Biology 1002B Lecture Notes - Lecture 14: Start Codon, Lac Operon, Alternative Splicing

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Published on 15 Apr 2013
School
Western University
Department
Biology
Course
Biology 1002B
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Lecture 14: Eukaryotic Gene Expression
Where is your gold today?
o Make pictures of genes showing he relative location of signals
o Make a chart of signals and how they are understand
o Make a list of RNA functions
o Make a diagram of gene expression that highlights complementary base pairing
o Make a chart comparing prokaryotes and eukaryotes
Eukaryotes can keep the ribosomes away from the mRNA just been translated from the nucleus
because of the nuclear membrane
Clicker question
o The synthesis and function of a typical tRNA molecule requires complimentary base-
pairing with:
Itself
yes
DNA
In transcription, it base-pairs
Other RNA
yes
Does not pair with amino acids, cannot pair, not bases
Operons bring several genes the control of one promoter
PHET lac operon simulation
Clicker Question
o How many stop codons (in DNA) are there in this picture?
4 stop codons in the picture
Every protein has a stop codon i.e. Lac I, Lac X, Lac Y, Lac Z
Keeping mRNA away from the ribosomes are very important
o Prokaryotes cannot do that
Eukaryotic regulation
o Transcriptional regulation
Regulation of transcription initiation
o Posttranscriptional regulation
o Translational regulation
o Posttranslational regulation
Nuclear gene structure is more complicated than in organelles
o TATA box
o Promoter proximal region, area where proteins bind (protein binding sites)
o How do eukaryotes stop transcription?
o Enhancers can be far away
o Genes do not have to have introns, eukaryotic often have introns, some have hundreds
of introns
RNA polymerase II does not bind to “naked” promoters
o More than one polymerase in eukaryotes
o Polymerase II transcribes protein genes (PCG)
Only find promoters attractive when they have protein on the gene
o They need the TATA promoter
Protein binds to the TATA promoter
Transcription factors regulate efficiency of polymerase binding
Helix-turn-Helix DNA binding motif
o Proteins are not making covalent bonds with DNA
o Just electro-static
o Lac repressor is a helix turn helix
Zinc Finger DNA binding motif binds the major groove
o Series of amino acids can associate with zinc cofactors
o Protein motifs
o DNA binding protein motifs
Leucine zippers hold two monomeric DNA binding proteins together
o Holding the dimers together, zips one dimmer onto another
o To some kind of DNA binding protein
Promoters and enhancers
o DNA can loop and bend
o Promoters are position dependent, move it far away from the gene, it no longer works
o Promoters are direction dependent
o Enhancers are less position dependent, it’ll work mostly everywhere
They bind to activators and trap the complex and maximize transcription
o There are silencers, which makes it all go away
o There are activators near the promoter proximal region and some activator on the
enhancer, and the enhancer will bond with co-activator and bends to and attach on to
the promoter
i.e. making a sandwich
enhancer makes the promoter more attractive
enhancer holds the co-activator in place to make promoter more attractive
Unique combinations of activators control specific genes
o Express different activators will produce different genes coding for different proteins in
different tissues
o Regulating their enhancers can regulate which genes to express by controlling the
activator it has
Cells tend to invest heavily in regulation of transcription
Polyadenylation signal
o Eukaryotes don’t have terminator loops
o They have a signal, the polyadenylation signal
o They transcribe the signal, mRNA recognized by RNase then an enzyme (RNase) that
cuts the mRNA at that site, poly A polyermase attaches As (only As)
Just added, no complementary pairing
There is no poly Ts
o Removes introns and putting a 5’ cap on it
Splicing
o In eukaryotes wants to remove the introns
o snRNA -> small nuclear (sn) RNA
snRNA pair with themselves
all RNA pair with themselves
o snRNPs (snRNA and proteins)
o making a spliceosome composed of snRNPs
o snRNAs have a complementary base pairs with the message, the complementary on the
mRNA to snRNA is called spicing signals
snRNA pair with themselves and mRNA
o and they cut off the introns making a mRNA with all exons
when we can do splicing
o an intron is not always an intron
o exons are not always exons
o cannot predict which ones are introns and which ones are exons
o it depends what type of cells, what stage of development, what proteins are needed
o cells have a choice, called alternative splicing
can be used to explain why we are more complex
can make multiple proteins from one gene
Drosophila DSCAM gene (in the brain, neurons) can generate nearly 40,000 peptides
o One gene can generate 40,000 proteins, to generate cells that are unique
There are lots of ribosomes on the nuclear membrane
o mRNA goes through the nuclear pore
o Messages goes through the nuclear pores
Translation initiation begins as ribosomes “scan” for start codon
o There are no SD box in eukaryotes
o They just scan to look for start codon to initiate translation, the small subunit scans for it,
then the big one joins
Eukaryote ribosomes are bigger, the process is slower, but everything else is the same, process
is the same, termination is the same
Synthesis of all proteins begin on cytosolic ribosomes
o All the proteins begin translation in the cytoplasm (nuclear genes)
o Except organelle genes
Organelle proteins are targeted for post-translational import via channels
o They have a tag on them, telling them where the protein goes
o Tag is amino acid tag

Document Summary

Eukaryotes can keep the ribosomes away from the mrna just been translated from the nucleus because of the nuclear membrane. Clicker question: the synthesis and function of a typical trna molecule requires complimentary base- pairing with: Does not pair with amino acids, cannot pair, not bases. Operons bring several genes the control of one promoter. Every protein has a stop codon i. e. lac i, lac x, lac y, lac z. Keeping mrna away from the ribosomes are very important: prokaryotes cannot do that. Regulation of transcription initiation: posttranscriptional regulation, translational regulation, posttranslational regulation. Rna polymerase ii does not bind to naked promoters: more than one polymerase in eukaryotes, polymerase ii transcribes protein genes (pcg) Only find promoters attractive when they have protein on the gene: they need the tata promoter. Transcription factors regulate efficiency of polymerase binding. Helix-turn-helix dna binding motif: proteins are not making covalent bonds with dna, lac repressor is a helix turn helix.