Chapter 17: Gene Expression: From Gene to Protein

TATA box

A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.

point mutation

A change in a single nucleotide pair of a gene.

mutation

A change in the nucleotide sequence of an organism's DNA or in the DNA or RNA of a virus.

mutagen

A chemical or physical agent that interacts with DNA and can cause a mutation.

ribosome

A complex of rRNA and protein molecules that functions as a site of protein synthesis in the cytoplasm; consists of a large and a small subunit. In eukaryotic cells, each subunit is assembled in the nucleolus.

domain

A discrete structural and functional region of a protein.

polyribosomes (or polysomes)

A group of several ribosomes attached to, and translating, the same messenger RNA molecule.

spliceosome

A large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons.

5' cap

A modified form of guanine nucleotide added onto the 5′ end of a pre-mRNA molecule.

insertion

A mutation involving the addition of one or more nucleotide pairs to a gene.

frameshift mutation

A mutation occurring when nucleotides are inserted in or deleted from a gene and the number inserted or deleted is not a multiple of three, resulting in the improper grouping of the subsequent nucleotides into codons.

nonsense mutation

A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.

deletion

A mutational loss of one or more nucleotide pairs from a gene.

intron

A noncoding, intervening sequence within a primary transcript that is removed from the transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed.

silent mutation

A nucleotide-pair substitution that has no observable effect on the phenotype; for example, within a gene, a mutation that results in a codon that codes for the same amino acid.

missense mutation

A nucleotide-pair substitution that results in a codon that codes for a different amino acid.

What polypeptide product would you expect from a poly-G mRNA that is 30 nucleotides long?

A polypeptide made up of 10 Gly (glycine) amino acids

What is a promoter? is it located at the upstream or downstream end of a transcription unit?

A promoter is the region of DNA to which RNA polymerase binds to begin transcription. It is at the upstream end of the gene (transcription unit).

signal-recognition particle (SRP)

A proteinRNA complex that recognizes a signal peptide as it emerges from a ribosome and helps direct the ribosome to the endoplasmic reticulum (ER) by binding to a receptor protein on the ER.

transcription unit

A region of DNA that is transcribed into an RNA molecule.

transcription factor

A regulatory protein that binds to DNA and affects transcription of specific genes.

poly-A tail

A sequence of 50-250 adenine nucleotides added onto the 3′ end of a premRNA molecule.

signal peptide

A sequence of about 20 amino acids at or near the leading (amino) end of a polypeptide that targets it to the endoplasmic reticulum or other organelles in a eukaryotic cell.

exon

A sequence within a primary transcript that remains in the RNA after RNA processing; also refers to the region of DNA from which this sequence was transcribed.

Describe how a polypeptide to be secreted reaches the endomembrane system.

A signal peptide on the leading end of the polypeptide being synthesized is recognized by a signal-recognition particle that brings the ribosome to the ER membrane. There the ribosome attaches and continues to synthesize the polypeptide, depositing it in the ER lumen.

promoter

A specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.

codon

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

messenger RNA (mRNA)

A type of RNA, synthesized using a DNA template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein. (In eukaryotes, the primary RNA transcript must undergo RNA processing to become mRNA.)

alternative RNA splicing

A type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.

nucleotide-pair substitution

A type of point mutation in which one nucleotide in a DNA strand and its partner in the complementary strand are replaced by another pair of nucleotides.

RNA splicing

After synthesis of a eukaryotic primary RNA transcript, the removal of portions of the transcript (introns) that will not be included in the mRNA and the joining together of the remaining portions (exons).

transfer RNA (tRNA)

An RNA molecule that functions as a translator between nucleic acid and protein languages by carrying specific amino acids to the ribosome, where they recognize the appropriate codons in the mRNA.

ribozyme

An RNA molecule that functions as an enzyme, such as an intron that catalyzes its own removal during RNA splicing.

aminoacyl-tRNA synthetases

An enzyme that joins each amino acid to the appropriate tRNA.

primary transcript

An initial RNA transcript from any gene; also called pre-mRNA when transcribed from a protein-coding gene.

A part of the promoter, called the TATA box, is said to be highly conserved in evolution. Which might this illustrate? A) The sequence evolves very rapidly. B) The sequence does not mutate. C) Any mutation in the sequence is selected against. D) The sequence is found in many but not all promoters. E) The sequence is transcribed at the start of every gene

Any mutation in the sequence is selected against.

Each of the following options is a modification of the sentence THECATATETHERAT. Which of the following is analogous to a frameshift mutation? A) THERATATETHECAT B) THETACATETHERAT C) THECATARETHERAT D) THECATATTHERAT E) CATATETHERAT

D) THECATATTHERAT

Crick and Brenner

Determined that deletion 1 or 2 bases near each other altered the entire polypeptide ("frameshift mutation"), but deletion of 3 bases resulted in a polypeptide that was normal after the deletion. The same is true for insertion of 1,2, or 3 bases

There are fewer than 21,000 human genes. how, then, can human cells make 75,000-100,000 different proteins?

Due to alternative splicing of exons, each gene can result in multiple different mRNAs and can thus direct synthesis of multiple different proteins.

What two processes ensure that the correct amino acid is added to a growing polypeptide chain?

First, each aminoacyl-tRNA synthetase specifically recognizes a single amino acid and attaches it only to an appropriate tRNA. Second, a tRNA charged with its specific amino acid binds only to an mRNA codon for that amino acid.

wobble

Flexibility in the base-pairing rules in which the nucleotide at the 5′ end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3′ end) of a codon.

What enables rna polymerase to start transcribing a gene at the right place on the Dna in a bacterial cell? in a eukaryotic cell?

In a bacterial cell, part of the RNA polymerase recognizes the gene's promoter and binds to it. In a eukaryotic cell, transcription factors mediate the binding of RNA polymerase to the promoter. In both cases, sequences in the promoter bind precisely to the RNA polymerase, so the enzyme is in the right location and orientation.

terminator

In bacteria, a sequence of nucleotides in DNA that marks the end of a gene and signals RNA polymerase to release the newly made RNA molecule and detach from the DNA.

What happens when one nucleotide pair is lost from the middle of the coding sequence of a gene?

In the mRNA, the reading frame downstream from the deletion is shifted, leading to a long string of incorrect amino acids in the polypeptide, and in most cases, a stop codon will arise, leading to premature termination. The polypeptide will most likely be nonfunctional.

start point

In transcription, the nucleotide position on the promoter where RNA polymerase begins synthesis of RNA.

How is RNA splicing similar to how you would watch a television show recorded earlier using a DVR? What would introns correspond to in this analogy?

In watching a show recorded with a DVR, you watch segments of the show itself (exons) and fast-forward through the commercials, which are thus like introns.

Which of these is the function of a poly (A) signal sequence? A) It adds the poly (A) tail to the 3ʹ end of the mRNA. B) It codes for a sequence in eukaryotic transcripts that signals enzymatic cleavage ~10 —35 nucleotides away. C) It allows the 3ʹ end of the mRNA to attach to the ribosome. D) It is a sequence that codes for the hydrolysis of the RNA polymerase. E) It adds a 7-methylguanosine cap to the 3ʹ end of the mRNA.

It codes for a sequence in eukaryotic transcripts that signals enzymatic cleavage ~10 —35 nucleotides away.

RNA processing

Modification of RNA primary transcripts, including splicing out of introns, joining together of exons, and alteration of the 5′ and 3′ ends.

reading frame

On an mRNA, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis.

What would be the effect of treating cells with an agent that removed the cap from mRNA?

Once the mRNA has exited the nucleus, the cap prevents it from being degraded by hydrolytic enzymes and facilitates its attachment to ribosomes. If the cap were removed from all mRNAs, the cell would no longer be able to synthesize any proteins and would probably die.

A site

One of a ribosome's three binding sites for tRNA during translation. The A site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. (A stands for aminoacyl tRNA.)

E site

One of a ribosome's three binding sites for tRNA during translation. The E site is the place where discharged tRNAs leave the ribosome. (E stands for exit.)

P site

One of a ribosome's three binding sites for tRNA during translation. The P site holds the tRNA carrying the growing polypeptide chain. (P stands for peptidyl tRNA.)

ribosomal RNAs (rRNAs)

RNA molecules that, together with proteins, make up ribosomes; the most abundant type of RNA.

template strand

The DNA strand that provides the pattern, or template, for ordering, by complementary base pairing, the sequence of nucleotides in an RNA transcript.

transcription initiation complex

The completed assembly of transcription factors and RNA polymerase bound to a promoter.

triplet code

The genetic instructions for a polypeptide chain written in the DNA as a series of nonoverlapping, three-nucleotide words.

Discuss the ways in which rrna structure likely contributes to ribosomal function.

The structure and function of the ribosome seem to depend more on the rRNAs than on the ribosomal proteins. Because it is single-stranded, an RNA molecule can hydrogen-bond with itself and with other RNA molecules. RNA molecules make up the interface between the two ribosomal subunits, so presumably RNA-RNA binding helps hold the ribosome together. The binding site for mRNA in the ribosome includes rRNA that can bind the mRNA. Also, complementary hydrogen bonding within an RNA molecule allows it to assume a particular threedimensional shape and, along with the RNA's functional groups, enables rRNA to catalyze peptide bond formation during translation.

translation

The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of "language" from nucleotides to amino acids.

Suppose X-rays caused a sequence change in the tata box of a particular gene's promoter. how would that affect transcription of the gene?

The transcription factor that recognizes the TATA sequence would be unable to bind, so RNA polymerase could not bind and transcription of that gene probably would not occur.

Which of the following is (are) true of snRNPs? A) They are made up of both DNA and RNA. B) They bind to splice sites at each end of the exon. C) They join together to form a large structure called the spliceosome. D) They act only in the cytosol. E) They attach introns to exons in the correct order.

They join together to form a large structure called the spliceosome.

In eukaryotic cells, mrnas have been found to have a circular arrangement in which proteins hold the poly-a tail near the 5¿ cap. how might this increase translation efficiency?

When one ribosome terminates translation and dissociates, the two subunits would be very close to the cap. This could facilitate their rebinding and initiating synthesis of a new polypeptide, thus increasing the efficiency of translation.

open reading frame (ORF)

a sequence of DNA that contains an ATG methionine start codon followed in frame by 33 or more codons before reaching a a stop codon.

When the ribosome reaches a stop codon on the mRNA, no corresponding tRNA enters the A site. If the translation reaction were to be experimentally stopped at this point, which of the following would you be able to isolate? A) an assembled ribosome with a polypeptide attached to the tRNA in the P site B) separated ribosomal subunits, a polypeptide, and free tRNA C) an assembled ribosome with a separated polypeptide D) separated ribosomal subunits with a polypeptide attached to the tRNA E) a cell with fewer ribosomes

an assembled ribosome with a polypeptide attached to the tRNA in the P site

When does translation begin in prokaryotic cells? A) after a transcription initiation complex has been formed B) as soon as transcription has begun C) after the 5ʹ caps are converted to mRNA D) once the pre-mRNA has been converted to mRNA E) as soon as the DNA introns are removed from the template

as soon as transcription has begun

Alternative RNA splicing A) is a mechanism for increasing the rate of transcription. B) can allow the production of proteins of different sizes from a single mRNA. C) can allow the production of similar proteins from different RNAs. D) increases the rate of transcription. E) is due to the presence or absence of particular snRNPs.

can allow the production of proteins of different sizes from a single mRNA.

Nirenberg and Mathaei

determined the sequence of the first codon, UUU that coded for the amino acid phenylalanine. The same technique was used to show that AAA codes for lysine, GGG for glycine, CCC for proline. Other more elaborate techniques were required to decode mixed triplets such a AUA and CGA.

When a tRNA molecule is shown twisted into an L shape, the form represented is A) its linear sequence. B) its 2-dimensional shape. C) its 3-dimensional shape. D) its microscopic image.

its 3-dimensional shape.

The process of translation, whether in prokaryotes or eukaryotes, requires tRNAs, amino acids, ribosomal subunits, and which of the following? A) polypeptide factors plus ATP B) polypeptide factors plus GTP C) polymerases plus GTP D) SRP plus chaperones E) signal peptides plus release factor

polypeptide factors plus GTP

RNA polymerase

pries the two strands of DNA apart and joins together RNA nucleotides complementary to the DNA template strand, thus elongating the RNA polynucleotide (are able to start a chain from scratch; they don't need a primer unlike DNA polymerase).

A mutant bacterial cell has a defective aminoacyl synthetase that attaches a lysine to tRNAs with the anticodon AAA instead of a phenylalanine. The consequence of this for the cell will be that A) none of the proteins in the cell will contain phenylalanine. B) proteins in the cell will include lysine instead of phenylalanine at amino acid positions specified by the codon UUU. C) the cell will compensate for the defect by attaching phenylalanine to tRNAs with lysine-specifying anticodons. D) the ribosome will skip a codon every time a UUU is encountered. E) None of the above will occur; the cell will recognize the error and destroy the tRNA

proteins in the cell will include lysine instead of phenylalanine at amino acid positions specified by the codon UUU.

H. Gobind Khorana

provided the final piece of puzzle by using organic synthesis to produce a defined artifical RNA and examine its protein sequence.

The TATA sequence is found only several nucleotides away from the start site of transcription. This most probably relates to which of the following? A) the number of hydrogen bonds between A and T in DNA B) the triplet nature of the codon C) the ability of this sequence to bind to the start site D) the supercoiling of the DNA near the start site E) the 3-dimensional shape of a DNA molecule

the number of hydrogen bonds between A and T in DNA

Gene expression

the process by which DNA directs the synthesis of proteins

transcription

the synthesis of RNA using information in the DNA.

Which of the following is a function of a signal peptide? A) to direct an mRNA molecule into the cisternal space of the ER B) to bind RNA polymerase to DNA and initiate transcription C) to terminate translation of the messenger RNA D) to translocate polypeptides across the ER membrane E) to signal the initiation of transcription

to bind RNA polymerase to DNA and initiate transcription