chapter 7

Question 1

RNA differs from DNA chemically in two respects: (1) the nucleotides in RNA are _—that is, they contain the sugar _ (hence the name ribonucleic acid) rather than the _ found in DNA; and (2) although, like DNA, RNA contains the bases adenine (A), guanine (G), and cytosine (C), it contains _ (U) instead of the _ (T)
found in DNA

Answer 1

ribonucleotides
ribose
deoxyribose
uracil
thymine

Question 2

The first step a cell takes in expressing one of its many thousands of genes is to copy the nucleotide sequence of that gene into RNA. The pro- cess is called _

Answer 2

transcription

Question 3

Whereas DNA always occurs in cells as a double-stranded helix, RNA is largely _.

Answer 3

single-stranded

Question 4

RNA polymer- ases make about one mistake for every _ nucleotides copied into RNA

Answer 4

10^4

Question 5

The majority of genes carried in a cell’s DNA specify the amino acid sequences of proteins. The RNA molecules encoded by these genes— which ultimately direct the synthesis of proteins—are called _ (_).

Answer 5

messenger RNAs
mRNAs

Question 6

When an RNA polymerase collides randomly with a DNA molecule, the enzyme sticks weakly to the double helix and then slides rapidly along its length. RNA polymerase latches on tightly only after it has encountered a gene region called a _.
As it binds tightly to this sequence, the RNA polymerase opens up the double helix immediately in front of the _ to expose the nucleotides on each strand of a short stretch of DNA.

Answer 6

promoter
promoter

Question 7

Elongation then continues until the enzyme encounters a second signal in the DNA, the _, where the polymerase halts and releases both the DNA template and the newly made RNA transcript

Answer 7

terminator (or stop site)

Question 8

The terminator sequence itself is _, and it is the interaction of this _ with the polymerase that causes the enzyme to let go of the template DNA.

Answer 8

also transcribed
3’ segment of RNA

Question 9

a segment of DNA will be transcribed only if _.

Answer 9

it is preceded by a promoter

Question 10

RNA polymerases I and III transcribe the genes encoding _, _ RNA, and various other RNAs that _ in the cell.

Answer 10

transfer RNA
ribosomal
play structural and catalytic roles

Question 11

RNA polymerases _ transcribe the genes encoding transfer RNA, ribosomal RNA, and various other RNAs that play structural and catalytic roles in the cell

Answer 11

I and III

Question 12

RNA polymerase _ transcribes the rest, including all those that encode _—which constitutes the majority of genes in eukaryotes

Answer 12

II
proteins

Question 13

WhereasthebacterialRNApolymerase(alongwithitssigmasubunit) is able to initiate transcription on its own, eukaryotic RNA polymerases require the assistance of a _ Principal among these are the _, which must assemble at each promoter, along with the polymerase, before transcription can begin.

Answer 13

large set of accessory proteins.
general transcription factors

Question 14

And before it can be exported to the cytosol, a eukaryotic RNA must go through several RNA processing steps, which include _, _, and _

Answer 14

capping
splicing
polyadenylation

Question 15

In short, capping modifies the _ of RNA, and polyadenylation adds _ to _ in eukaryotic cells. These changes help the RNA to be _, _, and _.

Answer 15

front (5’ end)
a long tail (poly-A tail)
the back (3’ end)
stable
exported
translated properly

Question 16

RNA splicing is carried out largely by RNA molecules rather than proteins. These RNA molecules, called _, are packaged with additional _ to form _

Answer 16

small nuclear RNAs (snRNAs)
_
proteins
_
small nuclear ribonucleoproteins (snRNPs, pro- nounced “snurps”).

Question 17

Together, these snRNPs form the core of the _, the large assembly of RNA and protein molecules that carries out RNA splicing in the nucleus.

Answer 17

spliceosome

Question 18

the transcripts of many eukaryotic genes can be spliced in different ways, each of which can produce a distinct protein called:_

Answer 18

alternative splicing

Question 19

the translation of mRNA into protein depends on adaptor molecules that bind to a codon with one part of the adaptor and to an amino acid with another. These adaptors consist of a set of small RNA molecules known as _, each about 80 nucleotides in length.

Answer 19

transfer RNAs (tRNAs)

Question 20

ecognition and attachment of the correct amino acid depend on enzymes called _

Answer 20

aminoacyl-tRNA synthetases

Question 21

This _ tRNA always carries
the amino acid methionine

Answer 21

initiator

Question 22

In eukaryotes, an initiator tRNA, charged with methionine, is first loaded into the _ site of the small ribosomal subunit, along with additional proteins called _

Answer 22

P
translation initiation factors

Question 23

These enzymes, which degrade proteins, first to short peptides and finally to individual amino acids, are known collectively as _.
proteins are broken down by large protein machines called _

Answer 23

proteases
proteasomes

Question 24

Proteins must then fold into the correct, three-dimensional shape (as we discuss in Chapter 4). Some proteins do so spontaneously, as they emerge from the ribosome. Most, however, require the assistance of _, which steer them along productive folding path- ways and prevent them from aggregating inside the cell

Answer 24

chaperone proteins

Question 25

The conversion of the genetic instructions in DNA into RNAs and proteins is termed _.

Answer 25

gene expression

Question 26

Cells make several functional types of RNAs, including messenger RNAs (mRNAs), which carry the instructions for making proteins; _, which are the crucial components of _; and transfer RNAs (tRNAs), which act as adaptor molecules in protein synthesis.

Answer 26

ribosomal RNAs (rRNAs) ribosomes

Question 27

To begin transcription, RNA polymerase binds to specific DNA sites called promoters that lie immediately upstream of genes. To initiate transcription, eukaryotic RNA polymerases require the assembly of a complex of general transcription factors at the promoter, whereas bacterial RNA polymerase requires only an additional subunit, called _.

Answer 27

sigma factor

Question 28

Introns are removed from the RNA transcripts in the nucleus by RNA splicing, a reaction catalyzed by _ known as snRNPs. Splicing removes the introns from the RNA and joins together the exons—often in a variety of combinations, allowing multiple proteins to be produced from the same gene.

Answer 28

small ribonucleoprotein complexes snRNPs

Question 29

Eukaryotic pre-mRNAs go through several additional RNA process- ing steps before they leave the nucleus as mRNAs, including 5ʹ RNA capping and 3ʹ polyadenylation. These reactions, along with splicing, take place _

Answer 29

as the pre-mRNA is being transcribed.

Question 30

tRNAs act as adaptor molecules in protein synthesis. Enzymes called _ covalently link amino acids to their appropriate tRNAs. Each tRNA contains a sequence of three nucleo- tides, the anticodon, which recognizes a codon in an mRNA through complementary base-pairing.

Answer 30

aminoacyl-tRNA synthetases

Question 31

The stepwise linking of amino acids into a polypeptide chain is catalyzed by an _ in the _, which thus acts as a _.

Answer 31

rRNA molecule large ribosomal subunit ribozyme

Question 32

The concentration of a protein in a cell depends on _. Protein degradation in the cytosol and nucleus occurs inside large protein complexes called _.

Answer 32

the rates at which the mRNA and protein are synthesized and degraded _ proteasomes

Question 33

From our knowledge of present-day organisms and the molecules they contain, it seems likely that life on Earth began with the evolution of _.

Answer 33

RNA molecules that could catalyze their own replication

Question 34

The chemical linkage between nucleotides in RNA—a _ bond—is the same as that in DNA.

Answer 34

phosphodiester

Question 35

The nontemplate strand of the gene (here, shown at the top) is sometimes called the _ because its _.

Answer 35

coding strand sequence is equivalent to the RNA product

Question 36

RNA molecule is usually depicted with its _ end, which is the first part to be synthesized.

Answer 36

5'

Question 37

Bacterial RNA polymerase (light blue) contains a subunit called _ (yellow) that recognizes the promoter of a gene (green). Once transcription has begun, _ is released, and the polymerase moves forward and continues synthesizing the RNA. Elongation continues until the polymerase encounters a sequence in the gene called the _ (red ). After transcribing this sequence into RNA (dark blue), the enzyme halts and releases both the DNA template and the newly made RNA transcript. The polymerase then reassociates with a _ and searches for another promoter to begin the process again.

Answer 37

sigma factor sigma factor terminator free sigma factor

Question 38

To begin transcription, eukaryotic RNA polymerase II requires _

Answer 38

a set of general transcription factors.

Question 39

Most eukaryotic promoters contain a DNA sequence called the _.

Answer 39

TATA box

Question 40

The TATA box is recognized by a _, called the _.

Answer 40

subunit of the general transcription factor TFIID TATA-binding protein (TBP)

Question 41

The binding of TFIID enables the adjacent _. The rest of the _, as well as the _ itself, then assemble at the promoter.

Answer 41

binding of TFIIB. general transcription factors RNA polymerase

Question 42

TFIIH _ at the transcription start point, using the energy of _, which exposes the template strand of the gene. TFIIH also _, releasing the polymerase from most of the general transcription factors, so it can begin transcription. The site of phosphorylation is a _ that extends from the polymerase.

Answer 42

pries apart the double helix ATP hydrolysis phosphorylates RNA polymerase II long polypeptide “tail”

Question 43

Once the polymerase moves away from the promoter, most of the general transcription factors are released from the DNA; the exception is _, which remains bound through multiple rounds of transcription initiation.

Answer 43

TFIID

Question 44

Splicing is carried out by a collection of _ called _.

Answer 44

RNA–protein complexes snRNPs

Question 45

In the first steps of splicing, U1 recognizes the _ and U2 recognizes the _ through complementary base-pairing.

Answer 45

5' splice site lariat branch-point site

Question 46

U6 then “_” the _ by displacing _ and base-pairing with this intron sequence itself.

Answer 46

re-checks 5' splice site U1

Question 47

In the next steps, conformational changes in _—triggered by the _ by spliceosomal proteins (not shown)— drive the formation of the _.

Answer 47

U2 and U6 hydrolysis of ATP spliceosome active site

Question 48

Once the splicing reactions have occurred (see Figure 7–21), the spliceosome deposits a group of _, known as the _(red ), on the mRNA to mark the splice site as successfully completed.

Answer 48

RNA-binding proteins exon junction complex

Question 49

Translation takes place in a _, which is repeated over and over during the synthesis of a protein.

Answer 49

four-step cycle

Question 50

In step 1 (translation), a charged tRNA carrying the next amino acid to be added to the polypeptide chain binds to the _ on the ribosome by forming base pairs with the mRNA codon that is exposed there.

Answer 50

vacant A site

Question 51

The A and P sites are sufficiently close together that their two tRNA molecules are _, with no stray bases in-between. This positioning of the tRNAs ensures that the correct _ will be preserved throughout the synthesis of the protein.

Answer 51

forced to form base pairs with codons that are contiguous _ reading frame

Question 52

In step 2, the carboxyl end of the polypeptide chain (amino acid 3 in step 1) is _ from the tRNA at the _ site and joined by a _ to the free amino group of the amino acid linked to the tRNA at the _ site. This reaction is carried out by a catalytic site in the _.

Answer 52

uncoupled P peptide bond A large subunit

Question 53

In step 3, a shift of the_ relative to the _ moves the two bound tRNAs into the _ sites of the _ subunit.

Answer 53

large subunit small subunit E and P large

Question 54

In step 4, the _ subunit moves exactly three nucleotides along the mRNA molecule, bringing it back to its original position relative to the _ subunit. This movement ejects the _ and resets the ribosome with an empty _ site so that the next charged tRNA molecule can bind

Answer 54

small large spent tRNA A

Question 55

Initiation of protein synthesis in eukaryotes requires _ and a _.

Answer 55

translation initiation factors special initiator tRNA

Question 56

efficient translation initiation also requires additional proteins that are bound at the _ of the mRNA. In this way, the translation apparatus can ascertain that both ends of the mRNA are _ before initiating translation.

Answer 56

5' cap and poly-A tail intact

Question 57

Proteins marked by a _ chain are degraded by the proteasome.

Answer 57

polyubiquitin

Question 58

Proteins in the _ (blue) recognize proteins marked by a specific type of polyubiquitin chain (red ). The _ unfolds the target protein and threads it into the _ (yellow), which is lined with _ that chop the protein to pieces.

Answer 58

stopper of a proteasome stopper proteasome’s central cylinder proteases