Transcription and splicing machinery
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DNA  primary mRNA  mature mRNA. Transcription + Processing. Transcription and Splicing machinery. Prokaryotic and Eukaryotic RNA Polymerases are similar in shape. Sigma ( σ ) subunit missing. -> Different number of subunits. Recognizes the promoter site (-10 box + -35 box).

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Transcription and splicing machinery

DNA  primary mRNA  mature mRNA

Transcription + Processing

Transcription and Splicing machinery

Prokaryotic and Eukaryotic RNA Polymerases are similar in shape

Sigma (σ) subunit missing

-> Different number of subunits

RNA polymerase mechanism shape

-> Similar to DNA polymerase

-> 3’-hydroxyl group of RNA chain attacks the a-phosphoryl group of the incoming NTP

-> Transition state stabilized by Mg2+

Transcription shape

AFM image of short DNA fragment with RNA polymerase molecule bound to transcription recognition site. 238nm scan size. Courtesy of Bustamante Lab, Chemistry Department, University of Oregon, Eugene OR

Prokaryotic promoter sites shape

-35 -10 +1

5’-----TTGACA--------------TATAAT---------start site----3’

σ subunit

Prokaryotic promoter sites shape

σ subunit interacts with

-10 box and -35 box

Alternative shapeE. coli promoters

Stanard Promoter -> σ70

Heat shock promoter -> σ32

N-starvation promoter -> σ54

DNA unwinding prior to Initiation of Transcription shape

-> Transition from closed to open complex

-> Unwinding done by RNA polymerase

1 RNA polymerase molecule -> 17bp segment -> 1.6 turns on B-DNA

Negative supercoiled DNA favors the transcription shape

-> neg. supercoiling facilitates unwinding

-> introduction of neg. supercoiling -> increases rate of transcription

-> Exception -> promoter of TopoII -> neg. Supercoiling -> decreases rate of transcription

Transcription bubble shape

First Nucleotide is pppG or pppA -> Transcription start

RNA-DNA hybrid separation shape

RNA polymerase forces the separation of the RNA-DNA hybrid

Transcription Termination shape

Rho independent termination

Termination by Rho protein

-> RNA polymerase pauses after production of hairpin

-> RNA-DNA hybrid of hairpin is unstable

=> RNA falls off

Rho interacts with RNA polymerase -> breaks the RNA-DNA hybrid helix -> functions as a helicase

Primary transcript of rRNA is modified shape

Modification: 1. Cleavage of primary transcript by Ribonuclease III

2. Modification of bases (Prokaryotes: methylation)

and ribose (Eukaryotes: methylation)

tRNA transcript is also modified shape

Modification: 1. Cleavage of primary transcript by Ribonuclease III

2. Addition of nucleotides at 3’ end (CCA)

3. Unusual bases

tRNA transcript processing shape

Modification: 1. Cleavage of primary transcript by Ribonuclease III

2. Addition of nucleotides at 3’ end (CCA)

3. Unusual bases

Antibiotic Inhibitors of Transcription shape

Rifampicin: - derivate of rifamycin (Streptomyces)

- inhibits initiation of RNA synthesis (binds to RNA polymerase -> in pocket

where RNA-DNA hybrid is formed)

Actinomycin D: - polypeptide-containing (Streptomyces)

- binds tightly (intercalates) to ds-DNA (cannot be template for RNA


- its ability to inhibit growth of rapid dividing cells makes it a effective

agent in cancer treatment

α shape-Amanitin:

produced by mushroom (Amanita phalloides)

-> cyclic peptide of 8 amino acids

-> binds tightly to RNA polymerase II

-> blocks elongation of RNA synthesis

-> deadly doses (LD50 is 0.1 mg/kg)

Different Eukaryotic RNA Polymerase promoters shape

Inr -> Initiator element

(found at transcription start)

DPE -> downstream core promoter element

Eukaryotic promoter elements (RNA polymerase II promoter) shape

-> -40 and -150

Normally between -30 and -100

Often paired with Inr -> -3 and -5

CAAT boxes and GC boxes can even be on noncoding strand active

DPE -> +28 and +32

Eukaryotic Transcription Initiation shape

TappingMode AFM image of an individual human transcription factor 2: DNA complex. Clearly resolved are the protein:protein interactions of two transcription factor proteins which facilitate the looping of the DNA, allowing two distal DNA sites to be combined. AFM provided the investigators' improved resolution of the looped DNA complexes compared to electron microscopy of rotary shadowed samples. 252 nm scan. Image courtesy of Bustamante Lab, Institute of Molecular Biology, University of Oregon, Eugene.

Eukaryotic Transcription Initiation shape

Basal transcription apparatus

(-> carboxylterminal domain)

TATA-box binding protein (TBP is a component of TFIID) recognizes the TATA box and forms complex with DNA

CTD plays a role in transcrition regulation -> binds to mediator

Phosphorylation of CTD by TFIIH -> elongation of transcription

Gene “Off” shape

Gene “On”

Eukaryotic transcription products (from RNA polymerase II) are processed




Polyadenylation of 3’ end

Capping 5’ end

RNA editing are processed

Splicing are processed

Anemia: defect synthesis of hemoglobin

Mutations affecting splice sites cause around 15% of all genetic diseases

Creates a new splice site

Spliceosome assembly are processed

The catalytic center of the spliceosome

Alternative splicing are processed

Self-splicing are processed

A rRNA precursor of Tetrahymena (protozoan) splices itself in the presence of guanosine (G) as co-factor

The L19 RNA is a intron that is catalytical active

This TappingMode scan of the protozoan, Tetrahymena, shows its cilia-covered body and mouth structures. The sample was dried onto a glass slide and scanned; no other preparation was required. 50 micron scan courtesy C. Mosher and E. Henderson, BioForce Laboratory and Iowa State University.

Ribosomal Factory are processed




Translation: are processed

mRNA -> Protein

Linkage of Amino Acids to tRNA are processed

2nd step

1st step

Linkages either 2’ or 3’

1st step: activation of AA by adenylation (Aminoacyl-AMP)

2nd step: linkage of AA to tRNA

Aminoacyl-tRNA synthetases couple Amino acids to tRNA are processed

Synthetases are highly specific for the amino acid (error rate 1 in 105)

Synthetases recognize the anticodon loops and acceptor stems of tRNA

Threonyl-tRNA synthetase complex

Class II synthetase

Glutaminyl-tRNA synthetase complex

Class I synthetase

Classification of Aminoacyl-tRNA synthetases of tRNA

  • Synthetases recognize different faces of the tRNA molecule:

  • Class I acylates the 2’ OH group of the terminal adenosine of tRNA

  • Class II acylates the 3’ OH group of the terminal adenosine of tRNA

  • They bind ATP in different conformations

  • Most class I are monomeric, most class II are dimers

Ribosomal RNAs (5S, of tRNA16S, 23S rRNA)

16S rRNA

tertiary structure

secondary structure

Ribosomal Protein L19 of the 50S subunit of tRNA

Fits through some of the cavities within the 23S RNA

Protein synthesis in E. coli of tRNA

Polysomes: Transcription and Translation happens at the same time

Direction of Transcription: 5’->3’

Direction of Translation: 5’->3’

tRNA binding sites on Ribosomes tRNA -> fMet

A for aminoacyl -> tRNA enters Ribosomes

P for peptidyl -> tRNA passed on - peptide bonds are closed

E for exit -> tRNA exits Ribosomes

Polypeptide chain escape path tRNA -> fMet

Polypeptide synthesis tunnel

Elongation factor Tu tRNA -> fMet

Elongation factor G

EF-G mediates translocation within the Ribosome

EF-Tu delivers aminoacyl-tRNA to Ribosomes

Translocation mechanism tRNA -> fMet

EF-G (in GTP form) binds to EF-Tu site -> stimulates GTP hydrolysis

Conformational change of EF-G -> driving EF-G into A site

Causes translocation of tRNA and mRNA

Diphtheria Toxin blocks Protein Synthesis by Inhibition of Translocation

Disease: Diphtheria

Cause: Toxin from Corynebacterium diphtheriae

Toxin catalysis transfer of ADP-ribose to diphthalamide ( a modified AA in EF 2 – translocase)

Differences between Eukaryotic and Prokaryotic Protein Synthesis

Difference -> Translocation Initiation