Bio - Ch. 11 part 1

What is the consensus sequence of the Pribnow box?

-35 element

How many phosphates are initially found at the 5' ends of all RNAs (before capping occurs) - how many after the action of the enzyme "triphosphatase"?

3, 2

How many subunits make up the bacterial "core enzyme" of transcription?

5

Mature eukaryotic mRNAs have special modifications at their 5' and 3' termini - what are these?

5': methylated guanosine cap, 3': poly(A) tail

Briefly describe the process by which eukaryotic mRNAs obtain their methylguanosine cap.

All 5' end of RNAs have a triphosphate 1. The last of the three phospates is removed, converts 5' terminus to a diphosphate 2. GMP is added in an inverted orientation so that the 5' end of the guanosine is facing the 5' end of the RNA chain, results in the first two nucleosides being joinded by an unusual 5'-5' triphosphate bridge 3. The terminal inverted guanosine is methylated at the 7 positions on its guanine base, while the nucleotide on the internal side of the triphosphate bridge is methylated at the '' position of the ribose

Likewise, differentiate between 'upstream' vs. 'downstream' sequences relative to the initiation site.

DNA preceding the initiation site are upstream, those succeeding are downstream

Briefly describe the transient nature of the DNA-RNA hybrid during transcription - does this structure exist outside of the "transcription bubble"?

DNA reforms and the RNA chain does not stay associated with the template as a DNA-RNA hybrid outside of the bubble

What are the three different kinds of molecules in the central dogma - which is the 'intermediate' one?

DNA, RNA, protein intermediate: mRNA,

Of the four possible RNA nucleoside monophosphates, which is involved in 5' capping?

GMP

What are ribosomes composed of?

RNA and protein

In eukaryotes, which RNA polymerase is responsible for transcribing messenger RNA (mRNA) molecules?

RNA polymerase III

What name is given to the enzymes responsible for transcription?

RNA polymerases

According to the model of PIC assembly in our textbook, what are the last two GTFs to join the complex?

TFIIE and TFIIH

Of the several GTFs involved in establishing the eukaryotic PIC, which comes 'pre-attached' to RNAPII?

TFIIF

What is a "poly(A) tail".

a string of adenosine residues

What is the bacterial "sigma factor" and what role does it play in transcription?

accessory polypeptide, increases the enzymes affinity for promoter sites

What are "transcription factors" - what role do they play with regard to RNA polymerase activity?

additional proteins that recognize promoters for the RNA polymerase

What is "poly(A) polymerase" and what role does it play in synthesizing the poly(A) tail?

adds about 250 adensoines

In general, what role do general transcription factors (GTFs) play during PIC formation?

allow RNAPII to bind to the promoter

Briefly describe the process by which eukaryotic mRNAs obtain their poly(A) tail.

approximately 20 nucleotides downstream form the AAUAAA recognition site 1. Complex of proteins cleaves the pre-mRNA downstream of the recognition site 2. An enzyme, poly(A) polymerase, adds 250 or so adenosines without needing a template

What is the role of tRNA in the above process?

delivers amino acids to the ribosome

With reference to the above question, what is "rho" and what role does it play in bacterial termination of transcription - be specific.

encircles the 5' end of the new RNA and moves along the strand in a 3' direction to the polymerase where it separates the RNA transcript from the DNA to which it is bound via its helicase activity

Broadly speaking, what are the functions of the -35 element and the Pribnow box with regard to transcription initiation in bacteria?

identifying the precise number of nucleotides at which transcription begins

Clearly differentiate between "protein-independent" vs. "rho-dependent" transcriptional termination in bacteria.

independent: specific nucleotide sequence called terminator, rho-dependent: a protein (rho)

How is the above molecule incorporated into the RNA chain of the pre-mRNA - it what orientation and by what kind of bond?

inverted orientation through facing the 5' end, through a triphosphate bond

What is a "5'-5' triphosphate bridge" and what role does it play in 5' capping?

joins first 2 nucleosides

Likewise, what is a "transcriptional elongation complex", when does it form, and what effect does its formation have upon the sigma factor?

major change in conformation of the polymerase, releases the sigma factor

With reference to the above question, which as catalytic activity?

make the enzyme active

What kind of chemical modification occurs at the 7 position of the inverted guanosine - at the 2' position of the ribose of the next nucleotide?

methylated

Is the central dogma true of all things?

no, retroviruses

By itself, is the core enzyme of the bacterial RNA polymerase functional or nonfunctional?

nonfunctional

How many types of RNA polymerases do bacteria possess?

one

What role does the AAUAAA recognition site play in pre-mRNA processing prior to the addition of the poly(A) tail?

poly(A) tail begins 20 nucleotides downstream

With reference to a messenger RNA (mRNA) molecule, what are 'noncoding segments' - where are they found?

portions that do not direct the assembly of amino acids, 5' and 3' ends

What is a eukaryotic "preinitiation complex" (PIC)?

preinitiation complex: RNAPII binds the promoter with the cooperation of a number of general transcription factors

Briefly describe three different functions of the 5' methylguanosine cap.

prevents the 5' end of the mRNA from being digested by exonucleases, aids in the transport of mRNA out of the nucleus, plays an important role in the initiation of mRNA translation

What is the function of the poly(A) tail?

protects the mRNA form premature degradation by exonucleases

What roles do the GTFs "TFIIA" and "TFIIB" play in recruiting RNA polymerase II (RNAPII) to the transcription start site?

provide a platform for the subsequent binding of the multi-subunit RNA polymerase with its attached TFIIF

Differentiate between "pyrophosphatases", "pyrophosphate", and "inorganic phosphate" in the context of RNA polymerase activity.

pyrophosphatase: hydrolyzes the pyrophosphate (PPi) produced in the first reaction to inorganic phosphate (Pi)

Briefly describe two different roles of ribosomal RNA (rRNA) with regard to ribosome function.

rRNA: provides structural support, catalyzes peptide bond formation

Briefly describe the 5' or 3' 'directionality' of RNA polymerases - both in terms of 'reading' and 'writing'.

reads 3' to 5', writes 5' to 3'

Of the above, which process is a function of ribosomes?

ribosomes are the function of translation

With regard to bacterial transcription, what is the "holoenzyme", when and how is it formed, and what role does it play?

sigma factor with the core enzyme, binds to a suitable promoter region and separates the two strands of DNA making the start site

What is the first step in assembly of the PIC - differentiate among "TATA"-binding protein" (TBP), the "TATA box", and the general transcription factor (GTF) "TFIID".

the binding of TATA-binding protein to the TATA box, TBP is present as a subunit of TFIID

Briefly describe the numbering scheme used to refer to the initiation start site of transcription, as well as the sequences before or after this location.

the nucleotide where transcription is initiated is +1, the prededing nucleotide is -1,

What specific reaction does RNA polymerase actually catalyze?

the reaction in which ribonucleoside TRIphosphate substrates are cleaved into ribonucleoside MONOphosphates

With regard to transcription, what is a "promoter" - what role does it play in the process?

the sire of the DNA to which an RNA polymerase molecule binds prior to transcription

What does the "central dogma" of molecular genetics state?

the slow of information is from DNA to RNA to protein

Differentiate between transcription and translation.

transcription: synthesis of an RNA molecule from a DNA template, translation: synthesis of a polypeptide from mRNA template

Briefly describe the catalytic activity of TFIIH, what RNAPII domain is affected, and the outcome that TFIIH activity has upon release of the PIC from the promoter DNA.

transform the polymerase into an active, transcribing complex, phosphorylation of the polymerase at the c-terminus domain by TFIIH trigger that uncouples the enzyme from the GTFs and the promoter DNA is releases

With respect to transcription vs. translation - which involves transfer RNA (tRNA)?

translation

With reference to the above question, what are "ribonucleoside tri- and mono-phosphates"?

tri: starting, mono: end