Chapter 15

Question 1

The enzymatic process whereby the genetic information contained in one strand of DNA is used to specify a complementary sequence of bases in an RNA strand

Answer 1

transcription

Question 2

A class of RNA molecules, each of which is complementary to one strand of DNA, that carry the genetic message from the chromosome to the ribosomes

Answer 2

messenger RNA (mRNA)

Question 3

A class of RNA molecules (Mr 25,000 to 30,000), each of which combines covalently with a specific amino acid for use in protein synthesis.

Answer 3

transfer RNA (tRNA)

Question 4

A class of RNA molecules serving as components of ribosomes.

Answer 4

Ribosomal RNA (rRNA)

Question 5

One of the three eukaryotic RNA polymerases; Pol I transcribes genes encoding large rRNA precursors

Answer 5

RNA Polymerase I

Question 6

One of the three eukaryotic RNA polymerases; Pol II transcribes most of the protein-coding genes.

Answer 6

RNA Polymerase II

Question 7

One of the three eukaryotic RNA polymerases; Pol III transcribes genes encoding tRNAs, some snRNAs, 5S ribosomal RNA, and other small functional RNAs.

Answer 7

RNA Polymerase III

Question 8

A transient subunit of the bacterial RNA polymerase that directs the enzyme to the promoter. Different sigma factors are specific for different promoters. The core RNA polymerase plus the sigma factor constitutes the RNA polymerase holoenzyme.

Answer 8

sigma factor

Question 9

the first 3 stages of synthesis of DNA, RNA, and proteins

Answer 9

initiation

Question 10

(1) The second of three stages of RNA synthesis, in which ribonucleotides are added to the 3′ end of the growing RNA molecule.

(2) The second of three stages of protein synthesis, in which amino acids are added to the C-terminal end of the growing peptide chain.

Answer 10

elongation

Question 11

(1) The third of three stages of RNA synthesis, in which the RNA polymerase and the RNA product are released from the DNA template.

(2) The third of three stages of protein synthesis, in which the ribosome and the peptide product are released from the mRNA template.

Answer 11

termination

Question 12

A DNA sequence at which RNA polymerase may bind, leading to initiation of transcription.

Answer 12

promoter

Question 13

A DNA or amino acid sequence consisting of the residues that most commonly occur at each position in a set of similar sequences.

Answer 13

consensus sequence

Question 14

An AT-rich sequence between positions −40 and −60 in the promoters of some highly expressed bacterial genes. The sequence is bound by an α subunit of RNA polymerase, improving the efficiency of transcription initiation for that gene.

Answer 14

upstream promoter (UP) element

Question 15

A strand of nucleic acid used by a polymerase as a template to synthesize a complementary strand.

Answer 15

template strand

Question 16

The strand of a double-stranded DNA that has the same sequence as the RNA transcript (with T in place of U) and is complementary to the template strand. Also called the nontemplate strand.

Answer 16

coding strand

Question 17

A complex of the RNA polymerase bound to a promoter, in which the DNA is intact and double-stranded. Compare open complex

Answer 17

closed complex

Question 18

(1) A complex of the RNA polymerase bound to a promoter, in which the bound DNA is partially unwound. Transcription initiation occurs in the open complex. Compare closed complex.

(2) A complex assembled on the E. coli origin of replication, oriC, at an early stage of replication initiation. It includes an oligomer of the AAA+ protein DnaA, ATP, and the histonelike protein HU.

Answer 18

open complex

Question 19

The complex of proteins required for efficient synthesis of the RNA transcript after the RNA polymerase has moved beyond the promoter.

Answer 19

elongation complex

Question 20

candidate DNA sequences are radiolabeled at one end. Then, a DNA-binding protein is added. Finally, chemical or enzymatic reagents are added to the mix in order to cleave the DNA randomly.

Answer 20

dna footprinting

Question 21

Release of an 8 to 10 base pair RNA transcript from the bacterial RNA polymerase initiation complex before it clears the promoter and enters the elongation stage.

Answer 21

abortive initiation

Question 22

The reverse of a nucleotide polymerization reaction, in which pyrophosphate reacts with the 3′-nucleotide monophosphate of an oligonucleotide, releasing the corresponding nucleotide triphosphate.

Answer 22

pyrophosphorolysis

Question 23

A mechanism for error correction in complex biological processes that maximizes the speed of correct reactions while stalling and allowing incorrect reactions to reverse.

Answer 23

kinetic proofreading

Question 24

A pathway for the correction of errors in an RNA transcript in which the RNA polymerase reverses direction by one or a few nucleotides on the template, and its endonuclease activity hydrolyzes the phosphodiester backbone of the transcript proximal to the mismatched base.

Answer 24

nucleolytic proofreading

Question 25

A DNA sequence, at the end of a transcriptional unit, that signals the end of transcription.

Answer 25

termination sequence

Question 26

In eukaryotes, a protein that affects the regulation and transcription initiation of a gene by binding to a regulatory sequence near or within the gene and interacting with RNA polymerase and/or other transcription factors

Answer 26

transcription factor

Question 27

A eukaryotic transcription factor that binds all three RNA polymerases as well as the AT-rich region of many promoters known as the TATA box.

Answer 27

TATA-binding protein (TBP)

Question 28

In eukaryotic cells, the DNA sequence elements common to promoters used by Pol II. The TATA box and initiator sequence (Inr) are required elements of a core promoter; a TFIIB recognition element (BRE) and downstream promoter element (DPE) may also be involved in transcription initiation from some core promoters

Answer 28

core promoter

Question 29

A eukaryotic nucleoprotein complex consisting of intact, double-stranded promoter DNA, Pol II, and various transcription factors.

Answer 29

preinitiation complex

Question 30

A large, multiprotein complex in eukaryotic cells that serves as the mediator between the Pol II transcription complex and any upstream transcription activators or enhancers regulating Pol II–catalyzed transcription.

Answer 30

mediator complex