bio unito 3 (142) more

what is the central dogma again?

• Genetic information passes from DNA to protein in a one-way information pathway

BASIC steps of producing a phenotype from the genotype

1. DNA / genes →

2. transcription to RNA →

3. translation to protein

what’s transcription, define ?

• synthesis of a single stranded RNA molecule from a template DNA strand.

• highly selective process: individual genes are transcribed only as their products are need

how selective is transcription ?

• highly !!

what’s a gene? ?

a DNA sequence that is transcribed into an RNA molecule.

RNA structure is an allows for….

• different RNA molecules can assume different structures.

• because their structure determines their function, RNA has tremendous variation in function

what’s the RNA types that come from MODERATELY REPETITIVE DNA

• tRNA

• rRNA

• snRNA

what’s the RNA types that come from UNIQUE SEQUENCE DNA

• mRNA

• _{think… me is special and unique}

what is mRNA

• function: encodes proteins

• unique sequence DNA

what is tRNA

• function: act as adaptor between mRNA and amino acids

• moderately repetitive DNA

• _{think… transfers the info}

what is rRNA

• function: forms ribosomes

• moderately repetitive DNA

• _{think… “r” is for ribsome}

what is snRNA

• function: functions in various nuclear processes (like splicing)

• unique sequence DNA

• _{think… “n” is for nucelar processes}

where does transcription happen in PROkaryotes ?

• cytoplasm !

where does transcription happen in EUkaryotes ?

• nucleus !

messenger RNA (mRNA) is transcribed in…

• both eukaryotes & prokaryotes!

ribosomal RNA (rRNA) is transcribed in…

• both eukaryotes & prokaryotes!

transfer RNA (tRNA) is transcribed in…

• both eukaryotes & prokaryotes!

transfer RNA (tRNA) is transcribed in…

• both eukaryotes & prokaryotes!

pre-messenger RNA (pre-mRNA) is transcribed in…

• only eukaryotes!

small nuclear RNA (snRNA) is transcribed in…

• only eukaryotes!

micro RNA (miRNA) is transcribed in…

• only eukaryotes!

small nucleolar RNA (snoRNA) is transcribed in…

• only eukaryotes!

small interfering RNA (siRNA) is transcribed in…

• only eukaryotes!

piwi-interacting RNA (piRNA) is transcribed in…

• only eukaryotes!

CRISPR RNA (crRNA) is transcribed in…

• prokaryotes only!

TEMPLATE stand….

• nucleotide strand used for trascription

NON-TEMPLATE stand….

• nucleotide strand not ordinarily transcribed

features of RNA ?

• is complementary and antiparallel to the DNA template strand

• has the same polarity and base sequence as nontemplate strand BUT WITH URACIL

can different genes be transcribed from different strands ?

• yes!

transcription unit ?

• a stretch of DNA that encodes an RNA molecule and the sequences necessary for its transcription

  • 1 gene in eukaryotes

  • 1 or + genes in prokaryotes

promoter and terminator sequences are responsible for ___ while transcribed sequences are essential for ____

• promoter & terminator = signaling

• transcribed = template

promoter is….

• DNA sequence that proteins/enzymes recognizes and binds (nontemplate strand)

• Located next to the transcription start site but is not itself transcribed.

where is the promoter located

• NONTEMPLATE STRAND

• located next to transcription start site but it isn’t transcribed !

what indicates which of the two DNA strands is to be read as the template and the direction of

transcription.

• promoter!

where’s the promoter of these genes?? ('-')?

here

what determines the transcription start site aka the first nucleotide that will be transcribed into RNA

• promoter!

if the TEMPLATE STRAND is 5’ - 3’, then the RNA is…

3’ - 5’ !!

if the TEMPLATE STRAND is 3’ - 5’, then the RNA is…

5’ - 3’ !!

RNA has same sequence as….

• the non-template strand !!

core promoter in EUKARYOTES

• -35 = TFIIB

• -25 = TATA box

1 transcription unit = _____

1 gene !

PRIBNOW BOX associated with…

• transcription → promoter → PROKARYOTES

TATA BOX associated with…

• transcription → promoter → EUKARYOTES

the initial RNA-coding sequences in eukaryotes has…

introns AND extrons

poly A signal associated with…

• transcription → terminator → EUKARYOTES

what are the rRNA’s in prokaryotes ??

• 16S rRNA

• 23S rRNA

• 5S rRNA

what are the rRNA’s in eukaryotes ??

• 18S rRNA

• 28S rRNA

• 5.8S rRNA

• _{think… eukaryotes are bigger so they need more!}

steps of transcription >?

1) intiation

2) elongation

3) termination

BASIC tools of transcription ?

• DNA gene

• RNA polymerase enzyme

• transcription factors

• RNA nucleotides (ATP, CTP, UTP, GTP)

• RNA

what makes up the RNA polymerase in PROKARYOTES

• core enzyme + sigma factor

  • _{think… prokaryotes are sigmas not alphas}

what are the EUKARYOTIC RNA polymerases

• RNA polymerase I

• RNA polymerase II

• RNA polymerase III

  • RNA polymerase IV

  • RNA polymerase V

what does RNA polymerase I do and where is it present ?

• transcribe large rRNA’s

• all eukaryotes

what does RNA polymerase II do and where is it present ?

• transcribe pre-mRNA, snoRNAs, some snRNA’s & miRNA’s

• all eukaryotes

what does RNA polymerase III do and where is it present ?

• transcribe tRNA, small rRNAs, some snRNA’s & miRNA’s

• all eukaryotes

RNA polymerase IV & V only in…

plants!

steps of transcription intitiaton in bacteria ?

1. RNA polymerase holoenzyme forms

2. promoter recognized

3. transcription bubble formed

4. transcription apparatus leaves promoter and transcription starts

what kind of enzyme is the RNA polymerase in bacteria ?

• holoenzyme !!

what determines the position of the start site in prokaryote initation ??

the location of consensus sequence in promoter

for initiation RNA synthesis in transcription no ___ is required

• primer!

purpose of CHROMATIN MODIFICATIOn ??

• DNA gets into more open configuration and available to transcription proteins

where do the enhancers of transcription in EUKARYOTES live ?

• underneath the promoter-ish

list the TRANSCRIPTION FACTORS in eukaryotes

• mediator

• TFIIA

• TFIIB

• TFIID & TBP

• TFIIE

• TFIIF

• TFIIH

  • think… no GC :(

steps for transcription INITATION in eukaryotes

1. TFIID binds to TATA in core promoter

   1. think… D goes in first and chases the TATAs

2. the transcription factors & RNA poly II bind to core promoter

3. transcription factors bind to sequences in enhancers (they loop around)

4. DNA loops out so that the proteins bound to enhancer can interact with basal transcription apparatus

5. transcription factors bind to sequences in the regulatory promoter and interact with the basal transcription apparatus through mediator

steps of transcription ELONGATION for both eu- and pro-karyotes

1. new nucleotides added to 3’ end of the RNA molecule

2. DNA unwinds at the front of the transcription bubble

3. rewinds after

what end of RNA are new nucleotides added to ???

3’ end !!

rho-dependent termination in bacteria ???

• uses rho-factor

• Rho Utilization site (RUT) makes RNA rich in C’s that makes RNA poly pause

rho-independent termination in bacteria ???

• hairpin structure forms through inverted repeats followed by a crap-ton of uracils

• the extra u’s cause RNA poly to pause

• and the hairpin destabilizes the DNA-RNA pairing and they seperate

what process involves Rat1 exonuclease ???

• transcription → TERMINATION → eukaryotes

steps for termination of transcription in eukaryotes ?

1. RNA poly keeps transcribing past coding sequence

2. cleavage at 3’ end of CODING PART of RNA

3. Rat1 exonuclease attaches to 5’ end of total RNA

4. moves towards RNA poly, degrading RNA and ending termination

pprocessing of prokaryotic mRNA is _____ because….

• uneccessary !

• its already colinear

what is colinearity

• number of nucleotides in a gene is proportional to the number of amino acids in the encoded protein

what does it mean when mRNA is polycistonic ….

• two or more separate proteins are encoded on a single molecule of mRNA

• PROKARYOTES

  • ex) lac operon

what does it mean when mRNA is monocistonic ….

• only one polypeptide is encoded on a single molecule of mRNA

• EUKARYOTES

  • ex)yeast stuff

what interrupts colinearity in eukaryotes, causing the need for pre-mRNA proccessing

• introns!

what needs to happen to pre-mRNA for it to become normal mRNA

• 5’ capping

• RNA splicing

• 3’ polyadenylation

what does the addition of the 5’ cap to pre-mRNA do ?

• facilitates binding of ribosome to 5' end of mRNA

• increases mRNA

what does the 3’ cleavage and addition of poly A tail to pre-mRNA do ?

• increases stability of mRNA

• facilitates binding of ribosome to mRNA

what does RNA splicing to pre-mRNA do ?

• removes noncoding introns from pre-mRNA,

• facilitates export of mRNA to cytoplasm,

• allows for multiple proteins to be produced

what does RNA editing to pre-mRNA do ?

• Alters nucleotide sequence of mRNA

when does the adding of the 5’ cap to pre-mRNA during transcription happen ?

• during elongation (so its co-transcriptional)

when does the adding of the poly-A to pre-mRNA during transcription happen ?

• immediately after termination (so post-transcriptional)

how is the poly-A tail added during pre-mRNA processing?

• pre-mRNA is cleaved in the 3’ untranslated region

• polyadenylation (addition of adenine) happens at the 3’ end

when does the split genes and RNA splicing to pre-mRNA during transcription happen ?

• post-transcriptional !

what does the pre-mRNA splicing?

• a splicosome!

what part of pre-mRNA is removed during processing?

• introns

rRNAs are ___cistronic, and must be cut into individual RNA molecules using ___

• polycistonic!

• methylation

do tRNAs have introns?

• yes!

where does translation happen in prokaryotes ??

• cytoplasm !

where does translation happen in eukaryotes ??

• cytoplasm

polypeptide ??? is…

• chain of amino acids joined by peptide bonds

protein ??? is…

• one or more polypeptides that work together to carry a specific function.

what are the components of an amino acid again ?

• amino group

• carboxyl group

• alpha carbon

• side chain (R-group)

list the actors in translation

• mRNA

• ribosome

• initation factos

• elongation factors

• release factors

• aminoacyl charged tRNA

what are the essential components of mature mRNA

• • 5’ UTR and 3’ UTR

• • AUG start codon

• • Triplet codons in sequence

• • Stop codon

• • 5’ cap and poly A tail (eukaryotesonly)

parts of RIBSOME in PROKARYOTES

• large subunit (50S)

  • 23S rRNA

  • 5S rRNA

• small subunit (30S)

  • 16S rRNA

parts of RIBSOME in EUKARYOTES

• large subunit (60S)

  • 28S rRNA

  • 5.8S rRNA

  • 5S rRNA

• small subunit (40S)

  • 18S rRNA

• _{think… eukaryotes need more, just more complex!}

ribsome structure ???

• EPA

with NO amino acid, tRNA are…

• uncharged !

aminoacyl-tRNA synthetases are responsible for…

• The correct matching up of tRNA and amino acid

• recognizes a particular amino acid as well as all the tRNAs that accept that amino acid

with a PAIRED amino acid, tRNA are…

• charged !