Cell Biology

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MSH2,3, MLH1, PMS2

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mismatch repair

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Xeroderma pigmentosum (XP)
groups A-G

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nucleotide excision-repair

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XP variant

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translesion synthesis by DNA polymerase

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Ataxia telangiectasia (AT)

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ATM protein, a protein kinase activated by double-strand breaks

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BRCA2

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Repair by homologous combination

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Werner Syndrome

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accesory DNA helicase for replication

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Fanconi anemia groups A-G

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DNA interstrand cross-link repair

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46BR patient

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DNA ligase I

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RNA polymerase I

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rRNA genes

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RNA polymerase II

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all protein-coding genes, ++sno RNA genes, miRNA genes, siRNA genes and most snRNA genes

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RNA polymerase III

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tRNA
some snRNA and genes for other small RNAs

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During transcription, RNA polymerase only requires sigma factor

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Prokaryotes

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During transcription, RNA polymerase requires general transcription factors: other proteins that control polymerase function

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Eukaryotes

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Eukaryotic Transcription

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-Find TATA box by TFIID (transcription factor II D). TDIID has a region called TATA binding protein (TBP)
-TBP helps to find TATA box and binds to it
-TFIIA
-TFIIB
-TFIIF
-TFIIE
-TFIIH has helicase and kinase activity
-RNA polymerase
-Other factors
----Formation of a transcription initiation complex.
-The RNA polymerase has a tail. This tail is called CTD (C terminal domain).
CTD is phosphorilated.
Phosphorilation changes the shape of RNA polymerase

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TFIIH

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Roles:
It unwinds the DNA at the transcription starting point (helicase activity), phosphorilates Ser5of RNA polymerase CTD.

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Activators bind to

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enhancers.

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TBP

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TATA binding protein

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TBP

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recognizes TATA box

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RNA Polymerase II requires

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activator, mediator, and chromatin modifying proteins

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Transcription in eukaryotes is tightly linked to

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RNA processing

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Different steps in eukaryotic mRNA processing are:

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-Capping
-Splicing
-Polyadenylation
-Editing (rare)

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Activators

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Activators attract another proteins including RNA polymerase.
Activators brings to the promoter RNA polymerase

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Enhancer + activator

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increases transcription

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Scafold

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Scafold is a mediator protein. It holds the transcription factors together.

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Reasons of a preinitiator transcription complex

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1) Gene expression should be specific
2) When all the proteins come together, the expression of the genes increases

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Enhanceosome

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It is the bigger complex during the initiation step of transcription

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Capping factors bind to the

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5' end

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RNA factory

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Proteins required for RNA processing associate with the RNA polymerase

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RNA polymerase is associated with

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Capping factors
Splicing factors
Polyadenylatio factors

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Name of the cap

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7-methyl guanosine cap

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Splicing

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Removal of introns from pre-RNA

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RNA processing is couple with ______

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wlongation

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Introns

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Intervening sequences
= non coding sequences

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exons

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expressed sequences
= coding sequences

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pre mRNA contains

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a mixed of introns and exons

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You need to remove introns to produce a

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mature RNA

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----- are required for the splicing reaction

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snRNPs

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In the splicing rxn,____ is essential

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Adenine

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RNA is not processed

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Prokaryotes

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Translation can occur co-transcriptionally

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Prokaryotes

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RNA polymerase requires general transcription factors

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Eukaryotes

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RNA is modified extensively

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Eukaryotes

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RNA must be exported to the cytoplasm

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Eukaryotes

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Start codon & also codes for methyonine

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AUG

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Stop codons

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UAA
UAG
UGA

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The direction of transcription determines the sequence of the

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protein

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Tetracycline

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Bacterial Inhibitor
Blocks a.a.-tRNA to A-site of ribosom

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Streptomycin

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Prevents chain elongation by ribosomes

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Chloramphenicol

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Blocks peptidyl transferase rxn

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Erythromycin

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Blocks translocation of ribosome

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Rifamycin

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Prevents RNA synthesis

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Puromycin

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Bacteria & Eukaryotes inhibitor
premature release of nascent polypeptide

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Actinomycin D

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Blocks RNA polymerase
Bacteria and Eukaryotic inhibitor

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Cycloheximide

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Eukaryotes inhibitor
Blocks translocation of ribosomes

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alpha-amanitin

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Inhibits RNA polymerase II

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Chaperone proteins

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they assist in the folding of newly formed polypeptides
They are also called heat shock proteins

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Cellular garbage disposal

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Proteosomes

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A protein that has to be destroyed is first marked by the addition of

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ubiquitn

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Proteases

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Enzymes inside of the proteosome.
These enzymes basically chew up the polypeptide, one a.a. at a time