Transcription Flashcards by Lance Andrie Malana

The synthesis of RNA molecules using DNA strands as the templates so that the genetic information can be transferred from DNA to RNA.

Transcription

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code for proteins

mRNAs

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form the basic structure of the ribosome and catalyze protein synthesis

rRNAs

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central to protein synthesis as the adaptors between mRNA and amino acids

tRNAs

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Serves as the template for the telomerase enzyme that extends the ends of chromosomes

Telomerase RNA

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Function in a variety of nuclear processes including the splicing of pre-mRNA

snRNAs (small nuclear RNAs)

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Help to process and chemically modify rRNAs

snoRNAs (small nucleolar RNAs)

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________________, not all of which appear to have a function; some serve as scaffolds and regulate diverse cell processes, including X-chromosome inactivation

lncRNAs (long noncoding RNAs)

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Regulate gene expression by blocking expression of specific mRNAs and causing their degradation

miRNAs (microRNAs)

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Turn off gene expression by directing the degradation of selective mRNAs and helping to establish repressive chromatin structures

siRNAs (small interfering RNAs)

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Bind to piwi proteins and protect the germ line from transposable elements

piRNAs (Piwi-interacting RNAs)

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DNA regions that can be transcribed (includes promoter, operator, and structural genes)

Operon

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Is the strand from which the RNA is actually transcribed

Template strand (antisense strand)

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Is the strand whose base sequence specifies the amino acid sequence of the encoded protein.

Coding strand (sense strand)

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*The enzyme responsible for the RNA synthesis

RNA Polymerase

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What factor binds to the core RNA polymerase to become an RNA polymerase holoenzyme

Sigma factor (σ)

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In E. coli is consists of 5 different subunits:

α2 = Determine the DNA to be transcribed
β = Catalyze polymerization
β’ = Bind & open DNA template
ω = Non-essential smallest subunit that facilitates the assembly of RNA polymerase
σ = Recognize the promoter for synthesis initiation

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*Drug for tuberculosis, can bind specifically to the β subunit of RNA-pol and inhibit the RNA synthesis.

Rifampicin

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Each transcriptable region is called

Structural gene

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*Is the DNA sequence that RNA-pol can bind.

*Is a region of DNA where transcription of a gene is initiated.

promoter

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Repressor protein binding site

Operator

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In a bacterial promoter, the TTGACG region is at __________ and the Pribnow region is at _________

-35 element
-10 element

Note: *Promoter + 1 is the transcription start site

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Eukaryotic promoter

TATA box

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Transcription of Prokaryotes:

*Initiation phase: RNA-pol recognizes the promoter and starts the transcription.

*Elongation phase: the RNA strand is continuously growing.

*Termination phase: the RNA-pol stops synthesis, and the nascent RNA is separated from the DNA template.

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a. Initiation * The first nucleotide on RNA transcript is always _______.

purine triphosphate

(GTP, ATP) is more often than (GTP, ATP).

GTP; ATP

In which phase of transcription is the sigma factor released

Elongation phase

Which factor enters during termination phase

rho factor

Which phase? Free nucleotide triphosphates are added sequentially to the 3’OH of the nascent RNA strand.

Elongation phase

Two types of termination in bacteria:

1. intrinsic (determined by specific sequences (termination sites) 2. rho-dependent (no formation of hairpin structure)

______ is a protein that binds to nascent RNA and tracks along the RNA to interact with RNA polymerase and release it from the elongation complex.

Rho factor

____ is a hexameric and ATP-dependent RNA translocase, that terminates transcription at certain specific genomic sites called a _____.

Rho; rut (rho utilization)

r-independent termination Termination sites consist of 3 features:

* Inverted repeats, rich in G:C which form a stem-loop structure (hairpin) in RNA transcript * Series of 7 U residues following the hairpin stem

In rho-independent termination, which structure causes the RNA polymerase to pause

Stem-loop

While RNA polymerase pauses, the U-rich sequence in the open complex is unable to hold the RNA-DNA hybrid together. Termination occurs

The 3 RNA Polymerases in Eukaryotic Cells

Types of polymerase and the genes they transcribe 1. RNA polymerase I = 5.8S, 18S, and 28S genes 2. RNA polymerase II = All protein-coding genes, plus snoRNA genes, miRNA genes, siRNA genes, lncRNA genes, and most snRNA genes 3. RNA polymerase III = tRNA genes, 5S rRNA genes, some snRNA genes, and genes for other small RNAs

The rRNAs were named according to their "S" values, which refer to their _________. The larger the S value, the larger the rRNA.

rate of sedimentation in an ultracentrifuge

a specific inhibitor of RNA-pol found in mushroom

Amanitin

RNA-pol of Eukaryotes sensitivity to Amanitin

RNA-pol I = No RNA-pol II = High RNA-pol III = Moderate

are the specific sequences on the DNA template that regulate the transcription of one or more genes.

Cis-acting element

Cis-acting element includes...

Enhancer GC box CAAT box (-75) TATA box (Hogness box) (-25)

Transcription Factor: Recognizes TATA box and other DNA sequences near the transcription start point

TFIID

Transcription Factor: Recognizes BRE element in promoters; accurately positions RNA polymerase at the start site of transcription

TFIIB

Transcription Factor: Not required in all promoters; stabilizes binding of TFIID

TFIIA

Stabilizes RNA polymerase interaction with TFIIB; helps attract TFIIE and TFIIH

TFIIF

Transcription Factor: Attracts and regulates TFIIH

TFIIE

Transcription Factor: Unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase C-terminal domain (CTD); releases RNA polymerase from the promoter

TFIIH

Pre-initiation complex (PIC)

* TBP (TATA binding proteins) of TFIID binds TATA * TFII A and TFII B bind TFII D * TFII F-RNA-pol complex binds TFIIB * TFII F and TFII E open the dsDNA (helicase and ATPase) * TFII H: completion of PIC

Gene regulatory proteins that help RNA pol, the general factors, and the mediator all to assemble at the promoter

Activators

Binding site for activator protein

Enhancer

*Allows the activator proteins to communicate properly with the Pol II and with the general transcription factors.

Mediators

Elongation factors in eukaryotes (___, ____, and ____) that stabilizes RNA pol

Spt4; Spt5; Elf

* Enzymes that rapidly remove superhelical tension in DNA

DNA topoisomerase

*A specialized topoisomerase in bacteria that Uses the energy of ATP hydrolysis to pump supercoils continuously into the DNA, thereby maintaining the DNA under constant tension

DNA gyrase

In eukaryotic transcription, the termination sequence is _________ followed by ____ repeats

AATAAA; GT

Post-transcriptional modifications in the nucleus

5' capping RNA splicing 3' polyadenylation

* Primary transcripts of mRNA are called as ______

heteronuclear RNA (hnRNA)

The capping occurs before the splicing.

A gene consisting of introns and exons.

Split gene

are the coding sequences that appear on split genes and primary transcripts, and will be expressed to matured mRNA.

Exons

are the non-coding sequences that are transcripted into primary mRNAs, and will be cleaved out in the later splicing process.

Introns

the large assembly of small nuclear RNA (snRNAs) and protein molecules that performs pre-mRNA splicing in the cell.

Spliceosome

Changes (insertion, deletion, base substitution) to specific nucleotide sequences within an RNA molecule after it has been generated.

RNA editing

Significance of RNA editing

multiple functions of gene, localization and stability of RNAs has been linked to human diseases

Excised intron is in the shape of ________

lariat

post-transcriptional modifications

5 methyl capping poly-A tail splicing in the nucleoplasm

What factor? Delivers aa-tRNAs to the A-site of the ribosomes

EF-Tu (elongation factor thermos unstable)

The enzyme ___________ catalyzes the conversion of cytidine (C) to uridine (U) in RNA

APOBEC1 (Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 1)

C to U APOBEC1 Glutamine to Stop Codon Unedited RNA: Produces the full-length Apo-B100 protein, primarily found in the liver (hepatic form). Edited RNA: Generates a truncated protein called Apo-B48, found in the intestines (intestinal form).

The enzyme _____________ catalyzes the A-to-I (adenosine to inosine) conversion in double-stranded RNA regions.

ADAR2 (Adenosine Deaminase Acting on RNA 2)

A to I ADAR2 Glutamine to Arginine Unedited GluR2 (Q form): Permits Ca²⁺ permeability, which is crucial for neuronal excitability. Edited GluR2 (R form): Becomes impermeable to Ca²⁺, stabilizing neuronal function and preventing excessive excitability.