ap biology 2005-2006 chapter 17. from gene to protein
TRANSCRIPT
2005-2006 AP Biology
Chapter 17.
From Gene to Protein
2005-2006AP Biology
Metabolism teaches us about genes Metabolic defects
studying metabolic diseases suggested that genes specified proteins
alkaptonuria (black urine from alkapton) PKU (phenylketonuria)
each disease is caused by non-functional enzyme
A B C D E
Genescreate
phenotype
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1 gene – 1 enzyme hypothesis Beadle & Tatum
Compared mutants of bread mold, Neurospora fungus
created mutations by X-ray treatments X-rays break DNA inactivate a gene
wild type grows on “minimal” media sugars + required precursor nutrient to synthesize
essential amino acids mutants require added amino acids
each type of mutant lacks a certain enzyme needed to produce a certain amino acid
non-functional enzyme = broken gene
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Beadle & Tatum 1941 | 1958
George Beadle
Edward Tatum
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Beadle & Tatum’s Neurospora experiment
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So… What is a gene? One gene – one enzyme
but not all proteins are enzymes but all proteins are coded by genes
One gene – one protein but many proteins are composed of several
polypeptides but each polypeptide has its own gene
One gene – one polypeptide but many genes only code for RNA
One gene – one product but many genes code for
more than one product …
Where doesthat leave
us?!
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Defining a gene…“Defining a gene is problematic because… one gene can code for several protein products, some genes code only for RNA, two genes can overlap, and there are many other complications.”
– Elizabeth Pennisi, Science 2003
gene
polypeptide 1
polypeptide 2
polypeptide 3
RNAgeneIt’s hard to
hunt for wabbits,if you don’t knowwhat a wabbitlooks like.
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proteinRNA
The “Central Dogma”
DNAtranscription translation
replication
How do we move information from DNA to proteins?
For simplicity sake,let’s go back togenes that codefor proteins…
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From nucleus to cytoplasm… Where are the genes?
genes are on chromosomes in nucleus Where are proteins synthesized?
proteins made in cytoplasm by ribosomes How does the information get from
nucleus to cytoplasm? messenger RNA
nucleus
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RNA ribose sugar N-bases
uracil instead of thymine U : A C : G
single stranded mRNA, rRNA, tRNA,
siRNA….
RNADNAtranscription
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Transcription Transcribed DNA strand = template strand
untranscribed DNA strand = coding strand Synthesis of complementary RNA strand
transcription bubble Enzyme
RNA polymerase
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Role of promoter1. Where to start reading
= starting point
2. Which strand to read
= template strand
3. Direction on DNA
= always reads DNA 3'5'
Transcription in Prokaryotes Initiation
RNA polymerase binds to promoter sequence on DNA
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Transcription in Prokaryotes Promoter sequences
RNA polymerase molecules bound to bacterial DNA
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Transcription in Prokaryotes Elongation
RNA polymerase unwinds DNA ~20 base pairs at a time
reads DNA 3’5’ builds RNA 5’3’ (the energy governs the synthesis!)
No proofreading 1 error/105 bases many copies short life not worth it!
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Transcription
RNA
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Transcription in Prokaryotes Termination
RNA polymerase stops at termination sequence
mRNA leaves nucleus through pores
RNA GC hairpin turn
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Transcription in Eukaryotes
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Prokaryote vs. Eukaryote genes Prokaryotes
DNA in cytoplasm circular
chromosome naked DNA
no introns
Eukaryotes DNA in nucleus linear
chromosomes DNA wound on
histone proteins introns vs. exons
eukaryoticDNA
exon = coding (expressed) sequence
intron = noncoding (inbetween) sequence
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Transcription in Eukaryotes 3 RNA polymerase enzymes
RNA polymerase I only transcribes rRNA genes
RNA polymerase I I transcribes genes into mRNA
RNA polymerase I I I only transcribes rRNA genes
each has a specific promoter sequence it recognizes
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Transcription in Eukaryotes Initiation complex
transcription factors bind to promoter region upstream of gene
proteins which bind to DNA & turn on or off transcription
TATA box binding site only then does RNA
polymerase bind to DNA
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A A A A A3' poly-A tail
CH3
mRNA
5'
5' cap
3'
G PPP
Post-transcriptional processing Primary transcript
eukaryotic mRNA needs work after transcription Protect mRNA
from RNase enzymes in cytoplasm add 5' cap add polyA tail
Edit out introns
eukaryoticDNA
exon = coding (expressed) sequence
intron = noncoding (inbetween) sequence
primary mRNAtranscript
mature mRNAtranscript
pre-mRNA
spliced mRNA
50-250 A’s
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Transcription to translation Differences between
prokaryotes & eukaryotes time & physical separation
between processes RNA processing
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Translation in Prokaryotes Transcription & translation are
simultaneous in bacteria DNA is in
cytoplasm no mRNA
editing needed
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mRNA
From gene to protein
DNAtranscription
nucleus cytoplasm
mRNA leaves nucleus through nuclear pores
proteins synthesized by ribosomes using instructions on mRNA
aa
aa
aa
aa
aa
aa
aa
aa
ribosome
proteintranslation
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How does mRNA code for proteins?
TACGCACATTTACGTACGCGGDNA
AUGCGUGUAAAUGCAUGCGCCmRNA
Met Arg Val Asn Ala Cys Alaprotein
?
How can you code for 20 amino acids with only 4 nucleotide bases (A,U,G,C)?
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Cracking the code Nirenberg & Matthaei
determined 1st codon–amino acid match UUU coded for phenylalanine
created artificial poly(U) mRNA added mRNA to test tube of
ribosomes, tRNA & amino acids mRNA synthesized single
amino acid polypeptide chain
1960 | 1968
phe–phe–phe–phe–phe–phe
2005-2006AP Biology Marshall NirenbergHeinrich Matthaei
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Translation Codons
blocks of 3 nucleotides decoded into the sequence of amino acids
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AUGCGUGUAAAUGCAUGCGCCmRNA
mRNA codes for proteins in triplets
TACGCACATTTACGTACGCGGDNA
AUGCGUGUAAAUGCAUGCGCCmRNA
Met Arg Val Asn Ala Cys Alaprotein
?
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The code For ALL life!
strongest support for a common origin for all life
Code is redundant several codons for
each amino acid
Why is this a good thing?
Start codon AUG methionine
Stop codons UGA, UAA, UAG
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How are the codons matched to amino acids?
TACGCACATTTACGTACGCGGDNA
AUGCGUGUAAAUGCAUGCGCCmRNA
aminoacid
tRNA
anti-codon
codon
5' 3'
3' 5'
3' 5'
UAC
MetGCA
ArgCAU
Val
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proteinaa
aa
aa
aa
aa
aa
aa
aaaa
aa
aa
transcription
cytoplasm
nucleus
translation
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tRNA structure “Clover leaf” structure
anticodon on “clover leaf” end amino acid attached on 3' end
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Loading tRNA
Aminoacyl tRNA synthetase enzyme which bonds
amino acid to tRNA endergonic reaction
ATP AMP energy stored in
tRNA-amino acid bond unstable so it can release amino acid
at ribosome
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Ribosomes Facilitate coupling of
tRNA anticodon to mRNA codon organelle or enzyme?
Structure ribosomal RNA (rRNA)
& proteins 2 subunits
large small
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Ribosomes P site (peptidyl-tRNA site)
holds tRNA carrying growing polypeptide chain
A site (aminoacyl-tRNA site) holds tRNA carrying next amino acid to
be added to chain E site (exit site)
empty tRNA leaves ribosome from exit site
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Building a polypeptide Initiation
brings together mRNA, ribosome subunits, proteins & initiator tRNA
Elongation Termination
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Elongation: growing a polypeptide
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Termination: release polypeptide Release factor
“release protein” bonds to A site bonds water molecule to polypeptide chain
Now what happens to the polypeptide?
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Protein targeting Signal peptide
address label
Destinations: secretion nucleus mitochondria chloroplasts cell membrane cytoplasm
start of a secretory pathway
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Can you tell the story?
DNA
pre-mRNA
ribosome
tRNA
aminoacids
polypeptide
mature mRNA
5' cap
polyA tail
large subunit
small subunit
aminoacyl tRNAsynthetase
E P A
5'
3'
RNA polymerase
exon intron
tRNA
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Put it all together…
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Any Questions??
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Chapter 17.
Mutations
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Code is redundant several codons for
each amino acid “wobble” in the tRNA “wobble” in the
aminoacyl-tRNA synthetase enzyme that loads the tRNA
Universal code
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Mutations
When do mutations affect the next generation?
Point mutations single base change base-pair
substitution silent mutation
no amino acid change redundancy in code
missense change amino acid
nonsense change to stop codon
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Point mutation leads to Sickle cell anemiaWhat kind of mutation?
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Sickle cell anemia
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Mutations Frameshift
shift in the reading frame
changes everything “downstream”
insertions adding base(s)
deletions losing base(s)
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What’s thevalue of
mutations?
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Chapter 17.
RNAProcessing
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Transcription -- another look The process of transcription includes
many points of control when to start reading DNA where to start reading DNA where to stop reading DNA editing the mRNA protecting mRNA as it travels through
cell
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Primary transcript Processing mRNA
protecting RNA from RNase in cytoplasm add 5’ cap add polyA tail
remove introns
AUG UGA
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Protecting RNA 5’ cap added
G trinucleoside (G-P-P-P) protects mRNA
from RNase (hydrolytic enzymes)
3’ poly-A tail added 50-250 A’s protects mRNA
from RNase (hydrolytic enzymes) helps export of RNA from nucleus
UTR UTR
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Dicing & splicing mRNA Pre-mRNA mRNA
edit out introns intervening sequences
splice together exons expressed sequences
In higher eukaryotes 90% or more of gene can be intron no one knows why…yet
there’s a Nobel prize waiting…
“AVERAGE”…“gene” = 8000bpre-mRNA = 8000bmature mRNA = 1200bprotein = 400aalotsa “JUNK”!
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Discovery of Split genes1977 | 1993
Richard Roberts Philip Sharp
NE BioLabs MITadenovirus
common cold
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snRNPs small nuclear RNA RNA + proteins
Spliceosome several snRNPs recognize splice site
sequence cut & paste
RNA as ribozyme some mRNA can
splice itself RNA as enzyme
Splicing enzymes
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Ribozyme RNA as enzyme
Sidney Altman Thomas Cech
1982 | 1989
Yale U of Colorado
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Splicing details No room for mistakes!
editing & splicing must be exactly accurate a single base added or lost throws off the
reading frame
AUG|CGG|UCC|GAU|AAG|GGC|CAU
AUGCGGCTATGGGUCCGAUAAGGGCCAUAUGCGGUCCGAUAAGGGCCAU
AUG|CGG|GUC|CGA|UAA|GGG|CCA|U
AUGCGGCTATGGGUCCGAUAAGGGCCAUAUGCGGGUCCGAUAAGGGCCAU
Met|Arg|Ser|Asp|Lys|Gly|His
Met|Arg|Val|Arg|STOP|
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Alternative splicing Alternative mRNAs produced from same gene
when is an intron not an intron… different segments treated as exons
Hardto definea gene!
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Domains Modular architecture
of many proteins separate
functional & structural regions
coded by different exons in same “gene”
2005-2006AP Biology AAAAAAAAGTP
20-30b
3'
promoter transcriptionstop
transcriptionstart
introns
The Transcriptional unit (gene?)
transcriptional unitTAC ACT
DNA
DNATATA5'RNA
polymerase
pre-mRNA
5' 3'
translationstart
translationstop
mature mRNA
5' 3'
UTR UTR
exonsenhancer
1000+b
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Any Questions??
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20-30b
3'
introns
The Transcriptional unit
transcriptional unitTAC ACTDNATATA
5'RNApolymerase
5' 3'
5' 3'
exonsenhancer
1000+b