AP Biology, Chapter 17 From Gene to Protein Summary Introduction 1.

Explain why dwarf peas have shorter stems than tall varieties a. Dwarfs lack the plant hormone gibberellin; applied gibberellin cures them b. Missing an enzyme required for gibberrellin synthesis THE CONNECTION BETWEEN GENES AND PROTEINS Introduction The study of metabolic defects provided evidence that genes specify proteins: science as a process 2. Explain the reasoning that led Archibald Garrod to first suggest that genes dictate phenotypes through enzymes. a. Garrod was an MD b. Focused on rare and unusual birth defects; inborn errors of metabolism c. Example: alkaptonuria i. Urine turns black; contains alkapton ii. Hypothesized a missing enzyme for brealing down alkapton 3. Describe Beadle and Tatum's experiments with Neurospora and explain the contribution they made to our understanding of how genes control metabolism. a. Neurospora can grow on a minimal medium (MM): sucrose, salts, + biotin i. Can synthesize all other biomolecules: amino acids, nitrogen bases, etc. ii. Biomolecules are made stepwise by a series of enzymes b. Beadle and Tatum collected mutants that required arginine in their MM i. Intermediates in the pathway were known ii. Intermediates: precursorornithinecitrullinearginine iii. Mutants can be grouped by which intermediate cures them c. Concluded that each group of mutants lack a different enzyme in the pathway 4. Distinguish between the "one gene-one enzyme" hypothesis and the "one gene-one polypeptide" hypothesis and explain why the original hypothesis was changed. a. One gene-one enzyme i. Each gene makes an enzyme ii. But some proteins are not enzymes iii. Counter examples: insulin, keratin, hemoglobin b. One gene-one polypeptide i. More inclusive ii. Counter examples: RNA genes, regulatory sequences Transcription and translation are the two main processes linking gene to protein: an Overview 5. Explain how RNA differs from DNA. a. Uracil instead of thymine b. Usually single-stranded c. Used to express traits rather than store and transmit traits 6. Briefly explain how information flows from gene to protein. a. In DNA, order of bases = information b. Copied by base-pairing rule into mRNA = transcription c. Ribosome clamps onto mRNA, moves along three bases at a time d. Each mRNA codon matches and anticodon on a specific tRNA

e. tRNA carries a specific anticodon at one end, amino acid matching that anticodon at the other end f. Ribosomes align proper tRNAs and form the peptide bonds 7. Distinguish between transcription and translation. a. Transcription = DNA bases RNA bases by complementarity b. Translation = RNA bases amino acid sequence 8. Compare where transcription and translation occur in prokaryotes and in eukaryotes. a. Prokaryotes i. No nucleus ii. Transcription and translation both in the cytoplasm b. Eukaryotes i. Transcription in the nucleus; pre-mRNA processed to mRNA ii. Translation in the cytoplasm (with possible exceptions) In the genetic code, nucleotide triplets specify amino acids 9. Define "codon" and explain the relationship between the linear sequence of codons on mRNA and the linear sequence of amino acids in a polypeptide. a. Codon = three base sequence signifying the position of an amino acid b. Order of codons gives the order of amino acids in protein c. In general, conserved; but with taxonomic variations, and mutant forms 10. Explain the early techniques used to identify what amino acids are specified by the triplets UUU, AAA, GGG, and CCC. a. Nirenberg, 1961 b. Synthesized poly-uracil to serve as an artificial mRNA c. In vitro protein synthesis made only poly-phenylalanine 11. Explain why polypeptides begin with methionine when they are synthesized. a. Don't always, see code variation link above b. Codon for met often signifies the starting place for the ribosome c. Often removed after translation 12. Explain in what way the genetic code is redundant and unambiguous. a. Redundant: more than one codon for most amino acids b. Unambiguous: in an organism, each codon codes for a specific amino acid 13. Explain the significance of the reading frame during translation. a. mRNAs are read first three, next three, next three, etc. b. Shifting the start one base changes the triplets downstream The genetic code must have evolved very early in the history of life 14. Explain the evolutionary significance of a nearly universal genetic code. a. Lateral transfer (species-to-species) of genetic material is fruitful b. Homologous structures signify a common ancestor with the structure c. Universal code indicates a single common ancestor for all living systems THE SYNTHESIS AND PROCESSING OF RNA Transcription is the DNA- directed synthesis of RNA: a closer look 15. Explain how RNA polymerase recognizes where transcription should begin. Describe the promoter, the terminator, and the transcription unit. a. RNA polymerase binds at the promoter i. Promoter includes transcription start point ii. Extends upstream iii. Determines template strand b. Eukaryotes i. Protein transcription factors bind to the promoter first ii. + RNA polymerase = transcription initiation complex iii. In prokaryotes, proteins bound to RNA polymerase specify binding c. Transcription unit extends from within the promoter past the terminator

d. Palindromic terminator sequence may form a hairpin loop 16. Explain the general process of transcription, including the three major steps of initiation, elongation, and termination. a. Initiation i. Eukayotes: half of promoters have TATAAAA; binds transcription factor ii. Prokaryotes: TATAAAT is a common RNA polymerase binding site b. Elongation i. RNA polymerase adds nucleotides to 3' end ii. No proofreading function c. Termination i. Terminator sequence is transcribed ii. Transcribed sequence forms hairpin in prokaryotes iii. AAUAAA termination sequence in eukaryotes reveals 3' processing site Eukaryotic cells modify RNA after transcription 17. Explain how RNA is modified after transcription in eukaryotic cells. a. 5' cap i. Methyl-G and PPP added ii. Protects from degradation and allows ribosome binding b. 3' poly(A) tail i. Pre-mRNA cut downstream from AAUAAA; poly(A) added ii. Same functions as 5' cap c. Introns removed i. Exon = expressed sequence; intron = interspersed sequence ii. Precise, complex excision involving spliceosomes 18. Define and explain the role of ribozymes. a. RNA-only enzymes involved in RNA processing b. Introns may also catalyze their own excision 19. Describe the functional and evolutionary significance of introns. a. Functional i. Introns may control gene activity ii. Alternate splicing can give >1 protein from the same gene b. Evolutionary i. Exons code for functional domains of proteins ii. Widely spaced functional components allows recombination new proteins THE SYNTHESIS OF PROTEIN Introduction Translation is the RNA-directed synthesis of a polypeptide: a closer look 20. Describe the structure and functions of tRNA. a. Structure i. Short, about 80 nucleotides ii. Folded with four base-paired regions iii. Amino acid attachment site at 3' end iv. Anticodon at the other end of folded molecule v. Modified after transcription b. Functions i. Transfer amino acids to ribosome ii. Anticodon matches amino acid iii. Anticodon hydrogen bonds to mRNA codon iv. Wobble allows fewer than 61 tRNAs c. Charging i. Amino acids added by aminoacyl-tRNA synthetases

ii. Only 20, not one to recognize each anticodon iii. Recognize the end with the amino acid attachment site 21. Describe the structure and functions of ribosomes. a. Structure i. Large with 60% rRNA and 40% protein ii. Two subunits found separately unless actively translating iii. Groove for mRNA iv. P-, A-, and E- sites for tRNA binding b. Function i. Clamp onto mRNA at start codon ii. Align tRNAs iii. Form peptide bonds iv. Move codon-by-codon along mRNA 22. Describe the process of translation (including initiation, elongation, and termination) and explain which enzymes, protein factors, and energy sources are needed for each stage. a. Initiation i. Small subunit binds to mRNA leader or 5' cap and tRNAmet in P-site ii. Large subunit then binds iii. Protein initiation factors and energy from GTP are required b. Elongation i. Next tRNA binds codon under A-site; uses elongation factors and GTP ii. Peptide bond formed iii. Growing polypeptide chain bound to tRNA in A-site c. Translocation i. Ribosome, mRNA, and tRNAs shift over one codon ii. tRNA in E-site is released iii. Uses GTP d. Termination i. Release factor binds stop codon (UAA, UAG, or UGA) under A-site ii. Water molecule added (hydrolysis) iii. New polypeptide released from last tRNA 23. Describe the significance of polyribosomes. a. Ribosomes can sequentially attach to mRNAs b. Allows many copies of a protein to be made using the same message Signal peptides target some eukaryotic polypeptides to specific destinations in the cell 24. Explain what determines the primary structure of a protein and describe how a polypeptide must be modified before it becomes fully functional. a. Primary structure = amino acid order dictated by mRNA b. Chaperone proteins enable folding c. Sugars, lipids, or phosphates may be added d. Pieces may be removed e. More than one chain may be bound together 25. Describe what determines whether a ribosome will be free in the cytosol or attached to the rough endoplasmic reticulum. a. Membrane-bound ribosomes make endomembrane and secreted proteins b. Amino-terminal signal peptide is bound by signal-peptide recognition particle c. Complex binds to rough ER d. Signal peptide is removed from finished protein RNA plays multiple roles in a cell: a review 26. Describe two properties of RNA that allow it to perform so many different functions. a. Can hydrogen bond to other nucleic acids

b. Can fold by forming complementary base pairs with itself Comparing protein synthesis in prokaryotes and eukaryotes: a review 27. Compare protein synthesis in prokaryotes and eukaryotes. a. RNA polymerases i. Eukaryotes have 3, prokaryotes have 1 ii. Initiation factors bind to promoter first in eukaryotes b. Different termination signals and ribosome sizes c. Prokaryotes can have simultaneous transcription and translation Point mutations can affect protein structure and function 28. Define "point mutations." Distinguish between base-pair substitutions and base-pair insertions. Give examples of each and note the significance of such changes. a. Point mutations change one or a few base pairs b. Substitutions i. Change a single base, maybe a single amino acid (missense) ii. Don't affect codons downstream iii. Usually have less drastic effects iv. Example: sickle-cell; one amino acid changed, altered protein shape c. Base insertions/deletions i. Change the reading frame = frameshift mutations ii. Change all codons downstream often to a stop codon (nonsense) iii. May change all amino acids downstream and can truncate 29. Describe several examples of mutagens and explain how they cause mutations. a. Mutagens i. Radiation: gamma, X, UV, cosmic rays ii. Chemical: nitrous acid, sodium azide, bromine, arsenic, base analogs b. Mechanisms i. Radiation can break bonds holding DNA together ii. Base analogs are incorporated but base-pair incorrectly iii. Reactive chemical mutagens react with bases in DNA What is a gene: revisiting the question 30. Describe the historical evolution of the concept of a gene. a. Mendel: discrete unit of inheritance that affects phenotype b. Morgan: place on a chromosome, locus c. Region of a specific nucleotide sequence d. DNA sequence coding for a protein e. Any sequence that change be changed to alter phenotype