Transcription and RNA Processing

Flashcards covering the anatomy of genes, the biochemistry of transcription, nuclear structure, and eukaryotic RNA processing steps including capping, polyadenylation, and splicing.

Transcription

The DNA-directed RNA synthesis where RNA is synthesized by RNA polymerase to produce a single-stranded RNA molecule complementary to one strand of the DNA double helix.

Human Genome Size

Approximately $3000\,Mb$ ($3 \times 10^9$ base pairs) of DNA containing about $25,000$ protein-coding genes.

Promoter

A DNA sequence that specifies where RNA polymerase will initiate transcription and tells RNA pol which DNA strand to use as the template.

Termination site

A DNA sequence that specifies where RNA polymerase stops transcription and releases the DNA template.

General transcription factors

Specific proteins that RNA polymerase needs to bind to the promoter in eukaryotic cells.

Initiation

1. RNA Pol binds to the promoter

2. RNA Pol unwinds short region of DNA to expose template strand.

3. RNA Pol begins synthesizing RNA complementary to template strand (at the 5' end of the RNA).

Elongation

4. RNA Pol adds nucleotides complementary to the template strandto 3’OH of RNA one at a time.

5. RNA transcript is released as it is made; DNA double helix immediately reforms.

Termination

The final stage of transcription where RNA Pol reaches the termination site and the RNA transcript is released.

net result: RNA molecule produced

DNA molecule not altered

Transcription unit

The molecular biologists' definition of a gene; a region of DNA that encodes an RNA, defined by a promoter, transcribed region, and termination site.

Regulatory elements

Specific DNA sequences that serve as binding sites for regulatory proteins that activate or repress transcription.

Nuclear envelope

A double-membrane structure that separates the cytoplasm from the nucleoplasm and contains nuclear pores.

Nucleolus

A structure within the nucleus known as the cell's "ribosome factory."

Nuclear pores

Selective transport channels approximately $100\,nm$ across that allow mRNAs to exit the nucleus and nuclear proteins to enter.

Capping

The addition of a modified guanine nucleotide to the $5'$ end of the pre-mRNA.

Polyadenylation

The post-transcriptional addition of $200 \text{-} 300$ adenine nucleotides to the $3'$ end of the pre-mRNA.

UTR

Untranslated region; found at the $5'$ and $3'$ ends of eukaryotic mRNA.

ORF

Open-reading frame; the coding region of the mRNA.

Introns

Internal, intervening segments of pre-mRNA that are removed during the splicing process.

Exons

The regions of RNA that remain after introns are removed and are joined back together.

Spliceosome

A complex of small nuclear RNAs (snRNAs) and associated proteins (snRNPs) that recognizes splice sites to remove introns and join exons back together

Alternative splicing

The pairing of different combinations of $5'$ and $3'$ splice sites, allowing some genes to encode more than one RNA.

Ribozymes

Catalytic RNA molecules.

snRNAs

Small nuclear RNAs which are involved in translation as components of spliceosomes.

how many times is Dan replicated per cell division

once

how many strands of DNA used at template for transcription

one

how many subsets of DNA (genes is transcribed in a given cell

one

what percentage of human DNA encodes proteins

1%

most of human genome is not transcribed

true

what sequences in DNA determine which regions of DNA will be transcribed

promoter

termination site

promoters and termination sites define the regions of DNA that are transcribed

true

in prokaryotes, RNA pol binds promoter

directly

in eukaryotes, what does RNA pol need to bind promoter

other proteins

both ran and dna require

template strand

DNA pol, not RNA pol requires a

primer

RNA polymerase uses

ATP, CTP, GTP and UTP

DNA polymerase use

dATP, dCTP, dGTP and dTTP

what do prokaryotic cells lack

nucleus

Ribosomes can begin translating mRNAs as soon as

they’re made

Eukaryotic cells have a

nucleus

where’s DNA in eukaryotic cells

nucleus

where are ribosomes in eukaryotic cells

cytoplasm

nuclear membrane shields the RNA from ______ until it is exported to the cytoplasm.

ribosomes

gene expression in eukaryotic cells allows for what

RNA processing

The nucleus of eukaryotic cells provides

a specialized environment for gene expression

what does the nucleus contain

- DNA and associated proteins (histones)

- the enzymes that replicate, transcribe and repair

DNA

- many other structural and regulatory proteins

- nucleolus = the cell's "ribosome factory"

Transport through nuclear pore is selective

- mRNAs exit the nucleus

- Nuclear proteins enter the nucleus

Transcription and translation occur in ____ succession.

rapid

Capping and polyadenylation can alter the stability and _____ of eukaryotic mRNAs

translation

splicing

removal of internal fragments of pre mRNA = introns

How are introns recognized and removed?

spliceosome

why splice?

• Introns must be removed to convert primary transcript to mature RNA

• allows some genes to encode more than one RNA via alternative splicing: pairing of different combinations of 5' and 3' splice sites.