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,

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

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).

Transcription

Transcription

...the synthesis of mRNA from a DNA template,

- now it is important to understand when and where, as well as how.

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).

E. coli RNA Polymerase

RNA Transcriptionprokaryote

E. coli Promoter Sequencesconcensus sequence alignment

Promoter Regions

Core Promoter ( ~ 0 to ~ -40 bp)Proximal ( ~ 100 - 200)

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”.

Negative Regulation(Inducible)

…default state is “on”, i.e., the gene is transcribed.

Protein!

Protein, or metabolite, etc.

Negative Regulation(Repressible)

…default state is “on”, i.e., the gene is transcribed.

Protein!

Protein, or metabolite, etc.

Positive Regulation

…default state is “off”, i.e., the gene is not transcribed.

Eukaryotic Initiation

Transcription is regulated by activators, repressors, co-activators and basal transcription factors.

Promoter Bashing

Modulators of expression can act at great distances.

Drosophila Guts and Such

dpp locus

...(c)LE and (d) ID enhancer driven, give rise to fly

appenages.

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.

Chromatin Remodeling

Expressed Proteins

Post-Transcriptional Events

• RNA processing,

– splicing,– poly adenylation,

• Alternate RNA processing.

RNA can be Autocatalytic

• Group I and Group II introns,

– found in mitochondria, chloroplasts, and sometimes in bacteria,

Group II Introns

Eukaryotic Intron Excision(not autocatalytic)

Eukaryotic Intron Excision(sequence is important)

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.

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.

mRNA Processingsplicing

Polyadenylation

AAUAA: concensus poly-A recognition site.

…complicated biochemistry, lots of sub-units.

Alternate mRNA Processing

…recognition of different poly-A sites. …alternate splicing.

Complexity

Calcitonin gene.

Central Dogma

DNA

RNA

Protein

transcription

replication

translation

?

(alternately processed)

• 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

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.

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.

What to Study?

• What regulates gene expression,

• How is gene expression modulated?

– Transcriptionally,– Post-Transcriptionally,– Translationally.