Molecular Biology of the Cell
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1 Alberts Johnson Lewis Raff Roberts Walter Molecular Biology of the Cell Fifth Edition Chapter 6 How Cells Read the Genome: From DNA to Protein Copyright Garland Science 2008
2 Figure 6-1 Molecular Biology of the Cell ( Garland Science 2008) 2
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5 25 APRIL 2013 VOL 496 NATURE 419
6 Amaral, P. P., Dinger, M. E., Mercer, T. R., & Mattick, J. S. (2008). Science, 319(5871),
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8 DNA has hereditary information. DNA can be passed on unchanged through DNA replication. How does the cell decode and use the information?
9 How do genetic instructions written in an alphabet of just four letters direct the formation of a bacterium, a fruit fly, or a human? Central dogma of molecular biology The flow of genetic information in cells is from DNA to RNA to protein.
10 Figure 6-2 Molecular Biology of the Cell ( Garland Science 2008) 10
11 Figure 6-3 Molecular Biology of the Cell ( Garland Science 2008) 11
12 mrna contains same genetic information as the genetic storage, DNA does. Then, why is mrna necessary for the expression of proteins in cells?
13 Many identical RNA copies can be made from the same gene. Each RNA molecule can direct the synthesis of many identical protein molecules. Each gene can be transcribed and with a different efficiency. This provides the cell with a way to make vast quantities of some proteins and tiny quantities of others.
14 Portions of DNA Sequence Are Transcribed into RNA Transcription ( ) and translation ( ) are the means by which cells read out, or express their genetic instructions genes. Transcription is the first step a cell reads out genes.
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16 RNA (ribonucleic acid) A linear polymer made of four different nucleotides liked together by phosphodiester bonds. 16 Figure 6-4 Molecular Biology of the Cell ( Garland Science 2008)
17 RNA differs from DNA chemically Nucleotides : Ribonucleotides (contain the sugar ribose rather than deoxyribose). Bases : A, G, C, and U (uracil) instead of T. Very small chemical differences
18 Figure 6-4a Molecular Biology of the Cell ( Garland Science 2008) 18
19 Figure 6-4b Molecular Biology of the Cell ( Garland Science 2008) 19
20 Figure 6-4c Molecular Biology of the Cell ( Garland Science 2008) 20
21 Figure 6-5 Molecular Biology of the Cell ( Garland Science 2008) 21
22 RNA differs from DNA in structure Single-stranded (DNA: double-stranded helix). Fold up into a variety of shapes (intramolecular base pairs; double-stranded DNA cannot fold). Carry out functions + convey information. Structural and even catalytic functions. Quite dramatic differences in overall structure
23 RNA molecule can form intramolecular base pairs and fold into specific structure (A) Conventional (pink) base pairing (Watson-Crick) (B) Nonconventional (green) base-pairing (e.g., A-G) Figure 6-6 Molecular Biology of the Cell ( Garland Science 2008) 23
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25 Transcription ( [ ], ;from DNA to RNA)
26 Transcription produces RNA complementary to one strand of DNA Figure 6-7 Molecular Biology of the Cell ( Garland Science 2008)
27 All of the RNA in a cell is made by transcription. Transcription begins with the opening and unwinding of a small portion of the DNA double helix. One of the two strands of the DNA acts as a template for the synthesis of RNA. Transcript : the RNA chain produced by transcription, which is elongated one nucleotide exactly complementary to the strand of DNA used as a template.
28 Transcription vs DNA replication Does not remain hydrogen-bonded to the template. The RNA chain is displaced. DNA helix re-forms. Only one strand of the DNA is transcribed. mrnas are much shorter than DNA. Human chromosome, 250 million nucleotide pairs (for the largest chromosome, Chromosome 1) RNAs, a few thousand.
29 Figure 6-8a Molecular Biology of the Cell ( Garland Science 2008) RNA polymerase
30 Figure 6-8b Molecular Biology of the Cell ( Garland Science 2008) 30
31 RNA polymerase (vs. DNA polymerase). Immediate release of the mrna as it is synthesized. Many RNA copies can be made in a short time. Simultaneously transcribing. The synthesis of next RNA is usually started before the first RNA has been completed. Speed: 30 bp/s (cf. DNA synthesis: 100 bp/s) A medium-sized gene (1.5 kb) requires about 50 s.
32 Simultaneously transcribing 32 Figure 6-9 Molecular Biology of the Cell ( Garland Science 2008)
33 RNA polymerase vs DNA polymerase Ribonucleotides not deoxyribonucleotides. No primer needed. Need not be as accurate as DNA replication. RNA is not used as the permanent storage form of genetic information, so mistakes in transcription have relatively minor consequences. Mistake rate: 1 error / 10 4 nt (cf. 1 error / 10 7~9 nt by DNA polymerase).
34 Several types of RNA are produced in cells mrna copied from genes, direct the synthesis of proteins
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36 Figure 6-10 Molecular Biology of the Cell ( Garland Science 2008) 36
37 mrna in euk vs. prok In eucaryotes Each mrna typically carries information transcribed from just one gene, coding for a single protein. In bacteria A set of adjacent genes is often transcribed as a single mrna that therefore carries the information for several different proteins (see Operon).
38 Non-mRNAs like proteins, serve as structural and enzymatic components of cells, and play key parts translating the genetic message into protein. 1. rrna : ribosomal RNA forms the core of the ribosomes, on which mrna is translated into protein. 2. trna : transfer RNA forms the adaptors that select amino acids. 3. small RNAs : used in pre-mrna splicing, regulation of gene expression, transport of proteins to the ER, etc.
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40 Signals in DNA tell RNA polymerase where to start and finish The initiation of transcription is an especially critical process because it is the main point at which the cell can select which proteins or RNAs are to be produced and at what rate.
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42 Promoter (start signal) The specific DNA sequences (starting point) for RNA synthesis. RNA polymerase latches tightly onto the a promoter. RNA polymerase opens up the promoter immediately. One of the DNA strands acts as a template. Chain elongation then continues until the enzyme encounters a second signal, terminator. Terminator (stop signal) Polymerase halts and releases both the DNA template and the newly made RNA chain.
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45 Sigma (σ) factor A subunit of bacterial polymerase. Is responsible for recognizing the promoter sequence. Once the polymerase has latched onto the promoter and synthesized about 10 nt of RNA, sigma factor is released. Releasing enables the polymerase to move forward. The polymerase reassociates with a free sigma factor after termination. The polymerase (+ σ factor) searches for a promoter, where it can begin the process of transcription again.
46 Figure 6-11 Molecular Biology of the Cell ( Garland Science 2008) 46
47 Figure 6-11 (part 1 of 7) Molecular Biology of the Cell ( Garland Science 2008) 47
48 Figure 6-11 (part 2 of 7) Molecular Biology of the Cell ( Garland Science 2008) 48
49 Figure 6-11 (part 3 of 7) Molecular Biology of the Cell ( Garland Science 2008) 49
50 Figure 6-11 (part 4 of 7) Molecular Biology of the Cell ( Garland Science 2008) 50
51 Figure 6-11 (part 5 of 7) Molecular Biology of the Cell ( Garland Science 2008) 51
52 Figure 6-11 (part 6 of 7) Molecular Biology of the Cell ( Garland Science 2008) 52
53 Figure 6-11 (part 7 of 7) Molecular Biology of the Cell ( Garland Science 2008) 53
54 Figure 6-12a Molecular Biology of the Cell ( Garland Science 2008) 54
55 Figure 6-12b Molecular Biology of the Cell ( Garland Science 2008) 55
56 RNA polymerase II
57 Because DNA is double-stranded, two different RNA molecules could in principle be transcribed from any gene, using each of the two DNA. Is it true?
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60 The promoter is asymmetrical and binds the polymerase in only one direction. RNA polymerase transcribes only one DNA strand in the 5 -to-3 direction. Only a portion of DNA can be transcribed only if it is preceded by a promoter sequence. In bacteria, genes tend to lie very close to one another. In humans, individual genes are widely dispersed, with stretches of DNA up to 100,000 nt long between one gene and the next.
61 Figure 6-14 Molecular Biology of the Cell ( Garland Science 2008) 61
62 Initiation of eukaryotic gene transcription is a complex process Polymerase II also requires activator, mediator, and chromatin modifying proteins
63 Eucaryotic vs Bacterial in transcription initiation 1. RNA polymerase 3 RNA polymerases (cf. single bacterial polymerase)
64 Table 6-2 Molecular Biology of the Cell ( Garland Science 2008) 64
65 Figure 6-15 Molecular Biology of the Cell ( Garland Science 2008) 65
66 2. Accessory proteins Require the assistance of a large set of accessory proteins (cf. bacterial polymerase initiate transcription on its own). General transcription factors, Co-activators ( ) and so on. 3. Elaborate control mechanism Chapter Nucleosome structure Chapter 4,
67 Eukaryotic RNA polymerase requires general transcription factors Purified eucaryotic RNA polymerase II could not on its own initiate transcription in vitro.
68 Figure 6-16 Molecular Biology of the Cell ( Garland Science 2008) 68
69 Figure 6-16 (part 1 of 3) Molecular Biology of the Cell ( Garland Science 2008) 69
70 Figure 6-16 (part 2 of 3) Molecular Biology of the Cell ( Garland Science 2008) 70
71 Figure 6-16 (part 3 of 3) Molecular Biology of the Cell ( Garland Science 2008) 71
72 Table 6-3 Molecular Biology of the Cell ( Garland Science 2008) 72
73 Figure 6-17 Molecular Biology of the Cell ( Garland Science 2008) 73
74 Figure 6-18 Molecular Biology of the Cell ( Garland Science 2008) 74
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76 General [Basal] transcription factors (TFIIA), TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. Assemble on the promoter. Assembly begins with TFIID binding to TATA box. Upon binding, TFIID causes a local distortion (landmark for the subsequent assembly of others). About 25 nt upstream from transcription start site. The actual order of assembly differs in the cell. Position the RNA polymerase (PIC, Preinitiation complex) Pull apart the double helix (Helicase activity by TFIIH). Launch the RNA polymerase.
77 TFIIH Helicase activity After RNA polymerse II has been tethered to the promoter, it must be released to begin the synthesis of mrna. Contains a protein kinase enzyme as a subunit. Phosphorylates the tail of RNA polymerase (C-terminal domain (CTD), Serine 5 of the CTD of RNApII). Phosphorylation of the CTD help the polymerase disengage from the cluster of transcription factors.
78 ?? The synchronized code of the histones and the CTD in regulating gene transcription ( : + CTD )
79 Phosphorylation of RNA polymerase II Transcribing polymerase : massively phosphorylated. Transcription finished by polymerase: phosphatases strip off the phosphates. Unphosphorylated polymerase: recruited to and initiate RNA synthesis at a promoter.
80 Figure 6-19 Molecular Biology of the Cell ( Garland Science 2008) 80
81 Figure 6-20a Molecular Biology of the Cell ( Garland Science 2008) 81
82 Figure 6-20b Molecular Biology of the Cell ( Garland Science 2008) 82
83 Figure 6-20c Molecular Biology of the Cell ( Garland Science 2008) 83
84 RNA processing ( RNA processing transcription coupling co-transcriptional process )
85 Figure 6-21 Molecular Biology of the Cell ( Garland Science 2008) 85
86 Eucaryotic RNAs are transcribed and processed simultaneously in the nucleus Bacterial vs eucaryotic system As mrnas transcribed, ribosomes immediately attach to the free 5 end of the RNA transcript and protein synthesis starts.
87 Figure 6-21a Molecular Biology of the Cell ( Garland Science 2008) 87
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89 The functions of two major mrna processing modifications. 1. Increase the stability of the mrna. 2. Aid its export from the nucleus to the cytoplasm. 3. Identify the RNA molecules as an mrna. 4. Indication by the protein synthesis machinery that both ends of the mrna are present and that the message is therefore complete. 5. Quality control of the RNA
90 Porrua, O. & Libri, D. RNA quality control in the nucleus: The Angels' share of RNA. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1829, (2013).
91 1. Bacterial system DNA lies directly exposed to the cytoplasm, which contains the ribosomes on which protein synthesis takes place. 2. Eucaryotic system DNA is enclosed within the nucleus. Transcription takes place in the nucleus, but protein synthesis takes place on ribosomes in the cytoplasm. So, before a eucaryotic mrna can be translated, it must be transported out of the nucleus and it must go through several different mrna processing steps.
92 1. 5 RNA capping Modification of the 5 end of the mrna transcript. Addition of G with a methyl group (7-methylguanosine). Occurs after the RNA pol II has produced about 25 nt of RNA. 2. Splicing 3. 3 Polyadenylation
93 Figure 6-22a Molecular Biology of the Cell ( Garland Science 2008) 93
94 Figure 6-22b Molecular Biology of the Cell ( Garland Science 2008) 94
95 3. 3 Polyadenylation 3 end of eucaryotic mrnas are first trimmed by an enzyme that cuts the RNA chain (mrna cleavage factors). Addition of a series of repeated A (a poly-a tail) onto the cut end (poly(a) factors + poly(a) polymerase). Generally a few hundred nucleotides long.
96 1. 5 RNA capping Modification of the 5 end of the mrna transcript. Addition of G with a methyl group (7-methylguanosine). Occurs after the RNA pol II has produced about 25 nt of RNA. 2. Splicing 3. 3 Polyadenylation
97 mrna (Transcription) : Transcript Initiation Elongation Termination (Processing) : RNA Capping Splicing Poly(A) Coupled or Connected
98 Cotranscriptional Regulation 98 Figure 6-23 Molecular Biology of the Cell ( Garland Science 2008)
99 Figure 6-24 Molecular Biology of the Cell ( Garland Science 2008) 99
100 Cotranscriptional Regulation mrna processing steps are tightly coupled to transcription. They take place as the RNA is being transcribed. Key enzymes : RNA polymerase II C-terminal domain (CTD : repeats of YSPTSPS ) The recruitment of mrna processing factors are depend on the phosphorylation of CTD residues Two major mrna processing steps; 1. RNA capping 2. Polyadenylation (poly(a)) *Others include mrna Splicing, mrna export, mrna surveillance, mrna packaging, and mrna cleavage, etc.
101 RNA-processing enzymes generates the 3 end of eucaryotic mrnas 5 capping enzymes of mrna recruitment (S-5-P of CTD) Spliceosome recruitment (S-2, or 5-P of CTD) 3 end processing enzymes of mrna (S-2-P of CTD) CstF (cleavage stimulation factor F) CPSF (cleavage and polyadenylation specificity factor) Poly-A polymerase: Add app. 200 A nucleotide. Poly-A binding proteins: Assemble onto the poly-a tail.
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103 Figure 6-38 Molecular Biology of the Cell ( Garland Science 2008) 103
104 Figure 6-38 (part 1 of 3) Molecular Biology of the Cell ( Garland Science 2008) 104
105 Figure 6-38 (part 2 of 3) Molecular Biology of the Cell ( Garland Science 2008) 105
106 Figure 6-38 (part 3 of 3) Molecular Biology of the Cell ( Garland Science 2008) 106
107 Buratowski, S. (2005). Connections between mrna 3' end processing and transcription termination. Current Opinion in Cell Biology, 17(3),
108 mrna (Transcription) : Transcript Initiation Elongation Termination (Processing) : RNA Capping Splicing Poly(A) Coupled or Connected
109 RNA splicing Splicing: Intron sequences are removed from the newly synthesized RNA and the exons are stitched together. Once a transcript has been spliced and its 5 end 3 ends have been modified, the RNA is a functional mrna., RNA splicing? small nuclear ribonucleoproteins (snrnps, [snurps])
110 Bacterial system: no Introns. Eucaryotic system: coding sequences are interrupted by noncoding sequences (introns). * Exon: expressed sequences, shorter than the introns. * The existence intron + exon found only in 1977.
111 Figure 6-25 Molecular Biology of the Cell ( Garland Science 2008) 111
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113 How does the cell determine which part of the primary transcript to remove during splicing? R: stands for either A or G Y: stands for either C or U N: stands for one of A, U, G, or C Special nucleotide sequences signal the beginning and the end of an intron. Act as cues for its removal. Found at or near each end of the intron.
114 RNA (ribonucleic acid)
115 Figure 6-26a Molecular Biology of the Cell ( Garland Science 2008) 115
116 Figure 6-26b Molecular Biology of the Cell ( Garland Science 2008) 116
117 3 steps 1 st step: Adenine nucleotide (A) in the intron attacks the 5 splice site. 2 nd step: Cuts the sugar-phosphate backbone of the RNA at this point. The cut 5 end of the intron becomes covalently linked to the A to form a branch structure. 3 rd step: The free 3 -OH end of the exon sequence then reacts with the start of the next exon, joining the two exons together and releasing the intron in the form of lariat. * The lariat containing the intron is eventually degraded.
118 Figure 6-27 Molecular Biology of the Cell ( Garland Science 2008) 118
119 Figure 6-28 Molecular Biology of the Cell ( Garland Science 2008) 119
120 Splicing is carried out largely by RNA molecules (small nuclear RNAs, snrnas). Recognized by small nuclear ribonucleoproteins (snrnps, [snurps]),
121 U2, U5, and U6 snrnps
122 snrnp Recognize and pair with the nucleotide sequences that mark the beginning and the branch point of each intron. Form the core of the spliceosome protein molecules that performs RNA splicing in the cells., the large assembly of RNA and RNA splicing process by spliceosome. A group of spliceosome components, is called the SR proteins (they contain a domain rich in serine and arginines)
123 Figure 6-30a Molecular Biology of the Cell ( Garland Science 2008)
124 Figure 6-30b Molecular Biology of the Cell ( Garland Science 2008)
125 Figure 6-30c Molecular Biology of the Cell ( Garland Science 2008)
126 Figure 6-31 Molecular Biology of the Cell ( Garland Science 2008) 126
127 Figure 6-32a Molecular Biology of the Cell ( Garland Science 2008) 127
128 Figure 6-32b Molecular Biology of the Cell ( Garland Science 2008) 128
129 Figure 6-33 Molecular Biology of the Cell ( Garland Science 2008) 129
130 Figure 6-34a Molecular Biology of the Cell ( Garland Science 2008) 130
131 Figure 6-34b Molecular Biology of the Cell ( Garland Science 2008) 131
132 Figure 6-35 Molecular Biology of the Cell ( Garland Science 2008) 132
133 Figure 6-36 Molecular Biology of the Cell ( Garland Science 2008) 133
134 Figure 6-37 Molecular Biology of the Cell ( Garland Science 2008) 134
135 The earliest cells may have had introns in their genes Argument for intron Early cells contained introns? Procaryotes would have been able to reproduce more rapidly and efficiently by shedding introns and adopting a smaller, more streamlined genome. Simple eucaryotes (e.g. yeast) have relatively few introns and introns are much shorter. Introns were originally parasitic mobile genetic elements?
136 Mature Eucaryotic mrnas are selectively exported from the nucleus Of the total mrna that is synthesized, only a small fraction is useful to the cell. The remaining RNA fragments excised introns, broken RNAs, and aberrantly spliced transcripts are not only useless but also could be dangerous to the cell. Degraded by Quality Control System: Exosomecontaining complexes., mrna?
137 How does the cell distinguish between the relatively rare mature mrna molecules it needs to keep and the overwhelming amount of debris generated by RNA processing? *EJC: exon junction complex **hnrnp: Heterogeneous nuclear ribonucleoproteins
138 Figure 6-39b Molecular Biology of the Cell ( Garland Science 2008) 138
139 mrna export is highly selective, as it is closely coupled to correct RNA processing and transcription. The coupling is achieved by nuclear pore complex (NPC), which recognise and transport only completed mrnas. To be export ready, it seems that an mrna molecule must be bound to set of RNA binding proteins (including poly(a)- binding protein, a cap-binding complex, proteins that mark completed RNA splices, and a nuclear transport receptor). The entire set of bound proteins ultimately determines whether an RNA molecule will leave the nucleus. The RNAs that remain behind in the nucleus are degraded, and are reused for transcription.
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141 Figure 6-41 Molecular Biology of the Cell ( Garland Science 2008) 141
142 Figure 6-42 Molecular Biology of the Cell ( Garland Science 2008) 142
143 Figure 6-43 Molecular Biology of the Cell ( Garland Science 2008) 143
144 Figure 6-43a Molecular Biology of the Cell ( Garland Science 2008) 144
145 Figure 6-43b Molecular Biology of the Cell ( Garland Science 2008) 145
146 Figure 6-44 Molecular Biology of the Cell ( Garland Science 2008) 146
147 Figure 6-44a Molecular Biology of the Cell ( Garland Science 2008) 147
148 Figure 6-44b Molecular Biology of the Cell ( Garland Science 2008) 148
149 Figure 6-45 Molecular Biology of the Cell ( Garland Science 2008) 149
150 Figure 6-46 Molecular Biology of the Cell ( Garland Science 2008) 150
151 Figure 6-47 Molecular Biology of the Cell ( Garland Science 2008) 151
152 Figure 6-48 Molecular Biology of the Cell ( Garland Science 2008) 152
153 Figure 6-49 Molecular Biology of the Cell ( Garland Science 2008) 153
154 mrna molecules are eventually degraded by the cell The length of time that a mature mrna molecule persists in the cell affects the amount of protein. Different lifetimes of mrna are in part controlled by nucleotide sequences in 3 UTR Lifetime (mrnas in bacteria) = 3 minutes Lifetime (β-globin gene in human) = 10 hours Stability of mrna vs. needs of the cell
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![Translation ( [ ];](/docs-images/82/85085754/images/156-0.jpg "from RNA to")
156 Translation ( [ ]; from RNA to Protein)
157 topic 1. trna 2. Wobble base paring 3. Aminoacyl-tRNA synthetase 4. Ribosome 5. Translation cycles
158 Coding Problem How is the information in a linear sequence of nucleotide in RNA translated into the linear sequence of a chemically quite different set of subunits the amino acids in proteins? Genetic Code
159 An mrna sequence is decoded in sets of three nucleotides 4 different nucleotides Genetic Code 20 different types of amino acids Figure 6-50 Molecular Biology of the Cell ( Garland Science 2008)
160 Genetic code The rules by which the n.t. sequence of a gene is translated into the a.a. sequence of a protein. AUG - initiation codon that specifies methionine. Codon Three consecutive nucleotides in RNA that specifies one a.a. Universal in all present-day organisms. Reading Frames An RNA sequence can be translated in any one of three different, nonoverlapping frames. Only one of three possible reading frames encodes the required protein.
161 Figure 6-51 Molecular Biology of the Cell ( Garland Science 2008) 161
162 trna molecules match amino acids to codons in mrna The codons in an mrna do not directly recognize the amino acids they specify. Then, how does the translation proceed from mrna to protein? trnas (transfer RNAs)
163 Ψ : pseudouridine (derived from U) D : dihydrouridine(derived from U) 163 Figure 6-52 Molecular Biology of the Cell ( Garland Science 2008)
164 Figure 6-52a Molecular Biology of the Cell ( Garland Science 2008) 164
165 Figure 6-52b,c Molecular Biology of the Cell ( Garland Science 2008) 165
166 Figure 6-52d Molecular Biology of the Cell ( Garland Science 2008) 166
167 trnas (transfer RNAs) small RNAs (about 80 nt). Adaptors Recognize / bind both to the codon and to the a.a. Cloverleaf, L-shaped structure Four short segments, folded, double-helical and held together by hydrogen bonds. Anticodon : 3 consecutive nt that pairs with the codon. Amino acid at 3 end : a.a. that matches the codon is attached.
168 trnas are covalently modified before they exit from the nucleus trnas synthesized by RNA polymerase III are covalently modified. Porrua, O. & Libri, D. RNA quality control in the nucleus: The Angels' share of RNA. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1829, (2013).
169 A few of the unusual nucleotide found in trna (10% are modified)
170 A. Trimming and Splicing Precursor trnas are synthesized. Trimmed to produce mature trna. Some trna precursors must be spliced out. Quality-control steps in the generation of trnas. B. Covalent Modification Near 1/10 nt is altered. Over 50 different types of trna modifications. Inosine (deamination of guanosine): affect the conformation and base-pairing of anticodon and facilitate the recognition of the appropriate mrna codon by the trna. Others affect the accuracy with which the trna is attached to the correct amino acid.
171 topic 1. trna 2. Wobble base paring 3. Aminoacyl-tRNA synthetase 4. Ribosome 5. Translation cycles
172 Genetic redundancy and Wobble base pairing The genetic code is redundant; that is, several different codoens can specify a single amino acid. What does this genetic redundancy imply and what is the possible explanations of the redundancy in translation process?
173 genetic redundancy Two possibilities; 20 amino acids, 61 codons and 31 trna Some amino acids have more than one trna. Some trnas can base-pair with more than one codon.
174 Wobble base pairing Some trnas require accurate base-pairing only at the first two positions of the codon and can tolerate a mismatch (or wobble) at the third position. Explains why so many of the alternative codons for an amino acid differ only in their third nucleotide. Make it possible to fit the 20 amino acids to their 61 codons with as few as 31 kinds trna molecules (In bacteria).
175 Figure 6-53 Molecular Biology of the Cell ( Garland Science 2008) 175
176 Figure 6-54 Molecular Biology of the Cell ( Garland Science 2008) 176
177 topic 1. trna 2. Wobble base paring 3. Aminoacyl-tRNA synthetase 4. Ribosome 5. Translation cycles
178 Specific enzymes couple trnas to the correct amino acid Aminoacyl-tRNA synthetase Covalently couples each amino acid to its appropriate set of trna. 20 synthetases in all. Attaches the amino acid to the 3 end of the trna. Specific nucleotides in both anticodon and the amino-acidaccepting arm - allow the correct trna to be recognized by the synthetase.
179 Figure 6-55 Molecular Biology of the Cell ( Garland Science 2008) 179
180 Figure 6-56 Molecular Biology of the Cell ( Garland Science 2008) 180
181 Figure 6-57 Molecular Biology of the Cell ( Garland Science 2008) 181
182 Figure 6-58 Molecular Biology of the Cell ( Garland Science 2008) 182
183 Figure 6-57 Molecular Biology of the Cell ( Garland Science 2008)
184 Figure 6-59 Molecular Biology of the Cell ( Garland Science 2008) 184
185 Figure 6-59a Molecular Biology of the Cell ( Garland Science 2008) 185
186 Figure 6-59b Molecular Biology of the Cell ( Garland Science 2008) 186
187 Figure 6-60 Molecular Biology of the Cell ( Garland Science 2008) 187
188 topic 1. trna 2. Wobble base paring 3. Aminoacyl-tRNA synthetase 4. Ribosome 5. Translation cycles
189 The RNA message is decoded on Ribosome 189 Figure 6-62 Molecular Biology of the Cell ( Garland Science 2008)
190 Figure 6-61 Molecular Biology of the Cell ( Garland Science 2008) 190
191 Ribosome Protein manufacturing machine. Travels along the mrna chain. Captures complementary trna. Covalently links the amino acid. Ribosomal proteins + ribosomal RNAs (rrnas) Cell contains millions of ribosomes in its cytoplasm (Free in cytosol + attached to rer).
192 Unique banding patterns allow the identification of each human chromosome To stain the chromosomes with dyes that bind to certain types of DNA sequences. These dyes mainly distinguish between DNA that is rich in A-T nucleotide pairs and DNA that is G-C rich, and they produce a striking and reliable pattern of bands along each chromosome. Giemsa stain: produce dark bands in AT rich region. Text p180, Fig 5-11 legend
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195 A large complex of 4 RNAs and more than 80 proteins. One large and one small subunits. Small subunit: matches the trna to the codons. Large subunit: catalyzes the formation of the peptide bonds. Remarkable efficiency In eucaryote, add 2 a.a. /s to a polypeptide chain. In bacterial, 20 a.a. /s.
196 rrnas are cleaved and covalently modified before they exit from the nucleus Porrua, O. & Libri, D. RNA quality control in the nucleus: The Angels' share of RNA. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1829, (2013).
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198 Srivastava, Rakesh, Srivastava, R., & Ahn, S. H. (2016). The Epigenetic Pathways to Ribosomal DNA Silencing. Microbiology and Molecular Biology Reviews : MMBR, 80(3), doi.org/ /mmbr
199 topic 1. trna 2. Wobble base paring 3. Aminoacyl-tRNA synthetase 4. Ribosome 5. Translation cycles
200 mrna binding site and three binding sites for trna (A-site, P-site, E-site)
201 Figure 6-65 Molecular Biology of the Cell ( Garland Science 2008) 201
202 Figure 6-66 Molecular Biology of the Cell ( Garland Science 2008) 202
203 Figure 6-66 (part 1 of 4) Molecular Biology of the Cell ( Garland Science 2008) 203
204 Figure 6-66 (part 2 of 4) Molecular Biology of the Cell ( Garland Science 2008) 204
205 Figure 6-66 (part 3 of 4) Molecular Biology of the Cell ( Garland Science 2008) 205
206 Figure 6-66 (part 4 of 4) Molecular Biology of the Cell ( Garland Science 2008) 206
207 Figure 6-67 Molecular Biology of the Cell ( Garland Science 2008) 207
208 Figure 6-67 (part 1 of 7) Molecular Biology of the Cell ( Garland Science 2008) 208
209 Figure 6-67 (part 2 of 7) Molecular Biology of the Cell ( Garland Science 2008) 209
210 Figure 6-67 (part 3 of 7) Molecular Biology of the Cell ( Garland Science 2008) 210
211 Figure 6-67 (part 4 of 7) Molecular Biology of the Cell ( Garland Science 2008) 211
212 Figure 6-67 (part 5 of 7) Molecular Biology of the Cell ( Garland Science 2008) 212
213 Figure 6-67 (part 6 of 7) Molecular Biology of the Cell ( Garland Science 2008) 213
214 Figure 6-67 (part 7 of 7) Molecular Biology of the Cell ( Garland Science 2008) 214
215 Figure 6-68 Molecular Biology of the Cell ( Garland Science 2008) 215
216 Figure 6-69a Molecular Biology of the Cell ( Garland Science 2008) 216
217 Figure 6-69b Molecular Biology of the Cell ( Garland Science 2008) 217
218 Figure 6-70 Molecular Biology of the Cell ( Garland Science 2008) 218
219 Figure 6-71 Molecular Biology of the Cell ( Garland Science 2008) 219
220 Cycles of translation Step 1: The appropriated charged trna enters the A-site by base-paring with the codon on the mrna Step 2: Its amino acid is then linked to the peptide chain held by the trna in the P-site. Step 3: Ribosome shifts, and the spent trna is moved to the E-site
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222 Alberts Johnson Lewis Raff Roberts Walter Molecular Biology of the Cell Fifth Edition Chapter 6 How Cells Read the Genome: From DNA to Protein Copyright Garland Science 2008
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224 Codons in mrna signal where to start and to stop protein synthesis Figure 6-72 Molecular Biology of the Cell ( Garland Science 2008)
225 Eucaryotic initiation factors (eifs) Only the methionine-charged initiator trna is capable of tightly binding to P-site of the small ribosome subunit without the complete ribosome present. Loaded ribosomal small subunit binds to the 5 end of an mrna (signaled by the cap of mrna). Then, it moves forward searching for the first AUG. When this AUG is encountered, eifs dissociate. Large ribosomal subunit assembles and completes the ribosome. eif-2; eif-4e (which directly binds the cap); eif-4g.
226 Figure 6-72 (part 1 of 5) Molecular Biology of the Cell ( Garland Science 2008) 226
227 Figure 6-72 (part 2 of 5) Molecular Biology of the Cell ( Garland Science 2008) 227
228 Figure 6-72 (part 3 of 5) Molecular Biology of the Cell ( Garland Science 2008) 228
229 Figure 6-72 (part 4 of 5) Molecular Biology of the Cell ( Garland Science 2008) 229
230 Figure 6-72 (part 5 of 5) Molecular Biology of the Cell ( Garland Science 2008) 230
231
232 Figure 6-75 Molecular Biology of the Cell ( Garland Science 2008) 232
233 Initiation of translation Begins with AUG codon. It sets the reading frame for the whole message. The last point whether the mrna is to be translated. Initiator trna always carries methionine. Distinct from the trna that normally carries methionine. This methionine is usually removed later by a specific protease. Translation initiation factors.
234 Bacterial initiation Polycistronic
235 Bacterial initiation No 5 caps of mrna. Specific ribosome-binding sequences. Up to 6 nucleotides long. Located a few nucleotides upstream of the AUGs. A procaryotic ribosome binds directly to a start codon. Polycistronic Procaryotic mrna encode several different proteins. Each is translated from the same mrna molecule.
236
237
238 Termination of translation Stop codons (UAA, UAG, or UGA). Not recognized by a trna. Do not specify amino acid. Signal to the ribosome to stop translation. Releasing factors Bind to any stop codon. Alters the activity of the peptidyl transferase. Catalyze the addition of a water instead of an a.a. Completed protein chain is immediately released.
239 Transcription: Simultaneously transcribing Translation: Multiple initiation (Polysome)
240 Proteins are made on polyribosomes 240 Figure 6-76 Molecular Biology of the Cell ( Garland Science 2008)
241 Polyribosome
242 Multiple initiations Protein synthesis takes between 20 s and several min. But, multiple initiations usually take place. Polyribosomes (or polysomes): large cytoplasmic assemblies made up of several ribosomes (Spaced as close as 80 nucleotides apart). Many more protein molecules can be made in a given time Bacteria and eucaryotes.
243 Figure 6-77 Molecular Biology of the Cell ( Garland Science 2008) 243
244 Figure 6-77 (part 1 of 2) Molecular Biology of the Cell ( Garland Science 2008) 244
245 Figure 6-77 (part 2 of 2) Molecular Biology of the Cell ( Garland Science 2008) 245
246 Figure 6-78 Molecular Biology of the Cell ( Garland Science 2008) 246
247 Figure 6-79 Molecular Biology of the Cell ( Garland Science 2008) 247
248 Table 6-4 Molecular Biology of the Cell ( Garland Science 2008) 248
249 Figure 6-80 Molecular Biology of the Cell ( Garland Science 2008) 249
250 Figure 6-81 Molecular Biology of the Cell ( Garland Science 2008) 250
251 Figure 6-81 (part 1 of 3) Molecular Biology of the Cell ( Garland Science 2008) 251
252 Figure 6-81 (part 2 of 3) Molecular Biology of the Cell ( Garland Science 2008) 252
253 Figure 6-81 (part 3 of 3) Molecular Biology of the Cell ( Garland Science 2008) 253
254 Figure 6-82 Molecular Biology of the Cell ( Garland Science 2008) 254
255 Figure 6-83 Molecular Biology of the Cell ( Garland Science 2008) 255
256 Figure 6-84 Molecular Biology of the Cell ( Garland Science 2008) 256
257 Figure 6-85 Molecular Biology of the Cell ( Garland Science 2008) 257
258 Figure 6-86 Molecular Biology of the Cell ( Garland Science 2008) 258
259 Figure 6-87 Molecular Biology of the Cell ( Garland Science 2008) 259
260 Figure 6-87a Molecular Biology of the Cell ( Garland Science 2008) 260
261 Figure 6-87b Molecular Biology of the Cell ( Garland Science 2008) 261
262 Inhibitors of procaryotic protein synthesis are used as antibiotics Translation processes are very similar among organisms. Some subtle differences!! The basis of one of the most important advances in modern medicine.
263 proteolysis: Carefully controlled protein breakdown helps regulate the amount of each protein in a cell The number of copies of a protein : how quickly new proteins are made, how long they survive. Life-span of protein; Structural protein: last for months or years. Other proteins : last only days, hours, or even seconds.
264 Figure 6-88 Molecular Biology of the Cell ( Garland Science 2008) 264
265 Proteasome Large complexes of proteolytic enzymes. Contains a central cylinder. The proteases chop the protein into short proteins. 265 Figure 6-89 Molecular Biology of the Cell ( Garland Science 2008)
266 Figure 6-90 Molecular Biology of the Cell ( Garland Science 2008) 266
267 Figure 6-91a Molecular Biology of the Cell ( Garland Science 2008) 267
268 Figure 6-91b Molecular Biology of the Cell ( Garland Science 2008) 268
269 Proteolysis: enzymatically break proteins down into their amino acids. Proteases: degrade proteins, first to short peptides and finally to individual amino acids. The importance of eliminating improperly folded proteins Neurodegenerative disorders ( ) such as Huntington s, Alzheimer s and Creutzfeldt-Jacob diseases are caused by the aggregation of misfolded proteins. These proteins aggregates can severely damage cells and tissues and even trigger cell death.
270 An elaborating ubiquitin-conjugating system marks proteins for destruction. Ubiquitin, a small protein, contains 76 a. a. Figure 6-92a Molecular Biology of the Cell ( Garland Science 2008)
271 The C-terminus of ubiquitin is initially activated through its high-energy thioester linkage to a cystein side chain on the E1. E1 (Ubiquitin-activating enzyme) E2 (Ubiquitin-conjugase) E3 (Ubiquitin-ligase)
272 Roughly 300 distinct E2-E3 complexes
273
274 Figure 6-94a Molecular Biology of the Cell ( Garland Science 2008) 274
275 Figure 6-94b Molecular Biology of the Cell ( Garland Science 2008) 275
276 Figure 6-95a,b Molecular Biology of the Cell ( Garland Science 2008) 276
277 Figure 6-95c Molecular Biology of the Cell ( Garland Science 2008) 277
278 Figure 6-95d Molecular Biology of the Cell ( Garland Science 2008) 278
279 Figure 6-96 Molecular Biology of the Cell ( Garland Science 2008) 279
280 There are many steps between DNA and proteins The final concentration of a protein Depends on the efficiency with which each of the many steps is carried out.
281 Figure 6-97 Molecular Biology of the Cell ( Garland Science 2008) 281
282
283 More than 100 different covalent modifications of proteins
284 RNA and the origins of life Interdependent components (Genes & Proteins) Nucleic acids are required to direct the synthesis of proteins. Proteins are required to synthesize nucleic acids.
285 RNA serves as an intermediate between genes and proteins. RNA catalyst, including the ribosome and RNA-splicing machinery, is molecular fossils of an earlier world? Figure 6-98 Molecular Biology of the Cell ( Garland Science 2008)
286 Life requires autocatalysis The origin of life requires molecules that possess the special way to self-produce more molecules. Proteins cannot reproduce itself directly.
287 RNA can both store information and catalyze chemical reaction An RNA molecule can in principle guide the information of an exact copy of itself. Catalysts (e.g. peptidyl transferase). Unique folded shapes, can serve as enzymes (ribozyme). Ribozymes constructed in the lab (Table 7-4). All the properties required to catalyze its own synthesis.
288 Figure 6-99 Molecular Biology of the Cell ( Garland Science 2008) 288
289 Figure Molecular Biology of the Cell ( Garland Science 2008) 289
290 Figure Molecular Biology of the Cell ( Garland Science 2008) 290
291 Figure Molecular Biology of the Cell ( Garland Science 2008) 291
292 Figure Molecular Biology of the Cell ( Garland Science 2008) 292
293 Figure (part 1 of 3) Molecular Biology of the Cell ( Garland Science 2008) 293
294 Figure (part 2 of 3) Molecular Biology of the Cell ( Garland Science 2008) 294
295 Figure (part 3 of 3) Molecular Biology of the Cell ( Garland Science 2008) 295
296 Figure Molecular Biology of the Cell ( Garland Science 2008) 296
297 Figure (part 1 of 2) Molecular Biology of the Cell ( Garland Science 2008) 297
298 Figure (part 2 of 2) Molecular Biology of the Cell ( Garland Science 2008) 298
299 RNA is thought to predate DNA in evolution Ribose is readily formed form formaldehyde (HCHO). Deoxyribose is harder to make (produced from ribose catalyzed by a protein enzyme). Ribose presumably predates deoxyribose. DNA uses thymine rather than uracil. The double-helical structure. Stability: damaged nucleotides can be repaired by using the other strand as a template. Deamination is easier to detect and repair in DNA (deamination of cytosine is uracil).
300 Eventually DNA took over the primary genetic function, and proteins became the major catalysts, while RNA remained as the intermediary connecting the two.
301 Table 6-5 Molecular Biology of the Cell ( Garland Science 2008) 301
302 Figure Molecular Biology of the Cell ( Garland Science 2008) 302
303 Figure Molecular Biology of the Cell ( Garland Science 2008) 303
304 Figure Molecular Biology of the Cell ( Garland Science 2008) 304
305 Figure Molecular Biology of the Cell ( Garland Science 2008) 305
306 Figure Molecular Biology of the Cell ( Garland Science 2008) 306
307 Figure Molecular Biology of the Cell ( Garland Science 2008) 307
308 Figure 6-110(part 1 of 3) Molecular Biology of the Cell ( Garland Science 2008) 308
309 Figure (part 2 of 3) Molecular Biology of the Cell ( Garland Science 2008) 309
310 Figure (part 3 of 3) Molecular Biology of the Cell ( Garland Science 2008) 310
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Bio 119 Bacterial Genomics 6/26/10
BACTERIAL GENOMICS Reading in BOM-12: Sec. 11.1 Genetic Map of the E. coli Chromosome p. 279 Sec. 13.2 Prokaryotic Genomes: Sizes and ORF Contents p. 344 Sec. 13.3 Prokaryotic Genomes: Bioinformatic Analysis
Name Period The Control of Gene Expression in Prokaryotes Notes
Bacterial DNA contains genes that encode for many different proteins (enzymes) so that many processes have the ability to occur -not all processes are carried out at any one time -what allows expression
Lesson Overview. Gene Regulation and Expression. Lesson Overview Gene Regulation and Expression
13.4 Gene Regulation and Expression THINK ABOUT IT Think of a library filled with how-to books. Would you ever need to use all of those books at the same time? Of course not. Now picture a tiny bacterium