Chapters 15-16 Biology

The primary transcripts in eukaryotes are most accurately described as:

A faithful copy of the entire gene including exons and introns.

The _______ of histones tend to loosen the coiling of DNA, making it more accessible for transcription.

Acertylation

The "one-gene/one-enzyme" hypothesis was proposed by:

Beadle and Tatum.

The start codon has a dual function because it also codes for an amino acid.

True

During translation, amino acids are carried to the ribosome by

tRNA

During protein synthesis in eukaryotes, which molecule passes from the nucleus to the cytoplasm and specifies the sequence of amino acids in the new polypeptide?

mRNA

Place the following in order, starting with the smallest (#1) and ending with the largest (#4). CODON

2

You are excited because your lab is studying the first microorganisms retrieved from Mars! Interestingly, their genetic material consists of a single-stranded nucleic acid with six different nitrogenous bases. Like organisms from Earth, segments of the nucleic acid contain the code for making proteins. Your experiments indicate that a single deletion in the nucleotide chain almost always leads to loss of function in the coded protein. However, when you make two deletions very close together, the protein usually functions normally. Based on these results, you conclude that the genetic code in these organisms is read in groups of ______ nucleotides. (Enter your answer as a numeral not a word, e.g. use 5 not five.)

2

The mRNA, tRNA, and _______ ribosomal subunits dissociate from each other.

2 (10)

Place the following in order, starting with the smallest (#1) and ending with the largest (#4). GENE

3

Shown below is a hypothetical DNA sequence from a virus. Also shown is the sequence of the RNA that is synthesized from this DNA. DNA sequence: 5'-AGCGAAATAAGCCGATTATGCCTTAACGTGAATAAA-3' 3'-TCGCTTTATTCGGCTAATACGGAATTGCACTTATTT -5' RNA sequence (G* = G cap): 5'-G*AGCGAACCGAUUAAUGAAUAAAAAAA....-3' How many exons does this DNA segment contain? (Enter your answer as a numeral not a word, e.g. enter 5 not five.)

3

How many unique mRNA codons can be constructed from the four different RNA nucleotides?

64

Which region that is associated with the lac operon effects the binding of RNA polymerase?

A and B.

What is the difference between a gene that is derepressed and one that is induced?

A gene that is derepressed is turned on because a repressor molecule is absent. By comparison, a gene that is induced is turned on because an inducer molecule is present.

What would happen if snRNAs did not recognize the branch point within an intron?

A lariat would not form

The template strand of a DNA segment that codes for mRNA has the sequence: ATGCGT. Which tRNA anticodons would pair with the mRNA that is coded for by this sequence?

AUG CGU

One or a few base pairs are gained.

Addition

Although 61 different codons code for amino acids, cells contain fewer than 61 different tRNAs. Why?

Because the 5' base on the tRNA anticodon has some flexibility (wobble); thus, some tRNA anticodons can pair with more than one mRNA codon.

A protein that initiates gene transcription and allows for non-glucose molecules to be used is

CAP

In some cells, DNA combines with proteins to form a substance called:

Chromatin

Enhancers can act at a distance from the gene being transcribed because __________ can form loops.

DNA

The Central Dogma of biology can be stated as:

DNA→ RNA→ proteins.

The tRNA in the _______ site is ejected.

E (7)

In eukaryotes, _________ transcribes rRNA.

RNA Polymerase I

Most amino acids are specified by more than one codon.

True

Which base in an anticodon will pair with the base adenine in a codon?

Uracil

The ribosomes moves along the mRNA so that the tRNA that was in the ______ site is now in the P site and the tRNA that was in the P site is now in the E site. The movement of the ribosome is called ____________.

- A - Translocation (6)

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.

Match each event with the appropriate stage of translation. ELONGATION:

- A charged tRNA with a complementary anticodon to the codon in the A site enters and binds. - 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. - The ribosome moves along the mRNA so that the tRNA that was in the A site is now in the P site and the tRNA that was in the P site is now in the E site. - The tRNA in the E site is ejected.

Match each event with the appropriate stage of translation. TERMINATION:

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

Match each event with the appropriate stage of translation. INITIATION:

- A tRNA molecule charges with it amino acid joins to the first AUG codon in the mRNA strand. - The small ribosomal subunit binds to mRNA. - The large ribosomal subunits binds to the small ribosomal subunit.

Classify each characteristic of transcription according to whether it is found in prokaryotes only, eukaryotes only, both, or neither. NEITHER:

- Four different RNA polymerases are used for transcription. - RNA polymerase unwinds and separates the 2 strands of the entire transcription unit before transcription begins.

Classify each characteristic of gene regulation according to whether it applies to prokaryotes only, eukaryotes only, both, or neither. BOTH

- Gene expression is usually controlled at the level of .... - Regulatory proteins act by binding to specific DNA sequences ... - Regulatory proteins may either inhibit or ...

Classify each characteristic of gene regulation according to whether it applies to prokaryotes only, eukaryotes only, both, or neither. EUKARYOTES ONLY

- Gene expression may be regulated by altering chromatin ... - Addition of ubiquitin marks ... - Major function of gene regulation include ... - Major functions of gene

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 remodel nucleosomes or completely remove them from DNA

Classify each characteristic of transcription according to whether it is found in prokaryotes only, eukaryotes only, both, or neither. BOTH:

- New RNA molecules are added to the 3' end of the growing RNA transcript. -Within the transcription bubble, RNA nucleotides match up with complementary bases on the template DNA strand.

Control of the lac operon and lactose utilization in bacteria is:

- Not induced in the presence of both glucose and lactose - Is a negative control, mediated by a repressor - Controlled by the expression of three downstream genes

Match each event with the appropriate stage of transcription. ELONGATION:

- RNA polymerase leaves the promoter. - A process called clearance or escape. - New nucleotides are added to the 3' end of the growing RNA transcript. - The transcription bubble created by RNA polymerase moves along the DNA template.

Match each event with the appropriate stage of transcription. TERMINATION:

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

Match each event with the appropriate stage of transcription. INITIATION:

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

Classify each characteristic of gene regulation according to whether it applies to prokaryotes only, eukaryotes only, both, or neither. PROKARYOTES ONLY

- The primary function of gene control is to adjust the cells activities ... - Functionally related genes are often ...

Classify each statement according to whether it applies to general transcription factors only, specific transcription factors only, both, or neither. SPECIFIC TRANSCRIPTION FACTORS ONLY:

- These transcription factors act in a tissue- or time- dependent manner to stimulate levels of transcription that are higher than the basal level. - These transcription factors bind to enhancer sequences that may be distant from the promoter.

Classify each statement according to whether it applies to general transcription factors only, specific transcription factors only, both, or neither. NEITHER:

- These transcription factors are found in both prokaryotes and eukaryotes.

Classify each statement according to whether it applies to general transcription factors only, specific transcription factors only, both, or neither. GENERAL TRANSCRIPTION FACTORS ONLY:

- These transcription factors are necessary to recruit RNA polymerase II to the promoter and initiate transcription at the basal level. - During formation of the transcription complex, these transcription factors are the first proteins to bind to the promoter. - One of these transcription factors binds directly to the TATA box in the core promoter. - These transcription factors include TFIID and TFIIE.

Classify each statement according to whether it applies to general transcription factors only, specific transcription factors only, both, or neither. BOTH:

- These transcription factors are proteins.

The best summary of gene splicing mechanisms are that:

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

Classify each characteristic of transcription according to whether it is found in prokaryotes only, eukaryotes only, both, or neither. EUKARYOTES ONLY:

- Transcription factors must bind to the promoter before RNA polymerase II binds to DNA. - A number of transcription factors interact with RNA polymerase II to form an initiation complex at the promoter. - After the mRNA molecules are transcribes, they are modified.

The eukaryotic transcription initiation complex is:

- Transcription of virtually all genes transcribes by RNA pol II requiring the same suite of general factors. - Responsible for highly regulated transcription levels. - Interactive with activators through DNA looping.

Classify each characteristic of transcription according to whether it is found in prokaryotes only, eukaryotes only, both, or neither. PROKARYOTES ONLY:

- Translation of the mRNA beings before transcription is finished. - Only one type of RNA polymerase is used for transcription. - The promoters contain 2 common 6-base sequences which are located 35 nt & 10 nt upstream from the start site.

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.

Examples of shapes in regulatory proteins that are used to bind to DNA include:

- Zinc Finger - Helix-Turn-Helix - Leucine Zipper

You synthesize three types of artificial mRNA: (x) 5' AAAGGGAAAGGGAAAGGGAAAGGGAAA 3' (y) 5' GGGCCCGGGCCCGGGCCCGGGCCCGGG 3' (z) 5' AGAGAGAGAGAGAGAGAGAGAGAGAG 3' When you analyze the polypeptides produced, you find that: x produces a polypeptide that is 50% glycine and 50%lysine. y produces a polypeptide that is 50% glycine and 50% proline. z produces a polypeptide that is 50% glutamate and 50% arginine. Based on these results only, the best conclusion to make is that:

AAA codes for lysine.

A(n) __________ is a regulatory protein that acts to increase the rate of transcription above the basal rate.

Activator

A charged tRNA with the _____ that is complementary to the codon in the A site enters and binds to the A site.

Anticodon (4)

The lac repressor:

Binds to the operator and prevents transcription.

Intracellular receptors usually contain binding sites for:

Both DNA and signaling molecules.

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.

The p300/CBP (CREB-binding protein) coactivator proteins are histone acetyltransferases that help regulate the transcription of many genes. Based on this information you can conclude that these proteins are involved in:

Chromatin Remodeling.

Some activators interact directly with RNA polymerase II while other require the assistance of a(n) ________.

Coactivator

The progesterone receptor (PR) is a steroid hormone receptor and transcription factor. The protein SRC-1, which does not bind DNA by itself, can bind to PR and increase expression of genes regulated by PR. Based on this information, SRC-1 is a(n):

Coactivator.

The strand of DNA that is not transcribed is called the _________ strand.

Coding

Crick and his colleagues proposed that the genetic code consists of a series of blocks of information, called ______, each corresponding to one amino acid in an encoded protein.

Codons.

Using your knowledge of the basic biological molecules, which of the following molecules is a glucocorticoid hormone?

Cortisol.

When glucose is present:

Cyclic AMP is low, CAP does not bind to the activator binding site, and transcription is turned off

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

DNA Replication.

Regulatory proteins can identify specific sequences on the DNA double helix without unwinding the helix. This is accomplished by inserting:

DNA-binding motifs into the major groove of the double helix where the edges of the nitrogen bases protrude.

One or a few base pairs are lost.

Deletion

Segments of a chromosome that are lost are called ____________.

Deletions

The protein ________ acts as an endonuclease in the first step of RNA interference.

Dicer.

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

Docking of ribosomes to the RER.

RNA interference is stimulated in the presence of ________ in the cell.

Double-stranded RNA.

The coding region of a gene is located __________ from its promoter.

Downstream

Intracellular receptors may be found:

Either in the cytoplasm or the nucleus.

Successive RNA nucleotides are added to the 3' end of the growing RNA chain during a process called.

Elongation (4)

Each specific transcription factor binds to a segment of DNA called a(n) __________.

Enhancer

Transcriptional control-proteins increase the rate of transcription by binding to:

Enhancer sequences within the DNA.

Through control of gene expression, a bacterial cell responds to changing __________ conditions.

Environmental

Gene ________ refers to the combined processes of transcription and translation.

Expression

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

False

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

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

Each regulatory protein has its own unique DNA-binding motif.

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

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

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

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

False

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

False

The trp operon consists of ________ genes that encode tryptophan biosynthesis enzymes.

Five.

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

Frameshift Mutation

The lac operon is expressed when:

Glucose is low and lactose is present.

Chromatin that contains high condensed DNA which is not being expressed is called:

Heterochromatin

The structure of chromatin can be modified by altering either the DNA or the _______ attached to DNA

Histones

One of the DNA-binding motifs in many eukaryotic organisms that contains a nearly identical sequence of 60 amino acids is known as the:

Homeodomain.

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.

Eukaryotic and prokaryotic organisms differ in how they process genetic information. Which statements best explain one of these differences?

In prokaryotes, translation of mRNA begins before transcription is complete Eukaryotes: transcription and modification of the mRNA is completed before translation begins.

In the absence of tryptophan, the trp repressor is:

Inactive and cannot bind to the operator.

Shown below is a hypothetical DNA sequence from a virus. Also shown is the sequence of the RNA that is synthesized from this DNA. DNA sequence: 5'-AGCGAAATAAGCCGATTATGCCTTAACGTGAATAAA-3' 3'-TCGCTTTATTCGGCTAATACGGAATTGCACTTATTT -5' RNA sequence (G* = G cap): 5'-G*AGCGAACCGAUUAAUGAAUAAAAAAA....-3' Based on the data provided, you can conclude that this virus:

Infects eukaryotic cells.

Evaluate the statements below and determine which is the BEST reason that bacterial cells use operons and polycistronic RNA.

Initiation of all genes in a biochemical pathway are regulated simultaneously.

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.

In eukaryotic cells, transcription occurs:

Inside the nucleus.

If you were given a sequence with a mutation in the -35 region of the trp operon the most likely effects would be the

Interference with RNA polymerase binding to the promotor.

Most eukaryotic genes contain noncoding sequences called ________ that are interspersed with the coding sequences.

Introns.

Segments of a chromosome that are repeated are called __________.

Inversions

The lac operon regulatory system is important to bacteria primarily because lactose:

Is only rarely available; producing enzymes all the time is costly.

What is the best way to describe our current understanding of the one-gene/one-polypeptide hypothesis?

It applies to prokaryotes but not to eukaryotes.

Tighter coiling of the chromatin makes the DNA ____ accessible for transcription.

Less

The fruit fly D. melanogaster has a gene dsx which helps to regulate sex development. When this gene is expressed in males, it produces a transcriptional regulatory protein that is required for male development. However, when the exact same gene is expressed in females, it produces a transcriptional regulatory protein that is required for female development. What is the most likely explanation for this observation?

Males and females use different transcription initiation factors when expressing the gene.

_________ is translated by the ribosomes and contains the code that specifies the sequence of amino acids in a polypeptide chain.

Messenger RNA

The _____ of histones i correlated with tighter coiling of the DNA and inactive regions of chromatin.

Methylation

Vertebrate cells possess a protein that binds to clusters of 5-methylcytosine and ensures the gene will stay in the "off" position. This control of gene regulation is a result of:

Methylation.

_________ acts to cleave target mRNAs or inhibit the translation of target mRNAs present in the cytoplasm of eukaryotes.

Micro RNA

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

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

None of these

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

The lowest level of chromatin structure consists of DNA wrapped twice around a group of histones to form a:

Nucleosome

Histones that are tightly wound by DNA and are the basic unit of chromatin are called:

Nucleosomes.

RNA interference is a mechanism for silencing gene expression at the:

Post-transcriptional but pre-translational level.

A site at the 5' end of a gene where RNA polymerase attaches to initiate transcription is called a(n).

Promoter

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

RNA Polymerase I Promoters

You are attempting to synthesize rRNA in a test tube using DNA isolated from mouse cells. In addition to the template DNA, ribonucleotides, and the necessary transcription factors, you should also add _________ to the test tube.

RNA Polymerase I.

General transcription factors, along with TAFs, recruit ________ and position it at the start of the protein-coding sequence.

RNA Polymerase II

In eukaryotes, __________ transcribes mRNA and some small nuclear RNAs.

RNA Polymerase II

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

RNA Polymerase II Promoters

In eukaryotes, _________ transcribes tRNA and some other small RNAs.

RNA Polymerase III

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

RNA Polymerase III Promoters

Transcription is carried out by the enzyme:

RNA Polymerase.

Ribosomes are complex aggregates of:

RNA and proteins.

The gene encoding apolipoprotein B exists in two isoforms, APOB100 and APOB48. These two forms are produced as a result of:

RNA editing.

Shown below is a hypothetical DNA sequence from a virus. Also shown is the sequence of the RNA that is synthesized from this DNA. DNA sequence: 5'-AGCGAAATAAGCCGATTATGCCTTAACGTGAATAAA-3' 3'-TCGCTTTATTCGGCTAATACGGAATTGCACTTATTT -5' RNA sequence (G* = G cap): 5'-G*AGCGAACCGAUUAAUGAAUAAAAAAA....-3' Based on the data provided, you can conclude that the RNA was transcribed by:

RNA polymerase core enzyme.

If a protein in the coactivator complex does not function properly, what would be a consequence?

RNA polymerase will not bind to the template DNA.

In eukaryotes, pre-mRNA processing may involve all of the following except:

Removal of exons from the pre-mRNA.

A protein that regulates transcription by binding to the operator is known as the:

Repressor.

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

Reverse Transcription.

A large ribosomal subunit associated with the _________ ribosomal subunit.

Small (3)

Glucocorticoids are ________ hormones secreted by ________ glands.

Steroid; endocrine.

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

Substitution

Glucocorticoid hormones activate genes that are involved in which of the following processes?

Synthesis of glucose, mobilization of fats, and breakdown of proteins.

The TFIID complex is formed by:

TATA-binding protein TBP and TAFs.

Assembly of basal transcription factors begins at the ________ sequence in the promoter.

TATA.

Shown below is a hypothetical DNA sequence from a virus. Also shown is the sequence of the RNA that is synthesized from this DNA. DNA sequence: 5'-AGCGAAATAAGCCGATTATGCCTTAACGTGAATAAA-3' 3'-TCGCTTTATTCGGCTAATACGGAATTGCACTTATTT -5' RNA sequence (G* = G cap): 5'-G*AGCGAACCGAUUAAUGAAUAAAAAAA....-3' What is the base sequence, in the DNA template strand, of the exon that is closest to the 3' end of this strand?

TCGCTT

The binding of TFIID is followed by the binding of a number of other general transcription factors. The correct order of binding of these factors would be:

TFIIB-TFIIA, TFIIF, TFIIE, TFIIH, TFIIJ

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.

During embryogenesis in angiosperms, it has been found that RNA silencing by the maternal genome is in effect. What effect will this have on the developing embryo?

The embryo will have more genes expressed by the maternal parent than by the paternal parent.

A mutation causes an activator to be nonfunctional. Which of the following statements best describes the consequences?

The gene will be expressed, but in less than optimal quantities.

In prokaryotes, the form of RNA polymerase that can accurately initiate synthesis of RNA is called:

The holoenzyme

How would a large chromosomal inversion affect the expression of a gene if the gene is located between the two break points but no breaks occur within the gene?

The inversion would probably have no effect on gene expression.

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.

If lacI were mutated, what effect would this have on lactose metabolism?

The repressor protein would not function properly, and the lac operon would be over expressed.

If lacO were mutated, what effect would this have on lactose metabolism?

The repressor would not properly bind to the operator, and the lac operon would be over expressed.

The inhibitor of an intracellular signal receptor is defective, such that even when stimulated by a signal molecule, the inhibitor stays bound to the receptor. What effect will this have on the signaling pathway?

The signal molecule will bind to the receptor, but it will not be able to activate it.

How could drug developers use RNA silencing in a medical application?

They could stop the production of a defective protein.

Evaluate the statements below and determine which is the best reason for why eukaryotes use basal transcription factors?

They give the cell tight control over transcription.

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.

The genetic code uses _________ nucleotide(s) to specify one amino acid.

Three

The correct order of gene expression control mechanisms in eukaryotes is:

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

Gene expression involves two phases, ___________ and translation.

Transcription.

As a microbiologist you have been asked to investigate gene regulation in a new bacteria. Given what is known about bacteria, the logical place to begin your investigation is:

Transcriptional control.

_________ transports amino acids to the ribosomes for use in protein synthesis.

Transfer RNA

Production of the iron-storing protein ferritin is regulated by aconitase, which binds to a 30-nucleotide sequence at the beginning of the ferritin mRNA and interferes with ribosome binding. Aconitase must be a:

Translation Repressor Protein.

RNA is used as a template to make a polypeptide.

Translation.

If a duplication occurs directly next to the original segment, it is termed a ___________ duplication.

Translocations

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

Triplet Repeat Expansion

When E. coli cells produce the amino acid tryptophan, a cluster of five genes is transcribed together. This cluster of genes is referred to as the:

Trp Operon.

In the presence of tryptophan, tryptophan binds to the:

Trp repressor.

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

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

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

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 some cases, it is possible to change the sequence of bases in a codon and it will still code for the same amino acid.

True

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

True

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

True

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

True

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

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 amino acid sequence of a protein determines its shape and specific function.

True

The final processed form of mRNA is called the mature mRNA.

True

The presence of glucose blocks induction of the lac operon.

True

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

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

Your research project involves the characterization of a recently identified transcription factor. As part of your project, you want to determine if this transcription factor binds directly to any of the general transcription factors. Unfortunately, however, you are having trouble expressing and purifying the full length protein. An option that may help you achieve your research goal would be to:

Try to express and purify only the activation domain, since transcription domains can be separated.

The assembly of transcription factors begins:

Upstream from the transcription start site.

When in a complex with ________, the CAP protein binds to the CAP site and ________ the expression of the lac operon.

cAMP; switches on.

Although the specific mechanism of RNA interference has not been fully defined, it involves:

double stranded RNA interference with mRNA.

In eukaryotes, the 3' poly-A tail is attached to:

mRNA

A small ribosomal subunit binds to a molecule of _______ near its 5' end.

mRNA (1)

Which molecule combines with proteins to form both the large and small ribosomal subunits?

rRNA.

Eukaryotic mRNA molecules may contain non-coding sequences that must be removed before translation. These are called:

Introns

What characteristic of glucocorticoid hormones allow them to act as intracellular receptors?

Glucocorticoid hormones are hydrophobic and can diffuse through the plasma membrane.

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.

False

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

False

Most codons code for more than one amino acid.

False

Only 20 different codons are used to code for amino acids.

False

Processing of mRNA transcripts occurs in prokaryotes only.

False

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

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

False

Stops 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

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

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

Transcript processing takes place in the cytoplasm.

False

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

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

Proteins called ________ transcription factors can initiate transcription only at the basal rate.

General

The sequence of nucleotides in a DNA molecule is called the ________ code.

Genetic

Why does the concentration of glucose have an effect on the transcription of the lac operon?

Glucose is the preferred sugar for the bacteria. If it is present, lactose metabolism is suppressed.

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.

In eukaryotes, translation takes place:

On Ribosomes.

The location of translation in prokaryotic cells is:

On ribosomes.

A site of negative genetic regulation where binding by repressor blocks transcription is the:

Operator.

A cluster of functionally-related genes that are regulated together and encoded into a single mRNA molecule is called a(n):

Operon.

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

P (5)

When a polypeptide is being assembled, the bond that forms between a newly added amino acid and the previous amino acid in the chain is a _________ bond.

Peptide

The release factor breaks the covalent bond that links the newly synthesized ________ to the tRNA in the P site.

Polypeptide Chain (9)

Messenger RNA molecules contain information that is used to synthesize ___________.

Polypeptides

Formation of the transcription initiation complex begins when general transcription factors bind to a segment of DNA called the ________.

Promoter

In eukaryotes, each type of RNA polymerase recognizes a different:

Promoter

The formation of nucleosomes may block the binding of transcription factors and RNA polymerase II to the:

Promoter

RNA polymerase binds to a region of the DNA called the __________.

Promoter (1)

The connection that exists between genes and hereditary traits is based on using the information encoded in genes to synthesize:

Proteins

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.

DNA affects the traits of an organism by providing the instructions for synthesizing _________.

Proteins.

Which of the following best describes translation?

RNA -> Protein

Transcription in prokaryotes is carried out by ______, which unwind(s) and transcribe(s) the gene.

RNA Polymerase

______ begins to unwind and separate the 2 strands of the DNA double helix.

RNA Polymerase (2)

The RNA was most likely transcribed by:

RNA Polymerase I.

What is the first step during transcription initiation in prokaryotes?

RNA polymerase binds to the promoter.

Segments of a chromosome that are broken in 2 places, reversed, and then put back together are called ______________.

Reciprocal

The basic tool of genetic regulation is the ability of certain proteins to bind to specific:

Regulatory DNA sequences.

When the ribosome encounters a stop codon, a _______ binds to the A site.

Release Factor (8)

What protein would not interact with a coactivator?

Repressors.

________ combines with protein to form the 2 ribosomal subunits.

Ribosomal RNA

The polypeptide-making organelles, which consist of protein combined with RNA, are called:

Ribosomes.

_________ combines with protein to form particles that help ribosomes attach to the endoplasmic reticulum in eukaryotes.

SRP RNA

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

Silent Mutation

________ plays a key role in the splicing reaction that removes introns from eukaryotic pre-mRNA.

Small nuclear-RNA

Enhancers are the binding sites for the:

Specific-transcription factors.

The A, P, and E sites are progressively occupied by amino acids being assembled into a polypeptide. These sites are part of:

The large ribosomal subunit.

You are studying regulation of a prokaryotic operon. Experimental results show that expression of the operon is increased when product levels are low. Based on this information, you conclude that the likely mode of regulation is:

The operon is OFF in the absence of its regulatory protein.

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

False

Gene splicing is a common regulatory mechanism in prokaryotes.

False

Chromatin is present in _______ cells only.

Eukaryotic

Classify each characteristic of gene regulation according to whether it applies to prokaryotes only, eukaryotes only, both, or neither. NEITHER

- In order to recognize the correct binding ... - Repressors are regulatory proteins that bind to DNA ... - Regulatory proteins always bind to DNA at sites that are ...

Classify each statement according to whether it applies to induction only, repression only, both, or neither. BOTH

- Involves the use of regulatory proteins to control the initiation of transcription

The ubiquitin-proteasome pathway:

- Is used to regulate expression of a number of cell surface receptors - Targets proteins in a stepwise fashion via ubiquitin ligase adding ubiquitin residues to the protein - Does not destroy the ubiquitin moiety, but rather cleaves it off for reuse.

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.

Classify each statement according to whether it applies to induction only, repression only, both, or neither. REPRESSION ONLY

- A cell turns off production of a certain enzyme in response to high levels of the product - Response of the trp operon to high levels of trypophan

Classify each statement according to whether it applies to induction only, repression only, both, or neither. NEITHER

- A cell turns on production of a certain enzyme in response to high levels of the product - A cell turns off production of a certain enzyme in response to high levels of the substrate

Classify each statement according to whether it applies to induction only, repression only, both, or neither. INDUCTION ONLY

- A cell turns on production of a certain enzyme in response to high levels of the substrate - Response of the lac operon to high levels of lactose

How many introns does this DNA segment contain? (Enter your answer as a numeral not a word, e.g. enter 5 not five.)

1

Place the following in order, starting with the smallest (#1) and ending with the largest (#4). NUCLEOTIDE

1

Arrange the following in the proper order in which they occur during glucocorticoid hormone action. 1. Binding of hormone to receptor 2. Release of HSP90 proteins 3. Entry of hormone into the nucleus.

1, 2, 3.

If the genetic code were read in groups of two bases, how many different codons would be possible?

16.

You are excited because your lab is studying the first microorganisms retrieved from Mars! Interestingly, their genetic material consists of a single-stranded nucleic acid with six different nitrogenous bases. Like organisms from Earth, segments of the nucleic acid contain the code for making proteins. If the genetic code in these organisms was read in groups of 2 bases instead of 3, what is the maximum number of amino acids that could be coded for assuming that only one codon functioned as a stop codon? (Enter your answer as a numeral not a word, e.g. enter 17 not seventeen.)

35

Place the following in order, starting with the smallest (#1) and ending with the largest (#4). CHROMOSOME

4

If proteins were composed of 18 different kinds of amino acids, the smallest possible codon size in a genetic system with just two different nitrogenous bases would be ______ nucleotides. (Enter your answer as a numeral not as a word, e.g. enter 3 not three.)

5

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.

You are studying an individual with very low levels of insulin in her blood. Further analysis indicates that cells of her pancreas are producing normal levels of this protein, but most of it is accumulating in the cytoplasm rather than being secreted from the cells. Which hypothesis to explain this observation makes the most sense?

A small deletion has removed the nucleotides that code for the signal sequence at the amino terminus of the protein.

A scientist makes three artificial mRNA strands: (x) 5' AAAUUUAAAUUUAAAUUUAAAUUUAAA 3' (y) 5' UUUCCCUUUCCCUUUCCCUUUCCCUUU 3' (z) 5' AUAUAUAUAUAUAUAUAUAUAUAUAU 3' When he analyzes the polypeptides produced, he finds that: x produces a polypeptide that is 50% phenylalanine and 50%lysine. y produces a polypeptide that is 50% phenylalanine and 50% proline. z produces a polypeptide that is 50% isoleucine and 50% tyrosine. Based on these results only, the best conclusion to make is that:

AAA codes for lysine.

In the absence of lactose, the lac repressor is:

Active and can bind to the operator.

The lac repressor is inactivated by binding to which of the following?

Allolactose

Elucidation of the histone code might:

Allow us to turn specific genes on or off.

You are working to characterize a novel protein in mice. Analysis shows that high levels of the primary transcript that codes for this protein are found in tissue from the brain, muscle, liver, and pancreas. However, an antibody that recognizes the C-terminal portion of the protein indicates that the protein is present in brain, muscle, and liver, but not in the pancreas. What is the most likely explanation for this result?

Alternative splicing in the pancreas yields a protein that is missing the portion that the antibody recognizes.

Specific amino acids are attached to tRNA molecules by:

Aminoacyl-tRNA synthetases.

The tRNA nucleotide sequence that pairs with bases on the mRNA is called a(n):

Anticodon

The genetic code includes specific start and stop codons.

True

What is required for formation of the transcription initiation complex in eukaryotes?

Binding of transcription factor to the TATA box, followed by recruitment of additional transcription factors and recruitment of RNA polymerase II.

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

True

Two 6-base sequences are present in bacterial promoters: TATAAT (located 10 nt upstream from the start site) and TTGACA (located 35 nt upstream from the start site). What is the significance of the fact that these two base sequences are different?

Both the location of the start site and the direction of transcription can be established.

Segments of a chromosome that break off and attach to another chromosome are called ___________.

Duplications

In vertebrates, methylation of ___ ensures that once a gene is turned off, it stays off.

DNA

Which of the following best describes transcription?

DNA -> RNA

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.

You are studying the effects of transcription factors on the activation of gene expression. However, when first starting your study you notice that some of the transcription factors bind further away from the DNA that it is aiming to transcribe. What description best explains this?

DNA looping transports the transcription factor closer to the promoter and initiates gene transcription.

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.

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

During translation, uncharged tRNA molecules leave the ribosome from the _________ site.

E.

Chromatin that contains loosely coiled DNA, which is accessible for transcription, is called:

Euchromatin

A gene that codes for a protein was removed from a eukaryotic cell and inserted into a prokaryotic cell. Although the gene was successfully transcribed and translated, it produced a different protein than it produced in the eukaryotic cell. What is the most likely explanation?

Eukaryotic genes often contain introns while prokaryotic genes do not.

All codons code for amino acids.

False

You are conducting a genetic screen to isolate nutritional mutants in yeast. Specifically, you want to isolate a double mutant that cannot synthesize histidine or leucine, two nutrients essential for growth. You start with a wild type yeast strain and mutagenize it with a UV light. Which of the following outlines the remaining steps for isolating such a mutant?

Grow mutagenized yeast on rich media. Then grow them on minimal media, as well as on minimal media containing histidine, minimal media containing leucine, and minimal media containing both histidine and leucine. Select for yeast that do not grow on minimal media, do not grow on media supplemented with only histidine or leucine, but do grow on minimal media supplemented with both histidine and leucine.

What is a major disadvantage to a bacterial cell of having an operon?

If there is a mutation in a regulatory region, none of the proteins will be synthesized.

The main form of glucose repression in the lac operon is:

Inducer exclusion.

The enzyme b-galactosidase acts on lactose to form galactose. In turn, the presence of galactose leads to expression of the enzymes responsible for the metabolism of galactose. In this case, lactose is serving as a carbon source and as a(n):

Inducer.

The lactose analog isopropyl-b-D-thio-galactoside (IPTG) is often used to regulate gene expression systems in bacteria. IPTG does not act as a substrate for b-galactosidase, but can bind to, and inactivate, the repressor. In this case, IPTG serves as a(n)

Inducer.

The lac repressor binds to what site within the lac operon?

LacO

Which of the following is not part of the lac operon?

Lacl

How does the cell recognize that lactose needs to be metabolized?

Lactose is converted into allolactose, which inhibits the lac repressor.

Which of the following cell signaling molecules crosses the cell membrane the easiest?

Molecules that are small and lipid-soluble.

Large chromatin-remodeling complexes alter the structure of chromatin in order to make the DNA ____ accessible to regulatory proteins which, in turn, affect gene expression.

More

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

Most eukaryotic genes contain introns.

During translation, translocation refers to:

Moving the ribosome along the mRNA molecule.

Which of the following molecules might be an intercellular signaling molecule?

NO

During transcription of mRNA in eukaryotes, some sequences are cut out of the primary transcript and the remaining sequences are joined together. This processing of mRNA is called _________.

Splicing.

Actual synthesis of the RNA transcript begins at the _________.

Start Site (3)

What is the base sequence, in the DNA template strand, of the intron that is closest to the 3' end of this strand?

TTACCCGGTTTA

You have discovered a way to damage proteins associated with initiating over-active inflammatory responses. You must now begin a study on the pathway that follows the clean up of those damaged proteins. Where would your study be focused?

Tagging of the protein with ubiquitin and then proteolysis of the protein by proteases in the proteasomes.

If two chromosomes are broken and they exchange non-homologous segments, this is called a ___________ translocation.

Tandem

When RNA polymerase reaches a __________, the RNA transcript and RNA polymerase separates from the DNA, and the DNA within the transcription bubble rewinds.

Terminator Sequence (5)

Evaluate the statements and determine which is the best explanation for why eukaryotes use so many regulatory elements, such as activators, repressors, coactivators, and basal transcription factors.

The complexity allows specific control over the timing and quantity of the protein produced.

In prokaryotes, the RNA polymerase holoenzyme consists of:

The core polymerase plus a sigma subunit.

Within the transcription bubble, the 9 most recently added nucleotides in the newly synthesized RNA strand temporarily form a helix with the template DNA strand. How might transcription be affected if helix formation did not occur?

The position of the 3' end of the RNA would be unstable, inhibiting elongation.

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.

Which of the following statement(s) about basal transcription factors is(are) TRUE?

They are essential for transcription and they cannot increase the rate of transcription by themselves.

Which of the following statements about basal transcription factors is TRUE?

They are essential for transcription and they cannot increase the rate of transcription by themselves.

Which of the following statements about enhancers is TRUE?

They are sequences to which activators bind.

When both glucose and lactose are present:

Transcription is turned off.

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

Transcription.

The codons do not overlap each other.

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

True

There is only one start codon.

True

At what point in gene expression do molecules go from being information storage molecules to metabolic and structurally functional molecules?

When RNA is translated into protein.

How does glucose effect the lac operon?

When glucose levels are low, it stimulates the production of cAMP, which binds to and activates the CAP protein, allowing it to bind to the DNA.

The enzyme dicer chops dsRNA molecules into small pieces of:

miRNA and siRNA

A charged _________ molecule with a UAC anticodon binds to the first AUG codon in the mRNA strand.

tRNA (2)