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Chapter 8 Gene Expression
Central Dogma
transcription translation
DNA mRNA protein
taking genetic information and using it to produce phenotypic traits
templatestrand
modificationgene
product
phenotype
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8.1 Polypeptide chains are linear polymers of amino acids.
Chapter 8 Gene Expression
proteins:
catalyzing reactions (enzymes)regulating gene expression (regulatory proteins)structural proteins
one or more chains of amino acids (20)linked by peptide bonds
polypeptide chains
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8.1 Polypeptide chains are linear polymers of amino acids.
Chapter 8 Gene Expression
amino acids
carboncarboxyl group -COOHamino group -NH2
side chain -R
connected to each other betweencarboxyl group and amino group
(dehydration synthesis)
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© 2006 Jones and Bartlett Publishers
Fig. 8.1. Amino acid structure
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Fig. 8.2. Chemical structures of amino acids specific in the genetic code
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© 2006 Jones and Bartlett Publishers
Fig. 8.3. Properties of a polypeptide chain
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8.1 Polypeptide chains are linear polymers of amino acids.
Chapter 8 Gene Expression
protein folding
interactions between amino acidsfolding to give 3-D structure
domains
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picture of beta chain of hemoglobinshowing folding/domains
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8.1 Polypeptide chains are linear polymers of amino acids.
Chapter 8 Gene Expression
protein folding
interactions between amino acidsfolding to give 3-D structure
some proteins are made of multiple chainseach one being a subunit
domains
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picture of hemoglobin
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8.1 Polypeptide chains are linear polymers of amino acids.
Chapter 8 Gene Expression
domain observations
vertebrate genomes have few protein domainsnot found in other organisms…
…but they are more complex because they haveput them together in more complex ways
only 7% of human proteins/domainsare specific to vertebrates
complexity is ~1.8 x fly or worm~5.8 x yeast
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8.2 linear order of amino acids is encoded in the DNA.
Chapter 8 Gene Expression
most genes code of a single polypeptide (protein)
order of nucleotides determines order of amino acids
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© 2006 Jones and Bartlett PublishersFig. 8.4. Colinearity of DNA and protein in the trpA gene of E. coli
genes and proteins are colinear
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8.2 linear order of amino acids is encoded in the DNA.
Chapter 8 Gene Expression REVIEW
8.1 Polypeptide chains are linear polymers of amino acids.
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
synthesis of RNA is similar to that of DNA
•RNA is made from single stranded DNA•monomers are ribonucleotides A, C, G and U
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© 2006 Jones and Bartlett Publishers
Fig. 8.5. Structural differences between ribose and deoxyribose and between uracil and thymine
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
synthesis of RNA is similar to that of DNA
•RNA is made from single stranded DNA•monomers are ribonucleotides A, C, G and U•sequence of bases is determined by DNA sequence•nucleotides connected 5’-P to 3’-OH•nucleotides only added at the 3’ end of RNA•enzyme is different - RNA polymerase(s)
can initiate without a primer
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Fig. 8.6A, B. RNA synthesis
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
RNA polymerases
prokaryotes - RNA polymerase holoenzyme six polypeptide chains
can process more than 104 nucleotides(while associated with the template)
processivity
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
RNA polymerases
eukaryotes - larger, more subunits
RNA polymerase IRNA polymerase IIRNA polymerase III
makes rRNAmRNA, snRNA’s, processingtRNA’s, 5S rRNA
processivity > 106 nucleotides
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
Transcription
which strandwhere to startwhere to stop ?
•promoter recognition•chain initiation•chain elongation•chain termination
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
which strandwhere to start
RNA polymerase binds to promoter
regions of DNA, 20-200 bp “recognized” by RNA polymeraseconsensus sequences (see fig. 8.8)
•promoter recognitionTranscription
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Fig. 8.8. Base sequences in promoter regions of several genes in E. coli
binding strength varies~ closer to consensus has stronger binding
(Eukaryotes also have enhancers that interact with promoters)
*TATA box
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
•promoter recognition•chain initiation
Transcription
after RNA polymerase bindingtranscription begins at +1
only one strand is transcribed
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
•promoter recognition•chain initiation•chain elongation
Transcription
next nucleotide added to 3’ endRNA made in 5’ to 3’ direction
about 17 bp of DNA are separateddouble helix reformsRNA trails off as separate strand
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Fig. 8.6C. RNA synthesis
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
•promoter recognition•chain initiation•chain elongation•chain termination
Transcription
special DNA sequencesRNA polymerase dissociates from DNA
self termination sequence only
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© 2006 Jones and Bartlett Publishers
Fig. 8.9. (A) Base sequence of a transcription termination region; (B) the 3' terminus of an RNA transcript
which strand ?
RNA polymerase terminates transcription when loop forms in transcript
RNA sequence ?
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
Transcription
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© 2006 Jones and Bartlett Publishers
Fig. 8.10. EM of part of newt DNA showing tandem repeats of genes . [Courtesy of Oscar Miller and Barbara R. Beatty]
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
•promoter recognition•chain initiation•chain elongation•chain termination
Transcription
special DNA sequencesRNA polymerase dissociates from DNA
self termination sequence only
termination protein sequence and protein
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
•promoter recognition•chain initiation•chain elongation•chain termination
Transcription
mutations
in coding regionin promotorin termination sequence
change amino acidsno transcript ?long transcript ?
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
Transcription
only one strand is transcribedmight be either one(either strand can have promoters/terminators)
genes usually don’t overlap
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Fig. 8.11. Typical arrangement of promoters and termination sites in a segment of a DNA molecule
A B C
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
mRNA
5’ 3’
3’ untrans-lated region
5’ untrans-lated region
open reading frame(ORF)
RNA transcript is called the primary( 1°) transcript
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8.3 DNA sequence determines RNA sequence.
Chapter 8 Gene Expression
RNA transcript is called the primary( 1°) transcript
in prokaryotes:used as mRNA directly for protein synthesisshort lifetime (minutes)
in eukaryotes:primary transcript is processed to become mRNAlonger lifetime (hours to days)
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8.4 Eukaryotic 1° transcript is processed to become mRNA
Chapter 8 Gene Expression
RNA processing
1. terminal cap is added
at 5’ endadd modified guanosine5’ to 5’ linkageneeded for mRNA to bind to ribosome
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8.4 Eukaryotic 1° transcript is processed to become mRNA
Chapter 8 Gene Expression
RNA processing
1. terminal cap is added2. poly-A tail is added
add up to 200 A to the 3’ end
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8.4 Eukaryotic 1° transcript is processed to become mRNA
Chapter 8 Gene Expression
RNA processing
1. terminal cap is added2. poly-A tail is added3. remove introns
take out unnecessary RNAresplice needed RNA
5’ 3’
exon exon exonintron intron
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Fig. 8.12. mRNA processing in eukaryotes
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8.4 Eukaryotic 1° transcript is processed to become mRNA
Chapter 8 Gene Expression
RNA processing
Many steps involved in processing are coupled
For example:
proteins involved with RNA polymerase to promote elongation also help recruit splicing machinery
the splicing machinery helps to:speed up elongationrecruit the polyadenylation machinery
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8.4 Eukaryotic 1° transcript is processed to become mRNA
Chapter 8 Gene Expression
RNA splicing (in the nucleus)
takes place at spliceosomesnuclear particlesprotein and small RNA’sforming snRNP’s
smallnuclearribo-nucleo-proteinparticles
U1, U2, U4, U5, U6
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8.4 Eukaryotic 1° transcript is processed to become mRNA
Chapter 8 Gene Expression
RNA splicing (in the nucleus)
5 snRNP RNA:
U1, U2, U4, U5, U6
U1 binds to both ends of the intron and brings them together
U4 and U6 are normally paired, U2 is stable alone
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8.4 Eukaryotic 1° transcript is processed to become mRNA
Chapter 8 Gene Expression
RNA splicing (in the nucleus)
U2 also binds to 3’ end of intron
U2 destabilizes U4-U6 complexand displaces U4 (U2 binds to U6)
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8.4 Eukaryotic 1° transcript is processed to become mRNA
Chapter 8 Gene Expression
RNA splicing (in the nucleus)
U1, U2, U4, U5, U6
U4 and U6 are normally paired, U2 is stable alone
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Fig. 8.13 . Interactions between small nuclear RNAs in snRNPs that are involved in splicing
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Fig. 8.14B. Drawing of DNA-RNA hybrid
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Chapter 8 Gene Expression
8.4 Eukaryotic 1° transcript is processed to become mRNA
RNA splicing
hybridize DNA with processed RNA(denature / renature)
mRNA
DNA
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Chapter 8 Gene Expression
8.4 Eukaryotic 1° transcript is processed to become mRNA
RNA splicing (in other places)
mitochondria happens w/out spliceosomesTetrahymena self slicing RNA
ribozymes
8.3 DNA sequence determines RNA sequence.
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Table 8.2. Characteristics of human genes
titin has 178
typical is about 87 bp
BRAC1 has 21 intronsspread over 100,000 bmRNA = 7800 bpeptide has 1863 a.a.
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Chapter 8 Gene Expression
8.4 Eukaryotic 1° transcript is processed to become mRNA
RNA splicing
human genes are spread outhave small exons separated
by long introns
only about 5% of a gene codes for protein
longest human gene is muscle protein, dystrophin2.4 Mb (79 exons)codes for over 3500 amino acids
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Chapter 8 Gene Expression
8.4 Eukaryotic 1° transcript is processed to become mRNA
RNA splicing
many exons correspond to domains of the assembled protein
suggests that some current genes may have been assembled from smaller pieces
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Chapter 8 Gene Expression
8.4 Eukaryotic 1° transcript is processed to become mRNA
many genes more proteins?
a single primary transcript can be spliced in different ways to give different mRNA (thus different proteins)
sxl-protein+
http://fig.cox.miami.edu/~cmallery/150/gene/split_genes.htm
non-functionalprotein
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Chapter 8 Gene Expression
8.4 Eukaryotic 1° transcript is processed to become mRNA
http://departments.oxy.edu/biology/Stillman/bi221/111300/processing_of_hnrnas.htm
tropomyosin
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
protein production includes two processes:
information transfergetting the amino acids in the correct order
chemical synthesishooking the amino acids together
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
protein production has 5 major components
•mRNA -
•ribosomes -
•tRNA -
•aminoacyl-tRNA synthetases -
•factors -
needed for assembly of ribosomehas information for amino acid sequence
2 subunits, align tRNA’s, attach a.a.’s
carry appropriate amino acid, have anticodon
puts a.a.’s on tRNA
for initiation, elongation and termination
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
Overview:
mRNA binds to ribosometRNA’s are brought in one by one with a.a.adjacent amino acids are joinedfinished protein is released from ribosome
initiationelongation
termination
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
Eukaryotic initiation:
eIF = eukaryotic Initiation Factorsnot elongation factors (pg. 294)
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
Eukaryotic initiation:
eIF4F binds to 5’ cap of mRNArecruits eIF4A and eIF4B
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Fig. 8.15. Initiation of protein synthesis
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
eIF4F binds to 5’ cap of mRNArecruits eIF4A and eIF4B
creates binding site for:
eIF2, eIF3, eIF5, tRNAMet
small 40S subunit of ribosomemaking initiation complex 48S
Eukaryotic initiation:
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
eIF4F binds to 5’ cap of mRNArecruits eIF4A and eIF4B
creates binding site for:
eIF2, eIF3, eIF5, tRNAMet
small 40S subunit of ribosomemaking initiation complex 48S
scans for AUGeiF5 causes release of initiation factors
and recruitment of the 60S subunit
Eukaryotic initiation:
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
Ribosome (60S subunit) has three binding sites
E
P
A
Exit
Peptidyl
Aminoacyl
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© 2006 Jones and Bartlett Publishers
Fig. 8.15. Initiation of protein synthesis
hydrogen bonding between codon and anticodon
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
Elongation (three steps)
•bring in next tRNA (with amino acid)
•form new peptide bond
•move to next codon on mRNA
Energy for elongation is provided by: EF-2EF-1
- GTP- GTP
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
Elongation
1. 40S subunit shifts one codon “down” the messagenew “charged” tRNA is brought to A site
2. coupled reaction forms new peptide bond(peptidyl transferase activity)
3. large subunit moves to “catch up” to small subunittRNA’s are shifted
1. from P and E site1. to the A and P site
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© 2006 Jones and Bartlett PublishersFig. 8.16A, B. Elongation cycle in protein synthesis
1
1
2
33
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
Elongation
completed one cyclerepeat for next codon
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© 2006 Jones and Bartlett PublishersFig. 8.16C, D. Elongation cycle in protein synthesis
11
3 3
2
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© 2006 Jones and Bartlett PublishersFig. 8.16. Elongation cycle in protein synthesis
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
Elongation
eukaryotes
40S60S12-15 aa/sec
EF-1EF-2
prokaryotes
30S50S20 aa/sec
EF-TuEF-G
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
Terrmination (release phase)
eukaryotic termination codons:
UAGUAAUGA
prokaryotes
UAAUAG
UAAUGA
RF-1
RF-2
RF
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Fig. 8.18. Termination of protein synthesis
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
InitiationElongationTermination
protein folding
most proteins fold as they are being synthesized
aa with hydrophilic R surfaceaa with hydrophobic R internal
-helix-pleated sheet
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alpha helix
Chapter 8 Gene Expression
http://wiz2.pharm.wayne.edu/biochem/nsphelix1.jpg
O
H
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Chapter 8 Gene Expression
beta pleated sheet
http://www.sciencecollege.co.uk/SC/biochemicals/bsheet.gif
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Fig. 8.19. A "ribbon" diagram of the path of the backbone of a polypeptide. [Adapted from W. I. Weiss, et al. 1992. Nature 360: 127.]
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Fig. 8.20. Alternative pathways in protein folding
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8.5 Translation takes place on a ribosome
Chapter 8 Gene Expression
eukaryotic prokaryotic
one protein / mRNAreads from 5’cap - to termination codon
may be polycistronic(multiple proteins / mRNA)
can initiate in other areasAGGAGG
(Shine-Dalgarno sequence)
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© 2006 Jones and Bartlett Publishers
Fig. 8.21. Products translated from a three-cistron mRNA molecule
for example, 10 enzymes needed for histidine synthesis - one mRNA
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Fig. 8.22. Direction of synthesis of RNA and of protein
by convention:write from L to RDNA 5’ to 3’protein amino to carboxyl
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8.6 Genetic code for amino acids is a triplet code
Chapter 8 Gene Expression
list of all codons and amino acids they encode
4 =4x4 =
4x4x4 =
41664
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Fig. 8.23. Reading bases in an RNA molecule
codons are linear and non-overlapping
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Fig. 8.24. Change in an amino acid sequence of a protein caused by the addition of an extra base
frameshift mutationreading frame
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Fig. 8.25. Interpretation of the rll frameshift mutations
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8.6 Genetic code for amino acids is a triplet code
Chapter 8 Gene Expression
make synthetic polynucleotides
AAAAAAAAAAAA…UUUUUUUUUUUU…CCCCCCCCCCCC…GGGGGGGGGGGG…
translate in vitro and look at peptides made
Lys Lys Lys Lys…Phe Phe Phe Phe…Pro Pro Pro Pro…Gly Gly Gly Gly…
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Fig. 8.26. Polypeptide synthesis in three different reading frames
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© 2006 Jones and Bartlett PublishersTable 8.3. The standard genetic code
redundancymore than one way to get most amino acids
universality (almost)minor differences in some protozoanssome organelles
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8.6 Genetic code for amino acids is a triplet code
Chapter 8 Gene Expression
tRNAs (how many different ones?)
small, single stranded RNA70-90 nucleotides long
5’ is monophosphate (instead of triphosphate)
folds on itself
anticodon region3’ end for attachment of a.a.
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Fig. 8.27. tRNA cloverleaf configuration
2-D
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Fig. 8.28B. Diagram of the three-dimensional structure of yeast tRNAPhe
5’
3’
“wobble” at the third position
3-D
number of distinct tRNAs is less than the # of codons
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Table 8.4. Wobble rules for tRNAs of E. coli and S. cervisiae
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8.7 Multiple ribosomes can move in tandem on mRNA
Chapter 8 Gene Expression
After ribosome has moves about 75 nucleotides another ribosome can initiate translation on the same message
in prokaryotes (no nucleus)
can have simultaneous transcription and translation
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Chapter 8 Gene Expression
8.7 Multiple ribosomes can move in tandem on mRNA
http://www.phschool.com/science/biology_place/biocoach/images/translation/polysome.gif