12. Gene Transcription and RNA Modification

Question 1

the process of synthesizing RNA from a DNA template.

Answer 1

Transcription

Question 2

a segment of DNA that contains the information to make a functional product, either RNA or a polypeptide.

Answer 2

Gene

Question 3

genes that produce mRNA and encode polypeptides

Answer 3

Protein-Coding (Structural) Genes

Question 4

a type of RNA that is transcribed from a protein-encoding gene and contains the information for the synthesis of a polypeptide.

Answer 4

Messenger RNA (mRNA)

Question 5

the process in which the sequence of codons within mRNA provides the information to synthesize the sequence of amino acids that constitute a polypeptide.

Answer 5

Translation

Question 6

the idea that the usual flow of genetic information is from DNA to RNA to polypeptide (protein). In addition, DNA replication serves to copy the information so that it can be transmitted from cell to cell and from parent to offspring.

Answer 6

Central Dogma of Genetic

Question 7

the process by which the information within a gene is accessed, first to synthesize RNA and polypeptides, and eventually to affect the phenotype of the organism.

Answer 7

Gene Expression

Question 8

a sequence within a gene that initiates (i.e., promotes) transcription.

Answer 8

Promoter

Question 9

a sequence within a gene that signals the end of transcription.

Answer 9

Terminator

Question 10

a strand of DNA that is used to synthesize a complementary strand of DNA or RNA.

Answer 10

Template Strand

Question 11

a strand of DNA that is not used as a template during transcription.

Answer 11

Nontemplate Strand

Question 12

the strand in DNA that is not used as a template for mRNA synthesis.

Answer 12

Coding (Sense) Strand

Question 13

a category of proteins that influence the ability of RNA polymerase to transcribe DNA into RNA.

Answer 13

Transcription Factors

Question 14

a segment of DNA that is recognized by a regulatory transcription factor. The binding of the transcription factor affects the rate of transcription.

Answer 14

Regulatory Sequence (Element)

Question 15

a short sequence in bacterial mRNA that binds to a ribosome and initiates translation.

Answer 15

Ribosome-Binding Site (Shine-Dalgarno Sequence)

Question 16

a sequence of three nucleotides in mRNA that functions in translation.

Answer 16

Codon

Question 17

a three-base sequence in mRNA that initiates translation. It is usually 5′-AUG-3′ and encodes methionine.

Answer 17

Start Codon

Question 18

a three-base sequence in mRNA that signals the end of translation of a polypeptide. The three are 5′–UAA–3′, 5′–UAG–3′, and 5′–UGA–3′.

Answer 18

Stop Codon

Question 19

(1) in transcription, the stage that involves the initial binding of RNA polymerase to the promoter in order to begin RNA synthesis; (2) in translation, the formation of a complex between mRNA, the initiator tRNA, and the ribosomal subunits.

Answer 19

Initiation

Question 20

(1) in transcription, the release of the newly made RNA transcript and RNA polymerase from the DNA; (2) in translation, the release of the polypeptide and the last tRNA and the disassembly of the ribosomal subunits and mRNA.

Answer 20

Termination

Question 21

an enzyme that synthesizes a strand of RNA using a DNA strand as a template.

Answer 21

RNA Polymerase

Question 22

the region of separation of two DNA strands produced by RNA polymerase during transcription.

Answer 22

Open Complex

Question 23

the site in a gene where transcription begins.

Answer 23

Transcriptional Start Site

Question 24

the TATAAT sequence that is often found at the −10 site of a bacterial promoter.

Answer 24

Pribnow Box

Question 25

the most commonly occurring bases within a specific type of sequence.

Answer 25

Consensus Sequence

Question 26

an enzyme composed of subunits that are needed for catalytic activity, as in the core enzyme of RNA polymerase.

Answer 26

Core Enzyme

Question 27

a transcription factor that recognizes bacterial promoter sequences and facilitates the binding of RNA polymerase to the promoter.

Answer 27

Sigma (σ) Factor

Question 28

an enzyme containing all of the functional subunits, such as the RNA polymerase holoenzyme that has σ factor along with the core enzyme.

Answer 28

Holoenzyme

Question 29

a structure found in transcription factor proteins that promotes binding to the major groove of DNA.

Answer 29

Helix-Turn-Helix Motif

Question 30

the complex between transcription factors, RNA polymerase, and a promoter before the DNA has denatured to form an open complex.

Answer 30

Closed Complex

Question 31

transcriptional termination that requires the participation of the ρ (rho) protein.

Answer 31

ρ-Dependent Termination

Question 32

transcription termination that does not require the ρ (rho) protein

Answer 32

ρ-Independent (Intrinsic) termination

Question 33

a relatively short DNA sequence that is necessary for transcription to take place. It provides the binding site for general transcription factors and RNA polymerase.

Answer 33

Core Promoter

Question 34

a sequence found within eukaryotic core promoters that determines the starting site for transcription. The TATA box is recognized by a TATA-binding protein, which is a component of TFIID.

Answer 34

TATA Box

Question 35

in eukaryotes, a low level of transcription produced by the core promoter. The binding of transcription factors to enhancer elements may increase transcription above the basal level.

Answer 35

Basal Transcription

Question 36

a DNA sequence that functions as a regulatory element in eukaryotes. The binding of a regulatory transcription factor to an enhancer increases the rate of transcription.

Answer 36

Enhancer

Question 37

a DNA sequence that functions as a regulatory element in eukaryotes. The binding of a regulatory transcription factor to a silencer decreases the rate of transcription.

Answer 37

Silencer

Question 38

a sequence of DNA, such as a regulatory element, that exerts a cis-effect.

Answer 38

Cis-Acting Element

Question 39

a regulatory protein that binds to a regulatory element in DNA and exerts a trans-effect.

Answer 39

Trans-Acting Element

Question 40

one of several proteins that are necessary to initiate basal transcription at the core promoter.

Answer 40

General Transcription Factor (GTF)

Question 41

a closed complex formed by the assembly of RNA polymerase II and general transcription factors at the core promoter, which initiates transcription.

Answer 41

Preinitiation Complex

Question 42

the minimum components that are needed to transcribe a eukaryotic gene; these include TFIID, TFIIB, TFIIF, TFIIE, TFIIH, RNA polymerase II, and a DNA sequence containing a TATA box and transcriptional start site.

Answer 42

Basal Transcription Apparatus

Question 43

a large protein complex that interacts with RNA polymerase II and various regulatory transcription factors. Depending on its interactions with regulatory transcription factors, mediator may stimulate or inhibit RNA polymerase II.

Answer 43

Mediator

Question 44

the correspondence between the sequence of codons in the DNA coding strand and the amino acid sequence of a polypeptide.

Answer 44

Colinearity

Question 45

a region of an RNA molecule that remains after splicing has removed the introns. In mRNA, the coding sequence of a polypeptide is contained within the exons.

Answer 45

Exon

Question 46

A segment of RNA that is removed during RNA splicing.

Answer 46

Intervening Sequence (Intron)

Question 47

in eukaryotes, a long transcript corresponding to the entire sequence of a protein-encoding gene, which is produced within the nucleus during transcription. This pre-mRNA is usually altered by splicing and other modifications before it exits the nucleus.

Answer 47

pre-mRNA

Question 48

the process in which pieces of RNA are removed and the remaining pieces are covalently attached to each other.

Answer 48

RNA Splicing

Question 49

an organelle within the nucleus of eukaryotic cells where the assembly of ribosomal subunits occurs.

Answer 49

Nucleolus

Question 50

an enzyme that digests an RNA or DNA strand from the end.

Answer 50

Exonuclease

Question 51

an enzyme that can cleave a bond between adjacent nucleotides within a DNA or RNA strand.

Answer 51

Endonuclease

Question 52

a type of intron found in self-splicing RNA that uses free guanosine in its splicing mechanism.

Answer 52

Group I Intron

Question 53

a type of intron found in self-splicing RNA that uses an adenine nucleotide within the intron itself in its splicing mechanism.

Answer 53

Group II Intron

Question 54

RNA splicing mechanism that occurs without the aid of any other catalyst.

Answer 54

Self-Splicing

Question 55

a protein that enhances the rate of self-splicing of group I and II introns.

Answer 55

Maturase

Question 56

a multisubunit complex that plays a key role in the splicing of eukaryotic pre-mRNAs.

Answer 56

Spliceosome

Question 57

a subunit of a spliceosome that consists of small nuclear RNA and a set of proteins.

Answer 57

snRNP

Question 58

a catalytically active RNA that uses one or more metal ions in its catalytic action.

Answer 58

Metalloribozyme

Question 59

the phenomenon that a pre-mRNA can be spliced in more than one way.

Answer 59

Alternative Splicing

Question 60

an exon that is always found in mature mRNAs following splicing.

Answer 60

Constitutive Exon

Question 61

an exon that is not always found in mature mRNAs. It is only found in certain types of alternatively spliced mRNAs.

Answer 61

Alternative Exon

Question 62

a protein that regulates the choice of splice sites in the process of RNA splicing.

Answer 62

Splicing Factor

Question 63

a type of splicing factor.

Answer 63

SR Protein

Question 64

the splicing out of an exon from a pre-mRNA so that it is not included in the mature mRNA.

Answer 64

Exon Skipping

Question 65

the covalent attachment of a 7-methylguanosine to the 5′ end of mRNA in eukaryotes.

Answer 65

Capping

Question 66

the string of adenine nucleotides at the 3′ end of eukaryotic mRNAs.

Answer 66

polyA Tail

Question 67

the process of attaching a string of adenine nucleotides to the 3′ end of eukaryotic mRNAs.

Answer 67

Polydenylation

Question 68

the process in which a change is made in the nucleotide sequence of an RNA molecule that involves additions or deletions of particular bases or conversion of one type of base to a different type.

Answer 68

RNA Editing