Chapter 17 RQ

1. Chapter 17 RQ • Why do dwarf peas fail to make their own gibberellins? • What did the “one gene – one polypeptide” hypothesis used to be called? • What is the “bridge” between DNA and protein synthesis? • What is the process by which one gene is copied into an mRNA strand? • How many mRNA nucleotide bases equal a “codon”?

2. 1. Give early experimental evidence that implicated proteins as the links between genotype and phenotype. • Inherited instructions in DNA direct protein synthesis, thus proteins are the links between genotype and phenotype • Garrod suggested that genes dictate phenotypes through enzymes that catalyze reactions 

3. 2. Describe Beadle and Tatum’s experiments with Neurospora, and explain the contribution they made to our understanding of how genes control metabolism. • Relationship between genes and enzymes • Wild type (bread mold) can survive on minimal medium  looked for mutants or auxotrophs that could not live because they can’t synthesize molecules • Results  one gene – one enzyme hypothesis  the function of a gene is to dictate the production of a specific enzyme 

5. One gene – one enzyme Gene codes for a specific enzyme One gene – one polypeptide Most enzymes are proteins Many proteins are not enzymes Proteins that are not enzymes are still gene products Many proteins are comprised of 2 or more polypeptide chains, each chain specified by a different gene  3. Distinguish between “one gene-one enzyme” hypothesis and “one gene-one polypeptide”, and explain why the original hypothesis was changed.

6. 4. Explain how RNA differs from DNA. • Both are nucleic acids; polymers of nucleotides • RNA is different from DNA: - the 5 carbon sugar is ribose not deoxyribose - the nitrogen base is uracil not thymine 

7. Two processes: transcription and translation Transcription  the synthesis of RNA using DNA as a template Translation  the synthesis of a polypeptide which is directed by mRNA DNA  RNA  protein 5. Briefly overview, in your own words, how information flows from gene to protein.

8. Transcription  is the synthesis of RNA under the direction of DNA Translation  the actual synthesis of a polypeptide, which occurs under the direction of mRNA  6. Distinguish between transcription and translation.

9. 7. Describe where transcription and translation occur in prokaryotes and in eukaryotes; explain why it is significant that in eukaryotes, transcription and translation are separated in space and time. • Prokaryotes  lack nuclei so DNA is not segregated from ribosomes or the protein – synthesizing machinery (occurs in rapid succession) • Eukaryotes  have nuclear envelopes that segregate transcription in the nucleus from translation in the cytoplasm; mRNA (the intermediary) is modified before it moves from the nucleus to the cytoplasm where translation occurs 

11. 8. Define codon, and explain what relationship exists between the linear sequence of codons on mRNA and the linear sequence of amino acids in a polypeptide. • Codon  a 3-nucleotide sequence in mRNA that specifies which amino acid will be added to a growing polypeptide or that signals termination  the basic unit of the genetic code • Genes are not directly translated into amino acids but are first transcribed as codons into mRNA 

13. 9. List the three stop codons and the one start codon. StartAUG StopUAA UAG UGA

14. 10. Explain in what way the genetic code is redundant and unambiguous. • Redundant  two or more codons differing only in their 3rd base can code for the same amino acids (UUU & UUC = phenylalanine) • Unambiguous  codons code for only ONE amino acid (UUU ONLY codes for phenylalanine) 

15. 11. Explain the evolutionary significance of a nearly universal genetic code. • It indicates that the code was established very early in life’s history

16. 12. Explain the process of transcription including the three major steps of initiation, elongation, and termination. Initiation  a RNA polymerase attaches at a specific region of DNA called the promoter, and begins transcription (often called the TATA box) Elongation  as RNA polymerase moves along the DNA, 10 – 20 bases are exposed at a time for pairing with RNA nucleotides Termination  transcription proceeds until RNA polymerase transcribes the termination sequence 

18. 13. Describe the general role of RNA polymerase in transcription and explain how it recognizes where to begin. • RNA polymerases bind at the promoter and in eukaryotes they need transcription factors to recognize them • The enzyme separates the 2 DNA strands at the initiation site and transcription begins 

20. 14. Specifically, describe the primary functions of RNA polymerase II. • It untwists and opens a short segment of DNA exposing about 10 nucleotide bases  one of the exposed DNA strands is the template for base-pairing with RNA nucleotides • It links incoming RNA nucleotides to the 3’ end of the elongating strand, thus, RNA grows one nucleotide at a time in the 5’ to 3’ direction 

22. 15. Distinguish among mRNA, tRNA, and rRNA. • mRNA  messenger RNA; what the DNA nucleotide sequence is transcribed into • tRNA  transfer RNA • rRNA  ribosomal RNA; translation occurs on ribosomes, complex particles composed of rRNA and protein that facilitate the orderly linking of amino acids into polypeptide chains 

23. 16. Describe the structure of tRNA and explain how the structure is related to the function. • tRNA is transcribed from DNA templates, made in the nucleus and travels out into the cytoplasm • Used repeatedly – picks up its designated amino acid in the cytosol, deposits it at the ribosome, and leaves to pick up another • Consists of a single RNA strand that is only about 80 nucleotides long, has a protruding end which serves as the attachment site for the amino acid 

25. 17. Given the sequence of bases in DNA, predict the corresponding codons transcribed on mRNA and the corresponding anticodons of tRNA. DNA CTAGGATGCAAATGC mRNA GAUCCUACGUUUACG tRNA CUAGGAUGCAAAUGC 

26. 18. Describe the wobble effect. • It is a relaxation of the base-pairing rules • If one tRNA variety existed for each of the mRNA codons that specifies an amino acid, there would be 61 tRNAs, there are only 45 - this is because some tRNAs can recognize two or more codons 

27. 19. Explain how an aminoacyl-tRNA synthetase matches a specific amino acid to its appropriate tRNA; describe the energy source that drives this endergonic process. • There are 20 types of these enzymes in a cell, each specific for an amino acid • The active site of each enzyme fits only a specific combination of amino acid and tRNA • The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP (which loses 2 phosphates!)

28. 20. Describe the structure of a ribosome and explain how this structure relates to function. • A ribosome is made up of 2 subunits (large and small) – these are constructed of proteins and ribosomal RNA molecules, and are made in the nucleolus • Function is to bring mRNA together with the amino acid-bearing tRNAs, therefore they have binding sites for mRNA and tRNA 

30. 21. Describe the process of translation including initiation, elongation, and termination and explain what enzymes, protein factors, and energy sources are needed for each stage. • Initiation  when mRNA, tRNA and the first amino acid come together with the ribosome - protein initiation factors bring everything together to begin (GTP provides energy) 

31. Elongation… • Elongation  amino acids are added one by one, helped by protein elongation factors 1. Codon recognition – mRNA codon makes a hydrogen bond with the tRNA anticodon (requires GTP hydrolysis) 2. Peptide bond formation – a ribozyme catalyzes the peptide bond creating a polypeptide which then separates from it’s tRNA 3. Translocation – the tRNA moves to another part of the ribosome, and the next codon to be translated steps up; finally the tRNA leaves (requires hydrolysis of GTP) 

32. Termination… • Termination  elongation continues until there is a stop codon; a protein release factor binds and adds a water to finish the polypeptide 

34. 22. Explain what determines the primary structure of a protein and describe how a polypeptide must be modified before it becomes fully functional. • A gene determines the protein’s primary structure (it’s amino acid sequence) • Primary structure then determines conformation changes • Posttranslational modifications  chemical modification by adding sugars, lipids, phosphates, or others 

35. 23. Describe what determines whether a ribosome will be free in the cytosol or attached to rough ER. • Free  suspended in cytosol and mostly synthesize proteins that dissolve in the cytosol and function there • Bound  attached to the cytosol side of the ER and make proteins which are secreted from the cell (ex: insulin) - occurs if the growing polypeptide ITSELF cues the ribosome to attach to the ER – marked by a signal peptide, which targets the protein to the ER 

36. A signal peptide is recognized by the SRP (signal-recognition particle), and this dictates where that particular protein will be headed for work. - as the polypeptide is being synthesized, it begins to snake around to where it will be located within the cell (ER, mitochondria, chloroplast, etc.)  24. Explain how proteins can be targeted for specific sites within the cell.

38. Prokaryotic A transcription unit can contain several genes, so the resulting mRNA code may code for different, but functionally related, proteins Eukaryotic A transcription unit contains a single gene, so the resulting mRNA codes for synthesis of only one polypeptide  25. Describe the difference between prokaryotic and eukaryotic mRNA.

39. 26. Explain how eukaryotic mRNA is processed before it leaves the nucleus. • In eukaryotes, RNA transcripts are modified before leaving the nucleus to make functional mRNA • This can happen in two ways: 1. Covalent alteration of both the 3’ and 5’ ends 2. Removal of intervening sequences • “Pre-mRNA” is what the molecule is called prior to this alteration 

42. 27. Describe some biological functions of introns and gene splicing. • Introns – the noncoding segments of nucleic acid that lie between coding regions • Exons – segments which are eventually expressed through amino acid sequences • Splicing – occurs when the introns are cut out of the initial length to transcribe and translate the portion that will code for used information 

43. 28. Explain why base-pair insertions or deletions usually have a greater effect than base-pair substitutions. • Substitutions  the replacement of one nucleotide and its partner in the complementary DNA strand with another pair of nucleotides • Insertions and deletions  the additions or losses of one or more nucleotide pairs in a gene 

45. 29. Describe how mutagenesis can occur. • Mutagenesis  the creation of mutations - due to: errors in DNA replication, repair, or recombinations that result in base-pair substitutions, insertions, or deletions  The End!