Gene Expression Gene Expression Chapter 13 Chapter 13
Mar 19, 2016
Gene ExpressionGene Expression
Chapter 13Chapter 13
Learning Objective 1Learning Objective 1
• What early evidence indicated that most What early evidence indicated that most genes specify the structure of proteins?genes specify the structure of proteins?
Garrod’s WorkGarrod’s Work
• Inborn errors of metabolismInborn errors of metabolism• evidence that genes specify proteins evidence that genes specify proteins
• Alkaptonuria Alkaptonuria • rare genetic disease rare genetic disease • lacks enzyme to oxidize homogentisic acidlacks enzyme to oxidize homogentisic acid
• Gene mutationGene mutation• associated with absence of specific enzymeassociated with absence of specific enzyme
AlkaptonuriaAlkaptonuria
Fig. 13-1, p. 280
Tyrosine
Functional enzyme absent
Homogentisic acid Functional enzyme present
Disease condition Normal metabolism
ALKAPTONURIA Maleylacetoacetate
Homogentisic acid excreted in urine; turns black when
exposed to air
H2OCO2
Learning Objective 2Learning Objective 2
• Describe Beadle and Tatum’s experiments Describe Beadle and Tatum’s experiments with with NeurosporaNeurospora
Beadle and TatumBeadle and Tatum
• Exposed Exposed Neurospora Neurospora sporesspores• to X-rays or ultraviolet radiationto X-rays or ultraviolet radiation• induced mutations prevented metabolic induced mutations prevented metabolic
production of essential molecules production of essential molecules
• Each mutant strainEach mutant strain• had mutation in only one genehad mutation in only one gene• each gene affected only one enzymeeach gene affected only one enzyme
Beadle-Tatum ExperimentsBeadle-Tatum Experiments
Fig. 13-2, p. 281
Expose Neurospora spores to UV light or X-rays
Fungal growth (mycelium)
Each irradiated spore is used to establish culture on complete growth medium (minimal medium plus amino acids, vitamins, etc.)
2
Transfer cells to minimal medium
plus vitamins
Transfer cells to minimal medium plus amino acids
Transfer cells to minimal medium
(control)
Minimal medium
plus arginine
Minimal medium
plus tryptophan
Minimal medium
plus lysine
Minimal medium
plus leucine
Minimal medium plus other amino
acids
1
3
KEY CONCEPTSKEY CONCEPTS
• Beadle and Tatum demonstrated the Beadle and Tatum demonstrated the relationship between genes and proteins relationship between genes and proteins in the 1940sin the 1940s
Learning Objective 3Learning Objective 3
• How does genetic information in cells flow How does genetic information in cells flow from DNA to RNA to polypeptide?from DNA to RNA to polypeptide?
DNA to ProteinDNA to Protein
• Information encoded in DNAInformation encoded in DNA• codes sequences of amino acids in proteinscodes sequences of amino acids in proteins
• 2-step process:2-step process:1. Transcription1. Transcription2. Translation2. Translation
TranscriptionTranscription
• Synthesizes Synthesizes messenger RNA (mRNA)messenger RNA (mRNA) • complementary to template DNA strandcomplementary to template DNA strand• specifies amino acid sequences of specifies amino acid sequences of
polypeptide chainspolypeptide chains
TranslationTranslation
• Synthesizes Synthesizes polypeptide chainpolypeptide chain • specified by specified by mRNAmRNA• also requires also requires tRNAtRNA and and ribosomesribosomes
• CodonCodon • sequence of 3 mRNA nucleotide basessequence of 3 mRNA nucleotide bases• specifies one specifies one amino acidamino acid • or a or a startstart or or stopstop signal signal
DNA to ProteinDNA to Protein
Fig. 13-4, p. 283
Nontemplate strand
TranscriptionDNA
Template strandmRNA
(complementary copy of
template DNA strand)
Codon 1 Codon 2 Codon 3 Codon 4 Codon 5 Codon 6
Polypeptide Met Thr Cys Glu Cys Phe
Translation
‘
‘
‘
‘
‘
‘
KEY CONCEPTSKEY CONCEPTS
• Transmission of information in cells is Transmission of information in cells is typically from DNA to RNA to polypeptidetypically from DNA to RNA to polypeptide
Learning Objective 4Learning Objective 4
• What is the difference between the What is the difference between the structures of DNA and RNA?structures of DNA and RNA?
RNARNA
• RNA nucleotidesRNA nucleotides• riboseribose (sugar) (sugar)• bases (bases (uraciluracil, adenine, guanine, or cytosine), adenine, guanine, or cytosine)• 3 phosphates3 phosphates
• RNA subunits RNA subunits • covalently joined by 5covalently joined by 5′′ – 3 – 3′′ linkages linkages• form alternating sugar-phosphate backboneform alternating sugar-phosphate backbone
RNA StructureRNA Structure
Fig. 13-3, p. 282
Uracil
Adenine
Cytosine
Guanine
Learning Objective 5Learning Objective 5
• Why is Why is genetic codegenetic code said to be redundant said to be redundant and virtually universal?and virtually universal?
• How may these features reflect its How may these features reflect its evolutionary history?evolutionary history?
Genetic CodeGenetic Code
• mRNA mRNA codonscodons• specify a sequence of amino acids specify a sequence of amino acids
• 64 codons64 codons• 61 code for amino acids61 code for amino acids• 3 codons are stop signals3 codons are stop signals
CodonsCodons
Genetic CodeGenetic Code
• Is redundantIs redundant• some amino acids have more than one codon some amino acids have more than one codon
• Is virtually universalIs virtually universal• suggesting all organisms have a common suggesting all organisms have a common
ancestorancestor• few minor exceptions to standard code found few minor exceptions to standard code found
in all organismsin all organisms
KEY CONCEPTSKEY CONCEPTS
• A sequence of DNA base triplets is A sequence of DNA base triplets is transcribed into RNA codonstranscribed into RNA codons
Learning Objective 6Learning Objective 6
• What are the similarities and differences What are the similarities and differences between the processes of between the processes of transcriptiontranscription and and DNA replicationDNA replication??
EnzymesEnzymes
• Similar enzymesSimilar enzymes• RNA polymerases RNA polymerases ((RNA synthesis)RNA synthesis)• DNA polymerases DNA polymerases ((DNA replication)DNA replication)
• Carry out synthesis in 5Carry out synthesis in 5′′ →→ 3 3′′ direction direction
• Use nucleotides with 3 phosphate groupsUse nucleotides with 3 phosphate groups
Antiparallel SynthesisAntiparallel Synthesis
• Strands of DNA are Strands of DNA are antiparallelantiparallel
• Template DNA strand and complementary Template DNA strand and complementary RNA strand are RNA strand are antiparallelantiparallel• DNA template read in 3DNA template read in 3′′ →→ 5 5′′ direction direction• RNA synthesized in 5RNA synthesized in 5′′ →→ 3 3′′ direction direction
Antiparallel SynthesisAntiparallel Synthesis
Fig. 13-9, p. 287
mRNA transcript mRNA transcriptPromoter region
Promoter region
Promoter regionRNA polymerase Gene 2
3’
Gene 1 Gene 3mRNA transcript
5’
5’
5’
3’
3’ 3’
5’
3’
5’
Base-Pairing RulesBase-Pairing Rules
• In RNA synthesis and DNA replicationIn RNA synthesis and DNA replication• are the sameare the same• exceptexcept uraciluracil is substituted for is substituted for thyminethymine
TranscriptionTranscription
Fig. 13-7, p. 286
Growing RNA strand Template DNA strand
5’ end 3’ direction
Nucleotide added to growing chain by RNA polymerase 3’end 5’ direction
Learning Objective 7Learning Objective 7
• What features of What features of tRNAtRNA are important in are important in decoding genetic information and decoding genetic information and converting it into “protein language”?converting it into “protein language”?
Transfer RNA (tRNA)Transfer RNA (tRNA)
• ““Decoding” molecule in Decoding” molecule in translationtranslation
• AnticodonAnticodon• complementary to mRNA codoncomplementary to mRNA codon• specific for 1 amino acidspecific for 1 amino acid
tRNAtRNA
Fig. 13-6a, p. 285
’ ’ Loop 3
Hydrogen bonds
Loop 1
Loop 2
Anticodon
Fig. 13-6b, p. 285
OH 3’ endAmino acid accepting end
P 5’ end
Hydrogen bonds
Loop 3Loop 1
Modified nucleotides
Loop 2
Anticodon
Fig. 13-6c, p. 285
Amino acid (phenylalanine)
Anticodon
‘ ‘
Transfer RNA (tRNA)Transfer RNA (tRNA)
• tRNAtRNA • attaches to specific amino acid attaches to specific amino acid • covalently bound bycovalently bound by aminoacyl-tRNA aminoacyl-tRNA
synthetasesynthetase enzymes enzymes
Aminoacyl-tRNAAminoacyl-tRNA
Fig. 13-11, p. 289
Phenylalanine AMP+
Aminoacyl-tRNA synthetase
+
AnticodonAmino acid tRNA Aminoacyl-tRNA
Stepped Art
Fig. 13-11, p. 289
AMP+Phenylalanine
Amino acid Aminoacyl-tRNAtRNA
+
Anticodon
Aminoacyl-tRNA synthetase
Learning Objective 8Learning Objective 8
• How do How do ribosomesribosomes function in polypeptide function in polypeptide synthesis?synthesis?
RibosomesRibosomes
• Bring together all machinery for Bring together all machinery for translationtranslation • Couple tRNAs to mRNA codonsCouple tRNAs to mRNA codons• Catalyze peptide bonds between amino acidsCatalyze peptide bonds between amino acids• Translocate mRNA to read next codonTranslocate mRNA to read next codon
Ribosomal SubunitsRibosomal Subunits
• Each ribosome is made ofEach ribosome is made of• 1 1 large ribosomal subunitlarge ribosomal subunit• 1 1 small ribosomal subunitsmall ribosomal subunit
• Each subunit containsEach subunit contains• ribosomal RNA (rRNA)ribosomal RNA (rRNA)• many proteinsmany proteins
Ribosome Ribosome StructureStructure
Fig. 13-12a, p. 290
Front view
Large subunit
E P A
Ribosome
Small subunit
Fig. 13-12b, p. 290
Large ribosomal subunit
E site
P site
A site
mRNA binding site
Small ribosomal subunit
KEY CONCEPTSKEY CONCEPTS
• A sequence of RNA codons is translated A sequence of RNA codons is translated into a sequence of amino acids in a into a sequence of amino acids in a polypeptidepolypeptide
Animation: Structure of a Animation: Structure of a RibosomeRibosome
CLICKTO PLAY
Learning Objective 9Learning Objective 9
• Describe the processes of Describe the processes of initiationinitiation, , elongationelongation, and , and terminationtermination in polypeptide in polypeptide synthesissynthesis
InitiationInitiation
• 1st stage of 1st stage of translationtranslation• Initiation factorsInitiation factors
• bind to small ribosomal subunitbind to small ribosomal subunit• which binds to mRNA at which binds to mRNA at start codon (AUG)start codon (AUG)
• Initiator tRNAInitiator tRNA• binds to start codonbinds to start codon• then binds large ribosomal subunitthen binds large ribosomal subunit
ElongationElongation
• A cyclic processA cyclic process• adds amino acids to polypeptide chainadds amino acids to polypeptide chain
• Proceeds in 5Proceeds in 5′′ →→ 3 3′′ direction along mRNA direction along mRNA
• Polypeptide chain growsPolypeptide chain grows• from amino end to carboxyl endfrom amino end to carboxyl end
TerminationTermination
• Final stage of Final stage of translationtranslation• when ribosome reaches when ribosome reaches stop codonstop codon
• AA sitesite binds to binds to release factorrelease factor• triggers release of triggers release of polypeptide chainpolypeptide chain• dissociation of translation complexdissociation of translation complex
Stages of TranscriptionStages of Transcription
RNA polymerase binds to promoter region in DNA
Termination sequence
Promoter region
Direction of transcription
RNA transcriptRewinding of DNA
Unwinding of DNA
RNA transcriptRNA polymerase
DNA
DNA
DNA template strand
Fig. 13-8, p. 287
Learning Objective 10Learning Objective 10
• What is the functional significance of the What is the functional significance of the structural differences between structural differences between bacterialbacterial and and eukaryoticeukaryotic mRNAs? mRNAs?
EukaryotesEukaryotes
• Genes Genes andand mRNA molecules mRNA molecules• are more complicated than those of bacteriaare more complicated than those of bacteria
Eukaryotic mRNAEukaryotic mRNA
• After transcriptionAfter transcription• 55′′ cap cap (modified guanosine triphosphate) is (modified guanosine triphosphate) is
added to added to 55′′ end end of mRNA molecule of mRNA molecule
• Poly-A tailPoly-A tail (adenine-containing nucleotides) (adenine-containing nucleotides)• may be added at 3may be added at 3′′ end of mRNA molecule end of mRNA molecule
Posttranscriptional ModificationPosttranscriptional Modification
Fig. 13-17, p. 295
1st exon
1st intron
2nd exon
2nd intron
3rd exon
mRNA termination sequencePromoter
Template DNA strand
7-methylguanosine cap Transcription, capping of 5’ end
5’ endStart codon Stop codon
Formation of pre-mRNASmall nuclear ribonucleoprotein complex
1st intron 2nd intron
5’ end –AAA... Poly-A tail
3’ endProcessing of pre-mRNA (addition of poly-A tail and removal of introns)
2nd exon
3rd exon
–AAA... Poly-A tail 3’ end5’ end
Protein-coding regionMature mRNA in nucleus Nuclear envelope
Nuclear pore
CytosolTransport through nuclear envelope to cytosol
–AAA... Poly-A tail 3’ end5’ end Start codon Stop codon
Mature mRNA in cytosol
1st exon
Introns and ExonsIntrons and Exons
• IntronsIntrons • noncoding regions (interrupt exons)noncoding regions (interrupt exons)• removed from original removed from original pre-mRNApre-mRNA
• ExonsExons• coding regions in eukaryotic genes coding regions in eukaryotic genes • spliced to produce continuous polypeptide spliced to produce continuous polypeptide
coding sequencecoding sequence
Learning Objective 11Learning Objective 11
• What is the difference between translation What is the difference between translation in in bacterialbacterial and and eukaryoticeukaryotic cells? cells?
Bacterial CellsBacterial Cells
• Transcription and translation are coupledTranscription and translation are coupled
• Bacterial ribosomesBacterial ribosomes• bind to 5bind to 5′′ end of growing mRNA end of growing mRNA• initiate translation before message is fully initiate translation before message is fully
synthesizedsynthesized
Bacterial mRNABacterial mRNA
Fig. 13-10, p. 288
Promoter region
mRNA termination sequenceTranscribed region
DNA
Upstream leader
sequences
Downstream trailing
sequences
Protein-coding sequences
Translated region
Start codon Stop codonmRNA
5 ′ end–OH 3 ′ end
Polypeptide
InitiationInitiation
Fig. 13-13a, p. 291
Leader sequence
mRNA
Small ribosomal subunit
Initiation factor
Start codon
Fig. 13-13b, p. 291
fMet
Initiator tRNA
Fig. 13-13c, p. 291
fMet Large ribosomal subunit
P site
E site A site
Initiation complex
ElongationElongation
Fig. 13-14, p. 292
tRNA with an amino acidAmino acids Amino acids
GDPGTP
E P A E P AAminoacyl-
tRNA binds to codon in A site
mRNA
Ribosome ready to accept another aminoacyl-tRNA
Peptide bond formation
Amino end of polypeptide New
peptide bondTranslocation
toward 3 ′ end of mRNA
E P A E P AGTP
GDP
TerminationTermination
Fig. 13-15a, p. 293
Release factor
E P A
mRNAStop codon (UAA, UAG, or UGA)
Fig. 13-15b, p. 293
Polypeptide chain is released
Stop codon (UAA, UAG, or UGA)
Fig. 13-15c, p. 293
Large ribosomal subunit
Release factor
AP
E
mRNASmall ribosomal subunit
tRNA
PolyribosomePolyribosome
• Many ribosomes bound to a single mRNAMany ribosomes bound to a single mRNA
KEY CONCEPTSKEY CONCEPTS
• Prokaryotic and eukaryotic cells differ in Prokaryotic and eukaryotic cells differ in the details of transcription and translationthe details of transcription and translation
Learning Objective 12Learning Objective 12
• Describe Describe retrovirusesretroviruses and the enzyme and the enzyme reverse transcriptasereverse transcriptase
RetrovirusesRetroviruses
• Synthesize DNA from an RNA template Synthesize DNA from an RNA template • HIV-1 (virus that causes AIDS)HIV-1 (virus that causes AIDS)
• Enzyme Enzyme reverse transcriptase reverse transcriptase • reverses flow of genetic information reverses flow of genetic information
Reverse TranscriptionReverse Transcription
Fig. 13-19a, p. 297
Chromosome DNA in nucleus of host cell Provirus inserted
into chromosome DNA
DNA provirusDNA replication
Digestion of RNA strandRNA /DNA hybrid Reverse transcription
RNA virus
Viral RNA
Fig. 13-19b, p. 297
Provirus DNA transcribed
Viral mRNA
Viral RNA
Viral proteins
RNA virus
2
Learning Objective 13Learning Objective 13
• Give examples of the different classes of Give examples of the different classes of mutations that affect the base sequence of mutations that affect the base sequence of DNA DNA
• What effects does each have on the What effects does each have on the polypeptide produced?polypeptide produced?
Base SubstitutionBase Substitution
• May alter or destroy protein function May alter or destroy protein function • missense mutationmissense mutation
• codon change specifies a different amino acidcodon change specifies a different amino acid• nonsense mutationnonsense mutation
• codon becomes a stop codoncodon becomes a stop codon
• May have minimal effectsMay have minimal effects• if amino acid is not alteredif amino acid is not altered• if codon change specifies a similar amino acidif codon change specifies a similar amino acid
Fig. 13-20a, p. 299
Normal DNA sequence
Normal mRNA sequence
Normal protein sequence
BASE-SUBSTITUTION MUTATIONS
Missense mutation
Nonsense mutation
(Stop)
(Stop)
(Stop)
Animation: Base-Pair Animation: Base-Pair SubstitutionSubstitution
CLICKTO PLAY
Frameshift MutationsFrameshift Mutations
• InsertionInsertion or or deletiondeletion of one or two base of one or two base pairs in a genepairs in a gene• destroys protein functiondestroys protein function• changes codon sequences downstream from changes codon sequences downstream from
the mutationthe mutation
Fig. 13-20b, p. 299
FRAMESHIFT MUTATIONS
Deletion causing nonsense
Deletion causing altered amino acid sequence
Normal DNA sequence
Normal mRNA sequence
Normal protein sequence
(Stop)
(Stop)
Animation: Frameshift Animation: Frameshift MutationMutation
CLICKTO PLAY
TransposonsTransposons
• Movable DNA sequencesMovable DNA sequences• ““jump” into the middle of a genejump” into the middle of a gene
• RetrotransposonsRetrotransposons• replicate by forming RNA intermediatereplicate by forming RNA intermediate• reverse transcriptase converts to original DNA reverse transcriptase converts to original DNA
sequence before jumping into genesequence before jumping into gene
KEY CONCEPTSKEY CONCEPTS
• Mutations can cause changes in Mutations can cause changes in phenotypephenotype
Animation: Protein Synthesis Animation: Protein Synthesis SummarySummary
CLICKTO PLAY