From Gene to Protein

1. From Gene to Protein Chapter 17

2. I. Connection of Genes to Protein A. Early Evidence - from the study of metabolic defects 1. Gerrod’s Hypothesis 1909 Archibald Gerrod - first to suggest that genes dictate phenotype through enzymes.

3. A. Early Evidence - from the study of metabolic defects 1. Gerrod’s Hypothesis 1909 Studied Alkaptonuria - absence of an enzyme that breaks down Alkapton Symptoms of disease due to inability to make an enzyme Enzymes needed for metabolic pathways

4. A. Early Evidence - from the study of metabolic defects 2. Beadle and Ephrussi, 1930s Mutations affecting drosophila eye color Blocks pigment by absence of a pathway enzyme. Mere hypothesis.

5. A. Early Evidence - from the study of metabolic defects 3. Beadle and Tatum Finally established the link between genes and enzymes Studied nutrition of bread mold Neurospora crassa (Study text for details)

6. A. Early Evidence - from the study of metabolic defects 4. One Gene - One Polypeptide Hypothesis Refined from Beadle and Tatum Not all proteins are enzymes Specific proteins require specific genes Used to be One gene - one protein Why the change?

7. B. The Process of Protein Synthesis - General Overview 1. Genes = instructions for a protein 2. RNA = bridge between DNA and protein RNA distinctives Single stranded Ribose sugar Uracil instead of Thymine

8. B. The Process of Protein Synthesis - General Overview 3. DNA nucleotide sequence translates to Amino Acid sequence

9. B. The Process of Protein Synthesis - General Overview 4. Two Stages in Protein Synthesis Transcription DNA code to RNA copy Messenger RNA (mRNA) Translation mRNA code to Amino Acid sequence

10. B. The Process of Protein Synthesis - General Overview 5. Eukaryotes and Prokaryotes Prokaryotes - no nucleus Transcription and translation are closely coupled Eukaryotes Transcription - in nucleus RNA processing - in nucleus Translation - cytoplasmic ribosome

11. B. The Process of Protein Synthesis - General Overview 6. Pathway summary DNA - RNA - Protein

12. C. Structure of the Genetic Code 1. Triplets of nucleotides specify amino acids 3 letters = dictate one amino acid With 4 letters = 64 triplet combinations 2. Each Triplet called a Codon

13. C. Structure of the Genetic Code 3. Matching codons to their amino acids began in the 1960s First - Marshall Nirenberg Mid 1960s - completed 61 code for amino acids AUG = start of a gene 3 codons = termination of a gene

15. C. Structure of the Genetic Code 4. Redundant, but not ambiguous Several codons can code for 1 amino acid (redundant) One codon can mean only 1 amino acid (not ambiguous)

17. II. Transcription and RNA A. DNA in the nucleus but Proteins built in cytoplasm Need an RNA copy of the gene to take code to the cytoplasm. Transcription - making the RNA copy

18. II. Transcription and RNA B. RNA Polymerase - opens up the specific gene and adds RNA nucleotides according to the DNA sequence. Prokaryotes - 1 kind RNA polymerase Eukaryotes - RNA Polymerases I, II, III C. Gene is read 3’ to 5’ RNA built 5’ to 3’

19. II. Transcription and RNA D. Beginning and end of gene Promotor sequence begins Terminator signals the end

20. II. Transcription and RNA E. Three stages in Transcription Initiation Elongation Termination

21. II. Transcription and RNA F. Initiation Promotor sequence start of a gene determines which strand is template provides a binding site for RNA Polymerase

22. II. Transcription and RNA F. Initiation In Eukaryotes Transcription factors find promotor (Often a TATA sequence) Bind to promotor RNA Polymerase binds onto Trans Fact makes Transcription Initiation Complex

24. II. Transcription and RNA G. Elongation RNA Polymerase moves down DNA Untwists and unzips DNA (10-20 bases) Adds in RNA nucleotides to 3’ end of growing RNA chain Behind this - DNA connects back and twists RNA copy peels away.

27. II. Transcription and RNA G. Elongation Many RNA Polymerases can be making a mRNA copy of the same gene at the same time. = More mRNAs increases the speed of protein production

28. II. Transcription and RNA H. Termination At end, RNA Polymerase copies a terminator In prokaryotes Transcription ends at end of terminator In Eukaryotes Transcription continues far beyond it This longer “pre-RNA” is then released

30. I. Modification of mRNA after transcription Enzymes modify the “pre-RNA” before its sent out to make protein 1. At 5’ end, a modified Guanine is added the 5’ Cap Function? Prevents erosion “Attach here” signal for ribosomes

31. I. Modification of mRNA after transcription Enzymes modify the “pre-RNA” before its sent out to make protein 2. At 3’ end - Poly A tail - 50 -250 letters Protects against hydrolysis damage Facilitates ribosome attachment Facilitates export from nucleus

32. I. Modification of mRNA after transcription 3. RNA Splicing mRNA has long stretches of non-coding nucleotides in between codes Called Introns Coding regions called Exons Splicing removes many intron portions

33. I. Modification of mRNA after transcription 3. RNA Splicing Accomplished by Spliceosome Composed of; Several proteins snRNP - small nuclear Ribonuclearproteins each snRNP has a RNA molecule, 150 letters

35. I. Modification of mRNA after transcription 3. RNA Splicing Functions 1.Contol which introns stay in 2.Regulate passage out of nucleus 3.Splice genes to code for more than one polypeptide

36. I. Modification of mRNA after transcription 3. RNA Splicing Alternative RNA Splicing More than one polypeptide from one gene. Depends on which segments are treated as exons

37. I. Modification of mRNA after transcription 4. Split genes facilitates protein evolution Proteins have different regions - domains different exons may code for different domains Presence of introns - facilitate crossing over at that point. Creates new genes by mixing exons from different genes. Leads to new proteins

39. III. Translation A. mRNA sequence to protein Transfer RNAs place amino acids in correct order according to the sequence of codons

40. III. Translation B. Transfer RNA - tRNA Made according to genes in the nucleus Can be used in the cytoplasm over and over 1. Action - picks up a specific amino acid places it in correct sequence at ribosome Returns to cytosol to get another of the same amino acid

42. III. Translation B. Transfer RNA - tRNA 2. Structure of tRNA 80 nucleotides Loops back on itself for a 3D shape At one end - attachment for a specific amino acid. At opposite end - Anticodon compliments and binds to the codon for the amino acid it carries

45. III. Translation B. Transfer RNA - tRNA 3. Some anticodons recognize more than one codon. Why? Two reasons - The third base in a codon includes some flexibility- called Wobble At this Wobble position U on anticodon can bind to A or G in third codon position - Some tRNA anticodons have Inosine A modified Adenine Can bond with U,C, or A.

46. III. Translation B. Transfer RNA - tRNA 4. Amino Acid joins to tRNA by Aminoacyl-tRNA Synthetase 20 different Synthetases to match the 20 different amino acids Each has active sites for a specific tRNA and A. Acid combo. Forms a covalent bond.

48. III. Translation C. Ribosomes Composed of large and small subunit made of proteins and rRNA (Active parts) Subunits form in the nucleolus exit nucleus through nuclear pores Large and small subunits only joins as a functional ribosome when they contact a mRNA molecule Prokaryotic ribosomes differ from eukaryotic ones

49. Ribosome Structure

50. III. Translation C. Ribosomes Binding Sites P - tRNA with chain A - tRNA with next A. Acid E - Discharges used tRNAs.