Chapter 12 Transcription

What region in eukaryotic genes usually contains the majority of regulatory elements such as GC and CAAT boxes?

-50 to -100

the consensus sequences at a bacterial promoter are 5' TTGACA 3' and 5' TATAAT 3' at -35 and -10 respectively. Which of the following sequences would be most easily recognized by σ factor?

5' TTGAAA 3' Sigma factor recognizes both the -35 and the -10 sequences. Among the sequences listed, 5' TTGAAA 3' has the fewest deviations from either of the consensus sequences, and would be most easily recognized by sigma factor.

Which of the following modifications occur to a eukaryotic pre-mRNA?

5' cap added, removal of introns, 3' poly A tail added

The template strand of a gene has the sequence: 5'-ATTGCC-3'. What is the sequence of the transcribed mRNA?

5'-GGCAAU-3'

Part of the coding region of a gene is shown here: 5'-TTCCCATTTCGATGGGATACGATGG-3' 3'-AAGGGTAAAGCTACCCTATGCTACC-5' What is the sequence of the transcribed mRNA, assuming transcription proceeds left to right?

5'-UUCCCAUUUCGAUGGGAUACGAUGG-3'

What percentage of human pre-mRNA is alternatively spliced?

70%

The low level of transcription caused by the presence of the core promoter by itself is known as

Basal transcription

Which of the following occurs first in prokaryotic transcription?

Formation of a holoenzyme

What do both the rho-dependent and rho-independent mechanisms of termination have in common?

Formation of a stem-loop structure

Where does splicing occur in the cell?

In the nucleus

What is a mechanism by which tRNA is processed in E. coli?

RNaseP acts as an endonuclease.

What is the correct order of elements that comprise a functional protein encoding gene in a prokaryote?

Regulatory region, promoter, transcribed region, terminator

Which of the following are the two mechanisms of transcription termination in E. coli?

Rho-dependent termination Rho-independent termination

In bacteria, a short sequence in the mRNA provides a location that recruits the machinery to start translation. This sequence is called the - site.

Shine-Dalgarno

Which of the following is correct regarding sigma factor?

It recognizes the promoter region

Who proposed the existence of messenger RNA in 1961?

Jacob and Monod

What is unusual about the 5' cap found on almost all eukaryotic mRNAs?

The nucleotide added is a guanine methylated at N7 and the bond is created between the phosphate group on the guanine and the phosphate on the terminal nucleotide

What marks the transition to the elongation stage of transcription in bacteria?

The release of the sigma factor from the RNA pol holoenzyme

The addition of a 7-methylguanosine to the 5' end of a mature mRNA is a process known as

capping

In E. coli, the RNA polymerase holoenzyme is composed of the ______ plus ______.

core enzyme; sigma factor

At the molecular level, ______ is the process by which a gene's information is used to produce a polypeptide or functional RNA molecule.

gene expression

The association of a sigma factor with the core enzyme forms a complex referred to as the RNA polymerase

holoenzyme

Basal transcription refers to the low level of transcription that ______.

involves only the core promoter

Francois Jacob and Jacques Monod hypothesized the existence of which molecule?

mRNA

The ribosome-binding site is a sequence in bacterial ______ that is involved in ______.

mRNA ; translation initiation

Which one is not a characteristic of bacterial transcription?

mRNA can be modified by RNA editing

You are working in a lab studying mRNAs from many different species. You need to distinguish between mRNAs in a mixed sample. You begin by having all of the mRNAs sequenced, including the mitochondrial mRNAs. You notice a high number of C to U conversions in the mitochondrial mRNAs from a certain portion of the sample. You conclude that this portion of the sample is from __________.

plants

Where does the process of transcription initiate?

promoter

In a gene, the DNA is transcribed into RNA from the ______ to the ______.

promoter; terminator

The sequence of a gene's DNA that is transcribed extends from the_______ end of the to the end of the_______

promoter; terminator

Match the eukaryotic RNA polymerase to the category of genes it transcribes. RNA polymerase I RNA polymerase II RNA polymerase III

rRNA protein-encoding genes tRNA and 5S rRNA

The nucleolus in eukaryotes is the site of processing of ______ RNA.

ribosomal RNA

What enables the splicing of group I and II introns?

ribozymes

Splicing that does not require the aid of other catalysts is known as

self splicing

Splicing joins together __________.

two exons

The holozyme is formed when the core enzyme associates with __________.

σ

Colinearity refers to the correspondence between ______.

the coding strand and the polypeptide amino acid sequences

3 things needed for basal transcription

RNA polymerase II general transcription factors mediator

Cis or trans-acting? 1. promoter 2. RNA polymerase 3. transcription factors 4. enhancer 5. silencer 6. TFIID

1. cis 2. trans 3. trans 4. cis 5. cis 6. trans Sequences that are physically part of the DNA are cis-acting. Proteins that bind to those sequences are trans-acting.

The TATA box of eukaryotic genes is usually located about ______ from the transcriptional start site.

25 bp upstream

What is a spliceosome?

A multicomponent structure that removes introns found in pre-mRNA

What is the core promoter?

A relatively short DNA sequence that is necessary for transcription to take place

The relationship between codons in DNA and AA seq of peptide?

Colinearity

What are snRNPs?

Components of the spliceosome

What is the purpose of phosphorylating the carboxy terminal domain (CTD)?

Convert from initiation to the elongation stage

Which of the following best describes transcription?

DNA -> RNA

Which best describes a terminator of a gene?

DNA sequence that specifies the end of transcription

To which will proteins known as transcription factors bind and what is the outcome?

DNA sequences to facilitate transcription

True or False. The 3' splice site contains a GU, whereas the 5' splice site contains an AG.

False

True or False. The terminator of a gene is located upstream of the coding region.

False

True or False. Unwinding of the DNA during prokaryotic transcription is the result of the activity of a helicase enzyme downstream of the RNA polymerase.

False

What is the biological advantage of alternative splicing?

Multiple proteins can be derived from a single gene

Is the promoter sequence part of the DNA that is transcribed?

Neither the -35 nor the -10 sequences are present on the new transcript.

What modification acts to stabilize eukaryotic mRNA?

Polyadenylation

You isolate a mature mRNA from a mixed experimental sample. You want to determine if it is a eukaryotic or prokaryotic mRNA. What can you look for in the mRNA to distinguish between mature prokaryotic and eukaryotic mRNAs?

Presence or absence of a 5' cap Presence or absence of edited nucleotides not directly encoded by the DNA The key to understanding this question is recognizing that it refers to mature mRNA. Although eukaryotic pre-mRNA contains introns, mature eukaryotic mRNA does not, so that would not be a useful way to distinguish between mature prokaryotic and eukaryotic mRNAs. Similarly, both prokaryotic and eukaryotic mRNAs can have a 3' tail, so this would not be helpful in distinguishing. In contast, only eukaryotic mRNAs have a 5' cap and RNA editing, so these would both be useful ways to distinguish between prokaryotic and eukaryotic mRNAs.

You have an RNA molecule that contains introns. You wish to carry out an in vitro splicing reaction with this RNA and cellular extracts. You want to determine if splicing is occuring via self-splicing or through the spliceosome. What enzyme could you add to the reaction to make this determination?

Protease Because splicing via the splicesome requires proteins, and self-splicing does not, if you added a protease, which degrades proteins, to the reaction you would be able to tell if your RNA was being spliced via self-splicing or via the spliceosome.

If a nucleotide in a eukaryotic mRNA coding sequence does not appear in the genomic DNA sequence, the most likely modification to have occurred is __________.

RNA editing

The process by which the nucleotide sequence of a mRNA molecule is changed after it has been transcribed is called

RNA editing

The enzyme that accomplishes transcription is termed __________.

RNA polymerase

A mutation occurs in one of the general transcription factors necessary for eukaryotic transciption. A pre-intiation complex forms, but the open complex does not form. Further, TFIIB, TFIIE, and TFIIH are not released from the DNA. The mutation is most likely in which general transcription factor?

TFIIH

Which of the following are features of transcription in eukaryotes only?

Termination occurs according to the allosteric or torpedo model Addition of 7-methylguanosine cap Mediator controls the switch to the elongation phase Presence of three types of RNA polymerases

An exonuclease binds to the 5'-end of the RNA that is being transcribed and degrades it in the 5' to 3' direction. The exonuclease then catches up to RNA polymerase II and causes termination. This describes the ______model of transcription termination in eukaryotes.

Torpedo model

A prokaryotic promoter is shown. Where does transcription start?

Transcription starts at the +1 site.

True or False. The RNA transcript being produced by the RNA polymerase is complementary to the template strand of the DNA.

True

True or False: Prokaryotic genes are colinear with their proteins, but this is not true for many eukaryotic genes.

True

After RNA polymerase II transcribes the polyadenylation signal, it is destabilized and dissociates from the DNA. This describes the _______model of transcription termination in eukaryotes.

allosteric

The phenomenon whereby different combinations of exons are joined to produce different mRNAs from the same transcript is called

alternative splicing

What sequences are not considered to be regulatory elements?

are NOT: General transcription factors are: Enhancers Silencers Core promoters Cis-acting elements

Arrange the following in the proper sequence in which they occur during RNA splicing.a. Lariat is formedb. U2 binds to branch sitec. 3' splice site is cut

b, a, c

The snRNPs are also called __________.

snurps

Pre-mRNA splicing requires the aid of a multicomponent structure called the

splicesome

The base sequence of the RNA transcript is ______complementary to the strand of DNA.

template

The Rho protein is involved in the __________ stage of transcription.

termination

The sequence in DNA that signals the end of transcription is known as the

terminator

Proteins that bind to DNA and facilitate RNA synthesis are collectively called

transcription factors

The first DNA base used as a template for RNA synthesis is called the

transcriptional start site