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Chapter 17

Chapter 17. From Gene to Protein. Proteins. Proteins have many structures , resulting in a wide range of functions Proteins do most of the work in cells and act as enzymes Proteins are made of monomers called amino acids. Table 5.1. An overview of protein functions. 2. 2.

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Chapter 17

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  1. Chapter 17 From Gene to Protein

  2. Proteins • Proteins have many structures, resulting in a wide range of functions • Proteins do most of the work in cells and act as enzymes • Proteins are made of monomers called amino acids

  3. Table 5.1 • An overview of protein functions

  4. 2 2 Substrate binds to enzyme. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) Enzyme (sucrase) Glucose OH H2O H O Fructose 3 Substrate is converted to products. 4 Products are released. Figure 5.16 • Enzymes • Are a type of protein that acts as a catalyst, speeding up chemical reactions

  5. Amino acids • Are organic molecules possessing both carboxyl and amino groups • Differ in their properties due to differing side chains, called R groups

  6. CH3 CH3 CH3 CH CH2 CH3 CH3 H CH3 H3C CH3 CH2 CH O O O O O H3N+ H3N+ H3N+ H3N+ C H3N+ C C C C C C C C C O– O– O– O– O– H H H H H Valine (Val) Leucine (Leu) Isoleucine (Ile) Glycine (Gly) Alanine (Ala) Nonpolar CH3 CH2 S H2C CH2 O NH CH2 H2N C C CH2 CH2 O– CH2 O O O H H3N+ H3N+ C C C C H3N+ C C O– O– O– H H H Phenylalanine (Phe) Proline (Pro) Methionine (Met) Tryptophan (Trp) Figure 5.17 Twenty Amino Acids • 20 different amino acids make up proteins

  7. OH NH2 O C NH2 O C OH SH CH2 CH3 OH Polar CH2 CH CH2 CH2 CH2 CH2 O O O O O O H3N+ H3N+ H3N+ H3N+ H3N+ H3N+ C C C C C C C C C C C C O– O– O– O– O– O– H H H H H H Glutamine (Gln) Tyrosine (Tyr) Asparagine (Asn) Cysteine (Cys) Serine (Ser) Threonine (Thr) Basic Acidic NH3+ NH2 NH+ O– O –O O CH2 C NH2+ C C NH Electrically charged CH2 CH2 CH2 CH2 CH2 O O H3N+ H3N+ CH2 CH2 C CH2 C C C O O– H3N+ O– CH2 C CH2 C H O H H3N+ O– C C CH2 H O O– H3N+ C C H O– H Lysine (Lys) Histidine (His) Arginine (Arg) Glutamic acid (Glu) Aspartic acid (Asp)

  8. Amino Acid Polymers • Amino acids • Are linked by peptide bonds

  9. Polypeptides • Polypeptides • Are polymers (chains) of amino acids • A protein • Consists of one or more polypeptides

  10. Protein Conformation and Function • A protein’s specific conformation (shape) determines how it functions

  11. Amino acid subunits +H3NAmino end Pro Thr Gly Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Arg Val Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Tyr Trp Lys Ala Leu Gly lle Ser Pro Phe His Glu His Ala Glu Val Thr Phe Val Ala Asn lle Thr Asp Ala Tyr Arg Ser Ala Arg Pro Gly Leu Leu Ser Pro Tyr Ser Tyr Ser Thr Thr Ala o Val c Val Glu – Lys o Thr Pro Asn Carboxyl end Figure 5.20 Four Levels of Protein Structure • Primary structure • Is the unique sequence of amino acids in a polypeptide

  12. H H H H H H O O O O O O O H H H H H H R R R R R R R C C C C C C C C C C C C C N N N N N N N N N N N N N C C C C C C C C C C C C C C R R R R R R H H H H H H H O O O O O O O H H H H H H H  pleated sheet H O H H Amino acidsubunits C C N N N C C C R H O H H H H H H N N N N N N  helix C C O C H H H C C C R R R R R H H C C C C C C O O O O H C R O C C O H C O N N H C C H R H R Figure 5.20 • Secondary structure • Is the folding or coiling of the polypeptide into a repeating configuration • Includes the  helix and the  pleated sheet

  13. Hydrophobic interactions and van der Waalsinteractions CH CH2 CH2 H3C CH3 OH Polypeptidebackbone H3C CH3 Hydrogenbond CH O HO C CH2 CH2 S S CH2 Disulfide bridge O -O C CH2 CH2 NH3+ Ionic bond • Tertiary structure • Is the overall three-dimensional shape of a polypeptide • Results from interactions between amino acids and R groups

  14. Polypeptidechain Collagen  Chains Iron Heme  Chains Hemoglobin • Quaternary structure • Is the overall protein structure that results from the aggregation of two or more polypeptide subunits

  15. +H3N Amino end Amino acid subunits helix Review of Protein Structure

  16. Sickle-Cell Disease: A Simple Change in Primary Structure • Sickle-cell disease • Results from a single amino acid substitution in the protein hemoglobin

  17. Normal hemoglobin Sickle-cell hemoglobin Primary structure Primary structure . . . . . . Exposed hydrophobic region Val His Leu Thr Pro Glul Glu Val His Leu Pro Glu Thr Val 5 6 7 3 4 5 6 7 1 2 1 2 3 4 Secondaryand tertiarystructures Secondaryand tertiarystructures  subunit  subunit     Quaternary structure Hemoglobin A Quaternary structure Hemoglobin S     Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced. Function Molecules donot associatewith oneanother, eachcarries oxygen. Function 10 m 10 m Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen Red bloodcell shape Red bloodcell shape Figure 5.21 Fibers of abnormalhemoglobin deform cell into sickle shape.

  18. What Determines Protein Conformation? • Protein conformation Depends on the physical and chemical conditions of the protein’s environment • Temperature, pH, etc. affect protein structure

  19. Denaturation Normal protein Denatured protein Renaturation Figure 5.22 Denaturation is when a protein unravels and loses its native conformation(shape)

  20. The Protein-Folding Problem • Most proteins • Probably go through several intermediate states on their way to a stable conformation • Denaturated proteins no longer work in their unfolded condition • Proteins may be denaturated by extreme changes in pH, temperature, salinity or heavy metals

  21. Correctlyfoldedprotein Polypeptide Cap Hollowcylinder The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comesoff, and the properlyfolded protein is released. Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end. Chaperonin(fully assembled) 2 3 1 Figure 5.23 • Chaperonins • Are protein molecules that assist in the proper folding of other proteins

  22. What happens if a protein isn’t folded correctly?

  23. Prions can be formed – misfolded versions of normal proteins

  24. Prions • Prions are slow-acting, virtually indestructible infectious proteins that cause brain diseases in mammals • Prions propagate by converting normal proteins into the prion version • Scrapie in sheep, mad cow disease, and Creutzfeldt-Jakob disease in humans are all caused by prions

  25. Overview: The Flow of Genetic Information • The information content of DNA • Is in the form of specific sequences of nucleotides along the DNA strands

  26. The DNA inherited by an organism • Leads to specific traits by dictating the synthesis of proteins • The process by which DNA directs protein synthesis, gene expression • Includes two stages, called transcription and translation

  27. The ribosome • Is part of the cellular machinery for translation, polypeptide synthesis Figure 17.1

  28. Concept 17.1: Genes specify proteins via transcription and translation

  29. Evidence from the Study of Metabolic Defects • In 1909, British physician Archibald Garrod • Was the first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell • DO NOT COPY

  30. Nutritional Mutants in Neurospora: Scientific Inquiry • Beadle and Tatum causes bread mold to mutate with X-rays • Creating mutants that could not survive on minimal medium

  31. EXPERIMENT RESULTS Class I Mutants Class II Mutants Class III Mutants Wild type Minimal medium (MM) (control) MM + Ornithine MM + Citrulline MM + Arginine (control) • Using genetic crosses • They determined that their mutants fell into three classes, each mutated in a different gene Working with the mold Neurospora crassa, George Beadle and Edward Tatum had isolated mutants requiring arginine in their growth medium and had shown genetically that these mutants fell into three classes, each defective in a different gene. From other considerations, they suspected that the metabolic pathway of arginine biosynthesis included the precursors ornithine and citrulline. Their most famous experiment, shown here, tested both their one gene–one enzyme hypothesis and their postulated arginine pathway. In this experiment, they grew their three classes of mutants under the four different conditions shown in the Results section below. The wild-type strain required only the minimal medium for growth. The three classes of mutants had different growth requirements Figure 17.2

  32. CONCLUSION From the growth patterns of the mutants, Beadle and Tatum deduced that each mutant was unable to carry out one step in the pathway for synthesizing arginine, presumably because it lacked the necessary enzyme. Because each of their mutants was mutated in a single gene, they concluded that each mutated gene must normally dictate the production of one enzyme. Their results supported the one gene–one enzyme hypothesis and also confirmed the arginine pathway. (Notice that a mutant can grow only if supplied with a compound made after the defective step.) Class I Mutants (mutation in gene A) Class II Mutants (mutation in gene B) Class III Mutants (mutation in gene C) Wild type Precursor Precursor Precursor Precursor Enzyme A Gene A A A A Ornithine Ornithine Ornithine Ornithine Enzyme B Gene B B B B Citrulline Citrulline Citrulline Citrulline Enzyme C Gene C C C C Arginine Arginine Arginine Arginine

  33. Beadle and Tatum developed the “one gene–one enzyme hypothesis” • Which states that the function of a gene is to dictate the production of a specific enzyme

  34. From AP Outline – Do not copy • Obj. 3.4 TSIAT describe representations and models illustrating how genetic information is translated into polypeptides • 3.6 TSC predict how a change in a specific DNA or RNA sequence can result in changes in gene expression.

  35. From AP Outline – Do not copy • 3.19 TSIAT describe the connection between the regulation of gene expression and observed differences between individuals in a a population • 3.25 THS can create a visual representation to illustrate how changes in a DNA nucelotide sequence can result in a change in the polypeptide produced.

  36. The Products of Gene Expression: A Developing Story • As researchers learned more about proteins • The made minor revision to the one gene–one enzyme hypothesis • Genes code for polypeptide chains or for RNA molecules

  37. Basic Principles of Transcription and Translation • Transcription • Is the synthesis of RNA under the direction of DNA • Produces messenger RNA (mRNA) • Translation • Is the actual synthesis of a polypeptide, which occurs under the direction of mRNA • Occurs on ribosomes

  38. DNA TRANSCRIPTION mRNA Ribosome TRANSLATION Polypeptide (a) Prokaryotic cell. In a cell lacking a nucleus, mRNAproduced by transcription is immediately translatedwithout additional processing. • In prokaryotes • Transcription and translation occur together Figure 17.3a

  39. Nuclear envelope DNA TRANSCRIPTION Pre-mRNA RNA PROCESSING mRNA Ribosome TRANSLATION (b) Eukaryotic cell. The nucleus provides a separatecompartment for transcription. The original RNAtranscript, called pre-mRNA, is processed in various ways before leaving the nucleus as mRNA. Polypeptide Figure 17.3b • In eukaryotes • RNA transcripts are modified before becoming true mRNA

  40. Cells are governed by a cellular chain of command • DNA RNA protein CENTRAL DOGMA

  41. The Genetic Code • How many bases correspond to an amino acid?

  42. Codons: Triplets of Bases • Genetic information • Is encoded as a sequence of nonoverlapping base triplets, or codons

  43. Gene 2 DNA molecule Gene 1 Gene 3 DNA strand (template) 5 3 A C C T A A A C C G A G TRANSCRIPTION A U C G C U G G G U U U 5 mRNA 3 Codon TRANSLATION Gly Phe Protein Trp Ser Figure 17.4 Amino acid • During transcription • The gene determines the sequence of bases along the length of an mRNA molecule

  44. Second mRNA base U C A G U UAU UUU UCU UGU Tyr Cys Phe UAC UUC UCC UGC C U Ser UUA UCA UAA Stop Stop UGA A Leu UAG UUG UCG Stop UGG Trp G CUU CCU U CAU CGU His CUC CCC CAC CGC C C Arg Pro Leu CUA CCA CAA CGA A Gln CUG CCG CAG CGG G Third mRNA base (3 end) First mRNA base (5 end) U AUU ACU AAU AGU Asn Ser C lle AUC ACC AAC AGC A Thr A AUA ACA AAA AGA Lys Arg Met or start G AUG ACG AAG AGG U GUU GCU GAU GGU Asp C GUC GCC GAC GGC G Val Ala Gly GUA GCA GAA GGA A Glu Figure 17.5 GUG GCG GAG GGG G Cracking the Code • A codon in messenger RNA • Is either translated into an amino acid or serves as a translational stop signal

  45. Codons must be read in the correct reading frame • For the specified polypeptide to be produced

  46. Evolution of the Genetic Code • The genetic code is nearly universal • Shared by organisms from the simplest bacteria to the most complex animals

  47. In laboratory experiments • Genes can be transcribed and translated after being transplanted from one species to another Figure 17.6

  48. Concept 17.2: Transcription is the DNA-directed synthesis of RNA: a closer look

  49. Molecular Components of Transcription • RNA synthesis • Is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides • Follows the same base-pairing rules as DNA, except that in RNA, uracil substitutes for thymine

  50. 3 1 2 Promoter Transcription unit 5 3 3 5 Start point DNA RNA polymerase Initiation. After RNA polymerase binds to the promoter, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand. Template strand of DNA 5 3 3 5 Unwound DNA RNA transcript Elongation. The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5  3 . In the wake of transcription, the DNA strands re-form a double helix. Rewound RNA 5 3 3 5 3 RNA transcript 5 Termination. Eventually, the RNA transcript is released, and the polymerase detaches from the DNA. 5 3 3 5 3 5 Completed RNA transcript Figure 17.7 Synthesis of an RNA Transcript • The stages of transcription are • Initiation • Elongation • Termination

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