Commack High School HL Biology

Topic

Two:

Biochemistr

y

Seven Quest

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2.1 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. What are the four most common elements found in living things? (Slide 6)

2. Provide a brief describe the role these four elements may play in a living thing (Slides 7-10)

3. The structure of DNA was discovered in 1953, since then molecular Biology has transformed our understanding of living processes.a. Outline the relationship between genes (DNA) and polypeptides. (Slide21)

b. Describe the reductionist approach that a molecular biologist uses discover the working of a metabolic pathway. (page 21-22)

c. Explain why ultimately the reductionist approach used by molecular biologists might be a limited one. (page 21-22)

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

4. 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? (page 23)

b. Explain why Carbon can form four bonds with up to four different atoms, and explain why. (slide 23)

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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.

5. Vitalism is a theory that nowadays has no credit.a. Describe the central tenant that Wöhler falsified.

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

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

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

Key features Examples

Carbohydrates

(Slide 26)

Lipids(Slides 29-30)

Proteins(Slide 32)

nucleic acids(Slide 33)

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

7. Draw structures of alpha and beta glucose and ribose. Number the carbon atoms correctly. Which sugar is a pentose? Which is a hexose? (Slides 27-28)

8. 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 29)

9. Draw a lipid molecule. (Slide 30)

10. Draw the generalized structure of an amino acid. Label and annotate the diagram to show the different groups that comprise amino acids. (Slide 34)

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

11. Which type of molecule is shown in the diagram to the right?

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12. 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. (Slide 39-42)

13. Distinguish between the terms anabolism and catabolism.

anabolism catabolism

Synthesis or breakdown?Energy required or released

Name a process

Products

Water produced or used?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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14. Annotate the diagram below to complete your notes on anabolism and catabolism. In the carbohydrate section add a named example, include both the names of the molecules and enzymes.

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

15. Draw a minimum of three molecules to show the hydrogen bonding between them. The diagram should be labelled and annotated to indicate: (Slide 46)

Large oxygen atom Small hydrogen atom Covalent bond: δ+ (indicate the region of each molecule which possesses a slightly positive charge)

and δ- (indicate the region of each molecule which possesses a slightly negative charge) Weak hydrogen bond between δ+ and δ- parts of neighboring water molecules.

16. Explain why the water molecule is polar. Refer to electrons and covalent bonding in your answer.(Slide 46)

2.2 A.2 Use of water as a coolant in sweat. (Slides 47-50)

17. Outline the consequences, to cells, of not cooling the human body.

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18. What property of water means it is useful as a coolant?

19. Explain how the body exploits this property of water to cool the body using sweat.

20. Referring to the table on page 13 outline how the polarity of water has affected the thermal properties of water and its ability to remain a liquid at most temperatures found on the surface of the planet.

2.2 A.1 Comparison of the thermal properties of water with those of methane. (Slide 51)

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

Methane Water

Formula H2O

Molecular mass 16

Bonding Single covalent

Polarity polar

Density (g cm-3) 0.46

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

Latent heat of vaporization (J g-1)

Melting point (oC) 0

Boiling point (oC) 100

2.2 U.2 Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water.

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22. 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 52)

Adhesive (Slide 53)

Thermal (Slide 54)

Solvent (Slide 55)

2.2 U.3 Substances can be hydrophilic or hydrophobic.

23. Define the terms:a. Hydrophilic (Slide 56)

b. Hydrophobic (Slide 57)

24. Complete the table to give examples of hydrophilic and hydrophobic molecules.

Polar, non-polar, charged? Examples

Hydrophilic

Hydrophobic

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.

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Complete the table to describe the transport of key substances in the blood. 25.

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

Glucose(Slide 58)

Amino acids(Slide 59)

Cholesterol(Slide 60)

Fats(Slide 61)

Oxygen(Slide 63)

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

26. List the three types of carbohydrates below. (Slide 66)

27. 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 72)

b. What else is needed to make the reaction occur? (Slide 72)

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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 72))

d. Monosaccharides are quickly and absorbed and readily used in cell respiration to release energy List the three key examples of 6-carbon monosaccharides. (Slides 73-75)

28. Complete the table to summarise the common forms of disaccharides. (Slides 73-75)

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.

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29. All three common polysaccharides are formed by the condensation of glucose molecules. Their properties however are markedly different complete the table to summarise how and why. (worksheet 43 & 44/internet)

Polysaccharide

Cellulose(Slide 78)

Starch (Slides 79-80)Glycogen(Slide 81)

Amylose Amylopectin

Size / number of glucose

molecules

variable, typically 1,500 units

up of 300-3,000 glucose units

Orientation and / or bonding of

glucose molecules

1-4 bonds between alternately oriented (upwards and downwards) glucose molecules

Condensation reactions link carbon atom 1 to carbon atom 4 on the next α-glucose

chain - straight or bent? curved bent

chain - branched or un-branched? un-branched branched

Properties of the molecule

Insoluble, does not affect the osmotic balance of cells

Molecule vary in size, easy to add / remove glucose units

Function/use

Useful for glucose, and consequently energy, storage, e.g. in seeds and storage organs such as potato cells.

Temporary store in leaf cells when glucose is being made faster by photosynthesis than it can be exported.

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

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30. The easiest way to use jmol is to use the ready-made models from on the Biotopics website (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 atoms

Carbon –

Hydrogen –

Oxygen –

b. Using the models identify and describe the differences between glucose, sucrose and fructose (hint: descriptions will be clearest if you refer to the numbered carbon atoms, see 2.3 U.1)

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. Select the amylopectin model and zoom in on the branch point. This glucose sub-unit is bonded how many others and which carbon atoms are used for bonded compared with the un-branched amylose molecule?

f. 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.

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.

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31. 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 87)

b. Describe the type of reaction that brings together the fatty acids to glycerol (Slide 88)

c. Write out the condensed formulas for glycerol and a fatty acid. (Slide 89)

d. Describe the term saturated when used in reference to fatty acids. (Slide 90)

e. For each of the following fatty acids deduce whether it is saturated, monounsaturated or polyunsaturated, Give reasons for each answer. (Slide 92) Oleic Acid

Caproic Acid

α-Linolenic Acid

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

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32. Unsaturated fatty acids are described as being cis or trans isomers depending on the structure of the double bonds in the fatty acids. (Slide 93)a. Complete the table to compare and contrast cis and trans isomers.

Cis-isomers Trans-isomers

Structural diagram

Natural / synthesised

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

Positioning of the hydrogen atoms

Shape of the fatty acid chain

The double bond causes a bend in the fatty acid chain

Packing of the fatty acids (density)

Trans-isomers can be closely packed

Triglyderides formed are liquid or solid at room temperature?

33. Identify which isomer is cis and which is trans. Give reasons for your decisions. (Slide 95)

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

______ -

______ -

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34. 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 98)

b. The chemical energy stored in the form of glucose is for immediate use in what process? (Slide 98)

c. Glycogen is the medium-term energy storage molecule in animals. (Slide 98) Where is it stored?

d. The lipids used in energy storage are fats in mammals. State one reason why? (Slide 100)

e. Explain some of the other functions of lipids in mammals. (Slide 101)

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

35. What does the term trans-fat evaluation mean? (Slide 102)

36. List some reasons why trans fats were invented. (Slide 102)

37. How does the shape of a trans-fat change? (Slide 102)

38. What are the advantages to eating lipids containing the fatty acid omega-3? (Slide 103)

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39. Fill in the chart used to evaluate claims (Slide 106)

Fatty Acids Sources & Examples Possible Effects EvidenceOmega-3 Reduced blood

pressure and triglycerides

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

Strong clinical & epidemiological evidence

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

40. Describe some of the key considerations for limitations for evidence of a study (Slide 108)

41. Read the analysis on the article on “Health Warning: Exercise Makes You Fat” published on Bad Science (http://www.badscience.net/2009/08/health-warning-exercise-makes-you-fat/).

a. Is the health claim a valid one?

b. Review the analysis and identify which key considerations of strengths and limitations were addressed.

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

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42. There have been many claims about the effects of different types of fat on human health. The main concern is coronary heart disease (CHD). (Slide 109)

a. Outline a causes of CHD. (Slide 109)

b. Discuss the evidence that CHD is caused by a diet high in trans fats and saturated fatty acids. (Bottom of Slide 109)

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

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 metres)2

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

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

43. 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)

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

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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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)

45. 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.

http:// helid.digicollection.org /documents/h0211e/p434.gif

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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.

46. 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 119)

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 119)

c. Draw and annotate a structural diagram below of a generalized amino acid (label the two functional groups in the diagram). (Slide 120)

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

47. How many different amino acids do we know of? (Slide 120)

42. List three examples of amino acids synthesised by ribosomes. (Slide 122)

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

43. State the three key ideas that explain the huge range of possible polypeptides: (Slides 123-125)

48. If a polypeptide contains just 5 amino acids calculate the how many different polypeptides can be created.

49. State both the name of the longest polypeptide known and approximately how many amino acids it contains. (Hint: Cover page)

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2.4 U.4 The amino acid sequence of polypeptides is coded for by genes. 50. Outline the central dogma of genetics. (Slide 127)

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 . 51. The R-groups of an amino acid are classified as having one of a number of different properties. List the

properties can they possess. (Slide 128)

52. Outline the four different levels of protein structure. (Slide 134)

Notes Fibrous or Globular

Primary (polypeptide)

• The order / sequence of the amino acids of which the

protein is composed

• Formed by covalent peptide bonds between adjacent

amino acids

• Controls all subsequent levels of structure

Neither (– will fold to

become one of the

subsequent levels of

structure)

Secondary(Slide 119/page 96-97/worksheet

219)

Tertiary(Slide 122/page 96-97/worksheet

219)

Quaternary(Slide 123/page 96-97/worksheet

219)

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53. Distinguish between globular and fibrous proteins (Slide 136)

Fibrous Globular

Shape

Function/Role

Solubility

Amino acid sequence

Stability

Examples

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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.

54. Complete the table to describe each of different functions that proteins have in and outside of cells. (Slides 137-138)

Function Description Key examples

Rubisco

Muscle contraction Actin and myosin together cause the muscle contractions used in

locomotion and transport around the body.

Tubulin is the subunit of microtubules that give animals cells their

shape and pull on chromosomes during mitosis.

Fibrous proteins give tensile strength needed in skin, tendons,

ligaments and blood vessel walls. collagen

Blood clotting

Proteins in blood help transport oxygen, carbon dioxide, iron and

lipids.

Cell adhesion

Membrane transport

Insulin

Receptors

Binding sites in membranes and cytoplasm for hormones,

neurotransmitters, tastes and smells, and also receptors for light in

the eye and in plants.rhodopsin

Packing of DNA

This is the most diverse group of proteins, as cells can make huge

numbers of different antibodies. immunoglobulins

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2.4 U.8 Every individual has a unique proteome.

55. The proteome is unique to every individual.a. Define the term proteome. (Slide 145)

b. What affects the type of proteome exists? (Slide 145)

c. What is a genome? (Slide 146)

2.4 A.2 Denaturation of proteins by heat or by deviation of pH from the optimum.

56. Describe the term denaturation. Refer to the structure of the protein in your answer. (Slide 148)

57. What factors can commonly cause denaturation and how? (Slide 148)

58. What is an adaptation the Thermophiles have that make life possible of them? (Slide 149)

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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.)

59. Label and annotate the structures of this single nucleotide (number each Carbon). (Slide 153)

a.

b.

c.

60. State the type of bond that joins a to b and b to c. (Slide 154)

61. Complete the table below to show the pairings of the bases in DNA and RNA. (Slide 155)

Purine Pyramidine

62. 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.

63.

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64. Explain why the DNA helix is described as anti-parallel. (Slide 160)

65. Explain the relevance of the following in the double-helix structure of DNA:(Slides 155-158)a. Complementary base pairing

b. Hydrogen bonds

c. Relative positioning of the sugar-phosphate backbone and the bases

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.)

66. In the space below, draw a section of DNA, showing two anti-parallel strands of four nucleotides each. (Slide 160)

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

67. Complete the table to distinguish between RNA and DNA. (Slide 162)

RNA DNA

Bases

Adenine (A)Guanine (G)Uracil (U)

Cytosine (C)

Sugar

Number of strandsTwo anti-parallel,

complementary strands form a double helix

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2.6.A1 Crick and Watson’s elucidation of the structure of DNA using model making.

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

68.a. State two benefits of modelling over an experimental approach.

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

c. 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.

d. 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.

Citations:

Allott, Andrew. Biology: Course Companion. S.l.: Oxford UP, 2014. Print.Paine, Chris http://bioknowledgy.weebly.comTaylor, Stephen. "Essential Biology 03.3 07.1 DNA Structure.docx." Web. 1 Oct. 2014.