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1974 1977 1979 1982 1984 1985 1986 1987 1990
DNA QUESTION: 1974 L. PETERSON/ECHS Describe protein synthesis in terms of molecular structures of the nucleic acids and, using a specific example, explain how a new phenotypic characteristic may result from a change in DNA. STANDARDS: 1/2 point each for each of the following (upper limit of points per section) DNA: __ double stranded __ helical form __ nucleotide __ phosphate-deoxyribose-purine or pyrimidine __ base pairing, A-T, G-C __ hydrogen bonds form the cross linkage __ separation of strands, "unzipping" __ strands antiparallel, sense and nonsense __ 2 hydrogen bonds (A-T), 3 hydrogen bonds (G-C) (max. = 4 points) mRNA: __ synthesized on DNA sense strand template, bases complementary __ nucleotides __ phosphate-ribose-purine or pyrimidine (U, A, G, C) __ RNA polymerase bonds nucleotides together __ mRNA synthesized in nucleus, moves to cytoplasm __ codon(s), triplets of bases, specific for an amino acid __ start, stop, and nonsense codons (43 possible combinations) __ attachment to ribosomes __ ribosomes move along it, reading message codon by codon __ instructions for synthesis of polypeptides __ amino acid sequence is ordered along it __ specific examples of "start" and "stop" __ mention of rRNA (max. = 5 points) tRNA: __ temporary attachment to mRNA, base-pairing __ anticodon complements codon of mRNA __ each tRNA is specific for one amino acid __ carries it to ribosome __ peptidyl transferase - joins amino acids by peptide bonds __ specific enzymes, glutathione, Mg ++ required for attachment of amino acids __ amino acid must first be activated by ATP __ ATP energy goes to peptide bond formation EXAMPLES (only one may be used): (max. = 3 points) one point for legitimate examples (sickle cell anemia, E. coli, tryptophan synthetase, Neurospora work, alkaptonuria, albinism) __ hypothetical case __ change in DNA, resulting __ change in mRNA code __ change in tRNA __ change in protein __ change in phenotype (max. = 3 points)
DNA QUESTION: 1977 L. PETERSON/ECHS Proteins are composed of amino acid subunits which form stable three-dimensional structures. a. Describe how the genetic instructions coded in DNA are translated into the primary structure (sequence of amino acid subunits) of a protein molecule. b. Explain how interactions among the individual amino acid subunits influence the transformation of the molecule into its three-dimensional structure and how they stabilize it. STANDARDS: Ten was the maximum number of points for part a. Six points were given for a good description of the structure and/or function of DNA, mRNA, tRNA (two points each). One point was given for a reasonable explanation of amino acid linkage to the ribosomes and one point for mentioning polysomes. The student received an additional point for a good discussion of the overall process of protein synthesis. Ten was the maximum number of points for part b. For mentioning any one of the four (primary, secondary, tertiary, quaternary) structures of protein, the student would receive one point. For mentioning two or more structures the student received two points. Up to four points could be earned for mentioning the different kinds of bonds which hold the protein molecule in its various forms (one point for each kind of bond mentioned). Another four points were given for describing or explaining the significance of the structures or bonds (one point for each structure or bond adequately handled). Although the number of points totals 20, only a maximum of 15 is awarded because the scale used is 0 to 15. The 20 points represent a fair way to treat the students' varied answers. However, because the maximum for each part was 10, a student could not answer only half of the question and score 15. LIST OF STANDARDS: PART A: STRUCTURE AND/OR FUNCTION IN PROTEIN SYNTHESIS DISCUSSION OF DNA = 2 points DISCUSSION OF mRNA = 2 points DISCUSSION OF tRNA = 2 points AMINO ACID LINKAGE/RIBOSOME (one point for discussion of each or possible two points for either one if done well/ but not two points for each one) OVERVIEW OF PROTEIN SYNTHESIS = 1 point MENTION OF POLYSOMES = 1 point [Part A Total = 10 points] PART B: STRUCTURES (primary, secondary, tertiary, quaternary) MENTION ONE = 1 point MENTION OF TWO OR MORE = 2 points / max. of 2 points SIGNIFICANCE OR DESCRIPTION OF EACH STRUCTURE OR BOND = 1 point / max. of 4 points MENTION OF A BOND = 1 point each / max os 4 points [Part B Total = 10 points] THE TERMS PRIMARY, SECONDARY, TERTIARY STRUCTURE OF PROTEINS ARE OFTEN USED AS FOLLOWS: PRIMARY = amino acid sequence; SECONDARY = coiling of polypeptide chain into alpha helix or interaction of two polypeptides to produce a beta configuration; TERTIARY = folding of the alpha helix to produce more or less globular proteins; ACTUALLY, THESE TERMS REFER TO TYPES OF FORCES STABILIZING A PROTEIN MOLECULE, AND NOT TO ANY ACTUAL GEOMETRIC SHAPE. THUS: PRIMARY = covalent bonding of peptides or peptide bond; SECONDARY = refers to hydrogen bonding as well as various ionic and so-called salt bonds; TERTIARY = refers to covalent bonds; interactions between atoms placed close to each other (i.e. Disulfide bonds); [QUATERNARY STRUCTURE = alpha & beta chains interacting as in the hemoglobin molecule]
DNA QUESTION: 1979 L. PETERSON/ECHS In relation to the chemical nature of the gene, describe: a. the chemical structure of the gene b. the replication (self-copying) of the gene c. gene mutations, including chromosomal aberrations STANDARDS: A. CHEMICAL STRUCTURE: max. = 6 points (one point for any of the following) __ genes are composed of units of DNA __ name 3 out of 4 nitrogen bases __ N bases are paired (proper pairs: A-T, G-C) __ components of nucleotid/DNA __ N bases are purines (AG) and pyrimidines (TC) __ DNA is a double stranded helix __ H bonds between N bases in base-pairing __ the two DNA strands are antiparallel (mirror/ complements) __ DNA codes for amino acid sequence in proteins __ each gene has a start and stop nucleotide sequence __ operon concept (Discuss) __ RNA genes (recognize) __ DNA dimensions B. REPLICATION: max. = 6 points (one point for any of the following) __ double stranded DNA "unzips" __ exposed N bases serve as a template for sequential base-pairing in forming new DNA __ new DNA formed in the 5'->3' direction __ both old DNA strands are complementarily copied at the same time __ only short sections are copied at one time __ DNA polymerase (I or III) enzymically controls DNA polymerization __ ligase is the enzyme for tying the new short sections (Okazaki sections) together __ pyrophosphatase catalyzes hydrolysis of pyrophosphate (from the polymerization) __ deoxynucleotide triphosphates are the precursor molecules (substrates of DNA polymerase) __ energy for the bonds holding the DNA polymer together comes from nucleoside triphosphates [NTP -> NMP + PPi -> 2 Pi] __ Replication occurs in interphase before mitosis/meiosis __ Additional replication information (e.g., endonuclease, nicking enzyme, swivelase, RNA polymerase initiation of DNA replication, etc.) C. MUTATIONS: max. = 6 points (one point for any of the following) __ POINT MUTATIONS (Describing each change in a N-base or base pair with the subsequent genetic effect; describing the effect of each mutagenic agent: radiation, chemicals, heat) __ CHROMOSOMAL ABERRATIONS (Description of: deletion, duplication, inversion, translo- cation, trisomy, monosomy, polyploidy)
DNA QUESTION: 1982 L. PETERSON/ECHS A portion of a specific DNA molecule consists of the following sequence of nucleotide triplets: TAC GAA CTT CGG TCC This DNA sequence codes for the following short polypeptide: methionine - leucine - glutamic acid - proline - arginine Describe the steps in the synthesis of this polypeptide. What would be the effect of a deleltion or an addition in one of the DNA nucleotides? What would be the effect of a substitution in one of the nucleotides? STANDARDS: In the transcription phase of protein synthesis, students were given a point for a correct definition of transcription. They were awarded one point for mentioning each of the following: __ DNA as the template molecule for messenger RNA __ The proper base pairing (including the uracil substitution) __ The chemical characteristics of nucleotides __ A comparison of RNA and DNA (other than uracil substitution) __ The triplet arrangement of codons and/or anticodons __ The control of transcription (Operon, etc.) __ Promoters __ The role of polymerase __ Intervening sequences in eukaryotic cells __ Factors involved in the release of mRNA from DNA __ 5' - 3' arrangement with attachment at -OH end A definition of translation was worth an additional point with one point given for mention of each of the following: __ Movement of mRNA from nucleus to ribosome __ Association of mRNA with the ribosome and ribosomal RNA __ Location of ribosomes __ Description of ribosome/polyribosome structure __ Role of transfer RNA in transporting amino acids __ Specific characteristics of tRNA __ Amino acid-tRNA complex activation __ Role of ATP and enzymes __ tRNA initiator molecules (met or f-met) __ Initiation factors (GTP, etc.) resulting in union of 30s and 50s __ Bonding of tRNA to 50s (A site) __ Role of amino transferase __ Initiation codons __ Examples of initiator codons (AUG, GUG) __ mRNA codon exposed at A site __ Peptide bond formation (dehydration synthesis) between amino acids __ Translocation of ribosome (shift from A to P site) __ Termination (nonsense) codons __ Examples of termination codons (UGA, UAA) __ Factors that function in the release of the polypeptide A maximum of twelve points could be earned from this part of the question. In order for a student to score fifteen points, three or more points must have been from the discussion of changes in the code. A student was given one point for recognizing that an addition or deletion may alter a large portion of the resulting polypeptide. An additional point was given for explaining the importance of where the deletion or addition occurred, and another point for demonstrating knowledge of the frame shift concept. Mentioning the role of repair DNA was worth another point. A student who explained that a substitution of a nucleotide alters only one amino acid was given a point. Additional points could be earned by stating that, in some cases, the polypeptide may not be altered, that the position of the nucleotide substituted is important ("wobble" effect) and that these changes in the code are important to natural selection and evolution.
DNA QUESTION: 1984 L. PETERSON/ECHS Experiments by the following scientists provided critical information concerning DNA. Describe each classical experiment and indicate how it provided evidence for the chemical nature of the gene. a. Hershey and Chase - bacteriophage replication b. Griffith and Avery - bacterial transformation c. Meselson and Stahl - DNA replication in bacteria STANDARDS: one point for each of the following with a max. of 6 points per section EXPERIMENTS OF HERSHEY AND CHASE: __ Hypothesis or problem statement Experimental procedure: __ phage cultured in 32P and 35S labeled E. coli __ recovery of labeled virus __ reinfection of cold bacteria with hot virus Results: __ recovery of endogenous 32P label __ recovery of exogenous 35S label __ recognition of protein (35S) and DNA (32P) association __ Interpretation and Extension to DNA as genetic material EXPERIMENTS OF GRIFFITH AND AVERY: __ Hypothesis or problem statement __ Restatement of Griffith's work (in vivo) __ Description of Griffith's work __ Recognition of "transforming principle" Description of Avery, MacLeod and McCarty's work: __ In vitro mix of inactivated III S cocci and active II R cocci leads to small number of plated III S forms __ Exposure of II R cocci to DNA extracted from III S phenotype __ Transformation of II R to III S DNA (DNAase implications) __ Interpretation EXPERIMENTS OF MESELSON AND STAHL: __ Hypothesis or problem statement __ Description of the design of Meselson and Stahl's Experiment __ In vitro work with E.coli using nutrients with 15N or heavy nitrogen __ Use of density gradient centrifugation __ Parent DNA (strands heavy) -> Offspring DNA (one strand heavy/one strand light) __ Interpretation of results: Semiconservative Replication
DNA QUESTION 1985: L. PETERSON/ECHS Describe the operon hypothesis and discuss how it explains the control of messenger RNA production and the regulation of protein synthesis in bacterial cells. STANDARDS: BACKGROUND: Max. = 2 points __ Definition of operon (functionally related genes whose expression is controlled) __ DNA consists of genes coding for both structural and regulating proteins (Hypothesis) __ Authors of Hypothesis DESCRIPTION OF OPERON (likely the Lac Operon): Max. = 8 points Structure (diagram) Max. 4 __ promoter site __ repressor site __ operator site __ structural genes __ inducer Function Max. 4 __ binds RNA polymerase* at 3' site on DNA (* also cAMP-CAP) __ produces repressor protein: stops RNA polymerase attaching to promoter __ site of attachment of repressor protein __ codes for sequential protein __ serves to inactivate repressor CONTROL OF mRNA PRODUCTION & CONSEQUENCES re PROTEIN SYNTHESIS: __ Inducible model: derepression (lactose example) [gene always off] = 3 points __ Repressible model: corepression (tryptophan-histidine) [gene always on] = 3 points __ CAP model: catabolite induction: with decrease in glucose -> increase in cAMP cAMP-CAP binds to promoter site therefore, transcription -> lactose metabolism = 3 points (above require explanation & example) __ Adaptive significance = 2 points __ Final fate of mRNA transcribed = 2 points Max. = 5
DNA QUESTION 1986: L. PETERSON/ECHS Describe the biochemical composition, structure, and replication of DNA. Discuss how recombinant DNA techniques may be used to correct a point mutation. STANDARDS: COMPOSITION AND STRUCTURE Max. = 10 points __ nucleotide = sugar and phosphate and nitrogen base/polymer __ sugar = deoxyribose (explain) __ bases = A T G C (mentioned) __ sugar - phosphate backbone/pyrimidine-purine "rungs" (general) __ 3'5' phosphodiester bonds / 3'5' phosphate __ hydrogen bonds Max. = 2 points __ A & T, G & C pairing/ratio = 1:1 __ A=T (2 H bonds), G=C (3 H bonds) __ molecular "fit" (purine = large, pyrimidine = small) __ complementary __ purine (double ring) pyrimidine (single ring) __ purines = AG; pyrimidine = CT Max. = 2 points __ direction, 3'5' ends, OH 3'/P 5' __ antiparallele/opposite direction/3'5' - 5'3' __ helix Max. = 2 points __ 10 bases/turn __ 3.4 A (0.34 nm) between base pairs __ 34 A (3.4 nm)/ turn __ 20 A (2.0 nm) wide Max. = 2 points __ B DNA / Z DNA __ association with proteins __ base stacking __ major/minor groove __ methylation/modification Max. = 2 points REPLICATION: Max. = 6 points __ "unzipping" - semiconservative - template/complement/break H bonds (Meselson & Stahl) __ enzymes - unwinding topoisomerases/helicases/destabilizing protein/swivelase __ discontinuous - Okazaki fragments - bubbles ("puffs") __ direction (5'3') __ bidirectional/leading -lagging/replication forks __ RNA primers (initiation sequence) __ enzymes (max. = 2) primase polymerases I, II, III, endonuclease (correct use w/polymerization) ribonuclease H - remove primers __ ligase - attaches fragments (correct use) Total Max. for Composition, Structure, & Replication = 13 points RECOMBINANT DNA: Max. = 6 points __ mutation - definition __ recombinant/recombinant - general definition __ restriction enzymes (max. = 2) (specific sequence, sticky or blunt ends, bacterial origin, reannealing) __ plasmids - library __ example __ technique
DNA QUESTION 1987: L. PETERSON/ECHS Describe the production and processing of a protein that will be exported from a eukaryotic cell. Begin with the separation of the messenger RNA from the DNA template and end with the release of the protein at the plasma membrane. STANDARDS: PRODUCTION: Max. = 8 points (Points found in many papers) (Points less frequently mentioned) RNA types: __ a) m-RNA single stranded __ DNA termination signal exists __ b) t-RNA clover leaf and functions to dislodge the __ c) r-RNA + protein = ribosome growing RNA message. __ Ribosome consists of large and small subunits __ m-RNA moves through pores in the nuclear envelope __ m-RNA enters cytoplasm __ m-RNA associates with ribosomes or rough ER __ introns removed; exons spliced (pre m-RNA). __ initiating codon (AUG) exists on m-RNA __ 5' end of m-RNA is capped __ m-RNA read in 3 nucleotide groups/codons (methylated guanine &/or __ amino acids joined to specific t-RNAs poly-A tail added to the 3' end). __ anticodon binds to codon on m-RNA __ codon sequence determines amino acid sequence __ t-RNA has anticodon loop. __ PA sites exist in the ribosomes (2 codons fit in) __ peptide bonds form between the amino acids __ ribosomes and m-RNA move __ translation of m-RNA ends at stop codon with respect to each other. (UAA, UAG, UGA) __ separation protein frees C terminal COOH from the t-RNA. __ synthesis of the protein in N -> COOH direction. __ m-RNA is read in the 5' -> 3' direction. PROCESSING AND EXPORT: NO MAX. __ ribosomes attach to outside of (rough) ER __ peptide enters ER (lumen) __ may be processing signal for entry into ER __ peptide moves to smooth ER __ transport vesicles form around polypeptide __ vesicles go to membrane or Golgi __ changes may occur in the protein in the Golgi Complex (- H2O, + sugar, + other peptides) __ proteins (vesicles) move to older parts (edge of Golgi) __ sorting of molecules into different types of Golgi sacs (lysosome) occur __ secretion vesicles bud off Golgi [movement] __ vesicles fuse with plasma membrane __ membranes break followed by release of contents
1990 DNA QUESTION: L. PETERSON/ECHS Describe the steps of protein synthesis, beginning with the attachment of a messenger RNA molecule to the small subunit of a ribosome and ending with the release of the polypeptide from the ribosome. Include in your answer a discussion of how the different types of RNA function in this process. STANDARDS: INITIATION (until peptide bond formation): Max. = 4 points __ site of attachment on mRNA (near start codon or near 5' end, or groove in ribosome) __ usually AUG is start codon __ 1st tRNA enters P site directly or 1st aa is met or fmet __ initiation factors __ large subunit then binds __ A + P sites (Entry/Donor) ELONGATION (from 1st peptide bond until last aa added) Max. = 4 points __ anticodon/codon; complementary to mRNA __ elongation factors __ peptidyl transferase __ bond broken between tRNA and aa __ formation of peptide bond __ tRNA leaves __ translocation (movement of mRNA relative to ribosome TERMINATION Max. = 4 points __ stop codon is reached __ stop codons are UGA, UAA, or UAG __ no corresponding tRNA for stop codons __ releasing factors __ hydrolysis of tRNA from polypeptide __ dissociation of ribosomal subunits OTHER (may be found in above sections): Max. = 3 points __ tRNA: e.g. tRNA carries aa to ribosome; charging of tRNA with cognate aa; recycling of tRNA; formation of aminoacyl tRNA; __ mRNA: what a codon is; mRNA carries information from DNA; cap/tail; leader/trailer; signal sequence; __ rRNA: sites on ribosome for attachment; protein plus rRNA forms a complete functional ribosome; __ GTP as energy source __ rate of translation __ polysomes