Chapter 12 - Gene Transcription and RNA Modification

What is the primary function of the genetic material, DNA?

Store information necessary to create a living organism contained in genes

What is a gene?

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

What is transcription?

The process of synthesizing RNA from a DNA template; making a copy

What is the template/product relationship for transcription

DNA template; RNA product

What is the template/product relationship for reverse transcription

RNA template; DNA product

What are protein-coding genes?

Genes that carry the information to produce mRNA and that code the amino acid sequence of polypeptides

What is messenger RNA (mRNA)?

A type of RNA that’s transcribed from a protein-coding gene and contains the information for the synthesis of a polypeptide

What is translation?

The synthesis of a polypeptide molecule from an mRNA template

What is the central dogma of genetics?

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 genetic information so that it can be transmitted from cell to cell and from parent to offspring

What is gene expression?

The process by which the information within a gene is accessed, first to synthesize RNA and polypeptides, and eventually to affect the properties of cells and the phenotype of multicellular organisms

What is the difference between promoter and terminator base sequences?

The promoter provides a site for beginning transcription

The terminator specifies the end of transcription

What is a template strand/non-coding strand?

A strand of DNA that’s used to synthesize a complementary strand of DNA or RNA

What is a non-template strand/coding strand?

A strand of DNA that’s not used as a template during transcription. It can also be the strand of DNA in protein-coding genes that’s not used as a template for mRNA synthesis

What are transcription factors?

A category of proteins that influence the ability of RNA polymerase to transcribe DNA into RNA; bind to genes and facilitate transcription

What are regulatory elements?

A short segment of DNA that’s recognized by a regulatory transcription factor. The binding of the transcription factor affects the rate of transcription. Also called regulatory sequences or response elements

What is the ribosome-binding site?

A short sequence in bacterial mRNA that binds to a ribosome and initiates translation. Also known as the Shine-Dalgarno sequence

What are codons?

A sequence of three nucleotides in mRNA that functions in translation

What is the difference between a start and a stop codon?

A start codon, which usually specifies methionine, initiates translation

A stop codon terminates translation

What are the three stages of transcription?

1) Initiation: Involves the initial binding of RNA polymerase to the promoter in order to begin RNA synthesis
2) Elongation: The synthesis of an RNA transcript using DNA as a template
3) Termination: The release of the newly made RNA transcript and RNA polymerase from the DNA

What is RNA polymerase?

An enzyme that synthesizes a strand of RNA using DNA as a template

What is the open complex?

The region of separation of two DNA strands where RNA polymerase can use one of the strands as a template for transcription

What is the transcriptional start site?

The site in a gene where transcription begins

Promoters are typically located just ______ of the site where transcription of a gene begins

Upstream

In promoters found in bacteria, two sequences, which are located at approximately the ______ in the promoter, are particularly important

-35 and -10 sites

What is the Pribnow box?

The TATAAT sequence that’s often found at the -10 site of a bacterual promoter

What is the consensus sequence?

The set of the most commonly occurring bases within a specific type of sequence in DNA

Mutations in the -35 or -10 sequences that lessen their similarity to the consensus sequences typically ______ the rate of transcription

Slow down

What is a core enzyme?

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

In E. coli, the core enzyme is composed of ______

Five subunits

What is a sigma factor?

A transcription factor that recognizes bacterial promoter sequence and facilitates the binding of RNA polymerase to the promoter

How is RNA polymerase holoenzyme created?

Through the association of a sixth subunit, sigma factor, with the core enzyme

What is the primary role of RNA polymerase holoenzyme?

Required to initiate transcription

What is the primary role of the sigma factor?

Recognize the promoter

What is a helix-turn-helix motif?

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

Why is it necessary for portions of a sigma-factor protein to fit into the major groove?

Parts of the sigma-factor protein must fit into the major groove so that the protein can recognize a promoter and form hydrogen bonds with its bases

What is a closed complex?

A complex of RNA polymerase, transcription factors, and a promoter prior to the separation of DNA strands and the transcription of RNA

At the -10 site, why is the DNA in an AT-rich region more easily separated and unwound compared to a GC-rich region?

A-T base pairs form only two hydrogen bonds, whereas G-C pairs form three. Therefore, DNA in an AT-rich region is more easily separated because fewer hydrogen bonds must be broken

The release of the sigma factor marks the transition to the ______ phase of transcription

Elongation

The ______ is made during the elongation stage

RNA transcript

RNA polymerase always connects nucleotides in the ______ direction

5’ to 3’

In transcription, the template strand is read in the ______ direction, and the synthesis of the RNA transcript occurs in a ______ direction

1) 3’ to 5’ direction
2) 5’ to 3’ direction

What is rho protein?

A protein that’s involved in transcriptional termination for certain bacterial genes

What are the two types of mechanism for termination?

1) Rho-dependent termination: Requires rho protein
2) Rho-independent termination: Does not require rho protein where a uracil-rich sequence occurs at the end of the RNA; also referred to as intrinsic termination

What are the three reasons why gene transcription in eukaryotes is more complex?

1) Larger, more complex cells (organelles)
2) Added cellular complexity means more genes that encode proteins are required
3) Multicellularity adds another level of regulation

What are the three types of RNA polymerases?

1) RNA pol I: Transcribes most rRNA genes, except for the 5S rRNA
2) RNA pol II: Transcribes all protein-encoding (structural genes); synthesizes all mRNAs. Also transcribes some snRNA genes needed for splicing
3) RNA pol III: Transcribes all tRNA genes, the 5S rRNA gene, and microRNA genes

What two features do protein-coding genes have to ensure that transcription occurs at an appropriate rate?

1) A core promoter
2) Regulatory elements

What is a core promoter?

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

What is the TATA box?

A sequence found within eukaryotic core promoters that determines the starting site for transcription. If it’s missing from the core promoter, the transcription start site becomes undefined, and transcription may start at a variety of different locations. It’s also an example of a cis-acting element

What is basal transcription?

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

What are enhancers?

A DNA region in eukaryotes that contains one or more regulatory elements. The binding of an activator to an enhancer increases the rate of transcription, whereas the binding of a repressor to an enhancer decreases the rate of transcription

What are regulatory transcription factors (RTFs)?

A protein or protein complex that binds to a regulatory element and influences the rate of transcription via RNA polymerase

What are the two types of RTFS?

1) Activators/Enhancers: Stimulate transcription
2) Repressors/Silencers: Inhibit transcription

A possible location for regulatory elements is the ______

-50 to -100 region

What are cis-acting elements?

A sequence of DNA, such a regulatory element, that exerts a cis-effect; cis meaning “next to.” Always found within the same chromosome as the genes they regulate

What are trans-acting factors?

A regulatory protein that binds to a regulatory element in DNA and exerts a trans-effect; trans meaning “across from.” May be far away from the genes they control, even on a different chromosome

What is mediator?

A large protein complex that mediates interactions between RNA polymerase II and RTFs that bind to enhancers

What are the three categories of proteins are needed for basal transcription at the core promoter?

1) RNA polymerase II
2) General transcription factors
3) A complex called mediator

What are general transcription factors (GTFs)?

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

What is preinitiation complex?

A closed complex formed by the assembly of GTFs, mediator, and RNA polymerase II at the core promoter, which initiates transcription

Why is phosphorylation of the carboxyl-terminal domain (CTD) functionally important?

The phosphorylation of the CTD allows RNA polymerase to proceed to the elongation phase of transcription

What is the basal transcription apparatus?

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

What are the two models of transcriptional termination?

1) Allosteric model: RNA polymerase II becomes destabilized after it has transcribed the polyadenylation signal sequence and dissociates from the DNA
2) Torpedo model: RNA polymerase II is physically removed from the DNA

What is colinearity?

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

What is a pre-mRNA?

The mRNA of eukaryotes that’s produced in the nucleus and has yet to be processed

What is RNA splicing?

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

What are the four ways in which RNA transcripts can be modified?

1) Processing of rRNA and tRNA transcripts to smaller functional pieces
2) 5’ capping
3) 3’ poly-A tailing of mRNA transcripts
4) Splicing

What is a nucleolus?

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

What is the difference between an endonuclease and an exonuclease?

Endonuclease: An enzyme that can cleave the bond between adjacent nucleotides within a DNA or RNA strand

Exonuclease: An enzyme that digests an RNA or DNA strand from one end by cleaving the bond between the two nucleotides at that end

RNaseP is a catalyst that contains both ______ and ______

1) RNA
2) Protein subunits

Which portion of RNaseP has the catalytic ability to cleave the precursor tRNA

RNA

What is a ribozyme?

An RNA molecule with catalytic activity

Ex: RNaseP

______ is the removal of intron RNA and the covalent connection of the exon RNA

Splicing

What are the three splicing mechanism that remove introns?

1) Group I intron splicing: Uses free guanosine; occurs via self-splicing
2) Group II intron splicing: Use an adenine nucleotide within the intron itself; occurs via self-splicing
3) Spliceosome: Uses a complex known as a spliceosome

What two aspects do the three splicing mechanisms have in common?

1) Removal of the intron RNA
2) Covalent linkage of the exon RNA fragments

Which of the three mechanisms is very common in eukaryotes?

Splicing via a spliceosome is very common in eukaryotes

What is self-splicing?

RNA splicing mechanism that occurs without the aid of any proteins or other RNAs

What are maturases?

A protein that enhances the rate of self-splicing of groups I and II introns

What is a spliceosome?

A multisubunit complex that plays a key role in the splicing of eukaryotic pre-mRNAs; recognizes the boundaries of the intron so that it can be removed properly

What is a snRNP?

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

What are three functions of a spliceosome?

1) Bind to an intron sequence and precisely recognize the intron-extron boundaries
2) Hold the pre-mRNA in the correct configuration to ensure the splicing together of the exons
3) Catalyzes the chemical reactions that cause the intron to be removed and the exons to be covalently linked

What is a metalloribozyme?

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

What is alternative splicing?

The phenomenon that a pre-mRNA can be spliced in more than one way; also referred to as exon shuffling

The ______ within a polypeptide determines the structure and function of a protein

Sequence of amino acids

How is alternative splicing advantageous?

Because alternative splicing allows two or more different polypeptide sequences to be derived from a single gene. it’s speculated that this process allows an organism to carry fewer genes in its genome

What is the difference between constitutive and alternative exons?

Constitutive exons are always found in mature mRNAs following splicing

Alternative exons are not always found in mature mRNAs. They are only found in certain types of alternatively spliced mRNAs

What are splicing factors?

A protein that regulates the choice of splice sites during the process of alternative splicing of pre-mRNAs

Ex: SR proteins

What is exon skipping?

The splicing out of an exon from a pre-mRNA so that it’s not included in the mature mRNA

What are two ways splicing factors modulate the ability of a spliceosome to choose 5’ and 3’ splice sites?

1) Repressing
2) Enhancing

What is capping?

The covalent attachment of a 7-methylguanosine to the 5’ end of mRNAs in eukaryotes

What are three functional roles of the 7-methylguanosine cap?

1) Exit of mRNAs from the nucleus
2) Binding of pre-mRNA to a ribosome during initiation of translation
3) Efficient splicing of introns

What is a polyA tail?

The string of adenine nucleotides at the 3’ end of eukaryotic mRNAs. Important for mRNA stability, the exit of mRNA from the nucleus, and in the synthesis of polypeptides

What is polyadenylation?

The process of attaching a string of adenine nucleotides to the 3’ end of eukaryotic pre-mRNAs

What is RNA editing?

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

What are three effects of RNA editing?

1) Generating start codons
2) Generating stop codons
3) Changing the coding sequence for a polypeptide