chapter 18

central dogma of molecular biology

the idea that typical flow of genetic information moves from DNA → RNA by transcription → protein by translation

major players invovled in the genetic information flow

DNA, mRNA, rRNA, tRNA, RNA polymerase, ribosomes

examples of exceptions to the central dogma

retroviruses use RNA as template to synthesize DNA

some viruses use RNA as template to make more RNA

prokaryotes’ genetic information flow location

transcription and translation both occur in cytoplasm and are coupled

eukaryotes’ genetic information flow location

transcription occurs in the nucleus, translation occurs in the cytosol

characteristics of retroviruses

they have RNA genomes that are enclosed in a protein capsid then is enclosed by membranous envelope

characteristics of retroviruses’ reproductive cycle

each RNA copy has a molecule of reverse transcriptase attached to it, the virus binds to host cell and its membrane fuse with the host membrane releasing its content into the host cell → the reverse transcriptase makes a DNA copy of its RNA genome formatting a double stranded viral DNA → the DNA enters into the nucleus and integrates into the host cell’s genome → the provirus is replicated each time the host cell replicates its DNA and viral mRNAs are produced by host enzymes and are used to make viral proteins → some viral RNAs are packaged with the viral proteins into new viral particles → the new viruses bud from the plasma membrane of host cells

provirus

integrated viral genome

retrotransposons

type of transposable elements that move from one chromosomal site to another by a process in which the retrotransposon DNA is first transcribed into RNA and reverse transcriptase then uses the RNA as a template to make a DNA copy that is integrated into the chromosomal DNA at another site

genetic code

set of rules specifying the relationship between the sequences of bases in a DNA or mRNA molecule and the order of amino acids in the polypeptide chain encoded by that DNA or mRNA

has the definition of gene changed since 1940s

yes, from 1 gene-one enzyme → 1 gene-one polypeptide → functional units of DNA that encode 1 or more polypeptides or functional RNA

key features of genetic code

triplet, non-overlapping, degenerate, unambiguous, 3 stop codons, nearly universal

4 stages of transcription

RNA polymerase binding, initiation, elongation, termination

transcription unit

segment of DNA whose transcription gives rise to a single continuous RNA molecule

promoter

base sequence in DNA to which RNA polymerase binds when initiating transcription

what are the 2 highly conserved regions of bacterial promoters

-10 and -35 sequences

characteristics of bacterial RNA polymerase

large protein consisting of 2 α subunits, 1 β subunit, 1 β’ subunit, dissociable σ factor

σ factor recognizes and binds to promoter, β and β’ subunits form a clamp that holds the DNA and catalytic center is located near the joining point of these subunits

template DNA strand

serving as the template for RNA synthesis

non-template strand

complementary to template strand

why are occasional errors in RNA not as critical as errors in DNA replication

if DNA template is correct, many RNAs are transcribed from it, so a few inaccurate copies of RNA can be tolerated. But if the DNA template has errors, all RNA synthesized using this DNA will have mistakes, there is only one copy of each DNA molecule made when DNA is is replicated before cell division

similarities between transcription in bacteria and eukaryotes

both consist of 4 stages, regulatory regions including promoters

differences between transcription in bacteria and eukaryotes

transcription in eukaryotic is more complex, promoter is more varied, more regulatory regions with enhancers and insulateors, 3 different RNA polymerases, more regulatory proteins like transcription factors, chromatin structures, no specific termination sites

3 types of RNA polymerases

Pol I, Pol II, Pol III

Pol I target genes

rRNAs

Pol II target genes

mRNAs

Pol III target genes

small RNAs, tRNAs

general transcription factor

protein that is always required for RNA polymerase to bind to its promoter and initiate RNA synthesis regardless of the identity of the gene involved

major members of the general TFs for RNA Pol II

TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH

which TFs contains TBP

TFIID

which TFs has helicase function

TFIIH

what does TBP stand for

TATA-binding protein

how are transcripts terminated for RNA PoL II mediated transcription

poly(A) signal acts in a conjunction with a poly(U) sequence downstream, recognized and bound by CPSF

primary transcript

any RNA molecule newly produced by transcription before any processing has occured

eukaryotic rRNA gene organization

100s to 1000s  copies of rRNA genees organized in transcription unit forming tandem repeats, each transcription unit contains one of 5.8S, 18S, 28S

what is the most abundant and stbale form of RNA

rRNA

types of pre-mRNA processing

5’ capping, splicing, poly(A) addition

5’ capping 

guanosine that is methylated at position 7 of the purine ring

splicing

removal of introns

5’ capping and poly(A) addition functions

protection against exonucleases, exportation of the cytoplasm, regulation of translation

what is the RNA-protein complex invovled in mRNA splicing

spliceosome

splice sites features

GU at 5’ splice site, AG at 3’ splice site, a branch site made of A residue in the middle, polypyrimidine tract

introns functions

alternative splicing to produce multiple polypeptides from the same DNA producing new proteins by exon shuffling or exon duplications. may contain regulatory elements for transcription