Topic 7: Nucleic acids and proteins

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1 Topic 7: Nucleic acids and proteins

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3 Topic 7: Nucleic acids and proteins 7.1 DNA structure Assessment Statement IBO Notes Student Notes Describe the structure of DNA, including the antiparallel strands, 3 5 linkages and hydrogen bonding between purines and pyrimidines. Outline the structure of nucleosomes. State that nucleosomes help to supercoil chromosomes and help to regulate transcription. Distinguish between unique or single copy genes and highly repetitive sequences in nuclear DNA. State that eukaryotic genes can contain exons and introns. Major and minor grooves, direction of the twist, alternative B and Z forms, and details of the dimensions are not required. Limit this to the fact that a nucleosome consists of DNA wrapped around eight histone proteins and held together by another histone protein. ighly repetitive sequences (satellite DNA) constitutes 5 45% of the genome. The sequences are typically between 5 and 300 base pairs per repeat, and may be duplicated as many as 10 5 times per genome. TOK: ighly repetitive sequences were once classified as junk DNA, showing a degree of confidence that it had no role. This addresses the question: To what extent do the labels and categories used in the pursuit of knowledge affect the knowledge we obtain?

4 1. Draw a diagram of the molecular structure of a portion of DNA. (Total 4 marks) 2. Draw a diagram showing the molecular structure of a section of the DNA molecule. (Total 5 marks) 3. What is the composition of the backbone of DNA? A. Alternating sugar and phosphate molecules B. Complementary base pairs C. Alternating sugar and base molecules D. A polysaccharide 4. Which of the following are connected by a hydrogen bond? A. The hydrogen and oxygen atoms of a water molecule B. A base pair of a DNA molecule C. Two amino acid molecules of a dipeptide D. Two glucose molecules in a disaccharide 5. The structure of the DNA double helix was described by Watson and Crick in Explain the structure of the DNA double helix, including its subunits and the way in which they are bonded together. (Total 8 marks)

5 6. To which parts of the deoxyribose molecule do phosphates bind in DNA? V C O 2 O I IV O II III O A. I and V B. III and IV C. II and III D. III and V

6 7.2 DNA replication Assessment Statement IBO Notes Student Notes State that DNA replication occurs in a direction. Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates. State that DNA replication is initiated at many points in eukaryotic chromosomes. The 5 end of the free DNA nucleotide is added to the 3 end of the chain of nucleotides that is already synthesized. The explanation of Okazaki fragments in relation to the direction of DNA polymerase III action is required. DNA polymerase III adds nucleotides in the direction. DNA polymerase I excises the RNA primers and replaces them with DNA.

7 1. What is the function of helicase? A. It forms bonds between DNA nucleotides. B. It adds new nucleotides to the DNA helix. C. It forms the DNA helix. D. It separates DNA strands. 2. Which enzyme removes the RNA primer during replication? A. RNA primase B. DNA polymerase I C. DNA ligase D. elicase 3. State a role for each of four different named enzymes in DNA replication. (Total 6 marks) 4. The diagram below shows a short section of DNA molecule before and after replication. If the nucleotides used to replicate the DNA were radioactive, which strands in the replicated molecules would be radioactive? G C T A C C G A T G A. II and III only B. I and III only C. I and II only G C T A C C G A T G G C T A C C G A T G I II III IV D. I, II, III and IV

8 5. Living organisms use DNA as their genetic material. Explain how DNA is replicated within the cells of living organisms. (Total 8 marks) 6. A biochemist isolated and purified molecules needed for DNA replication. When some DNA was added replication occurred, but the DNA molecules formed were defective. Each consisted of a normal DNA strand paired with segments of DNA a few hundred nucleotides long. Which of the following had been left out of the mixture? A. DNA ligase B. elicase C. Nucleotides D. DNA polymerase

9 7.3 Transcription Assessment Statement IBO Notes Student Notes State that transcription is carried out in a direction. Distinguish between the sense and antisense strands of DNA. Explain the process of transcription in prokaryotes, including the role of the promoter region, RNA polymerase, nucleoside triphosphates and the terminator. State that eukaryotic RNA needs the removal of introns to form mature mrna. The 5 end of the free RNA nucleotide is added to the 3 end of the RNA molecule that is already synthesized. The sense strand (coding strand) has the same base sequence as mrna with uracil instead of thymine. The antisense (template) strand is transcribed. The following details are not required: there is more than one type of RNA polymerase; features of the promoter region; the need for transcription protein factors for RNA polymerase binding; TATA boxes (and other repetitive sequences); and the exact sequence of the bases that act as terminators. Further details of the process of posttranscriptional modification of RNA are not required. 7.4 Translation Assessment Statement IBO Notes Student Notes Explain that each trna molecule is recognized by a trna activating enzyme that binds a specific amino acid to the trna, using ATP for energy. Outline the structure of ribosomes, including protein and RNA composition, large and small subunits, three trna binding sites and mrna binding sites. State that translation consists of initiation, elongation, translocation and termination. Each amino acid has a specific trnaactivating enzyme (the name aminoacyl trna synthetase is not required). The shape of trna and CCA at the 3 end should be included. State that translation occurs in a direction. During translation, the ribosome moves along the mrna towards the 3 end. The start codon is nearer to the 5 end. Draw and label a diagram showing the structure of a peptide bond between two amino acids. Explain the process of translation, including ribosomes, polysomes, start codons and stop codons. State that free ribosomes synthesize proteins for use primarily within the cell, and that bound ribosomes synthesize proteins primarily for secretion or for lysosomes. Use of methionine for initiation, details of the T factor and recall of actual stop codons are not required.

10 1. Describe the consequence of a base substitution mutation with regards to sickle cell anaemia. (Total 7 marks) 2. The following diagram shows the lac operon which helps to regulate the expression of genes. Permease -galactosidase Acetylase DNA lac I Promoter Operator lac Z lac Y lac A [Source: Riki Lewis, uman Genetics, 3rd Edition, William C Brown, (1999), page 158] (a) Outline the term operon.. (2) (b) Outline the relationship between the lac operon and transcription... (3) (Total 5 marks) 3. Explain the process of translation. (Total 9 marks)

11 4. What is removed to form mature eukaryotic mrna? A. RNA primers B. Exons C. RNA polymerases D. Introns 5. Outline the process of translation. (Total 5 marks) 6. A certain gene codes for a polypeptide that is 120 amino acids long. Approximately how many nucleotides long is the mrna that codes for this polypeptide likely to be? A. 30 B. 40 C. 360 D Sickle cell anemia is a serious disease caused by a single base substitution mutation. Explain how a single base substitution mutation can have significant consequences for an individual. (Total 6 marks) 8. Compare DNA transcription with translation. (Total 4 marks) 9. (a) Define the term degenerate as it relates to the genetic code.

12 (b) Apart from international cooperation, outline two positive outcomes of the uman Genome Project. (2) (c) State the catalytic activity of reverse transcriptase. (d) State one use of monoclonal antibodies in diagnosis and one use in treatment. Diagnosis:... Treatment:... (2) (Total 6 marks) 10. Distinguish between the structure of DNA and RNA. DNA RNA (Total 3 marks)

13 11. It had always been assumed that eukaryotic genes were similar in organization to prokaryotic genes. owever, modern techniques of molecular analysis indicated that there are additional DNA sequences that lie within the coding region of genes. Exons are the DNA sequences that code for proteins while introns are the intervening sequences that have to be removed. The graph shows the number of exons found in genes for three different groups of eukaryotes. Percentage of genes Saccharomyces cerevisiae (a yeast) Drosophila melanogaster (fruit fly) Mammals <30<40<60>60 Number of exons [Source: Benjamin Lewin, (1999) Genes VII, OUP, page 55] (a) Calculate the percentage of genes that have five or less exons in mammals.

14 (b) Describe the distribution of the number of exons and the percentage of genes in D. melanogaster. (2) (c) (i) Compare the distributions of the number of exons found in genes of S. cerevisiae and mammals (2) (ii) Suggest one reason for the differences in the numbers of exons found in genes of S. cerevisiae and mammals uman DNA has been analysed and details of certain genes are shown in the table below. Gene Gene size / kb* mrna size / kb Number of introns Insulin Collagen Albumin Phenylalanine hydroxylase Dystrophin *kilobase pairs [Source: William S Klug and Michael R Cummings, (2002), Concepts of Genetics, 7th edition, Prentice all, page 314]

15 (d) Calculate the average size of the introns for the albumin gene. (2) (e) Analyse the relationship between gene size and the number of introns. (2) (f) Determine the maximum number of amino acids that could be produced by translating the phenylalanine hydroxylase mrna. emoglobin is a protein composed of two pairs of globin molecules. During the process of development from conception to adulthood, human hemoglobin changes in composition. Adult hemoglobin consists of two alpha- and two beta-globin molecules. Two globin genes occur on chromosome 16: alpha- and zeta-globin. Four other globin genes are found on chromosome 11: beta, delta, epsilon and gamma. The graph below illustrates the changes in expression of the globin genes over time. Percentage of hemoglobin Key: alpha-globin gamma-globin beta-globin delta-globin epsilon-globin zeta-globin weeks of gestation birth month of age [Source: adapted from M Cummings, uman eredity, 4th edition, West/Wadsworth Publishing Company]

16 (g) State which globin genes are the first to be expressed after fertilization. (h) Compare the expression of the gamma-globin gene with the beta-globin gene. (3) (i) Deduce the composition of the hemoglobin molecules at 10 weeks of gestation months after birth (2) (Total 17 marks) 12. Describe the genetic code. (Total 6 marks) 13. Where do transcription and translation occur in eukaryotic cells? Transcription Translation A. Cytoplasm Cytoplasm B. Cytoplasm Mitochondria C. Nucleus Cytoplasm D. Nucleus Nucleus

17 14. The lac operon model of gene control in the bacterium Escherichia coli explains how the production of the enzyme β-galactosidase is controlled. Which conditions are necessary for β-galactosidase enzyme to be produced in this bacterium? A. Glucose is present and lactose is absent B. Glucose and lactose are present C. Glucose is absent and lactose is present D. Glucose and lactose are both absent 15. The process of translation involves the use of transfer RNA (trna) and amino acids. Outline the structure of trna. (Total 5 marks) 16. Explain the process of translation. (Total 9 marks)

18 7.5 Proteins Assessment Statement IBO Notes Student Notes Explain the four levels of protein structure, indicating the significance of each level. Outline the difference between fibrous and globular proteins, with reference to two examples of each protein type. Explain the significance of polar and non polar amino acids. State four functions of proteins, giving a named example of each. Quaternary structure may involve the binding of a prosthetic group to form a conjugated protein. Aim 7: Simulation exercises showing three dimensional molecular models of proteins are available. Limit this to controlling the position of proteins in membranes, creating hydrophilic channels through membranes, and the specificity of active sites in enzymes. Membrane proteins should not be included.

19 1. Outline the production of a dipeptide by a condensation reaction. Include the structure of a generalized dipeptide in your answer. (Total 5 marks) 2. List four functions of proteins, giving an example of each. (Total 4 marks) 3. Outline the role of condensation and hydrolysis in the relationship between amino acids and dipeptides. (Total 4 marks) 4. The complex structure of proteins can be explained in terms of four levels of structure, primary, secondary, tertiary and quaternary. (a) Primary structure involves the sequence of amino acids that are bonded together to form a polypeptide. State the name of the linkage that bonds the amino acids together. (b) Beta pleated sheets are an example of secondary structure. State one other example. (c) Tertiary structure in globular proteins involves the folding of polypeptides. State one type of bond that stabilizes the tertiary structure. (d) Outline the quaternary structure of proteins. (2) (Total 5 marks)

20 5. Which of the following reactions occurs when a dipeptide is formed from amino acids? A. ydrolysis B. Denaturation C. Condensation D. Oxidation 6. Which is not a primary function of protein molecules? A. ormones B. Energy storage C. Transport D. Structure 7. Distinguish between fibrous and globular proteins, giving one example of each. (Total 5 marks) 8. Which structure represents an amino acid? A. O B. O N C C N C C O S C. O D. O N C C N C C O O 9. Draw the basic structure of an amino acid, and label the groups that are used in peptide bond formation. (Total 4 marks)

21 7.6 Enzymes Assessment Statement IBO Notes Student Notes State that metabolic pathways consist of chains and cycles of enzyme catalysed reactions. Describe the induced fit model. Explain that enzymes lower the activation energy of the chemical reactions that they catalyse. Explain the difference between competitive and noncompetitive inhibition, with reference to one example of each. Explain the control of metabolic pathways by endproduct inhibition, including the role of allosteric sites. This is an extension of the lock and key model. Its importance in accounting for the ability of some enzymes to bind to several substrates should be mentioned. TOK: Scientific truths are often pragmatic. We accept them as true because they give us predictive power, that is, they work. The German scientist Emil Fischer introduced the lock andkey model for enzymes and their substrates in It was not until 1958 that Daniel Koshland in the United States suggested that the binding of the substrate to the active site caused a conformational change, hence the induced fit model. This is an example of one model or theory, accepted for many years, being superseded by another that offers a fuller explanation of a process. Only exothermic reactions should be considered. Specific energy values do not need to be recalled. Competitive inhibition is the situation when an inhibiting molecule that is structurally similar to the substrate molecule binds to the active site, preventing substrate binding. Limit non competitive inhibition to an inhibitor binding to an enzyme (not to its active site) that causes a conformational change in its active site, resulting in a decrease in activity. Reversible inhibition, as compared to irreversible inhibition, is not required.

22 1. (a) Define the term active site of an enzyme. (b) Outline how enzymes catalyze biochemical reactions. (2) (c) Explain the effect of p on enzyme activity. (3) (d) State three functions of lipids. (2) (Total 8 marks) 2. Explain the effects of temperature, p and substrate concentration on enzyme activity. (Total 8 marks)

23 3. Consider the metabolic pathway shown below A B C D E If there is end-product inhibition, which product (B to E) would inhibit which enzyme (1 to 4)? Product Enzyme A. C 4 B. B 3 C. B 4 D. E 1 4. Alcohol dehydrogenase is an enzyme that catalyses the reversible reaction of ethanol and ethanal according to the equation below. NAD+C3C2O ethanol C3CO+NAD++ ethanal The initial rate of reaction can be measured according to the time taken for NAD to be produced. In an experiment, the initial rate at different concentrations of ethanol was recorded (no inhibition). The experiment was then repeated with the addition of l mmol dm -3 2,2,2-trifluoroethanol, a competitive inhibitor of the enzyme. A third experiment using a greater concentration of the same inhibitor (3 mmol dm -3 ) was performed. The results for each experiment are shown in the graph below. Initial rate of reaction / arbitrary units no inhibition 3 1 mmol dm inhibitor 3 3 mmol dm inhibitor Ethanol concentration / mmol dm 3 [Source: R Taber, Biochemical Education, (1998) 26, pages ]

24 (a) Outline the effect of increasing the substrate concentration on the control reaction (no inhibition). (2) (b) (i) State the initial rate of reaction at an ethanol concentration of 50 mmol dm 3 in the presence of the inhibitor at the following concentrations. 1 mmol dm 3 :... 3 mmol dm 3 :... (ii) State the effect of increasing the concentration of inhibitor on the initial rate of reaction (c) Explain how a competitive inhibitor works. (3) (Total 7 marks)

25 5. What can reduce the effect of a competitive inhibitor of an enzyme? A. Decrease the temperature at which the reaction takes place. B. Increase the temperature at which the reaction takes place. C. Increase the substrate concentration. D. Add a non-competitive inhibitor. 6. Outline enzyme-substrate specificity. (Total 5 marks) 7. Explain how allosteric control of metabolic pathways by end-product inhibition includes negative feedback and non-competitive inhibition. (Total 8 marks) 8. Explain the effect of substrate concentration on enzyme activity. (Total 3 marks) 9. What effect do enzymes have on the activation energy of exergonic and endergonic reactions? Activation energy of exergonic reactions Activation energy of endergonic reactions A. increases increases B. decreases decreases C. increases decreases D. decreases increases

26 10. The enzyme aspartate carbomyltransferase (ACTase) is a key regulatory enzyme in nucleotide metabolism in bacteria. The activity of this enzyme was studied in the bacterium elicobacter pylori, an important human pathogen. ACTase activity and the growth of. pylori were measured at different concentrations of carbomoyl aspartate (CAA), the end product of the reaction catalysed by ACTase ACTase activity / % of control Growth / % of control Key: 25 ACTase activity. pylori growth Concentration of carbamoyl aspartate / mmol dm 3 [Source: Burns, et al., Biological Procedures Online, (1998), (a) (i) State the growth of. pylori at a CAA concentration of 30 mmol dm (ii) Calculate the change in ACTase activity between CAA concentrations of 20 and 40 mmol dm (b) Compare the effect of increasing CAA concentration on the growth of. pylori and ACTase activity. (2)

27 (c) Explain the effect of CAA on ACTase activity. (2) (d) Suggest a direct medical application of this information. (Total 7 marks) 11. Which of the following could cause denaturation of an enzyme? A. Substrate concentration B. A competitive inhibitor C. igh temperature D. Low salt concentration

28 12. The graph below shows the effect of changing the substrate concentration on an enzyme controlled reaction. 40 % substrate 20 % substrate 10 % substrate Amount of product formed 5 % substrate 2.5 % substrate Time 0 % substrate What is the correct interpretation of these data? A. The rate of reaction increases continuously with increase in substrate concentration. B. The rate of reaction decreases continuously with increase in substrate concentration. C. The rate of reaction increases up to a point and then remains constant. D. The rate of reaction is not affected by any change in the substrate concentration. 13. ow does the enzyme pectinase help in fruit juice production? A. Pectinase increases the amount of protein in the juice extracted. B. Pectinase decreases the lipid content of the juice extracted. C. Pectinase increases the volume of the juice extracted. D. Pectinase eliminates toxins from the juice extracted.

29 14. In the enzyme controlled pathway shown below, which compound is most likely to inhibit enzyme (w)? enzyme enzyme enzyme enzyme w x y z Precursor I II III IV A. I B. II C. III D. IV 15. Explain competitive and non-competitive inhibition, including allostery. (Total 8 marks)