Student Notes

Com

mack

High

School HL

Biology

Topic

Three:

Nucleic

Acids

Seven Quest

7.1 S.1 Analysis of results of the Hershey and Chase experiment providing evidence that DNA is the genetic material.

16. What are bacteriophages? (Slides 3-4)

Use the hyperlink on slide 6 https://www.youtube.com/watch?v=Wxvd55XGrqc or the ppt. to view an animation about the Hersey-Chase experiment then answer the 3 questions below:

17. Explain why sulphur was used in one experiment and phosphorus in the other.

18. Explain why most of the radioactive sulphur (S35) was found in the supernatant.

19. Explain why little of the radioactive phosphorous (P32) was found in the supernatant, i.e. most remained in the pellet.

7.1 U.2 DNA structure suggested a mechanism for DNA replication.

20. What are the side of the ladder that makes up DNA (Slide 8)

21. Outline the basic components of a nucleotide with a drawing (Slides 9 &10)

22. Describe how the complementary base pairing in DNA comes together below. (slide 11) Explain why it is only possible for cytosine to pair with guanine and adenine to pair with thymine in terms of the sugar deoxyribose in DNA

7.1 U.1 Nucleosomes help to supercoil the DNA.

23. Explain why a Prokaryotic DNA is described as being ‘naked’ (Slide 12

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24. Outline how supercoiling occurs (Slide 12)

25. What is one thing regulated by supercoiling. (Slide 12)

26. In the space below, draw and label the structure of a simplified nucleosome, including the H1 linker and octamer (which consists of two copies of four different types of histone proteins). (Slide 13)

27. Which stage of Mitosis would be supercoiled begin? (Slide 15)

7.1 S.2 Utilization of molecular visualization software to analyse the association between protein and DNA within a nucleosome.

28. Use the RCSB Protein Bank to read about nucleosomes and examine Jmol images of them.Article on nucleosomes: http://www.rcsb.org/pdb/101/motm.do?momID=7Jmol visualisation of a nucleosome: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1AOI&bionumber=1

a. Identify the two copies of each histone protein. This can be done by locating the ‘tail of each protein’. The tails of the proteins are involved in regulating gene expression.

b. Suggest how the positive charges help to form the nucleosome with the negatively charged DNA molecule.

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2.7 S.2 Analysis of Meselson and Stahl’s results to obtain support for the theory of semi-conservative replication of DNA. (Slides 16-17)

14. Describe and explain the result found by centrifuging a mixture of DNA from generation 0 and 2. (2)

15. Outline with the aid of a diagram semi-conservation (Slide 16)

2.7 U.2 Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds. 2.7 U.3 DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as a template.

16. Complete and label the diagram below. (Slide 20)

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17. Explain how complementary base pairs are arranged. (Slide 24)

7.1 U.3 DNA polymerases can only add nucleotides to the 3’ end of a primer. (Slide 24)

18. Outline what a primer is and the role it has in DNA Replication. (Slide 26)

2.7 U.3 DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as a template.19. Where does DNA polymerase formed between nucleotides move along the template strand? (Slide 27)

2.7.U1 The replication of DNA is semi-conservative and depends on complementary base pairing.

20. Explain why DNA replication of this kind of referred to as being semi-conservative. (Slides 29-30)

7.1 U.4 DNA replication is continuous on the leading strand and discontinuous on the lagging strand.

21. Explain the process of DNA Replication:Distinguish between the lead strand and the lagging strand. (slides 31 and 32)

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7.1 U.5 DNA replication is carried out by a complex system of enzymes.

22. Summarize the roles of the enzymes of DNA Replication: (Slide 33)

Enzyme Function

DNA Gyrase(aka topoisomerase)

an enzyme that relieves strain while double-strand DNA is being unwound by helicase

SSBP

DNA Helicase unwinds DNA at origins of replication

DNA Polymerase III

RNA Primase puts down RNA primer to start replication

DNA Polymerase I

DNA Ligase

23. Construct a replication fork containing all the enzymes listed above. (Slide 34)

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7.1 A.2 Use of nucleotides containing deoxyribonucleic acid to stop DNA replication in preparation of samples for base sequencing. (slides 32-33))

24. State how dideoxyribonucleic acid affect DNA replication.

7.1 U.6 Some regions of DNA do not code for proteins but have other important functions. [The regions of DNA that do not code for proteins should be limited to regulators of gene expression, introns, telomeres and genes for tRNAs.]

25. Problems near the end of chromosomes can occur. Describe the problem (Slides 36-37)

1.6 U.1 Mitosis is division of the nucleus into two genetically identical daughter nuclei.

24. List four reasons of Mitosis to occur (Slide 40)

1.6 U.4 Interphase is a very active phase of the cell cycle with many processes occurring in the nucleus and cytoplasm.

25. Draw and label a pie chart to show the relative amount of time spent in each phase of the cell cycle, including the stages of interphase and mitosis, as well as cytokinesis. (Slide 42)

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26. Outline the stages of interphase. (Slide 43)

Stage Events

G0 a cell functioning as normal

G1

S synthesis of DNA

G2

27. List three metabolic reactions that occur during interphase (Think MR. POD Slide 44).

Metabolic reactions

P

Organelles numbers are increased

D

1.6 U.5 Cyclins are involved in the control of the cell cycle.

28. Define the term cyclin: (Slide 49)

29. Outline the roles of the four cyclins involved in control of the cell cycle: (Slide 46)

Function

Cyclin DTriggers cells to move from G0 to G1 and from G1 into

S phase.

Cyclin E

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Cyclin Aactivates DNA replication inside the nucleus in S phase.

Cyclin B .

30. The graph shows the concentrations of the four main cyclins at different points in the cell cycle. Label the graph to identify which line represents of the four main cyclins outlined above. (Slide 46)

1.6 U.2 Chromosomes condense by supercoiling during mitosis.

31. Distinguish between chromosomes and chromatids. (Slide 47)

32. Explain why cells need to supercoil their DNA molecules. (Slide 43)

33. Outline how DNA molecules are supercoiled. (Slide 44)

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34. Outline the stages of mitosis of an animal cell with a chromosome number of four. (Slides 46-50)

Diagram Outline

Prop

hase

• The nucleolus disappears.• Chromatin condenses into visible

chromosomes.• There are two sister chromatids held

together by a centromere.• The mitotic spindle forms in the cytoplasm.

Met

apha

seA

naph

ase

• Characterized by movement. It begins when pairs of sister chromatids pull apart.

• Sister chromatids move to opposite poles of the cell.

• Chromosomes look like a “V” as they are pulled.

• At the end of anaphase, the two poles have identical number and types of chromosomes.

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Tel

opha

se

• Microtubules elongate the cell.• Daughter nuclei begin to form• Nuclear envelopes re-form.• Nucleolus reappears.• Chromatin uncoils.• The cells cytoplasm begins to pinch.

1.6 U.3 Cytokinesis occurs after mitosis and is different in plant and animal cells.

35. Distinguish between mitosis and cytokinesis (Watch the animation on slide 56 and the using the picture on slide 56)

36. Outline cytokinesis in plant and animal cells (Slides 56-57)

Animal cells Plant cells

1.6 S.1 Identification of phases of mitosis in cells viewed with a microscope or in a micrograph.10

37. Label the micrograph to identify at least one example of a cell in each phase of mitosis. (Slide 53)

1.6 S.2 Determination of a mitotic index from a micrograph.

Micrograph of a pressed onion root meristem

38. Complete the table by classifying each cell (do not count cells wholly in the image) based on what phase of the cell cycle it is in.

Interphase MitosisProphase Metaphase Anaphase Telophase Total

Number of cells 46 1 2 1 3 53

% 100

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1.6 U.6 Mutagens, oncogenes and metastasis are involved in the development of primary and secondary tumors.

39. Define the term tumor (Slide 59)

40. Watch the video links: Cancer (also known as a malignant tumor) is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. List the names of five main types of cancer: (Hyperlink on Slide 59)

41. What is an oncogene? (Slide 60)

42. Mutagens are agents that cause gene mutations. Not all mutations result in cancers, but anything that causes a mutation has the potential to cause a cancer.

a. State the collective name given to chemicals that cause mutations. (Slide 56)

b. Give examples of non-chemical mutagens (Slide 55)

1.6 A.1 The correlation between smoking and incidence of cancers.

43. The graph below plots cigarette consumption and lung cancer deaths over time. (Slides 63-65)

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a. Describe the relationship shown.

b. How strong is the correlation? Justify your answer by discussing the evidence.

44. There are many other similar survey in different countries, with different demographics that show similar results. Along with lung cancer, cancers of mouth and throat are very common as these areas are in direct contact with the smoke too. Lists some examples of other cancers that are more common in smokers than non-smokers.

45. Correlation does not equal causation. Outline the direct evidence shows that it is tobacco smoke that causes the increased incidence of these cancers.

Protein Synthesis

2.7 U.4 Transcription is the synthesis of mRNA copied from the DNA base sequences by RNA polymerase. 2.7 U.5 Translation is the synthesis of polypeptides on ribosomes

46. What are the names of the two processes required for gene expression or protein synthesis? (Slide 67)

47. Give 3 examples of proteins constructed and their functions (Slides 67-70)13

48. Where do transcription and translation take place in the cell? (Slide 71)

7.2 U.2 Nucleosomes help to regulate transcription in eukaryotes.

49. State the name of the key chemical group that can be added to DNA to affect transcription. (Slide 73)

50. Outline how the modification of DNA and histones can activate or deactivate genes.(Slides 74-75)

Acetylation

Methylation

7.2 S.1 Analysis of changes in the DNA methylation patterns.

51. How does methylation effect gene expression? (Slides 73-74)

52. Outline gene expression of the length of your nose. How might changes in the production of the molecules morphogens effect nose length? (Slide 76)

53. Suggest how modified DNA or histones maybe inherited by offspring (Hyperlink on Slide 77).

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7.2 U.6 The environment of a cell and of an organism has an impact on gene expression.

54. What are some factors that cause genes to change? (Hyperlink Slide 77)

Diet, exercise…

55. Are genetic tags passed on to the next generation? (Hyperlink Slide 77)

They can change during your life time.

56. How does Norrbotten Sweden help us understand how genes work? (Hyperlink Slide 77)

Protein Synthesis Part 1 (TRANSCRIPTION)

7.2 A.1 The promoter as an example of non-coding DNA with a function.

57. Coding regions are used as a guide for the production of polypeptides, but non-coding regions are not. Non-coding regions do however have important functions, for example promoters. Outline how promoter regions called the TATA box of DNA molecules aid the production of polypeptides. (Slide79)

2.7 U.4 Transcription is the synthesis of mRNA copied from the DNA base sequences by RNA polymerase.

58. Outline the roles of RNA polymerase in the process of creating mRNA. (Slide 80)

7.2 U.1Transcription occurs in a 5’ to 3’ direction.

59. State the direction of transcription and draw a simple diagram to show the addition of an RNA molecule to a growing mRNA strand. (Hyperlink on Slide 81)

60. Identify the three states of Transcription (Slide 82)

Initiation

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Elongation Termination

7.2 U.3 Eukaryotic cells modify mRNA after transcription.

61. Distinguish between introns and exons in eukaryotic DNA. (Slide 83)

62. Outline the steps in transcription using a diagram (Slide 84)

63. Most of the eukaryotic genome is non-coding. There are two types of repetitive sequences: moderately repetitive sequences and highly repetitive sequences otherwise known as satellite DNA. Give an example of a region of DNA that contains highly repetitive sequences and outline the function of that region. What are telomeres?(Slide 85)

7.2 U.4 Splicing of mRNA increases the number of different proteins an organism can produce

64. a. Describe why the splicing process happens. (Slide 86)

b. Name an example of a protein family that is commonly alternatively spliced. (slide 87)

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7.1 A.3 Tandem repeats are used in DNA profiling.

65. State the sources of DNA used in paternal and maternal profiling. (Slides 88-89)

66. Suggest a reason why non-coding regions are more useful than coding regions in DNA profiling. (Slides 88-89)

67. Describe what is meant by the term tandem repeat sequence. (Slide 89)

7.2 U.6 The environment of a cell and of an organism has an impact on gene expression.

68. Outline how temperature effect gene expression Artic Hares. (Slide 90)

Protein Synthesis Part 2 (TRANSLATION)

7.3 U.1 Initiation of translation involves assembly of the components that carry out the process.

69. Identify the main components of translation (Slide 92)

2.7 U.5 Translation is the synthesis of polypeptides on ribosomes.

70. Describe the process of Translation? (Slide 93)

71. Draw a two diagrams to outline the structure of a ribosome. Label the following: (Slide 94)

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large subunit, small subunit, and the three rRNA binding sites (located on the large subunit)

72. Draw a two diagrams to outline the structure of a tRNA. Label the following (Slide 96)

Acceptor loop, D loop, T loop and Anticodon attachment site

7.3 A.1 tRNA-activating enzymes illustrate enzyme–substrate specificity and the role of phosphorylation.

73. What role does ATP playing the constructing a tRNA? (Slides 97-98)

2.7 U.8 Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA.

74. State the molecule on which anti-codons, which are complementary to codons, can be found. (Slide 99)

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7.3 U.1 Initiation of translation involves assembly of the components that carry out the process. AND 7.3 U.2 Synthesis of the polypeptide involves a repeated cycle of events. AND 7.3 U.3 Disassembly of the components follows termination of translation.

75. Complete the table to summarize the process of translation. (Slide 100)

a. Initiation

b. Elongation

c. Termination

2.7 U.6 The amino acid sequence of polypeptides is determined by mRNA according to the genetic code. 2.7 U.7 Codons of three bases on mRNA correspond to one amino acid in a polypeptide.

76. Define role of the 3 types of RNA in Protein Synthesis (slide 101)

mRNA Transfer RNA rRNA

7.3 U.2 Synthesis of the polypeptide involves a repeated cycle of events

77. Outline the first step of translation. (slide 102)

78. Define step two, three and four of translation. (slides 102-103)Step two

Step three

Step Four

7.3 U.3 Disassembly of the components follows termination of translation.

79. Why does the process stop? (Slide 104-105)

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80. Sketch diagrams below to show translation after watching the animation from the hypelink. (Slide 106)

2.7 U.6 The amino acid sequence of polypeptides is determined by mRNA according to the genetic code.

81. Describe why the length of the gene code can vary. (Slide 108)

1.7 U.7 Codons of three bases on mRNA correspond to one amino acid in a polypeptide. 2.7 S.3 Use a table of mRNA codons and their corresponding amino acids to deduce the sequence of amino acids coded by a short mRNA strand of known base sequence. (Review Slides 109-112)

Use the genetic code table to help answer the questions below.

82. Deduce the codon(s) that translate for Aspartate.

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2.7 S.1 Use a table of the genetic code to deduce which codon(s) corresponds to which amino acid.

83. If mRNA contains the base sequence CUG-ACU-AGG-UCC-GGAa. deduce the amino acid sequence of the polypeptide translated.

2.7 S.4 Deducing the DNA base sequence for the mRNA strand.

b. deduce the base sequence of the DNA antisense strand from which the mRNA was transcribed.

c. If mRNA contains the base sequence ACU-AAC deduce the base sequence of the DNA sense strand.

84. Transcribe and translate this DNA sequence.

DNA T A C G G G G T G A C A A C T

mRNA A U G G G G C G G

Amino acid

Met

85. An mRNA strand has 75 codons. How many amino acids will be in the polypeptide?

86. A polypeptide contains 103 amino acids. What is the length of the gene (unit = base pairs)?

87. A gene is 105kbp (kilobase pairs). How many amino acids are in the polypeptide?

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7.3 S.1 Identification of polysomes in electron micrographs of prokaryotes and eukaryotes.

88. A polysome is a structure that consists of multiple ribosomes attached to a single mRNA translating it simultaneously to quickly create many copies of the required polypeptide. Describe how polysomes in prokaryotes may differ in structure from polysomes in eukaryotes.(Slides 124-125)

7.3 U.6 Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane.

89. State two reasons why translation can occur immediately after transcription in prokaryotes. (Slide 128)

2.5 U.1 Enzymes have an active site to which specific substrates bind. (Use the hyperlink below) http://highered.mheducation.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

90. Define the following terms: (Slide 139)a. Enzyme: b. Active site: c. Substrate: d. Product:

8.1 U.2 Enzymes lower the activation energy of the chemical reactions that they catalyse.

91. What suffix is commonly applied to enzymes? (Slide136)

92. What effect do enzymes have on the activation energy of a reaction? (Slide 135)

93. Define activation energy? (Slide 134) is the energy needed barrier to starting a reaction

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94. Complete the sketch graph to show how enzymes reduce the activation energy required for a reaction to occur. (Slide 138)

95. Explain enzyme-substrate specificity, using a diagram and referring to the lock-and-key model.(Slide 143)

a. enzyme

b

c

d

e

f

96. State the function of polar region of amino acids on the active site of the enzyme. (Slide 140)

97. Describe the induced-fit model of enzyme activity, with reference to the lock and key theory, conformational change and activation energy. (Slide 144)

a. As the substrate approaches, polar regions of the enzyme’s active site attract the substrate.

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b.

c. This stress reduces the activation energy or the reaction returns the enzyme to its original shape

2.5 U.2 Enzyme catalysis involves molecular motion and the collision of substrates with the active site Play with the animation, by changing concentrations .

98. State what is meant by the term collision in enzyme catalysis. (Slide 145)

99. Explain why not all collisions between enzymes and substrates result in catalysis. (Slide 141)

100. Explain why the presence of water is critical for most enzyme reactions.(Slide 142)

101. Enzymes can be immobilized (e.g. embedded in cell membranes). Enzymes can also be free to move, but they tend to move more slowly than substrates, explain why. (Slide 143)

102. Describe three examples of enzymes giving the substrates and products.(Slide 147)

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Enzyme Substrate Product

Lactase Lactose

Maltase 2 Glucose molecules

Sucrase

2.5 U.5 Immobilized enzymes are widely used in industry.

103. Enzymes used in industry are commonly immobilized. Describe the advantages of immobilizing enzymes. (Slide 148)

Remember CRSS

C oncentration R ecycled S eparation S tability

104. List three ways in which enzymes can be immobilized. (Slide 148)

105. List eight common uses of enzymes in industry.(Slide 149)

Biofuels Brewing

Medicine & Biotechnology Juice yield

2.5 U.3 Temperature, pH and substrate concentration affect the rate of activity of enzymes.

106. List the factors that affect the rate at which enzymes work (Slide 157)

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107. Explain the effects of temperature, pH and substrate concentration on the rate of an enzyme-controlled reaction.

Effect of Temperature (Slide 158 )a. Kinetic energy increasing, increase in

collisions, increase rate of reaction

2.5 U.4 Enzymes can be denatured (Slides 159-162) 108. With the use of annotated diagrams explain how the denaturing of an enzyme affects its ability to

catalyse reactions.

Effect of pH (Slide 161 )a. Decrease in pH H+ exposed to bond

sites changing the active sites shape

b. Optimum pH/Maximum rate of reaction

c. High pH destabilizes the enzyme due to exposer to OH- decreasing the rate of the reaction

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Effect of Substrate Concentration (Slide 164 )a. Increasing collisions, increase rate of

reaction

b.

c. Full saturation of active sites by substrate

8.1 U.1 Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.

109. Define metabolism.(Slide 165)

110. Describe what a metabolic pathway is and state how each step in the pathway is controlled. (Slides 165)

111. Give an example of a linear metabolic pathway. (Slide 165)

112. Give an example of a metabolic pathway that is a cycle. (Slide 167)

8.1 U.3 Enzyme inhibitors can be competitive or non-competitive .

113. Define an inhibitor. (Slides 168)

114. Using diagrams, explain the difference between competitive and non-competitive methods of inhibition.(Slides 168-169)

Competitive Non-competitive

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115. Outline one example of one non-competitive inhibitor. (Slides 172-173)

8.1 A.2 Use of databases to identify potential new anti-malarial drugs.

116. What causes the disease malaria? (Slide 174)

117. Bioinformatics has facilitated research into metabolic pathways is referred to as chemogenomics. Outline the process of chemogenomics. (Slide 177)

118. Describe what is meant by the term Bioinformatics.(Slide 176)

2.5 A.1 Methods of production of lactose-free milk and its advantages.

119. Although all children produce lactase some adults are lactose intolerant, they lose the ability to produce lactase in adulthood. Explain why. (Slide 178)

120. State the three other commercial reasons that lactose free milk is produced. (Slide 181)• Increase sweetness •• shortening the production time for yogurts or cheese

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121. Outline the process by which lactose-free milk is produced by immobilized enzymes. (Slide 181)1. Lactase obtained from yeast

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