Gene ExpressionGene Structure

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Gene Expression/Gene Structure

• September 18, 2001 (and beyond?)

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The DNA is in Charge
Today
Ribosome
Protein
I
III
II
AGCTAGTCGATAGCTGATCTGCTGATGCTGATGCTGATCATGCTAGCTAG
CTAGCTAGCTAGCATACGTAGCGA
rRNA
tRNA (5S rRNA, snRNAs)
mRNA
(Nucleolus)
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Flow of Genetic Information
DNA
RNA Transcription
DNA Replication
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Todays Exciting Topics

• Role of Messenger RNA
• Basic Steps of Transcription
• Prokaryotic Transcription
• Some Differences in Eukaryotic Transcription
• Enhancers
• Posttranscriptional Processing

5
rRNA and tRNA are Cogs in the Machinery

• rRNA is a structural part of the ribosome
• tRNA helps the protein machinery to read the mRNA
• Neither of these types of RNAs actually carries
  any information

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Messenger RNA

• Messenger RNA carries the information in the DNA
  to the protein translation machinery (ribosomes)
• Serves as the template for protein synthesis
• Which mRNAs are transcribed in a cell decide the
  fate of that cell since they dictate which
  information in the DNA is read by the protein
  translation machinery

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How do mRNAs Encode Protein?(Preview of Dr.
Hodels Lectures)

• Each three bases in the mRNA codes for a
  different one of the 20 amino acids
• In the ribosome these three bases are recognized
  by the tRNA that is charged with the
  appropriate amino acid
• That amino acid is then added to the peptide
  chain
• Recent structure of ribosome suggests RNA
  catalyzes the transfer

Methionine
Phenylalanine
Serine
5
3
UAGUUUUCC
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RNA Transcription

• RNA transcription can be broken down into three
  different steps
• Initiation
• Elongation
• Termination

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Regulation can occur at any of these steps

• Initiation- highly regulated step
• Elongation- the rate at which the mRNA is made
  can control how quickly its made
• Termination- premature termination can mean that
  the whole mRNA never gets made and neither does
  what it codes for
• Like receiving only part of the instructions on
  how to put together your easy to assemble
  bookcase/desk/whatever

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Todays Exciting Topics

• Role of Messenger RNA
• Basic Steps of Transcription
• Prokaryotic Transcription
• Some Differences in Eukaryotic Transcription
• Enhancers
• Posttranscriptional Processing

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Prokaryotic Transcription of mRNA

• In prokaryotes all RNA is transcribed by the same
  RNA polymerase
• There is no nucleus to separate the transcribed
  RNA from the protein translation machinery
• Translation start as soon as the RNA is
  transcribed
• This is called
• Coupled Transcription and Translation

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Coupled Transcription and Translation
RNA polymerase
Actively Transcribed Chromatin
Ribosomes
mRNA
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Initiation can occur at Multiple Sites
Bacterial Chromosome
Direction of Transcription
Initiation site
RNA Fibrils
Termination site
Initiation site
RNA Fibrils
Termination site
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Todays Exciting Topics

• Role of Messenger RNA
• Basic Steps of Transcription
• Prokaryotic Transcription
• Initiation, elongation, termination
• Some Differences in Eukaryotic Transcription
• Enhancers
• Posttranscriptional Processing

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Eukaryotic Transcription

• Has to be more control of how more complex
  genetic material is read to create more variety
  (multicellular)
• RNA has to be transcribed in the nucleus and then
  transported to the protein translation machinery
  in the cytoplasm before it can be read (compare
  to the Coupled transcription and translation of
  prokaryotes)

DNA
Nucleus
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Transcription of mRNA in Eukaryotes

• Steps involved are the same as in prokaryotes
• Initiation
• Elongation
• Termination
• Mediated by RNA polymerase II
• Very complex enzyme with many subunits

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Eukaryotic Intiation

• Initiation occurs at promoters as in prokaryotes-
  eukaryotic promoters are not well-characterized
  but have some well conserved elements- including
  the TATA box and CAAT box (both have AT pairs)
• In addition to the promoters there are region in
  the DNA called enhancers to which transcription
  factors bind and regulate which DNA is read and
  encoded in mRNA

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Transcription Factor Function
Pol
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Elongation and Termination

• Neither is understood in as much detail as in
  prokaryotes
• Elongation of the chain occurs by the addition of
  nucleotide to the 3-OH of the previous
  nucleotide
• Can be regulated by the rate at which nucleotides
  are added
• Termination occurs after a specific signal in the
  DNA

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Posttranscriptional ProcessingSplicing

• Often eukaryotic mRNAs have extra pieces in them
  called introns that have to be spliced out to
  make the mature message

Exons are spliced together to make the final mRNA
WHY?????
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More Posttranscriptional Processing

• Once the mRNA is made it has a long journey ahead
  to the cytoplasm
• mRNA gets processed to make it more stable
• Needs to be transported
• Needs to be relatively stable over time

AAAAAA
5
3
22
(No Transcript)
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Why is eukaryotic mRNA modified?
AAAAAA
5
3
Prokaryotic mRNA
Eukaryotic mRNA
5
3
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Basic Scheme The Life of an mRNA
DNA
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Todays Exciting Topics

• Role of Messenger RNA
• Basic Steps of Transcription
• Initiation, elongation, termination
• Prokaryotic Transcription
• Some Differences in Eukaryotic Transcription
• Enhancers
• Posttranscriptional Processing

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Gene Structure and the Human Genome
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What is a Gene??

• Definition of a Gene
• Description of a Generic Eukaryotic Gene
• Packaging of the Genome
• Chromosomes
• Chromosome Structure
• Specialized Regions of Chromosomes
• Makeup of the Human Genome

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What are Genes?

• Historically Defined as a Unit of Inheritance
• In 1866 Gregor Mendel described the Gene Theory
• Work Rediscovered in 1900
• Concept Existed Long Before the Chemical Nature
  of DNA was Understood

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What are Genes?

• The functional and physical unit of heredity
  passed from parent to offspring
• Genes are pieces of DNA, and most genes contain
  the information for making a specific protein

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Gene This is Your Life
DNA
Transcription
Processing
mRNA
AAA
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Organization of a GENE
Intron
Promoter
3-Untranslated Region (3-UTR)
5-Untranslated Region (5-UTR)
Exons
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Reading the Gene of the Gene
Processing
mRNA
AAA
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What is a Gene??

• Definition of a Gene
• Description of a Generic Eukaryotic Gene
• Packaging of the Genome
• Chromosomes
• Chromosome Structure
• Specialized Regions of Chromosomes
• Makeup of the Human Genome

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Cell
Histones
DNA
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2 nm
11 nm
RESULT

• Each DNA molecule is packaged into a chromosome
  50,000X shorter than its extended length

30 nm
300 nm
700 nm
1400 nm
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Packaging of DNA
30 nm
Nucleosomes
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Packaging of DNA
Interphase
Mitosis
1 µm
10 µm
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Chromosome Banding/Karyotype
Banding pattern is due to differential
staining of different regions of a given
chromosome
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What is a Gene??

• Definition of a Gene
• Description of a Generic Gene
• Packaging of the Genome
• Chromosomes
• Chromosome Structure
• Specialized Regions of Chromosomes
• Makeup of the Human Genome

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Specialized Regions of Chromosomes

• Origins of replication
• Eukaryotic chromosomes have many origins
• Centromere (1 per)
• Attaches chromosome to the mitotic spindle
  apparatus
• Telomere (2 per)
• Linear end of the chromosome

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Function of Centromeres

• Centromeres are at the center of the chromosome
• Allow a single copy of each chromosome to be
  pulled into each cell when a cell divides
• Protein complex termed a kinetocore attaches the
  chromosomes to the mitotic spindle

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Telomeres

• Serves as caps for the linear end of the
  chromosome
• Prevents DNA from being degraded
• Prevents recombination
• Made up of repeating sequences
• The End Replication Problem

3
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Origins of Replication
Centromeres
Telomeres
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What is a Gene??

• Definition of a Gene
• Description of a Generic Gene
• Packaging of the Genome
• Chromosomes
• Chromosome Structure
• Specialized Regions of Chromosomes
• Makeup of the Human Genome

45
Human Genome

• 3.2 x 109 base pairs of DNA
• 60-100,00 genes predicted (30,000)
• Arranged in 23 pairs of chromosomes
• 22 pairs of autosomal chromosomes
• 1 pair of somatic (either XX or XY)
• Only 1-2 of the genome encodes proteins

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Human Genome Contains a High Percentage of
Non-Coding DNA

• Introns
• Telomeres
• Highly repetitive DNA sequences
• Satellite DNA (repeats of up to 1,000,000 bp)
• Moderately repetitive DNA sequences
• Alu sequences

All these sequences may contribute to genetic
diversity
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Rate of Sequencing of the Human Genome
200
150
Millions of Base Pairs
100
50
1996
1997
1998
Completed by 2003
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What We Learned Today (what fun)

• Definition of a Gene
• Description of a Generic Gene
• Packaging of the Genome
• Chromosomes
• Chromosome Structure
• Specialized Regions of Chromosomes
• Makeup of the Human Genome