DNA RNA Protein Function

The Central Dogma

Transcription

ReplicationTranslation Work

The cell as a factoryThe cell as a factory DNADNA = Complete instructions for making and maintaining the = Complete instructions for making and maintaining the

product. (How to put together “Dave” and keep him running). product. (How to put together “Dave” and keep him running). Has to be kept safe and accurate.Has to be kept safe and accurate. Has to be kept organized. Has to be kept organized.

RNARNA = Portable copy of one part of the instructions. (Photocopy to = Portable copy of one part of the instructions. (Photocopy to run down to the factory floor. run down to the factory floor.

Also called “messenger” RNA or “mRNA”.Also called “messenger” RNA or “mRNA”. Just made when it’s needed and then it’s disposable.Just made when it’s needed and then it’s disposable.

ProteinProtein = Tools and materials used for actually building the = Tools and materials used for actually building the product. product.

““Enzymes” are proteins that act as machinery to make something the cell Enzymes” are proteins that act as machinery to make something the cell needs. needs.

““Structural proteins” are proteins used to form the structure of the cell. (like Structural proteins” are proteins used to form the structure of the cell. (like lumber and nails) lumber and nails)

Getting from the instructions to Getting from the instructions to the productthe product

Only one strand of DNA serves as Only one strand of DNA serves as a template for making the RNA a template for making the RNA (transcription).(transcription).

Different genes are transcribed Different genes are transcribed from different strands from different strands

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

Transcription

Transcription- making the mRNA Translation- making the protein

Gene Structure

Transcription start site

Translation start site

3’mRNA 5’AUG TTA GCG CCT ATC TAA

Transcription

Translation stop site

Ribosome

Protein

Off to work!

PromotersPromoters• 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.

~200 bp

gene

Promoters regulate gene Promoters regulate gene expressionexpression

The Promoter determines:The Promoter determines:

1.1. Which DNA strand will serve as a template.Which DNA strand will serve as a template.

2.2. When to start making the mRNA.When to start making the mRNA.

3.3. Where to start making the mRNA Where to start making the mRNA (Transcription starting point ).(Transcription starting point ).

4.4. When to stop making the mRNA (How much When to stop making the mRNA (How much to make).to make).

Bacterial Gene StructureBacterial Gene Structure Bacterial (prokaryotic) genesBacterial (prokaryotic) genes

One mRNA can contain several coding regions (ORFs).One mRNA can contain several coding regions (ORFs). Each ORF has it’s own translation start and stopEach ORF has it’s own translation start and stop

Gene

1 Gene 3

Gene 2

promoter

start stopstart stop

start stop

DNA with one promoter controlling several genes

mRNA containing several genes

transcription

Prokaryotic Gene Prokaryotic Gene ExpressionExpression

PromoterCistron1Cistron2Cistron3Terminator

Transcription

mRNA: 5’ 3’

Translation

1 2 3

Proteins: NC

NC N

C

1 2 3

DNA:

ORFs:

Plant and Animal Gene StructurePlant and Animal Gene Structure

Plant and animal (Eukaryotic) genesPlant and animal (Eukaryotic) genes One mRNA contains a single coding region (ORF).One mRNA contains a single coding region (ORF).

start stop

DNA with one promoter controlling one gene

mRNA containing a single ORF (gene).

Gene

promoter

transcription

Introns: Plant and Animal Genes Often Contain “Extra” Introns: Plant and Animal Genes Often Contain “Extra” DNADNA

The coding region in some Eukaryotic genes is interrupted by non-The coding region in some Eukaryotic genes is interrupted by non-coding regions that have to be removed before the protein is made.coding regions that have to be removed before the protein is made.

The ORFs in the gene are called ”Exons”The ORFs in the gene are called ”Exons” The extra DNA chunks are called “Introns”The extra DNA chunks are called “Introns”

The “pre-RNA” also contains the sequence information that tell the The “pre-RNA” also contains the sequence information that tell the cell where to trim out the “extra” DNA (splice junctions).cell where to trim out the “extra” DNA (splice junctions).

““Processed” mRNA has the normal translation starts and stops Processed” mRNA has the normal translation starts and stops needed to make the protein.needed to make the protein.

From Gene to ProteinFrom Gene to Protein

BioinformaticsBioinformatics

We’re getting REALLY good at sequencing We’re getting REALLY good at sequencing DNA and sequence databases now contain DNA and sequence databases now contain around a bazillion jillion bases from a around a bazillion jillion bases from a plethora of critters.plethora of critters.

““Mining” for useful information in that glut of Mining” for useful information in that glut of information is what bioinformatics is about.information is what bioinformatics is about.

Bioinformatics is basically the application of Bioinformatics is basically the application of some rules and strategies for finding genes.some rules and strategies for finding genes.

Fortunately, the rules aren’t all that hard.Fortunately, the rules aren’t all that hard.

Steps to finding genesSteps to finding genes

1.1. Find ORFsFind ORFs This is the biggest target, easiest to find- look for long This is the biggest target, easiest to find- look for long

stretches of triplet codons that don’t have a stop stretches of triplet codons that don’t have a stop codon.codon.

2.2. Find the “Start” Codon (where the protein Find the “Start” Codon (where the protein begins)begins)

Always an ATG (Methionine codon)Always an ATG (Methionine codon) Usually quite near the beginning of the ORF (5’ end)Usually quite near the beginning of the ORF (5’ end)

3.3. Find Promoter Elements (TATA and CAAT boxes)Find Promoter Elements (TATA and CAAT boxes) Should be before an ORF, (also referred to as Should be before an ORF, (also referred to as

“upstream” or 5’ of an ORF).“upstream” or 5’ of an ORF). May have ambiguous sequence. (TATA box may look May have ambiguous sequence. (TATA box may look

like “TATAA” or “TAATA” or “TATATA” or “TTATAA”).like “TATAA” or “TAATA” or “TATATA” or “TTATAA”).

LUNCH TIME !!!!!!