CFP Microbiology Lecture 3: Transcription

Explain mRNA (messenger RNA)

encodes the amino acid sequence of a polypeptide
mRNAs are the transcripts of protein coding genes

Explain tRNA (transfer RNA)

brings amino acids to the ribosome during the translation process

Explain rRNA (ribosomal RNA)

Combines with ribosomal proteins to form the ribosome
mRNA is translated into protein at the ribosome

Explain snRNA (Small nuclear RNA)

combines with certain proteins and is involved in RNA processing in eukaryotes

How many RNA polymerase does bacteria have?

One; composed of the core polymerase plus sigma factor

What are the 4 RNA molecules

mRNA, tRNA, rRNA, snRNA

What are the 3 different RNA polymerases in eukaryotes?

RNA polymerase I: 5.8s, 18s, 28s rRNA genes (ribosome)
RNA polymerase II: all protein-coding genes (mRNA) and some snRNA (messenger RNA)
RNA polymerase III: tRNA genes and some snRNAs

Explain the process of bacterial RNA polymerase transcription of DNA

RNA polymerase core enzyme is a multi-subunit complex that synthesizes RNA using DNA as a template
RNA polymerase + sigma factor (holoenzyme) adheres weakly to bacterial DNA and slides along DNA until it reaches a promoter region( -35BP and -10BP regions)

What are the eukaryotic promotor sequences and boxes?

GC box: GGGCGG -70 to -200 base pairs
TATA box: TATAAA -20 to -35 base pairs
CAAT box: CCAAT -80 base pairs

Explain the eukaryotic proteins needed for transcription initiation

TATA box binding protein: a subunit of TFIID; binds to TATA box of gene promoter
TFIID: causes a distortion in the DNA helix allowing for the recruitment of other transcription factors
TFIIB: involved in RNA polymerase interactions - start site recognitio

Explain transcription initiation in eukaryotes

Most common eukaryote promoter sequence is located at position -35 and contains the sequence - 5' - TATAAAA-3' (TATA box)
TBP/TFIID bind to the promoter at the TATA box (-25)
TFIIB binds to promoter
RNA polymerase, TFIIE, and TFIIH are recruited to the pr

For what level of transcription can you use basal transcriptional machine?

basal transcriptional machine; this is sufficient for only a low level of transcription; for increase levels of transcription or tissue specific transcription, the binding of an activator and mediator/adaptor molecule is required

What is the central dogma of molecular bio?

DNA -> RNA -> Protein

Transcription produces which product? (tRNA? mRNA?)

mRNA

Translation is the synthesis of a polypeptide using information from what?

mRNA

What is the site of translation?

Ribosomes

In prokaryotes, translation of mRNA can begin before transcription has finished, T/F?

True

A ____________ ______________ is the initial RNA transcript from any gene prior to processing?

Primary Transcript

Does RNA have one or strands of nucleotides?

One

The sequence of bases in DNA is the template for what?

mRNA

Can both strands of DNA code for genes to produce proteins?

Yes; depends which strand the gene is on

Visualize the antisense and sense strand and how they can be complementary to mRNA

The sense strand of DNA has the same sequence as the mRNA; however in mRNA all of the T's are replaced with U's
The antisense strand of DNA is complementary to mRNA and is used as the template for mRNA synthesis

What are the regions of a prokarytic gene?

Promoter: located upstream of the RNA coding sequence and ensure the proper location of transcription initiation
RNA coding sequence: the DNA sequence that is transcribed into RNA
Terminator: a sequence downstream of the RNA coding sequence and specifies

RNA synthesis is catalyzed by what?

RNA polymerase- pries the DNA strands apart and hooks together the RNA nucleotides

What are the 3 stages of transcription?

Initiation
Elongation
Termination

Explain the initiation stage of transcription

During transcription only one strand of DNA is required for template - the strand serving as the template is called the antisense strand and the other strand is called coding strand or sense strand

What is the number of base pairs where the prokaryotic promoter begins?

-35 bp : 5' - TTGACA- 3'
-10bp: 5' -TATAAT-3' (aka Pribnow box)

Explain the elongation stage

Coding strand and RNA transcript will have the same bases from 5' to 3' - uracil will be substituted for thymine though

Explain the termination stage

Termination occurs at termination site of DNA
RNA polymerase and ner mRNA transcript is released

Compare DNA synthesis to RNA synthesis.

RNA- RNA polymerase, NTPs precursor, no primer needed, uracil pairs with adenine
DNA- DNA polymerase, dNTP precursor, primer required for initiation, thymine pairs with adenine

What are the 4 types of RNA molecules

mRNA, tRNA, rRNA, snRNA

Can RNA polymerase proofread like DNA?

No

How accurate is transcription compared to replication?

Less accurate

How many nucleotide pairs per helical turn of double helix?

10
DNA with fixed ends, rotation is prevented
When 10 DNA base pairs is unwound, the DNA will form one supercoil to relieve tension
One supercoil forms for every 10 bp opened up

What causes positive and negative supercoils?

When a protein is tracking through DNA, the ends are unable to rotate
Excess helical turns ahead of RNA polymerase cause positive supercoils
Deficit of helical turns behind the RNA polymerase cause negative supercoils

Termination of transcription can involve intrinsic termination sequences found in the RNA transcript

Regions that form hairpins varying in length from 7-20 bps, include G-C rich regions and is followed by a run of U bases

Termination of transcription can involve extrinsic factors such as the rho protein in prokaryotes

Rho protein attaches to recognition site on the RNA
Rho moves along RNA following RNA polymerase
RNA polymerase pauses at terminator and rho catches up
RHO unwinds DNA-RNA hybrid and pull RNA from the RNA polymerase
Termination: RNA polymerase, rho, and R

Do eukaryotic cells modify RNA after transcription?

Yes; enzymes in the eukaryotic nucleus modify pre-mRNA (RNA processing) before the genetic messages are dispatched to the cytoplasm
During RNA processing, both ends of the primary transcript are usually altered
Also, usually some interior parts of the mol

What is the importance of introns?

Introns are DNA or RNA molecules which do not code for proteins and interrupts the sequence of genes
Some introns contain sequences that may regulate gene expression
Some genes can encode more than one kind of polypeptide, depending on which segments are