Module 11: From DNA to Proteins: Transcription

evidence suggests_____was original genetic material

RNA

Ribozymes:

catalytic RNA

The structure of RNA (2)

• Primary structure • Secondary structure

Primary Structure =

RNA molecule folds to form secondary structures, owing to hydrogen bonding between complementary bases on the same strand

Y/N DNA RNA: Composed of nucleotides

Yes, Yes

DNA RNA: Type of sugar

Deoxyribose, Ribose

Y/N DNA RNA: Presence of 2'-OH group

No, Yes

Y/N DNA RNA: Bases

A, G, C, T;

A, G, C, U

Y/N DNA RNA: Nucleotides joined by phosphodiester bonds

Yes, Yes

Y/N DNA RNA: Double or single stranded

Usually double, Usually single

Y/N DNA RNA: Secondary structure

Double helix, Many types

Y/N DNA RNA: Stability

Stable, Easily degraded

(Tp, Location and Function) Ribosomal RNA (rRNA)

Bacterial and eukaryotic, Cytoplasm, Structural and functional components of the ribosome

(Tp, Location and Function) Messenger RNA (mRNA)

Bacterial and eukaryotic, Nucleus and cytoplasm, Carries genetic code for proteins

(Tp, Location and Function) Transfer RNA (tRNA)

Bacterial and eukaryotic, Cytoplasm, Helps incorporate amino acids into polypeptide chain

(Tp, Location and Function) Small nuclear RNA (snRNA)

Eukaryotic, Nucleus, Processing of pre-mRNA

(Tp, Location and Function) Small nucleolar RNA (snoRNA)

Eukaryotic, Nucleus, Processing and assembly of rRNA

(Tp, Location and Function) MicroRNA (miRNA)

Eukaryotic, Cytoplasm, Inhibits translation of mRNA

(Tp, Location and Function) Small interfering RNA (siRNA)

Eukaryotic Cytoplasm Triggers degradation of other RNA molecules

(Tp, Location and Function) Piwi-interacting RNA (piRNA)

Eukaryotic, Nucleus and cytoplasm, Suppresses the transcription of transposable elements in reproductive cells

(Tp, Location and Function) Long noncoding RNA (IncRNA)

Nucleus and cytoplasm Variety of functions

(Tp, Function) CRISPR RNA (crRNA)

Prokaryotic, Assists in destruction of foreign DNA

Which class of RNA is correctly paired with its function?

Transcription Is the…

Synthesis of an RNA Molecule from a DNA Template

Some RNAs are transcribed in both prokaryotic and eukaryotic cells ?

mRNA, rRNA, tRNA

Some RNAs are transcribed only in eukaryotic cells ?

pre-mRNA, snRNA, snoRNA, miRNA, siRNA, IncRNA, piRNA

Some RNAs are transcribed only in prokaryote cells ?

crRNA (crispr RNA)

Some viruses copy RNA directly from…

RNA

All cellular types of RNA are transcribed from…

DNA

The transcribed strand:

template strand

The transcription unit contains:

• A promoter

• RNA-coding sequence

• Terminator

Under the electron microscope, DNA molecules undergoing transcription exhibit…

Christmas-tree-like structures

RNA molecules are synthesized that are complementary and antiparallel to…

one of the two nucleotide strands of DNA, the template strand

RNA is transcribed from one…

DNA strand.

What is the difference between the template strand and the nontemplate strand?

The template strand is the DNA strand that is transcribed into an RNA molecule; the nontemplate strand is not transcribed.

A transcription unit includes:

a promoter, a region that encodes RNA, and a terminator

A transcription unit Drawing

correct

The substrate for transcription

Ribonucleoside triphosphates (rNTPs) added to the 3 end of the RNA molecule

The transcription apparatus

Bacterial RNA polymerase, The sigma factor:

The sigma factor:

binding to the promoter when transcription starts

Ribonucleoside triphosphates are substrates used in…

RNA synthesis

In transcription, nucleosides are always added to the….

3’ end of the RNA molecule

In transcription, nucleosides are always added to the 3’ end of the RNA molecule Steps:

1. Initiation of RNA synthesis does not require a primer

2. New Nucleotides are added to the 3’ end of the RNA molecule

3. DNA unwinds at the front of the transcription bubble and then rewinds

What is the function of the sigma factor?

The sigma factor controls the binding of RNA polymerase to the promoter.

Bacterial Transcription Consists of…

Initiation, Elongation, and Termination

Initiation • Bacterial promoters

Consensus sequences:

Consensus sequences:

sequences that possess considerable similarity

Consensus sequences: examples

• –10 consensus: 10 bp upstream of the start site

• Pribnow box: • 5 TATAAT 3 3 ATATTA 5

• –35 consensus sequence: TTGACA

The consensus sequence comprises the most …

commonly encountered nucleotides at each site

In consensus sequences: Pyrimidines indicated by..

Y

In consensus sequences: Purines indicated by..

R

In consensus sequences: N means….

that no particular bases is more common

In consensus sequences: C/G means….

Cytosine and Guanine are equally common

A consensus sequence consists of the most….

commonly encountered bases at each position in a group of related sequences

In bacterial promoters, consensus sequences are found…

upstream of the start site, approximately at positions -10 and -35

Initial RNA synthesis: primer?

no primer is required

The location of the consensus sequence determines the…

position of the start site

Transcription in bacteria is catalyzed by….

RNA polymerase, which must bind to the sigma factor to initiate transcription

RNA transcription is initiated when …

core RNA polymerase binds to the promoter with the help of sigma

RNA transcription initiated in Bacteria 6 steps

1. The sigma factor associates with the core enzyme to form a holoenzyme

2. which binds to the -35 and -10 consensus sequences in the promoter

3. The holoenzyme binds the promoter tightly and unwinds the double-stranded DNA

4. A nucleoside triphosphate complementary to the DNA at the start site serves as the first nucleotide in the RNA molecule

5. Two phosphate groups are cleaved from each subsequent nucleoside triphosphate, creating an RNA nucleotide that is added to the 3’ end of the growing RNA molecule

6. The sigma factor is released as the RNA polymerase moves beyond the promoter

RNA elongation is carried out by….

the action of RNA polymerase

Termination: Rho-dependent termination:

uses rho factor

Rho-independent termination:

hairpin structure formed by inverted repeats, followed by a string of uracils

The termination of transcription in some bacterial genes requires the…

presence of the rho factor

Rho-independent termination in bacteria is a multistep process (steps)

1. inverted repeats are transcribed into RNA

2. The string of U’s causes the RNA polymerase to pause

3. the inverted repeats in RNA fold into a hairpin loop

4. this destabilizes the DNA-RNA pairing

5. The RNA transcript separates from the template, terminating transcription

Rho-independent terminator contains…

an inverted repeat followed by a strong of approximately 6 adenine nucleotides

Conclusion of Rho Independent termination

Transcription terminates when inverted repeats form a hairpin followed by a string of uracils

Number of nucleotides in a gene should be proportional to…

the number of amino acids in the encoded protein

DNA _____ than mRNA;

much longer

DNA much longer than mRNA; demonstrated through…

hybridization

The concept of colinearity suggests that a continuous sequence of nucleotides in DNA encodes a…

continuous sequence of amino acids in protein.

A continuous sequence of nucleotides in the DNA codes a ….

continuous sequence of amino acids in the protein

The noncolinearity of eukaryotic genes was discovered by…

hybridizing DNA and mRNA

Is the coding sequence in a gene always continuous?

Coding sequences in a gene may be interrupted by noncoding sequences

Experiment: coding sequence in a gene always continuous?

1. Mix DNA with Complimentary RNA and heat to a seperate DNA strands

2. cool the mixture complementary, sequences pair

Experiment: coding sequence in a gene always continuous? Results

DNA may reanneal with its complimentary strand

or with RNA (Noncoding regions of DNA are seen as loops)

What evidence indicated that eukaryotic genes are not collinear with their proteins?

When DNA was hybridized to the mRNA transcribed from it, regions of DNA that did not correspond to RNA looped out.

exons

coding sequences

introns

noncoding sequences

The coding sequences (exons) of many eukaryotic genes are disrupted by…

noncoding sequences (introns)

The gene includes:

DNA sequences that code for all exons and introns

• Those sequences at the beginning and end of the RNA that are not translated into a protein, including the entire transcription unit

Those sequences at the beginning and end of the RNA that are not translated into a protein, including the entire transcription unit

• The promoter

• The RNA coding sequence

• The terminator

Many RNA Molecules Are Modified After…

Transcription in Eukaryotes

A mature mRNA contains…

5′ untranslated region (5′ UTR, or leader sequence), protein coding region, 3’ untranslated region

Shine-Dalgarno sequence in….

Prokaryotes only

5′ untranslated region aka.

Shine–Dalgarno sequence

Draw a mature mRNA

correct

The addition of the 5′ cap

A nucleotide with 7-methylguanine; 5′-5′ bond is attached to the 5′- end of the RNA

The addition of the poly(A) tail

~ 50 to 250 adenine nucleotides are added to the 3′-end of the mRNA

Most eukaryotic mRNAs have a…

5’ cap

Most eukaryotic mRNAs have a…

3’ poly (A) tail

In pre-mRNA processing, a poly(A) tail is added through…

cleavage and polyadenylation.

pre-mRNA processing drawn

correct

RNA splicing

Consensus sequences, Spliceosome:

Consensus sequences

• 5′ consensus sequence

• 3′ consensus sequence:

• Branch point: the adenine “A”: ~18- 40 nucleotides upstream of 3′- splicing site

Spliceosome:

five RNA molecules + 300 proteins

The splicing of pre-mRNA requires…

consensus sequences.

Critical consensus sequences are present at the….

5’ splice site and the 3’ splice site.

Draw the splicing of pre-mRNA

correct

The splicing of pre-mRNA introns requires a ____ process

two-step