Chapter 17 From Gene to Protein
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- Jewel Hill
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1 Chapter 17 From Gene to Protein
2 Describe the structure of DNA. What is its elemental makeup? Name the subunit that makes up DNA. What components make up the DNA molecule? How are the two strands related and connected? How are they different?
3 Question? How does DNA control a cell? By controlling Protein Synthesis. Proteins are the link between genotype and phenotype.
4 Archibald Garrod Suggested genes control enzymes that catalyze chemical processes in cells. Inherited Diseases - inborn errors of metabolism where a person can t make an enzyme.
5 Example Alkaptonuria - where urine turns black after exposure to air. Lacks - an enzyme to metabolize alkapton.
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7 George Beadle and Edward Tatum Worked with Neurospora and proved the link between genes and enzymes. Neurospora Pink bread mold
8 Experiment Grew Neurospora on agar. Varied the nutrients. Looked for mutants that failed to grow on minimum agar.
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10 Results Three classes of mutants for Arginine Synthesis. Each mutant had a different block in the Arginine Synthesis pathway.
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12 Conclusion Mutations were abnormal genes. Each gene dictated the synthesis of one enzyme. One Gene - One Enzyme Hypothesis.
13 Current Hypothesis One Gene - One Polypeptide Hypothesis (because of 4 th degree structure).
14 Central Dogma Transcription DNA Translation RNA Polypeptide
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16 Explanation DNA - the Genetic code or genotype. RNA - the message or instructions. Polypeptide - the product for the phenotype.
17 Genetic Code Sequence of DNA bases that describe which Amino Acid to place in what order in a polypeptide. The genetic code gives the primary protein structure.
18 Code Basis If you use: 1 base = 1 amino acid 4 bases = 4 amino acids 4 1 = 4 combinations, which are not enough for 20 AAs.
19 If you use: 2 bases = 1 amino acid Ex AT, TA, CA, GC 4 2 = 16 amino acids Still not enough combinations.
20 If you use: 3 bases = 1AA Ex CAT, AGC, TTT 4 3 = 64 combinations More than enough for 20 amino acids.
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22 Genetic Code Is based on triplets of bases. Has redundancy; some AA's have more than 1 code. Proof - make artificial RNA and see what AAs are used in protein synthesis (early 1960 s).
23 Codon A 3-nucleotide word in the Genetic Code. 64 possible codons known.
24 DNA vs RNA DNA RNA Sugar deoxyribose ribose Bases ATGC AUGC Backbones 2 1 Size very large small Use genetic code varied
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26 Codon Dictionary Start- AUG (Met) Stop- UAA UAG UGA 60 codons for the other 19 AAs.
27 Code Redundancy Third base in a codon shows "wobble. First two bases are the most important in reading the code and giving the correct AA. The third base often doesn t matter.
28 Code Evolution The genetic code is nearly universal. Ex: CCG = proline (all life) Reason - The code must have evolved very early. Life on earth must share a common ancestor.
29 Reading Frame and Frame Shift The reading of the code is every three bases (Reading Frame) Ex: the red cat ate the rat Frame shift improper groupings of the bases Ex: thr edc ata tat her at The words only make sense if read in this grouping of three.
30 Transcription Process of making RNA from a DNA template.
31 Transcription Steps 1. RNA Polymerase Binding 2. Initiation 3. Elongation 4. Termination
32 RNA Polymerase Enzyme for building RNA from RNA nucleotides.
33 Binding Requires that the enzyme find the proper place on the DNA to attach and start transcription.
34 Binding Is a complicated process Uses Promoter Regions on the DNA (upstream from the information for the protein) Requires proteins called Transcription Factors.
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36 TATA Box Short segment of T,A,T,A Located 25 nucleotides upstream for the initiation site. Recognition site for transcription factors to bind to the DNA.
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38 Transcription Factors Proteins that bind to DNA before RNA Polymerase. Recognizes TATA box, attaches, and flags the spot for RNA Polymerase.
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40 Transcription Initiation Complex The complete assembly of transcription factors and RNA Polymerase bound to the promoter area of the DNA to be transcribed.
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42 Initiation Actual unwinding of DNA to start RNA synthesis. Requires Initiation Factors.
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44 Elongation RNA Polymerase untwists DNA 1 turn at a time. Exposes 10 DNA bases for pairing with RNA nucleotides.
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46 Elongation Enzyme moves 5 3. Rate is about 60 nucleotides per second.
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48 Comment Each gene can be read by sequential RNA Polymerases giving several copies of RNA. Result - several copies of the protein can be made.
49 Termination DNA sequence that tells RNA Polymerase to stop. Ex: AATAAA RNA Polymerase detaches from DNA after closing the helix.
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51 Final Product Pre-mRNA This is a raw RNA that will need processing.
52 Modifications of RNA 1. 5 Cap 2. Poly-A Tail 3. Splicing
53 5' Cap Modified Guanine nucleotide added to the 5' end. Protects mrna from digestive enzymes. Recognition sign for ribosome attachment.
54 Poly-A Tail Adenine nucleotides added to the 3' tail Protects mrna from digestive enzymes. Aids in mrna transport from nucleus.
55 Comment The head and tail areas often contain leaders and trailers, areas of RNA that are not read. Similar to leaders or trailers on cassette tapes.
56 RNA Splicing Removal of non-protein coding regions of RNA. Coding regions are then spliced back together.
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58 Introns Intervening sequences. Removed from RNA.
59 Exons Expressed sequences of RNA. Translated into AAs.
60 Spliceosome Cut out Introns and join Exons together. Made of snrna and snrnp.
61 snrna Small Nuclear RNA. 150 nucleotides long. Structural part of spliceosomes.
62 snrnps ("snurps") Small Nuclear Ribonucleoprotiens Made of snrna and proteins. Join with other proteins to form a spliceosome.
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65 Ribozymes RNA molecules that act as enzymes. Are sometimes Intron RNA and cause splicing without a spliceosome.
66 Introns - Function Left-over DNA (?) Way to lengthen genetic message. Old virus inserts (?) Way to create new proteins.
67 Final RNA Transcript
68 If a segment of DNA is 5 -TGA AGA CCG-3, the resulting RNA strand from the transcription of this would read: 5 -TGA AGA CCG-3 5 -UGA AGA CCG CGG UCU UCA ACU UCU GGC- 5
69 Translation Process by which a cell interprets a genetic message and builds a polypeptide.
70 Materials Required trna Ribosomes mrna
71 Transfer RNA = trna Made by transcription. About 80 nucleotides long. Carries AA for polypeptide synthesis.
72 Structure of trna Has double stranded regions and 3 loops. AA attachment site at the 3' end. 1 loop serves as the Anticodon.
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74 Anticodon Region of trna that base pairs to mrna codon. Usually is a compliment to the mrna bases, so reads the same as the DNA codon.
75 Example DNA - GAC mrna - CUG trna anticodon - GAC
76 Comment "Wobble" effect allows for 45 types of trna instead of 61. Reason - in the third position, U can pair with A or G. Inosine (I), a modified base in the third position can pair with U, C, or A.
77 Importance Allows for fewer types of trna. Allows some mistakes to code for the same AA which gives exactly the same polypeptide.
78 Aminoacyl-tRNA Synthetases Family of Enzymes. Add AAs to trnas. Active site fits 1AA and 1 type of trna. Uses a secondary genetic code to load the correct AA to each trna.
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80 Ribosomes Two subunits made in the nucleolus. Made of rrna (60%) and protein (40%). rrna is the most abundant type of RNA in a cell.
81 Large subunit Proteins rrna
82 Both sununits
83 Large Subunit Has 3 sites for trna. P site: Peptidyl-tRNA site - carries the growing polypeptide chain. A site: Aminoacyl-tRNA site -holds the trna carrying the next AA to be added. E site: Exit site
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85 Translation Steps 1. Initiation 2. Elongation 3. Termination
86 Initiation - Brings together: mrna A trna carrying the 1st AA 2 subunits of the ribosome
87 Initiation Steps: 1. Small subunit binds to the mrna. 2. Initiator trna (Met, AUG) binds to mrna. 3. Large subunit binds to mrna. Initiator trna is in the P-site
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89 Initiation Requires other proteins called "Initiation Factors. GTP used as energy source.
90 Elongation Steps: 1. Codon Recognition 2. Peptide Bond Formation 3. Translocation
91 Codon Recognition trna anticodon matched to mrna codon in the A site.
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93 Peptide Bond Formation A peptide bond is formed between the new AA and the polypeptide chain in the P-site. Bond formation is by rrna acting as a ribozyme
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95 After bond formation The polypeptide is now transferred from the trna in the P-site to the trna in the A-site.
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97 Translocation trna in P-site is released. Ribosome advances 1 codon, 5 3. trna in A-site is now in the P-site. Process repeats with the next codon.
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99 Comment Elongation takes 60 milliseconds for each AA added.
100 Termination Triggered by stop codons. Release factor binds in the A-site instead of a trna. H 2 O is added instead of AA, freeing the polypeptide. Ribosome separates.
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102 Polyribosomes Cluster of ribosomes all reading the same mrna. Another way to make multiple copies of a protein.
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104 Prokaryotes
105 Comment Polypeptide usually needs to be modified before it becomes functional.
106 Examples Sugars, lipids, phosphate groups added. Some AAs removed. Protein may be cleaved. Join polypeptides together (Quaternary Structure).
107 Signal Hypothesis Clue on the growing polypeptide that causes ribosome to attach to ER. All ribosomes are free ribosomes unless clued by the polypeptide to attach to the ER.
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109 Result Protein is made directly into the ER. Protein targeted to desired location (e.g. secreted protein). Clue (the first 20 AAs are removed by processing).
110 The flow of genetic information from DNA to protein in eukaryotic cells is called the central dogma of biology. Write the central dogma of biology as a flow chart What role does each of these structures play in protein synthesis? DNA mrna RNA polymerase Spliceosomes
111 Mutations Changes in the genetic makeup of a cell. May be at chromosome (review chapter 15) or DNA level
112 DNA or Point Mutations Changes in one or a few nucleotides in the genetic code. Effects - none to fatal.
113 Types of Point Mutations 1. Base-Pair Substitutions 2. Insertions 3. Deletions
114 Base-Pair Substitution The replacement of 1 pair of nucleotides by another pair.
115 Sickle Cell Anemia
116 Types of Substitutions 1. Missense - altered codons, still code for AAs but not the right ones 2. Nonsense - changed codon becomes a stop codon.
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118 Question? What will the "Wobble" Effect have on Missense? If the 3rd base is changed, the AA may still be the same and the mutation is silent.
119 Comment Silent mutations may still have an effect by slowing down the speed of making the protein. Reason harder to find some trnas than others.
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121 Missense Effect Can be none to fatal depending on where the AA was in the protein. Ex: if in an active site - major effect. If in another part of the enzyme - no effect.
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123 Nonsense Effect Stops protein synthesis. Leads to nonfunctional proteins unless the mutation was near the very end of the polypeptide.
124 Sense Mutations The changing of a stop codon to a reading codon. Result - longer polypeptides which may not be functional. Ex. heavy hemoglobin
125 Insertions & Deletions The addition or loss of a base in the DNA. Cause frame shifts and extensive missense, nonsense or sense mutations.
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127 Question? Loss of 3 nucleotides is often not a problem. Why? Because the loss of a 3 bases or one codon restores the reading frame and the protein may still be able to function.
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129 Mutagenesis Process of causing mutations or changes in the DNA.
130 Mutagens Materials that cause DNA changes. 1. Radiation ex: UV light, X-rays 2. Chemicals ex: 5-bromouracil
131 Spontaneous Mutations Random errors during DNA replication.
132 Comment Any material that can chemically bond to DNA, or is chemically similar to the nitrogen bases, will often be a very strong mutagen.
133 What is a gene? A gene is a region of DNA that can be expressed to produce a final functional product. The product can be a protein or a RNA molecule.
134 Protein vs RNA Protein usually structure or enzyme for phenotype RNA often a regulatory molecule which will be discussed in future chapters.
135 Summary Know Beadle and Tatum. Know the central dogma. Be able to read the genetic code. Be able to describe the events of transcription and translation.
136 Summary Be able to discuss RNA and protein processing. Be able to describe and discuss mutations. Be able to discuss what is a gene.