The cell as a factory

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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 its needed and then its
  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)

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

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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
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Transcription- making the mRNA
Translation- making the protein
Off to work!
Gene Structure
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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.

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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).
  

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Bacterial Gene Structure

• Bacterial (prokaryotic) genes
• One mRNA can contain several coding regions
  (ORFs).
• Each ORF has its own translation start and stop

transcription
DNA with one promoter controlling several genes
mRNA containing several genes
start
stop
start
stop
start
stop
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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
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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).
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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.

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From Gene to Protein
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Bioinformatics

• Were 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 arent all that hard.

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Steps to finding genes

• Find ORFs
• This is the biggest target, easiest to find- look
  for long stretches of triplet codons that dont
  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).

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LUNCH TIME !!!!!!