Commack High School HL Biology

Topic

Two:

Biochemistr

y

Seven Quest

Student Notes

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.1 U.1 Molecular biology explains living processes in terms of the chemical substances involved. 2.1 U.4 Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism.

1. Identify the three parts of an atom and there charge. (Slide 2)

2. What are the four most common elements found in living things and what is the total percentage of the four in living things? (Slide 3)

3. Provide a brief describe the role these four elements may play in a living thing (Slides 4-7)

4. Outline two other elements that are essential to living things (Slides 8-12)

2.1 U.2 Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist

5. Despite only being the 15th most abundant element on the planet carbon forms the backbone of every single organic molecule.a. What type of bonds can carbon molecules form? And how does the strength of these bonds compare with

other types of bond? (Slide 16)

b. Explain why Carbon can form four bonds with up to four different atoms, and explain why. (slide 16)

c. What are the minimum atom combinations need to be an organic compound? (Slide 16)

6. Describe the difference between molecular biologist reductions approach to understanding and emergent properties (Slide 17)

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2.1 A.1 Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.

7. Vitalism is a theory that nowadays has no credit.

a. Describe the central tenant that Wöhler falsified.(Slide 18)

b. Wöhler accidentally artificially synthesized urea, hence falsifying vitalism. What compound was he trying to produce? (Slide 18)

2.1 U.3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

8. Compare the key feature of the different groups of organic molecules by completing the table below.

Key features Examples

Carbohydrates(Slide 19)

Lipids(Slides 20)

Proteins(Slide 21)

nucleic acids(Slide 22)

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2.1 S.1 Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.

9. Draw structures of alpha and beta glucose and ribose. Number the carbon atoms correctly. Which sugar is a pentose? Which is a hexose? (Slide 23)

10. Draw out a fatty acid with the formula CH3(CH2)6COOH. Draw the structure of molecule and explain why it is

called a saturated fatty acid and a glycerol molecule. (Slide 23)

11. Draw the generalized structure of an amino acid. Label and annotate the diagram to show the different groups that comprise amino acids. (Slide 23)

12. Draw a Simplified Nucleotide (Slide 23)

2.1 S.2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams. 13. Which type of molecule is shown in the diagram to the right?

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14. The diagrams below show various molecular structures.

a. Identify which of the diagrams represent:i. the structure of glucose.

ii. the structure of an amino acid.

iii. the structure of fatty acids.

b. Discuss which of the molecules are most similar in structure.

2.1 U.5 Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.2.1 U.6 Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

15. Draw and annotate a diagram below of an anabolism and catabolism reaction (Slide 27)

16. Distinguish between the terms anabolism and catabolism. (Slide 27-29)

anabolism catabolism

Synthesis or breakdown? Breakdown

Energy required or released Requires energy

Name a processReduction Reactions/Condensation

Oxidation Reactions/Hydrolysis

Products Digestion milk

Water produced or used? Produced

enzymes/agent involved

C H C

C

C

CC

C

H

HH

H

H

HH

N C

R

C

O

O H

H

C H O H

C

H

H O H C

C

O H

H

C

H

O H

C

H

O H

OO

O

O H

O H

O H

O H

O H

(C H )3 2

2

n

I.

III .

II.

IV.2

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2.2 U.1 Water molecules are polar and hydrogen bonds form between them.

17. Draw a minimum of three molecules to show the hydrogen bonding between them. The diagram should be labelled and annotated to indicate: (Slide 31)

Large oxygen atom Small hydrogen atom Covalent bond Weak hydrogen bond between δ+ and δ- parts of neighboring water molecules.

18. What is the weak intermolecular force holding the five water molecules together (Slide 31)

19. Explain why the water molecule is polar. Refer to electrons and covalent bonding in your answer.(Slide 31)

2.2 A.2 Use of water as a coolant in sweat

20. What is a property of water that make it is useful as a coolant? (Slide 32)

21. Describe the heat of vaporization. (Slide 33)

22. Draw a heating curve of water and methane. (Make note of the difference in heat energy need to change states between a solid to a liquid and the heat energy need to change from a liquid to a gas.). Label heat of vaporization on your heating curves for both. (Slide 34)

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23. Outline the differences between the heating curves of both and how that might effect changes states for both. (Slide 34)

2.2 A.1 Comparison of the thermal properties of water with those of methane (Slide 35)

24. Complete the table to compare the thermal properties of water with methane.

Methane Water

Formula CH4 H2O

Molecular mass 16

Bonding Single covalent

Polarity nonpolar polar

Density (g cm-3) 0.46

Specific Heat Capacity (J g-1 oc-1) 2.2

Latent heat of vaporization (J g-1)2257

Melting point (oC) 0

Boiling point (oC) 100

25. Outline the consequences, to cells, of not cooling the human body. (Slide 36)

26. Explain how the body exploits this property of water to cool the body using sweat. (Slide 36)

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2.2 U.2 Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water.27. Summarize the key points on each property of water and how it relates to the structure of the water molecule.

Outline the property Give examples of how organisms exploit this property

Cohesive (Slide 37) Water is a polar molecule. Hydrogen bonds that exist between water molecules linking water molecules

Adhesive (Slide 38)

Trees use capillary action

Thermal (Slide 39) Water also has a high heat of vaporization which means it takes a lot of heat to evaporate water from a liquid to a vapor

important as a cooling mechanism for humans

Solvent (Slide 41) it allows water to act as a transport medium (blood and cytoplasm) of important molecules in biological organisms

2.2 U.3 Substances can be hydrophilic or hydrophobic.

28. Define the terms:a. Hydrophilic (Slide 42)

b. Hydrophobic (Slide 43)

29. Complete the table to give examples of hydrophilic and hydrophobic molecules. (Slides 42-43)

Polar, non-polar, charged? Examples

Hydrophilicglucose

Hydrophobic

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2.2 A.3 Modes of transport of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in blood in relation to their solubility in water.

30. Complete the table to describe the transport of key substances in the blood.

Describe the solubility in water Relate how it is carried in the blood to the solubility

Glucose(Slide 44) substances which it transports

Amino acids(Slide 45) R group determines the degree of

solubilityCholesterol

(Slide 57) carried in blood in lipoprotein complexes

Fats(Slide 46) hydrophilic phosphate heads of the

phospholipids face outwards and are in contact with water

Oxygen(Slide 47)

small size of an oxygen molecule it is soluble in water

Ionic Compounds (Slide 48)

carried in the blood plasma due to the polar nature of

water

31. Water is a great solvent of other polar molecules and ions. Outline the composition of blood below. (Back to Slide 40)Plasma 55%

Cellular Components 45%

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2.1 S.2 Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

32. Draw and number the carbons in the linear and ring structure of fructose (Slide 49)

33. Describe the linkage to the carbons the deoxyribose molecule on slide 50?

34. Identify one difference between the C6H12O6 molecules on slide 51.

35. How does the shape differ in a 1-4 ring structure and a 1-6 ring structure (Slide 53)

2.3 U.1 Monosaccharide monomers are linked together by condensation reactions to form disaccharides and polysaccharide polymers.

36. List the three types of carbohydrates below. (Slide 55)

37. What is the general formula for monosaccharides/? (Slide 56)

38. Draw alpha and beta glucose below. Circle the difference between the two monosaccharides. (Slide 57)

39. Where is Ribose found in you? (Slide 58)

40. Galactose is one component of milk. What does it bond to, to produce lactose? (Slide 58)

41. Draw Fructose below. How does it differ from the two monosaccharides alpha and beta glucose? (Slide 57)

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42. Condensation of monosaccharides is a polymerization reaction. It can continue to create a longer chain of saccharides (a carbohydrate). These building reactions are part of the anabolic metabolism.

a. Define polymer. (Slide 60)

b. What else is needed to make the reaction occur? (Slide 60)

c. Annotate and complete diagram below to outline how two monosaccharides are converted into a disaccharide through condensation, producing a glycosidic bond. Include a word equation. (Slide 60)

43. Complete the table to summarise the common forms of disaccharides. (Slides 61-63)

Disaccharide Produced by plants or animals?

Produced from which Monosaccharides?

Commonly found in

plant

Lactose animal milk

glucose + fructose sugar beet and sugar cane

2.3 A.1 Structure and function of cellulose and starch in plants and glycogen in humans.

44. What is it that give Cellulose its high tensile strength? (Slide 65)

45. What type of glucose is used to form Cellulose? What Carbon numbers do they bond to? (Slide 65)

46. Compare the linkage between the glucose molecules in Amylose and Amylopectin (Slides 67-68)

47. Compare the branching between the glucose molecules in Amylopectin and Glycogen. (Slide 67-68)

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48. Compare polysaccharides of glucose. (Slide 69)

Cellulose Starch GlycogenAmylose Amylopectin

Source Plant Plant

Subunit α−Glucose α−Glucose

Bonds 1-4 1-4 1-4 and 1-6

Branches No No Yes per 20 sub units

2.3 S.1 Use of molecular visualization software to compare cellulose, starch and glycogen.

49. The easiest way to use jmol is to use the ready-made models from on the Biotopics website (Slide 71) (http://www.biotopics.co.uk/jsmol/glucose.html#). Play with the models, move them and zoom in and out.a. Select the the glucose molecule and identify the colours used to represent carbon, hydrogen and oxygen

atomsCarbon –

Hydrogen –

Oxygen –

b. Using the models identify and describe the differences between glucose, sucrose and fructose

c. Look at the amylose model and zoom out from it. Describe the overall shape of the molecule.

d. Zoom in on the amylose molecule. Each glucose sub-unit is bonded to how many other sub-units? Which carbons atoms used to form the glycosidic bonds? Are there any exceptions to these rules?

e. Using a similar approach to that above investigate the structure of glycogen and find the similarities and differences between it and both amylose and amylopectin.

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2.3 U.2 Fatty acids can be saturated, monounsaturated or polyunsaturated. 2.3.U.4 Triglycerides are formed by condensation from three fatty acids and one glycerol.

50. Fatty acids in the production of lipids.a. In the space below, draw the generalized structure of a glycerol and a fatty acid (label the 2 functional groups

in the fatty acid). (Slide 72)

b. Describe the type of reaction that brings together the fatty acids to glycerol (Slide 72)

c. Describe the term saturated when used in reference to fatty acids. (Slide 74)

d. For each of the following fatty acids deduce whether it is saturated, monounsaturated or polyunsaturated, Give reasons for each answer. (Slide 74)

Oleic Acid Caproic Acid

α-Linolenic Acid

2.3 U.3 Unsaturated fatty acids can be cis or trans isomers.

51. What does the term trans-fat evaluation mean? (Slide 75)

52. List some reasons why trans fats were invented. (Slide 75)

53. How does the shape of a trans-fat change? (Slide 75)

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54. Outline the location of the carbon and hydrogens with a diagram for the three types of fats acids we are focusing on, Saturated, cis and trans fatty acids. (Slide 76) Saturated Cis Trans

55. Unsaturated fatty acids are described as being cis or trans isomers depending on the structure of the double bonds in the fatty acids. (Slide 77)a. Complete the table to compare and contrast cis and trans isomers.

Cis-isomers Trans-isomers

Structural diagram

Natural / synthesized

Rare in nature – usually artificially produced to produce solid fats, e.g. margarine from vegetable oils.

Positioning of the hydrogen atoms

the hydrogen atoms are on the same side of the two carbon atoms

Shape of the fatty acid chain

The double bond causes a bend in the fatty acid chain

Packing of the fatty acids (density)

Therefore, cis-isomers are only loosely packed

Triglycerides formed are liquid or solid at room temperature?

Triglycerides formed from trans-isomers have high melting points – they usually solid at room temperature

56. Identify which isomer is cis and which is trans.

2.3.A3 Lipids are more suitable for long-term energy storage in humans than carbohydrates.

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57. Lipids are normally used for long-term energy storage whereas carbohydrates are used for short-term energy storage.

a. When the energy in carbohydrates is released what is produced? (Slide 84)

b. The chemical energy stored in the form of glucose is for immediate use in what process? (Slide 84)

c. Glycogen is the medium-term energy storage molecule in animals. (Slide 84) Where is it stored?

d. The lipids in the form of fats are used as energy storage in mammals. State one reason why? (Slide 85)

e. Explain some of the other functions of lipids in mammals. (Slide 86)

2.3 A.4 Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids.

58. Three fatty acids and a glycerol make up a triglyceride, identify the reason this molecule needs to be transported in a lipoprotein. (Slide 87)

59. What makes trans fats bad? (Slide 88)

60. What is the 3 in omega-3 mean and why may these types of fats be a benefit? ((Slide 89)

61. Fill in the chart used to evaluate claims (Slide 91)

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Fatty Acids Sources & Examples

Possible Effects Evidence

Omega-3 Fish, nuts & Veg. oils Reduced blood pressure and triglycerides

Good clinical evidence

Trans-fats Partially hydrogenated veg. oils and margarines, deep fried food convenience foods

Saturated fats Inc. LDL & can lead to atherosclerosis, CHD, stroke & heart attacks

Strong clinical & epidemiological evidence (correlation with disease)

62. Describe some of the key considerations for limitations for evidence of a study, use the graph on slide 93 (Slides 92-93)

2.3 A.2 Scientific evidence for health risks of trans fats and saturated fatty acids.

https://www.dairynutrition.ca/scientific-evidence/cardiovascular-disease/the-facts-on-natural-trans-fats-and-cardiovascular-diseasehttp://www.efsa.europa.eu/en/press/news/040831

63. Briefly discuss the evidence that CHD is caused by a diet high in trans fats and saturated fatty acids after reading one of the articles above

2.3 S.2 Determination of body mass index by calculation or use of a nomogram.

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Body Mass Index (BMI) is used as a screening tool to identify possible weight problems, however, BMI is not a diagnostic tool. To determine if excess weight is a health risk further assessments are needed such as:

• skinfold thickness measurements• evaluations of diet• physical activity• and family history

BMI is calculated the same way for both adults and children. The calculation is based on the following formula:BMI = mass in kilograms

(height in meters)2

n.b. units for BMI are kg m-2

The BMI status of someone can be assessed using the table to the right.

64. A man has a mass of 75 kg and a height of 1.45 meters.a. Calculate his body mass. (1)

b. Deduce the body mass status of this man using the table. (1)

c. Outline the relationship between height and BMI for a fixed body mass. (1)

65. A woman has a height of 150 cm and a BMI of 40.

a. Calculate the minimum amount of body mass she must lose to reach normal body mass status. Show all of your working. (3)

b. Suggest two ways in which the woman could reduce her body mass. (2)

66. Use the nomogram to answer the following questions. a. A woman has a mas of 75 Kg and a height of 160cm. Determine her BMI status.

b. A man is 190cm tall and has an acceptable BMI. Estimate his body mass.

BMI Status

Below 18.5 Underweight

18.5 – 24.9 Normal

25.0 – 29.9 Overweight

30.0 and Above Obese

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2.4 U.2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

67. How many essential amino acids are there? (Slide 103) .

68. Outline the differences in the R group between the four groups of amino acids (Slide 103)

2.4 U.1 Amino acids are linked together by condensation to form polypeptides. AND 2.4 S.1 Drawing molecular diagrams to show the formation of a peptide bond.

69. Condensation of amino acids is a polymerization reaction. A chain of amino acids joined together is called a polypeptide. These building reactions are part of the anabolic metabolism.

a. What organelle controls the formation of polypeptides? (Slide 104) Ribosomes

b. Draw and annotate a structural diagram below to outline how two generalized amino acids (i.e. use the R-group nomenclature) into a dipeptide through condensation, producing a peptide bond. (Slide 103)

c. Draw and annotate a structural diagram below of a generalized amino acid (label the two functional groups in the diagram). (Slide 102)

70. List three examples of amino acids synthesised by ribosomes. (Slide 103)

2.4 U.3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

71. State the three key ideas that explain the huge range of possible polypeptides: (Slide 107)

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2.4 U.4 The amino acid sequence of polypeptides is coded for by genes.72. Outline the central dogma of genetics. (Slide 108)

2.4 U.6 The amino acid sequence determines the three-dimensional conformation of a protein.2.4 U.5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

73. Outline the four different levels of protein structure. (Slides 110-113)

Structural difference of the 4 levels of Proteins

Primary

Secondary In addition to the covalent bond in primary structure there is additional

bonding internally Hydrogen bonding causes the polypeptide to fold and coil

in two ways: Alpha Helix /Beta pleated sheets

Tertiary

Quaternary all the bond types of a tertiary structure quaternary structures have two or

more polypeptides strands that aggregate together

74. Outline the structural differences between fibrous and globular proteins with an example of each. (Slice 114)

Fibrous Proteins

Globular Proteins

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75. Distinguish between globular and fibrous proteins (Slide 115)

Fibrous Globular

Shape Rounded/spherical

Function/RoleStructural (Strength and support)

Solubility (Generally) soluble in water

Amino acid sequence

Repetitive amino acid sequence Irregular amino acid sequence

StabilityMore sensitive to changes in heat pH,

etc.

ExamplesCatalase, hemoglobin, insulin,

immunoglobulin

2.4.U7 Living organisms synthesize many different proteins with a wide range of functions. 2.4.A1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.

76. Complete the table to describe each of different functions that proteins have in and outside of cells. (Slides 118-123)

Function Description Key examples

CatalysisThree are thousands of different enzymes to catalyze specific chemical

reactions within the cell or outside it.Rubisco

(Slide 118)

Some such as insulin, FSH and LH are proteins, but hormones are

chemically very diverse.Insulin

(Slide 119

Tensile strengtheningActin and

myosin (Slide 120)

Receptors Rhodopsin( Slide 121)

Tensile strengthening Fibrous proteins give tensile strength needed in skin, tendons, ligaments

and blood vessel walls.Collagen

(Slide 122)

DraglineSpider Silk(Slide 123)

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77. List a few examples of how the proteins are use biotechnologically in industry. (Slide 117)

2.4 U.8 Every individual has a unique proteome.

78. The proteome is unique to every individual.a. Define the term proteome. (Slide 124)

b. What affects the type of proteome exists? (Slide 124)

2.6.U1 The nucleic acids DNA and RNA are polymers of nucleotides. (includes 2.6.S1 Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases.)

79. Label and annotate the structures of this single nucleotide (number each Carbon). (Slide 127)

1..

Phosphate group

2..

3.

80. State the type of bond that joins a to b and b to c. (Slide 127) Covalent Bonding

81. Draw the simplified version of purines and pyrimidines, include the bonding chart for A, T, G, and C below the drawing. (Slide 128)

82. Complete the table below to show the pairings of the bases types in DNA. (Slides 129-130)

Purine PyrimidineAdenine

Cytosine

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2.6 U.3 DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs. (includes 2.6 S.1 Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases.)

83. In the space below, draw a single strand of three nucleotides, naming the bonds between them and showing the correct relative position of these bonds. (Slide 132)

84. Explain why the DNA helix is described as anti-parallel. (Slide 133)

85. In the space below, draw a section of DNA, showing two anti-parallel strands of four nucleotides each. (Slide 133)

2.6 U.2 DNA differs from RNA in the number of strands present, the base composition and the type of pentose.

86. Complete the table to distinguish between RNA and DNA. (Slide 134)

RNA DNA

BasesAdenine (A) bonds Uracil (U)

Guanine (G) bonds Cytosine (C)

Sugar

Number of strands Two anti-parallel, complementary strands form a double helix

2.6 A.1 Crick and Watson’s elucidation of the structure of DNA using model making.

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Whilst others worked using an experimental basis Watson and Crick used stick-and-ball models to test their ideas on the possible structure of DNA. After reading the article Envisioning DNA: The Nature of Science and the Search for the Double Helix and watching Tedtalk James Watson: How we discovered DNA Answer the questions below

87.c. State two benefits of modelling over an experimental approach.

d. Outline the reasons was their first model was rejected.

e. Because of the visual nature of Watson and Crick’s correct model of DNA led to other discoveries. List the

two key discoveries concerning of DNA that were found quickly after the model was published.

f. Modelling alone cannot lead to discoveries. Watson and Crick’s work was based on the experiments and insight of others. Give an example of the work of other scientists that supported their discovery.