Transcription and Translation

First half only transcription and second half only translation =

Describe RNA polymerases

• Do not require primer nad lack 3-5 exonuclease

• Syn RNA in the 5 to 3 direcction

• Need ATP, GTP, CTP and UTP

Why do we need tranascitption?

Cell only has one or several copies —> not enough for cell meta

Protect a genomic DNA from cytoplasmic envrion (Euks only)

Reg the rate of protein syn via number of nRNA, life time of mRNA(degrade) and RNA binding factors (translation)

What is the difference between RNA poly in Euks vs Proks?

Proks - Single RNA poly for all RNA, E coli had 4 subs (sigma facotr —> promoter sigma 70

Euks - Have 3 types

• I - prod rRNA

• II - prod mRNA

• III - prod tRNA and 5S rRNA

***Same mech for all 3 but diff types of promoters

Describe the strucutre of a gene.

Reg sequences: promoter —>binding for RNA poly and trans factors

…………………Promoter proximal elements and enhancers bind nuclear rep, co act, and co repressors

***Start + terminaiton seq needed

Describe the template and coding strand using their specific terms

Template - made via Rna poly, Comp and antiparrallel to coding strand and RNA

Coding - Analogus to produced RNA (Can be used to determine AA seq of protein)

How do we started transcription? What is the regulation?

AT rich seqeunces

• E coli TATAAT - pribnow box (PROKS)

• Euks have TATA(A/T)A - TATA box

Also can have CAAT boxes, GC rich seq, and enchanters in EUKS

How is enlongation stopped?

Termination seq via

• Rho independent - formation of hairpin loop —> release of RNA polu and transcript

• Rhi dep - binding of rho causes release of poly and transcript

AHHour DNA is way too coiled what do we use to prevent this?

DNA topoisomerase

Describe binding of RNA poly in bacteria

• Recog and binds to promoter

• Unwinds and separates DNA

• Sigma factor dissaociates from DNA

• RNA poly transcribes DNA

What is a cistron?

Region of DAN that encodes for single polypeptide chain

***Relates to prok mRNA s which are ususal polycistronic transcripts

*8Proks lack of nucleus allows for coupling of transcription and translation

AHH patient Ivy Sharer has a positive sputum stain whihc reveals that she has TB, what will we treat her with?

• Multidrug regimen inclduing rifampin (Abx of the rifamycin family)

  Inh bacteria RNA poly however can also inhibit micro RNA polymerase (TB dosage below needed amount for inhibition)

What are the differences when comparing EUK transcription vs PROK counterpart?

• Occurs in Nuc and in chromatin

• More reg: Nucleosome mod enzymes (histone acetytransferases), chromatin remodeling

• 3 polymerases

• More processing :mod of RNA and splciing

• nMRNA = only one polypeptide

What do general transcription factors interact with?

GTFs interact with polymerase II —> initiate trans

Enhancers —>up or down stream to stim transctiption initiation, can bind to trans factors or activators.

What is thalassemias?

Group of hereditary anemias —> most common gene disorder

• Affects subunits of adult hemoglobin—>anemia

• Mutations with Beta + phenotype are withint he TATA box

  Messes with start point and red beta globin by 75%

Describe the synthesis of EUK tRNA.

tRNA synthesized by RNA poly III (Poly III)

• mature tRNA is made from precurosors via cleavge of 5 and 3 ends, splciing to remove introns, replacement of 3 termineal UU with CCA, or multiple mods of bases

Describe the syn and processing of EUK mRNA.

RNA Poly II syn primary transcript

• capped at 5 end during trans - 5 capm (recognition for ribosome binding + decreases degradation)

• Poly A tail at 3 end once released from RNA poly

• Introns spliced out

• —>cytoplasm once mature RNA done

Describe the synthesis of EUK rRNA

Via RNA poly I

• From repeating genes

• Mult RNA poly I can transcript from a single gene

• rRNAs for thje ribonucleoprotein complex ie ribosome

What kind of mutation causes sickle cell anemia

Missense mutation

• Single base change in each allele for B globin DNA ie GTG (Val) replaces normal GAG (Glu)

• - Oxygenated molescules (soluble) however upon deoxygenation then aggreattion to insluble fibers

  Defroms RBC into spiny and sickle shaped

What are the componenets needed for translation

template ie mRNA

ribosomes

tRNA

AAs

Translation factors

ATP and GTP - used to attach AA to tRNA, binding of aminoacyl tRNA to A site and trasnslocation

mRNA syn from 5 end producing a polypeptide syn from its amino terminal end

Describe the formation of aminoacyl tRNA

Attachemnt of AA to tRNA cat via aminoacyl tRNA synthetases

• AA atttachmed to 3 end of tRNA

• Req ATP

• Respon for specifcity and proofreading and high fidelity of translation

• each memeber recognizes specidc AA with corresponding tRNA

Describe the sites associated with ribosomes and where they are located?

APE sites

• A binds incoming aminoacyl tRNA and directs next AA added

• P occupied by peptidyl tRNA —>carries syn peptide’

• E - empty tRNA about to exit

Can be free or bound to the rough ER

Describe the initation of translation.

• 16s rRNA contains seq comp to shine dalgarno seq

  Posititons mRNA on 30s subunit

• in EUKS, 40S sub binds to cap strucutre of mRNA

• AUG is recognized via initator tRNA —> enters P site

  Reg via IF2 in E coli and several eIF in humans

  Proks + mitro iniator tRNA carries N formylated methionine

  ***IN EUK not formylated

  ***AA attacched to carbonxyl end via peptidyltransferase

What are some medications that take use of the translation system and where do they act? Ex clindamycin, diphtheria toxin. tetracycline

What happens when we do a shitty job and need to degrade our misfolded proteins?

Misfolded proteins labeled for degradation by polyubiq

• Polyubiq proteins degraded by 26S proteosome

What assists in folding these newly synthesized proteins? What do they do and what family are these apart of?

Chaperones - HSP60 or 70 family, disulfide bonds cat via protein disulfide isomerase (PDI)

Describe termination of translation?

Moves until a termination codon goes into the A site

Release factor binds to A site —>triggers hydrolyses of teh bond bertweenpeptide and tRNA by a peptidyltransferase —>released from ribosome—>ribosome dissoasited into subunits

What are some regulation of translation

regulatory proteins - either stabalize or prevent binding

rare codons - fewer tRNA, slow down, translation, usually at the beg of mRNA

Small interfering RNA

AHAH somes has been exposed to streptomycin, what subunit does this affect and what are the effects?

AHAH somes has been exposed to tetracycline, what subunit does this affect and what are the effects?

AHAH somes has been exposed to chloramphenicol, what subunit does this affect and what are the effects?

AHAH somes has been exposed to ricin, what subunit does this affect and what are the effects?