pre-miRNA is processed by Dicer nuclease to produce mature miRNA.

True

During translation in eukaryotes, some ribosomes remain free in the cytoplasm while others attach to protein channels embedded in the RER.

True

Hundreds of regulatory sequences have been identified and each one provides a binding site for a specific protein that is able to recognize the sequence.

True

In the lac operon, the 3 genes that code for proteins needed to metabolize lactose are transcribed as a unit, producing a single molecule of mRNA.

True

Regulatory proteins function by binding to specific sequences on the DNA called regulatory sequences.

True

Which of the following were used to decipher the genetic code? Check all that apply.

A cell-free biochemical system that could synthesize polypeptides Synthetic mRNA polymers with known base sequences Synthetic RNA triplets with known base sequences

Elongation (Stage of Transcription)

A process called clearance or escape. New nucleotides are added to the 3' end of the grown RNA transcript.

In eukaryotes, how can a single gene code for several different proteins?

A single pre-mRNA can be spliced to form different mature mRNAs by including different sets of exons

Initiation (Stage of Transcription)

The RNA polymerase holoenzyme binds to the promoter. Once bound to the promoter, RNA polymerase begins to unwind the DNA. The RNA polymerase holoenzyme is formed.

A patient you are working with has increased expression of genes dangerous to their health. The suggested treatment is to alter post-transcriptional regulation. Explain where in the process of gene expression this would occur and what types of regulation should be manipulated in order to save the patient's life?

This phase would occur between the transcription of the DNA to RNA and prior to protein formation, therefore manipulation of the capping, splicing or addition of poly A tails would stop expression.

A bacterial cell has a nonsense mutation in the gene that codes for hexokinase, an enzyme used during glycolysis. This mutation is most likely to affect the expression of this gene by

causing early termination during the elongation cycle of translation.

After completing research into chromatin structure and remodeling, you prepare a final presentation on your findings. To ensure maximum accuracy, your presentation of the function of chromatin-remodeling complexes would be they

help regulate transcription by altering the structure of chromatin. contain enzymes that can modify histones. contain enzymes that can modify DNA. have the ability to slide nucleosomes along DNA to reveal binding sites for proteins. have the ability to remodel nucleosomes or completely remove them from DNA. replace histones with different histones.

RNA is used as a template to make a complementary strand of RNA.

None of these

Changes a codon for one amino acid into a stop codon.

Nonsense mutation

During initiation of translation, the small ribosomal subunit joins to the mRNA and initiator rRNA, followed by the large ribosomal subunit.

False

During transcript processing, a methylated GTP is added to the 3' end of the transcript

False

During transcript processing, a series of adenine residues are added to the 5' end of the transcript

False

During transcript processing, noncoding regions, called exons, are removed and the coding regions, called introns, are spliced together

False

During translation, a charged tRNA first binds to the ribosome if its anticodon matches the codon in the E site.

False

During translation, an amino acid attached to a tRNA in the A site is transferred to a growing polypeptide attached to a tRNA in the P site.

False

During translocation of the ribosome, tRNA molecules move from the P site, to the A site, to the E site, and are then ejected from the ribosome.

False

Each regulatory protein has its own unique DNA-binding motif

False

Each siRNA is loaded into its own RISC, which cleaves target tRNAs. true incorrect

False

Gene splicing is a common regulatory mechanism in prokaryotes.

False

Special "spacer" proteins are used to mark the end of one codon and the start of the next codon.

False

Stop codons have a dual function because each one also codes for an amino acid.

False

Synthesis of the proteins needed to metabolize lactose is repressed by the presence of lactose.

False

Transcript processing takes place in the cytoplasm

False

When the level of glucose is high, cAMP is abundant and binds to CAP.

False

Changes a codon for one amino acid into a codon for a different amino acid.

Missense mutation

An addition or deletion that alters the codons upstream from the mutation

None of these

Termination (Stage of Transcription)

Reaching a terminator sequence causes formation of phosphodiester bonds to stop. RNA polymerase releases the DNA template. The RNA- DNA hybrid within the transcription bubble dissociates.

Scientists have identified many different types of small RNAs including miRNA and siRNA.

True

Small RNAs can regulate gene expression at both the transcriptional level and the posttranscriptional level.

True

The source of double-stranded RNA used to produce siRNAs can be either from within the cell or from outside the cell.

True