Chapter 12: Gene Transcription and RNA Modification

gene

a unit of heredity that may influence the outcome of a trait in an organism. At the molecular level, a gene is a segment of DNA that contains the information to make a functional product, either RNA or a polypeptide.

transcription

the process of synthesizing RNA from a DNA template

altered, RNA, information

* the structure of DNA is not _____ as a result of transcription
* rather, the DNA base sequence has only been accessed to make a copy in the form of _____
* therefore, the same DNA can continue to store _____

protein-coding genes

genes that produce mRNA and encodes polypeptides; also called structural genes

messenger RNA

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

translation

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

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

gene expression

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

regulatory sequence, promoter, terminator

sequences of DNA for transcription

ribosome binding site, 5’ UTR/3’ UTR, codons, start codon, stop codon

sequences of mRNA for translation

promoter, terminator

the _____ and _____ are base sequences used during gene transcription (cause RNA synthesis to occur within a defined location)

promoter

a sequence within a gene that initiates transcription

terminator

a sequence within a gene that signals the end of transcription

template (noncoding) strand

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

template (noncoding) strand

the strand of DNA that is the reverse complement of RNA and that RNA polymerase binds to

nontemplate (coding) strand

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

nontemplate (coding) strand

the strand of DNA that has the same sequence as the transcribed mRNA that encodes a polypeptide

transcription factors

* a category of proteins that influence the ability of RNA polymerase to transcribe DNA into RNA
* a category of proteins that controls the rate of transcription

promoter

some transcription factors bind directly to the _____ and facilitate transcription

regulatory sequences

other transcription factors recognize _____ _____

regulatory sequences

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

increase, inhibit

certain transcription factors bind to regulatory sequences and _____ the rate of transcription, whereas others _____ transcription

ribosome-binding site

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

codon

a sequence of three nucleotides in mRNA that functions in translation and contains the information for the polypeptide’s sequence

start codon

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

stop codon

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

5’ UTR/3’ UTR

untranslated region of mRNA that never goes farther than mRNA

initiation, elongation, and termination

the three stages of transcription

initiation

the stage that involves the initial binding of RNA polymerase to the promoter in order to begin RNA synthesis

elongation

the synthesis of an RNA transcript using DNA as a template

termination

the release of the newly made RNA transcript and RNA polymerase from the DNA

RNA polymerase

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

open complex

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

upstream

most of the promoter is located just ahead of, or _____ from, the site where transcription of a gene actually begins

transcriptional start site

the site in a gene where transcription begins

first, +1

the transcription start site is the _____ nucleotide used as a template for transcription and is denoted _____

\-35 and -10 sites

two particularly important sequences of bacterial promoters

Pribnow box

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

\-10 site

sequence of a bacterial promoter that is AT-rich and is where RNA polymerase binds

consensus sequence

the most commonly occurring bases within a specific type of sequence

TTGACA

consensus sequence of -35 site

TATAAT

consensus sequence of -10 site

slow

mutations in the -35 or -10 sequences that lessen their similarity to the consensus sequences typically _____ down the rate of transcription

less

more differences from consensus sequence = _____ tight binding

RNA polymerase

the enzyme that catalyzes the synthesis of RNA

six

total number of subunits of RNA polymerase

five

number of subunits of RNA polymerase core enzyme

one

number of subunits of RNA polymerase sigma factor

RNA polymerase holoenzyme

core enzyme + sigma factor

alpha subunits

important in the proper assembly of the holoenzyme and in the process of binding to DNA

beta subunits

also needed for binding to the DNA, and they carry out the catalytic synthesis of RNA

omega subunit

important for the proper assembly of the core enzyme

sigma factor

primary role is to recognize the promoter

sigma factor

the promoter is identified when the _____ _____ recognizes both the -35 and -10 sequences

helix turn helix

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

alpha, major, hydrogen

_____ helices within the protein fit into the _____ groove of the DNA double helix and _____ bonding occurs between nucleotides in the -35 and -10 sequences of the promoter and amino acid side chains in the helix-turn-helix motif of sigma factor

sigma factor, closed

the process of transcription is initiated when _____ _____ within the holoenzyme binds to the promoter to form a _____ complex

closed complex

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

open, TATAAT, AT, fewer

the unwinding into an _____ complex begins at the _____ sequence in the -10 site, which contains only _____ base pairs (DNA is more easily separated because _____ hydrogen bonds must be broken)

open

a short strand of RNA is made within the _____ complex, and then the sigma factor is released from the core enzyme

sigma factor

the release of _____ _____ marks the transition to the elongation phase of transcription

17

as RNA polymerase moves along the DNA, it creates an open complex that is approximately _____ bp long

5 to 3

RNA polymerase always connects nucleotides in the _____ direction

vary

in the case of the transcription of multiple genes within a chromosome, the direction of transcription and the DNA strand that is used as a template _____ among different genes

rho-dependent termination and rho-independent termination

two different mechanisms for termination

rho protein

a protein that is involved in transcriptional termination for certain bacterial genes

rho dependent termination

transcriptional termination that requires the participation of the rho protein

rut site

encodes a sequence in the RNA that acts as a recognition site for the binding of rho protein

helicase

rho protein functions as a _____, an enzyme that can separate RNA-DNA hybrid regions

terminator, stem-loop

at the _____ site, the DNA encodes an RNA sequence containing several GC base pairs that form a _____ structure

stem-loop, hydrogen

the rho protein catches up to the _____, passes through it, and breaks the _____ bonds between the DNA and RNA within the open complex

protein, stem-loop, hybrid

rho dependent termination:

instability caused by _____ interaction, _____, and DNA-RNA _____ breaks apart open complex

rho independent termination

transcription termination that does not require the rho protein

NusA

a protein that binds to RNA polymerase and promotes pausing at stem-loop sequences during rho independent termination

uracil, weak

_____-rich sequence of rho independent termination is relavatively _____, causing the RNA transcript to spontaneously dissociate from the DNA and stop further transcription

uracil, stem-loop, hybrid

rho independent termination:

instability caused by _____-rich sequence, _____, and DNA-RNA _____ breaks apart open complex

complex, larger, organelles, proteins, genes, multicellular

gene transcription in eukaryotes is more _____

* eukaryotic cells are _____ than bacterial cells and contain a variety of compartments known as _____
* eukaryotes make many more _____, and consequently they have many more protein-coding _____
* _____

three

the genetic material within the nucleus of a eukaryotic cell is transcribed by _____ different RNA polymerase enzymes

RNA polymerase I

transcribes all rRNA genes (except for the 5S rRNA)

RNA polymerase II

transcribes all structural (protein-encoding) genes (all mRNAs & some snRNA genes)

RNA polymerase III

transcribes all tRNA genes, the 5S rRNA gene, microRNA genes

core promoter and regulatory elements

two features of an eukaryotic protein-encoding gene

core promoter

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.

TATA box and transcriptional start site

two parts of a core promoter

TATA box

a sequence found within eukaryotic core promoters that determines the starting site for transcription (TATAAA sequence)

25, starting

the TATA box, which is usually about _____ bp upstream from the transcriptional start site, is important in determining the precise _____ point for transcription

basal transcription

in eukaryotes, a low level of transcription produced by the core promoter

regulatory elements

_____ _____ are short DNA sequences that affect the ability of RNA polymerase to recognize the core promoter and begin the process of transcription

enhancers and silencers

two categories of regulatory elements

enhancer

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

silencer

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

cis-acting element

DNA sequences, such as the TATA box, enhancers, and silencers, that exert their effects only on a particular gene

cis-acting element

within the same chromosome as the genes they regulate

trans-acting factor

a regulatory protein that binds to a regulatory element in DNA

RNA polymerase II

in eukaryotes, the enzyme that catalyzes the linkage of nucleotides in the 5’ to 3’ direction, using DNA as a template

general transcription factors (GTFs)

five different proteins that are necessary to initiate basal transcription at the core promoter

TFIID

_____ first binds to the TATA box and thereby plays a critical role in the recognition of the core promoter

TFIIB

after TFIID binds to the TATA box, it associates with _____ (promotes the binding of RNA polymerase II and TFIIF)

TFIIF

_____ is bound to RNA polymerase II

TFIIE, TFIIH, preinitiation complex

_____ and _____ bind to RNA polymerase II to form a _____ _____ (closed complex)