DNA  RNA  Protein  Function

1. The Central Dogma DNA  RNA  Protein  Function Replication Translation Work Transcription

2. The cell as a factory DNA = Complete instructions for making and maintaining the product. (How to put together “Dave” and keep him running). Has to be kept safe and accurate. Has to be kept organized. RNA = Portable copy of one part of the instructions. (Photocopy to run down to the factory floor. Also called “messenger” RNA or “mRNA”. Just made when it’s needed and then it’s disposable. Protein = Tools and materials used for actually building the product. “Enzymes” are proteins that act as machinery to make something the cell needs. “Structural proteins” are proteins used to form the structure of the cell. (like lumber and nails)

4. Getting from the instructions to the product

5. Only one strand of DNA serves as a template for making the RNA (transcription). • Different genes are transcribed from different strands

6. Transcription Catalyzed by RNA polymerase – a complex, multisubunit enzyme that catalyzes the formation of the phosphodiester bonds that link together the nucleotides in an RNA chain

7. Transcription Transcription start site Protein Ribosome AUG TTA GCG CCT ATC TAA 3’ mRNA 5’ Translation start site Translation stop site Transcription- making the mRNA Translation- making the protein Off to work! Gene Structure

8. ~200 bp gene Promoters • RNA polymerase must bind at the promoter to start making the mRNA (transcription). • Other proteins must bind to the promoter to regulate when the RNA polymerase is supposed to make the mRNA.

9. Promoters regulate gene expression • The Promoter determines: • Which DNA strand will serve as a template. • When to start making the mRNA. • Where to start making the mRNA (Transcription starting point ). • When to stop making the mRNA (How much to make).

10. promoter Gene 1 Gene 2 Gene 3 Bacterial Gene Structure • Bacterial (prokaryotic) genes • One mRNA can contain several coding regions (ORFs). • Each ORF has it’s own translation start and stop transcription DNA with one promoter controlling several genes mRNA containing several genes start stop start stop start stop

11. Translation Prokaryotic Gene Expression DNA: Promoter Cistron1 Cistron2 Cistron3 Terminator Transcription mRNA: 5’ 3’ ORFs: 1 2 3 N N C N Proteins: C C 1 2 3

12. transcription promoter Gene start stop Plant and Animal Gene Structure • Plant and animal (Eukaryotic) genes • One mRNA contains a single coding region (ORF). DNA with one promoter controlling one gene mRNA containing a single ORF (gene).

13. Introns: Plant and Animal Genes Often Contain “Extra” DNA • The coding region in some Eukaryotic genes is interrupted by non-coding regions that have to be removed before the protein is made. • The ORFs in the gene are called ”Exons” • The extra DNA chunks are called “Introns” • The “pre-RNA” also contains the sequence information that tell the cell where to trim out the “extra” DNA (splice junctions). • “Processed” mRNA has the normal translation starts and stops needed to make the protein.

14. From Gene to Protein

15. Bioinformatics • We’re getting REALLY good at sequencing DNA and sequence databases now contain around a bazillion jillion bases from a plethora of critters. • “Mining” for useful information in that glut of information is what bioinformatics is about. • Bioinformatics is basically the application of some rules and strategies for finding genes. • Fortunately, the rules aren’t all that hard.

16. Steps to finding genes • Find ORFs • This is the biggest target, easiest to find- look for long stretches of triplet codons that don’t have a stop codon. • Find the “Start” Codon (where the protein begins) • Always an ATG (Methionine codon) • Usually quite near the beginning of the ORF (5’ end) • Find Promoter Elements (TATA and CAAT boxes) • Should be before an ORF, (also referred to as “upstream” or 5’ of an ORF). • May have ambiguous sequence. (TATA box may look like “TATAA” or “TAATA” or “TATATA” or “TTATAA”).

17. LUNCH TIME !!!!!!