Translation

Large, small subunit

rRNA, proteins
RNAs play key role in almost every step of translation
Mediate interaction btwn mRNA and tRNA during initiation, catalyze peptide
bond formation in elongation
Know the three sites: A, P, E and whre they are located wrt the large subunit and the
mRNA
Initiation:
IF-1, IF-2 (G), -IF-3
Know which translation factors are the G proteins and which arent
IF-2 is the only G-protein; when the large subunit binds IF-2 hydrolyzes GTP
and IF-1 and IF-2 are released
Shine Dalgarno seq- recognized by base pairing with 16s Rrna
The AUG isnt enough for prokaryotes to initiate translation; they need the
shine dalgarno located in the 5 UTR to distinguish btwn start codon and
internal AUG. the small subunit goes along looking for the SD sequence, Hbonds to it, and if AUG is situated correctly in the P site, the small subunit
binds
Initiator tRNA and formylated MET
Formylated MET resembles peptide bond so can fit right into P site
Ternary complex formation: total ribosome, all of initiation factors are gone, ready
to go into elongation
Elongation:
EF-Tu, EF-G
Binding of aaTRNA to A site: bc our initiatiortRNA is in the P site
Peptide bond formation- know the chemistry- who is attacking who
N of aminoacyl tRNA attacks carbonyl of peptidyl tRNA
Translocation- facilitatedby the EF-G; EF-tu brings in the tRNA
Both of these are G rpoteins
Termination
RF1, RF2, RF3, RRF
EF-G-GTP and IF3 play role
EF-G-GTP helps in translocation; IF3 helps dissociate two subunits
Stop codon always in A site, release factors along with EF-G mimic the tRNA bc they
have to fit into the A site- anything that has to fit in the same site has to look the
same
Whole process begins with hydrolysis of polypeptide from the tRNA

Translocation- ribosome is moving relative to the mRNA. It is a relative movement.

The trnas stay associated with the codons that they came in. the tRNAs and mrNAs
are hydrogen bondedthey will stay fixed. The tRNA is still bonded to the mRNA
moving relative to ea/other
Prokaryotic gene regulation
Basal, repressed, activated levels of transcription
Basal is neither activated nor repressed; no transcription factors binding or
non-functioning transcription factors (ex. Is Gal4)
Effectors regulate the regulatorsthe proteins are sensitive to the environment so
they are there to regulate in response to something else. Effects allosterically
Arabinose regulates AraC
cAMP regulated CAP
Transcription factors all need to bind to DNA bc that is how they know what Gs to
regulate
They have seq. UPSTREAM of promoters in prokaryotes
Seq. identified by dna binding motifs
Run a gene thru a database and see if it has a dna binding motif
In porkaryotes helix turn helix is most common
Homeodomain found in eukaryotes which is slight variation
2 dimeric types: basic leu zipper and basic helix loop helix-=- BOTH HAVE TO BE
DIMERS TO BIND
Zn fingers are largest class; can be dimeric or monomeric
Dont memorize details of structure but know generalities of how they interact
w/DNA and how they interact w/themselves if they are dimers
Bacterial gene regulation
Lac opron
Inducers vs substrates (Xgal, IPTG, lactose) know why we can separate inducer from
substrate. LACTOSE CAN BE BOTH. Inducers are the allosteric effectors. Substrate is
converted to a product
In most cases there is two diff proteins involved inthese processes
Experiments leading to model of lac regulation
Lac repressor- inducer
Isolated mutation in repressor protein that bound the inducer
Later found out there was positive regulator -- CAP
CAP-cAMP- glucose sensor, DIRECT interaction w/RNA pol
Ara operon

First operon that was discovered that loops so u can have sites far away that are
regulating promoter region
AraC can act as repressor or activator; this is dependent on arabinose effector
It co-activates with the cap-cAMP so this is sensitive to level fo glucose in the media
Involves looping of the DNA
Ara and Lac are both combinatorial because they both are regulated by TWO
DIFFFERENT REGULATORS. ANYTHING THAT IS REGULATED BY MORE THAN ONE
PROTEIN
Combinatorial is found in prokaryotes but eukaryotes are more complex
Eukaryoteic transcription
Eukaryotic promoter (TATA box at -30). AT rich sequence; this is recognized by TBP
os this is really the first element that aws discovered in eukaryotes to define the
promoter
TBP was the first protein to be recognized to bind to promoter
Formation of preinitiation complex at Pol II promoters
Steps in initiation
Role of TFIID (TBP) nad TFIIH
Know F comes in with Pol II
D nad H have specific roles
TBP-DNA interaction bc it is so different than all the other ones we have talked
about which are alpha helices interacting with the major groove and TBP was one of
the first proteins to interact w/minor groove using Beta sheets osvery diff
interaction
CTD and phosphorylation 2 sites that are phospholryalted on 7 aa repeat; these
diff sites of phosphoryaltino are correlated w/diff steps in initiation and processing
Structure of 5 cap, poly A function and general structureit is added on after
cleavage of the message, add 200 As to end of message
Know function of cap and tail
Torpedo model of termination
Poly A is important for translation initiation bc of the circular transcript
cAP important for translation initiation bc it is recognized by eIF4
Splicing
in prokaryotes we can have polycistronic messages with multiple ORFs but since we
have SD sequences, ruibosomes can find internal AUGs but in eukaryotes they do
scanning mechanism which means u can only translate one open reading frame and
the later AUGs you wont find. So messages made with intron/exon have to be
spliced to one reading frame
hnRNA vs mRNA (pulse chase experiments)
showe that we reduce since of hnRNA in this processing and later
experiments looking at electron microscopy show that size is reduced bc introns are
taken out

snRNPS are involved in recognizing splice sites; where they bind, what they do
formation of spliceosomeonce final spliceosome is formed we can catalyze the 2
transesterfication rxns
splice sites (5 , branch, 3)be able to one a diagram know where is 5, 3, etc
what would happen if you knowcked one of these out
two transesterication reactionswhat is attacking what?
Structure branch A (A point with three phosphodiester bonds know what the bonds
are), lariat
Alternative splicing
Exon shuffling
Transaltion in eukaryotes
5 cap recognized and small subunit plus tRNA scans for first AUG
this is why u cant take prokaryotic rNA and get it to be translated, bc it doesnt have
a cap
small subunit is actually already bound by tRNAi
cap and polyA to form circular template so we can get re-initiation to occur quickly
no formy-Met, no RBS
kozak- ppl say ATG bc talking about sequence in DNA so AUG and ATG are used
synonymously it is the ATG of the coding strand not the template strand
regulation of eukaryotic transcription
enhancers: sites where activators and repressors bind
initially they were all having positive effects but later found u can have
repressors binding to these regions too
anything that binds to enhancer has to have speicifc DNA binding domain and has to
recognize a sequence but there are enzymes used in this process of activation or
repression that dont bind DNAcoactivators and corepressorsrecruited to
enhancers by activators and repressors; the co ones can modify chromatin or
interact w/general transcription factors or the mediatorthey can be interacting
w/other things and are BROUGHT IN BY ACTIVATORS/REPRESSORS
co-activators and co-repressors: no DNA binding domains, recruited by activators
and repressors, frequently involved in modifying chromatin
Eukaryotic examples
Gal gene control
Gal4 UAS, Gal