this week chapters 9, 10.1 and 10.4 - 10.7 for reference, –exam material will be on lecture...
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![Page 1: This Week Chapters 9, 10.1 and 10.4 - 10.7 for reference, –exam material will be on lecture content for the above, Chapter 11.5 (Friday). Monday Paper,](https://reader031.vdocuments.site/reader031/viewer/2022032800/56649d4c5503460f94a2a6a0/html5/thumbnails/1.jpg)
This Week
• Chapters 9, 10.1 and 10.4 - 10.7 for reference,
– exam material will be on lecture content for the above,
• Chapter 11.5 (Friday).
• Monday Paper,
![Page 2: This Week Chapters 9, 10.1 and 10.4 - 10.7 for reference, –exam material will be on lecture content for the above, Chapter 11.5 (Friday). Monday Paper,](https://reader031.vdocuments.site/reader031/viewer/2022032800/56649d4c5503460f94a2a6a0/html5/thumbnails/2.jpg)
Seminarsextra credit
• May 21 “Virgin Birth, Centrosomes, and Microbes”. William Sullivan, Molecular, Cell, & Developmental Biology, University of California, Santa Cruz
• May 28 "Proliferation & Caste Formation in a Polyembryonic Parasitoid Wasp". Laura Corley, Department of Entomology, Washington State University
• Wednesdays, 4:00 PM, BI 212
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Gene Expression
…the processes by which information contained in genes and genomes is decoded by cells,
...in order to produce molecules that determine the phenotypes observed in organisms,
– transcription (post-transcriptional modifications),
– translation (post-translational modifications).
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Transcription
![Page 5: This Week Chapters 9, 10.1 and 10.4 - 10.7 for reference, –exam material will be on lecture content for the above, Chapter 11.5 (Friday). Monday Paper,](https://reader031.vdocuments.site/reader031/viewer/2022032800/56649d4c5503460f94a2a6a0/html5/thumbnails/5.jpg)
Transcription
...the synthesis of mRNA from a DNA template,
- now it is important to understand when and where, as well as how.
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mRNA Synthesis
• Template (DNA) and Promoter,
• Nucleoside triphosphates (NTPs),
– N: A,U,G,or C,
• Enzymes (RNA polymerases),
• Energy (as in replication, from phosphate bonds).
![Page 7: This Week Chapters 9, 10.1 and 10.4 - 10.7 for reference, –exam material will be on lecture content for the above, Chapter 11.5 (Friday). Monday Paper,](https://reader031.vdocuments.site/reader031/viewer/2022032800/56649d4c5503460f94a2a6a0/html5/thumbnails/7.jpg)
E. coli RNA Polymerase
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RNA Transcriptionprokaryote
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E. coli Promoter Sequencesconcensus sequence alignment
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Promoter Regions
Core Promoter ( ~ 0 to ~ -40 bp)Proximal ( ~ 100 - 200)
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Regulation of Transcription(Prokaryotes)
• Regulation of gene expression is often at the transcription level,
– Negative regulation,
• inducible,
• repressible,
– Positive regulation
Gene native state is “on”.
Gene native state is “off”.
![Page 12: This Week Chapters 9, 10.1 and 10.4 - 10.7 for reference, –exam material will be on lecture content for the above, Chapter 11.5 (Friday). Monday Paper,](https://reader031.vdocuments.site/reader031/viewer/2022032800/56649d4c5503460f94a2a6a0/html5/thumbnails/12.jpg)
Negative Regulation(Inducible)
…default state is “on”, i.e., the gene is transcribed.
Protein!
Protein, or metabolite, etc.
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Negative Regulation(Repressible)
…default state is “on”, i.e., the gene is transcribed.
Protein!
Protein, or metabolite, etc.
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Positive Regulation
…default state is “off”, i.e., the gene is not transcribed.
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Eukaryotic Initiation
Transcription is regulated by activators, repressors, co-activators and basal transcription factors.
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Promoter Bashing
Modulators of expression can act at great distances.
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Drosophila Guts and Such
dpp locus
...(c)LE and (d) ID enhancer driven, give rise to fly
appenages.
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Terms
• cis-acting elements;
– DNA sequences that serve as attachments sites for the DNA-binding proteins that regulate the initiation of transcription.
• trans-acting elements;
– the DNA-binding proteins that regulate the initiation of transcription.
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Chromatin Remodeling
Expressed Proteins
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Post-Transcriptional Events
• RNA processing,
– splicing,– poly adenylation,
• Alternate RNA processing.
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RNA can be Autocatalytic
• Group I and Group II introns,
– found in mitochondria, chloroplasts, and sometimes in bacteria,
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Group II Introns
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Eukaryotic Intron Excision(not autocatalytic)
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Eukaryotic Intron Excision(sequence is important)
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Spliceosomes
... small nuclear RNAs (snRNAs):
– RNA molecules that act as catalysts in spliceosomes,
• catalytic RNAs that have probably evolved from ancient RNA enzymes (ribozymes).
…work in concert with > 100 proteins to facilitate intron identification and removal,
– snRNPs: RNA/Protein structures.
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U1 and U2
U1 binds to the 5’ exon/intron junction.
U2 binds to the adenosine at the branch site.
Psuedouradine (
Think about the required specificity for intron identification in cells.
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mRNA Processingsplicing
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Polyadenylation
AAUAA: concensus poly-A recognition site.
…complicated biochemistry, lots of sub-units.
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Alternate mRNA Processing
…recognition of different poly-A sites. …alternate splicing.
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Complexity
Calcitonin gene.
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Central Dogma
DNA
RNA
Protein
transcription
replication
translation
?
(alternately processed)
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• Genome... the dynamic complement of genetic material in an individual,
• Transcriptome... mRNA component in an individual,
– complexity increases resulting from transcription control and transcription and post-transcription
modification,
• Proteome... the protein component of an individual,
– complexity increases due to post-translational modification, protein-protein interactions, etc.
Expanded Central Dogma
Genome Transcriptome Proteome
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Translation
…the synthesis of a polypeptide. This occurs on ribosomes using the information encoded on mRNA,
– tRNA molecules mediate the transfer of information between mRNA and the growing polypeptide.
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Initiationcomplexity
1. Recent reports of “alternate” translation start sites indicate that further complexity in protein production may occur at the translational level.
2. Recent reports of “alternate” small sub-unit specificity affecting translation,
- different eIs,- different small sub-- units.
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What to Study?
• What regulates gene expression,
• How is gene expression modulated?
– Transcriptionally,– Post-Transcriptionally,– Translationally.