GN Exam 3 Ch. 13. Transcription

Pribnow TATAAT

(-10) Consensus Sequence -lies 10 bp upstream from the start site -sometimes called the __________ box -the -10 consensus sequence is ________

TTGACA

(-35) Consensus Sequence -lies 35 bp upstream from the start site -the -35 consensus sequence is _________

transcription unit

-A ______________ is a segment of DNA that codes for an RNA molecule and the sequences necessary for its transcription

replication transcription

In ___________, all the nucleotides in the DNA molecule are copied, but in ______________ only parts of the DNA molecule are made into RNA

polycistronic

In bacteria, a group of genes is often transcribed into a single RNA molecule; such a molecule is termed _____________ mRNA. -this is produced when a single terminator is present at the end of a group of several genes that are transcribed together, instead of each gene having its own terminator

RNA polymerase II

In eukaryotes, which RNA polymerase(s) transcribes the genes that encode proteins?

RNA polymerase I RNA polymerase III

In eukaryotes, which RNA polymerase(s) transcribes the genes that encode ribosomal RNAs?

core promoter

In eukaryotic cells, where does the basal transcription apparatus bind?

3' end

In transcription, to which end of the elongating strand are nucleotides always added?

+1 rNTP sigma

Initial RNA Synthesis -once the holoenzyme has bound to the promoter, RNA polymerase is positioned over the transcription start site (at position _____) & has unwound the DNA to produce a single stranded template -an _____ complementary to the base at the start site serves as the first nucleotide in the RNA molecule (no primer is required) -Two phosphate groups are cleaved from each subsequent rNTP, creating an RNA nucleotide that is added to the 3' end of the growing RNA molecule -the ______ factor is released as the RNA polymerase moves beyond the promoter

consensus sequence

Initiation -A ______________ is the set elf the most commonly encountered nucleotides among sequences that possess considerable similarity -a sequence that describes the nucleotides most often present in a segment of interest

bubble rNTPs

Initiation four steps: 1. promoter recognition 2. formation of the transcription _______ 3. creation of the first bonds between ______ 4. escape of the transcription apparatus from the promoter

promoter

Initiation the ________ sequence contains the information on where the transcription apparatus will start transcribing, which strand is to be read, and in which direction the RNA polymerase will move

transcription factors (TF) mediator

Initiation/ RNA polymerase II -Transcription in eukaryotes is initiated through the assembly of the transcription machinery on the promoter -machinery = RNA polymerase II and a series of _________ that form a giant complex consisting of 50+ polypeptides -The basal transcription apparatus consists of RNA polymerase II, a series of general transcription factors, and a complex of proteins known as the ______.

core promoter activator loops regulatory

Initiation/ RNA polymerase II Initiation steps 1. TFIID binds to TATA box in the core promoter, helping to center the RNA polymerase over the transcription start site 2. then transcription factors & RNA polymerase II bind to the _________ 3. transcriptional _________ proteins bind to sequences in enhancers 4. DNA _______ out, allowing the proteins bound to the enhancer to interact with the basal transcription apparatus 5. transcriptional activator proteins bind to sequences in the ___________ promoter and interact with the basal transcription apparatus through the mediator

pre-initation TF's

Initiation/ RNA polymerase II RNA polymerase II and the general transcription factors assemble at the core promoter, forming a _________ complex. (in bacteria, the sigma factor recognizes/binds to the promoter sequence; in eukaryotes, the function of sigma is replaced by general _____)

direct repeat

Inverted vs Direct Repeats AGGC**AGGC TCCG **TCCG

inverted repeat

Inverted vs Direct Repeats AGGC**GCCT TCCG**CGGA

hairpin *remember: in replication single strand binding proteins prevent hairpin formation*

Inverted vs Direct Repeats -A ________ forms when sequences of nucleotides on the same strand are inverted complements -these form on the RNA in transcription from an inverted repeat -these consists of a region of paired bases (the stem) and intervening unpaired bases (a loop)

holoenzyme holoenzyme core enzyme core enzyme

Regarding transcription in prokaryotes: For each stage listed below, select the holoenzyme of RNA polymerase if it is required for proper completion of the stage or select the core enzyme if it can accomplish this step without the rest of the enzyme. Template Binding: _______ Initiation: __________ Elongation: ___________ Termination: ___________

rho factor helicase

Rho Dependent terminators -can only cause termination of transcription if the ancillary protein ________ is present -Rho binds to the RNA and moves toward the 3' end, following the RNA polymerase -when RNA polymerase encounters a terminator sequence, it pauses, allowing rho to catch up (pauses at termination hairpin) -the rho factor has ______ activity, which it uses to unwind the RNA-DNA hybrid in the transcription bubble -transcription ends

adenine template

Rho Independent terminators *The hairpins are followed by a string of _________ residues on the _______ strand of the DNA. The A-U bonds are relatively weak and allow dissociation of the DNA-RNA pairing (A-U only have 2 H bonds; C-G have 3 H bonds)

adenine uracil adenine-uracil

Rho Independent terminators -in Rho independent terminators, a string of seven to nine _____________ nucleotides follows the inverted repeat in the template DNA. -the transcription of these nucleotides produces a string of __________ nucleotides after the hairpin in the transcribed RNA

destabilizes

Rho Independent terminators -the string of uracils in the RNA molecule causes the RNA polymerase to pause, and the inverted repeats in RNA fold in to a hairpin -the hairpin __________ the DNA-RNA pairing, causing the RNA to separate from the DNA template -separation may be facilitated by the ______ base pairings, which are relatively weak -transcription terminates

inverted repeats hairpin

Rho Independent terminators -Rho independent terminators contain ____________, which are sequences on the same strand that are inverted and complementary. When these are transcribed into RNA and bind to each other, a ________ forms.

DNA template raw materials proteins

Like replication, transcription requires 3 major components: 1. A DNA _________ 2. The ____________ (ribonucleotide triphosphates) needed to build a new RNA molecule 3. the transcription apparatus, consisting of the ________ necessary for catalyzing the synthesis of RNA

RNA polymerase II

Match the eukaryotic polymerase to the gene it transcribes: messenger RNA

RNA polymerase I = ribosomal RNA only (18s and 28s)

Match the eukaryotic polymerase to the gene it transcribes: ribosomal RNA only

RNA polymerase III

Match the eukaryotic polymerase to the gene it transcribes: transfer RNA

the holoenzyme (core enzyme + sigma factor)

what binds to the -10 consensus sequence found in most bacterial promotors?

sigma

What component/protein/subunit is present in the holoenzyme but is not present in the core enzyme in prokaryotes?

Rho

What component/protein/subunit is sometimes required for proper termination of transcription in prokaryotes?

antiparallel

-During transcription, an RNA molecule that is complementary and _________ to the DNA template strand is synthesized -The RNA transcript has the same polarity and base sequence as the nontemplate strand, except that it contains U rather than T

one

-RNA synthesis for a single gene is from ______ DNA strand -Different genes can be transcribed from different strands of the same DNA segment

promoter sigma sigma factor

-RNA transcription is initiated when core RNA polymerase binds to the _______ with the help of _______ -Transcription in bacteria is carried out by RNA polymerase, which must bind to the ________ to initiate transcription

template non-template (coding strand)

-The template for RNA synthesis (transcription), as for DNA synthesis (replication), is a single strand of the DNA double helix. Unlike replication, the transcription of a gene takes place on only one of the two nucleotide strands of DNA. -The nucleotide strand used for transcription is termed the ________ strand. The other strand is called the ___________ strand.

cis elements

-_____ elements are nucleotide sequences that are "close to" the coding region of a gene and help the cell to determine when the gene should be transcribed (elements that are on the same piece of DNA as the gene we are regulating) -Binding sites for proteins (or RNAs) -examples: -the core promoter and regulatory promoter

trans-acting factors

-_______ factors are proteins or RNAs from other genes (not on the same piece of DNA) - Attach to cis-elements or other transcription factors - Recruit RNA polymerase

binding initiation elongation termination

4 Stages of transcription: 1. template _________ 2. chain _________ 3. chain ___________ 4. chain _________

I II III

3 RNA polymerases RNA polymerase ___ = Large rRNA (28S,18S, 5.8S) RNA polymerase ___ = mRNA, snRNA, snoRNA, miRNA RNA polymerase ___ = small rRNA (5S), tRNA, snRNA

transcription

All cellular RNAs are synthesized from DNA templates through the process of _________

sigma weakly -10

Consensus Sequences -The _______ factor associates with the core RNA polymerase enzyme to form a holoenzyme, which binds to the -35 and -10 consensus sequences in the DNA promoter -The holoenzyme initially binds _______ to the promoter, but then undergoes a structural change that allows it toe bind more tightly and unwind the dsDNA. -Unwinding begins within the _____ consensus sequence and extended downstream for about 14 nucleotides, including the start site (-12 to +2)

-10 consensus sequence -35 consensus sequence

Consensus Sequences There are two commonly encountered consensus sequences found in almost all bacterial promoters:

upstream core regulatory

Core Promoter & Regulatory Promoter -the regulatory promoter is farther ______ of the gene -general transcription factors bind to the _______ promoter; transcription activator proteins bind to the _______promoter

core enzyme

Elongation -End of initiation: RNA polymerase undergoes a change in shape and the sigma factor is released -Elongation occurs 5' to 3' using only the _________ -RNA polymerase moves downstream, unwinding DNA ahead of the transcription bubble and joining nucleotides to the growing RNA molecule -RNA polymerase then rewinds the DNA behind the transcription bubble

30 bp 8 bp

Eukaryotic Elongation / RNA polymerase II -After about ~____bp are synthesized, RNA polymerase leaves the promoter and begins elongation -many transcription factors stay bound at the promoter to reinitiate transcription -transcription bubble contains about ____bp of DNA-RNA hybrid -The structure of RNA polymerase causes separation of the newly formed RNA strand from the DNA template strand

Rat1 exonuclease

Eukaryotic Termination - RNA polymerase II -The three eukaryotic RNA polymerases use different mechanisms for termination -The termination of transcription by RNA polymerase II requires the enzyme __________ -cleavage of the RNA occurs based on consensus sequence

cleavage Rat1 exonuclease rat1

Eukaryotic Termination - RNA polymerase II 1. RNA polymerase II transcribes well past the coding sequences of most genes 2. _________ is near the 3' end of the RNA, while RNA polymerase continues transcribing 3. the ______ attaches to the 5' end of the trailing RNA, and moves toward the RNA polymerase, degrading the RNA as it goes 4. when the _____ reaches the polymerase, transcription is terminated

primer 3' bubble

Overview of Transcription: 1. Initiation of RNA synthesis does not require a _______ 2. New nucleotides are added to the ____ end of the RNA molecule 3. DNA unwinds at the front of the transcription _______.... 4. ..... and then rewinds

translated

Polycistronic mRNA = one RNA molecule is produced, but it contains the information for more than one gene and is _________ into more than one gene product

5' 3'

Processing of pre-mRNA to form mRNA (RNA polymerase II makes mRNA's) 3 types of processing: -Capping of the ____ end (occurs immediately) -PolyA tail added to the ____ end -removal of introns (intron is spliced out)

top bottom

Prokaryote Transcription Summary -Under the electron microscope, DNA molecules undergoing transcription exhibit Christmas tree-like structures -The DNA molecule is the stem of the tree -The RNA molecules are the branches -transcription begins at the ____ of the tree (little DNA has been transcribed, and the RNA branches are short) -has transcription continues, RNA molecules lengthen, producing the long branches at the ________ of the tree

holoenzyme core enzyme Rho

Prokaryote Transcription Summary -The _________ is required for binding & initiation -the _________ can elongate and terminate without sigma -______ sometimes is involved in termination -1 piece of DNA may by simultaneously transcribed into many copies of RNA

cytoplasm nucleus cytoplasm

Prokaryote/Eukaryote Comparison -In Prokaryotes, transcription and translation occur in the _____________ (no nucleus in prokaryotes) -In Eukaryotes, transcription and processing occur in the ________, but translation occurs in the _________

processing eukaryotes

Prokaryote/Eukaryote Comparison -___________ in eukaryotes but not in prokaryotes -Eukaryotes make DNA in to pre-mRNA (add cap, tail, and splice) then moves out of nucleus to cytoplasm -Different RNA polymerases for different types of RNA in __________

CRISPR RNA (crRNA)

Prokaryotic vs. Eukaryotic -The type of RNA that are produced only in prokaryotes:

pre-mRNA snRNA snoRNA miRNA siRNA piRNA

Prokaryotic vs. Eukaryotic -The types of RNAs that are only produced in eukaryotes:

mRNA, rRNA, tRNA

Prokaryotic vs. Eukaryotic -The types of RNAs that are transcribed in both prokaryotic and eukaryotic cells:

Polycistronic no introns Monocistronic Introns

Prokaryotic vs. Eukaryotic Gene Expression -Prokaryotes: _____________ mRNA; no ________ (usually) -Eukaryotes: ___________ (usually); ___________

gene +1

RNA Polymerase III -transcribes tRNA, 5S rRNA, and snRNAs (it makes small rRNAs and tRNA) -*Promoters can be located within the ________* -The number and position of the internal promoter elements (boxes) varies from gene to gene. -Transcription factors interact with these internal promoter elements and with polymerase to position polymerase for proper initiation of transcription at _____ nucleotide.

RNA has a 2' OH

RNA is different from DNA in which of the following ways?

rRNA rRNA rRNA rRNA rRNA

RNA polymerase I -RNA polymerase I transcribes ______ genes in eukaryotes -_______ genes are transcribed into 1 pre-______ molecule that undergoes processing to release the 18S, 5.8S, and the 28S ________ -there are several tandem copies of _____ genes

regulatory promoter

RNA polymerase II -the _________ is located immediately upstream of the core promoter -variety of consensus sequences -this is not always the same for all genes that are transcribed by RNA polymerase II

core promoter TATA box

RNA polymerase II -the _________ is located immediately upstream of the gene and is the site to which the basal transcription apparatus binds. -has the ______ box_, which has the consensus sequence TATAAA and is located -25 to -30 bp upstream of the start site -this is the same for all genes that are transcribed by RNA polymerase II

proteins core promoter regulatory

RNA polymerase II -transcribes the genes that encode ________ -a promoter for a gene transcribed by RNA polymerase II typically consists of two primary parts: the _______ promoter and the _______ promoter

Ribose (RNA sugar) deoxyribose (DNA sugar)

Structural difference between DNA and RNA? -________ has one more -OH group than ________ (which has -H attached to the second 2' carbon in the ring)

terminator terminator

Termination -RNA polymerase adds nucleotides to the 3' end of the growing RNA molecule until it transcribes a ________ -transcription stops after the _________ has been transcribed -several overlapping events need to happen at this location: RNA polymerase must stop synthesizing RNA, the newly made RNA molecule must be released from RNA polymerase, the RNA molecule must dissociate from the DNA, and RNA polymerase must detach from the DNA template

Rho-dependent terminators Rho-Independent terminators

Termination Bacterial cells possess two major types of terminators:

template strand coding strand upstream downstream

Terminology review: _____________: strand of DNA that is transcribed _____________: other DNA strand (sequence is the same as the RNA transcribed from the template strand except for T/U difference) _____________: sequences prior to the start of transcription _____________: sequences after the start of transcription (+1 and up)

ribonucleoside triphosphates (rNTPs) two phosphodiester 3'

The Substrate For Transcription -RNA is synthesized from _____________, each consisting of a ribose sugar and a base (a nucleoside) attached to three phosphate groups. -In RNA synthesis, nucleotides are added one at a time to the 3'-OH group of the growing RNA molecule -_______ phosphate groups are cleaved from the incoming rNTP; the remaining phosphate group participates in a _________ bond that connects the nucleotide to the growing RNA molecule. -Nucleotides are always added to the ____ end of the RNA molecule, and the direction of transcription is there fore 5' to 3'

terminator

The Transcription Unit -The _________ is a sequence of nucleotides that signals where transcription is to end. -These are part of the RNA-coding sequence; transcription stops only after this has been copied into RNA

Promoter

The Transcription Unit -The ___________ is a DNA sequence that the transcription apparatus recognizes and binds. -it indicates which of the two DNA strands is to be read as the template and the direction of transcription. -It also determines the transcription start site, the first nucleotide that will be transcribed into RNA -it is located next to the transcription start site

RNA-coding region

The Transcription Unit -The ____________ is a sequence of DNA nucleotides that is copied into an RNA molecule

a promoter, an RNA-coding region, and a terminator

The Transcription Unit -The transcription Unit has 3 critical regions: ________, _______, and ___________

downstream upstream downstream

The Transcription Unit -The transcription apparatus is said to move _________ during transcription: it binds to the promoter (which is usually _________ of the transcription start site) and moves toward the terminator (which is _________ of the start site)

No (the promoter region is where everything gets together, and then transcription starts adjacent to it)

The Transcription Unit is the promoter transcribed into RNA in prokaryotes (typically)?

three proteins proteins

Transcription in EUKARYOTES -Eukaryotic cells possess _______ different RNA polymerases, each of which transcribes a different class of RNA and recognizes a different type of promotor (prokaryotic cells only have 1 RNA polymerase) -the different RNA polymerases recognize different promoters, different transcription factors and different termination factors -many accessory ________take part in the binding of eukaryotic RNA polymerases to DNA templates, and the different types of promoters require different ________

nucleus cytoplasm

Transcription in EUKARYOTES -Transcription in Eukaryotes occurs in the ___________, and then translation occurs in the _________

holoenzyme (α2ββ'σ)

Transcription in Prokaryotes -After the sigma factor has associated with the core enzyme (forming a __________), RNA polymerase binds stably only to the promoter and initiates transcription at the proper start site. -Sigma is required only for promoter binding and initiation; after a few RNA nucleotides have been joined together, sigma usually detaches from the core enzyme

RNA polymerase

Transcription in Prokaryotes -Bacterial cells typically only possess one type of __________, which catalyzes the synthesis of all classes of bacterial RNA: mRNA, tRNA, and rRNA.

core enzyme (α2ββ')

Transcription in Prokaryotes -at the heart of most bacterial RNA polymerases are 5 subunits (individual polypeptide chains) the make up the ___________: two copes of a subunit called alpha, and single copies of subunits beta, beta prime, and omega. -this enzyme catalyzes the elongation of the RNA molecule by the addition of RNA nucleotides

sigma factor

Transcription in Prokaryotes -the _________ controls the binding of RNA polymerase to the promoter; without this, RNA polymerase initiates transcription at a random point along the DNA.

+1

Transcription starts at the _____ nucleotide

hairpin rho

Transcription termination requires a ________, but may or may not require the enzyme ______

DNA primer 5' to 3' phosphate

Transcription: Synthesis of RNA -_________ is used as template (same as replication) -No _________ needed -rNTPs (note: Uracil pairs with adenine. No Thymine) -Nucleotides are added ____ to ____ -Two _______ groups are cleaved from the incoming rNTP as the nucleotide is added

Polymerase Ribonucleotides Promoter DNA template

Which of the following are required for transcription?

helicase cleft 3' 3'

structure of RNA polymerase II -note: RNA polymerase II has its own ______ activity -The DNA double helix enters RNA polymerase II through a ____ in the enzyme and unwinds -The DNA-RNA duplex is bent at a right angle, which positions the ____ end of the RNA at the active site of the enzyme -at the active site, new nucleotides are added to the ____ end of the growing RNA molecule

selective

transcription is a highly _________ process: individual genes are transcribed only as their products are needed