Biochemistry Exploring Biomolecules - biogenius -...

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RBiology

BiochemistryExploring Biomolecules

About this Lesson

Biochemistry is an important concept to teach the students before they enter a Biology I course. This activity connects bonding and molecular shapes in chemistry with structure and function in biology. The activity begins with an introduction to organic chemistry, the chemistry of carbon, which is essential to the chemistry of life.

This lesson is included in the LTF Biology Module 2.

Objectives

Students will:• Gain a better understanding of organic chemistry in a biological setting• Focus on the properties and functions of the four main classes of biomolecules

Level

Middle Grades Biology and Chemistry

Common Core State Standards for Science Content

LTF Science lessons will be aligned with the next generation of multi-state science standards that are currently in development. These standards are said to be develo ped around the anchor document, A Framework for K–12 Science Education, which was produced by the National Research Council. Where applicable, the LTF Science lessons are also aligned to the Common Core Standards for Mathematical Content as well as the Common Core Literacy Standards for Science and Technical Subjects.

Code Standard Level of Thinking

Depth of Knowledge

(LITERACY)W.1

Write arguments to support claims in an analysis of substantive topics or texts, using valid reasoning and relevant and suffi cient evidence.

Apply II

Connections to AP*

This lesson addresses concepts contained in Big Ideas 2, 3, and 4 in the revised AP Biology curriculum under the following sections: 2.A.2.b, 2.A.3.a, 3.A.1.a, 3.A.1.b, 4.A.1.a, and 4.A.1.b.*Advanced Placement and AP are registered trademarks of the College Entrance Examination Board. The College Board was not involved in the production of this product.

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RTeacher Overview – Biochemistry

Materials and Resources

Each lab group will need the following:1 set models, organic molecules

Assessments

The following assessment is located on the LTF website:• Middle Grades: Chemistry• Biology: Chemistry of Life Assessment

Teaching Suggestions

Biochemistry is an important concept to teach the students before they enter a Biology I course. This activity connects bonding and molecular shapes in chemistry with structure and function in biology. The activity begins with an introduction to organic chemistry, the chemistry of carbon, which is essential to the chemistry of life.

v. 2.0, 2.0

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Answer Key

Conclusion Questions

1. Carbon has four valence electrons, so it has four available bonding sites. Carbon can form single, double, and triple covalent bonds with itself and other atoms.

2. Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).

3. Student lists will vary; check the periodic table shown in Figure 1 to make sure they list appropriate elements.

One possible list might be: sodium (Na), potassium (K), sulfur (S), phosphorus (P), and iron (Fe).

4. A functional group is a side chain or group of atoms that attach to a carbon backbone. A functional group both identifi es the molecule and provides a site for chemical reactions.

Three common functional groups are hydroxyl (OH), carboxyl (COOH) and amine (NH2), with structures detailed in the text.

5. A polymer is series of linked repeating units known as monomers.

6. Polymers are formed when two monomers join together by means of a covalent bond in a condensation or dehydration synthesis reaction. When two monomers bond, a water molecule is released as a product.

Adding a water molecule across the bond between two units in a polymer is a hydrolysis reaction. This reaction allows the polymer to be broken apart.

7. a. Amino acids

b. Monosaccharides

c. Nucleotides

8. When two amino acids covalently bond to each other by means of a dehydration synthesis reaction, the bond formed is a peptide bond. It is formed between the amine group of one amino acid and the carboxylic acid group of the other amino acid.

A dipeptide consists of two amino acid monomers joined by a peptide bond.

9. The primary structure of a protein is the sequence of amino acids that are joined together. The slightest change in this order may change the function of the protein.

A secondary structure may either be an α-helix or a β-pleated sheet. The R groups that compose the protein will determine the type of folding and intermolecular forces that will occur within the protein. Emphasize that all of this folding and coiling is due to intermolecular forces, whether attractive or repulsive.

Other complex structures may exist. These are not listed in this activity but include tertiary structure, quaternary structure, and the globular structure (joining of two or more polypeptide chains) of proteins.

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Answer Key (continued)

10. A disaccharide consists of two monosaccharides joined together. They join by means of a covalent bond known as a glycosidic bond, which occurs due to a dehydration synthesis reaction.

One common example of a disaccharide is sucrose. It is formed when glucose and fructose join together by a dehydration synthesis reaction.

11. Glycogen – The way animals store energy in the liver and muscles (branched chains)

Starch – Used by plants to form glucose

Cellulose – Probably the most common organic compound on Earth (straight chains linked together to form all types of fi bers)

12. Hydrophobic means “water-fearing.” Hydrophilic means “water-loving.”

Molecules that are hydrophobic tend to be largely nonpolar, unlike polar water molecules. Hydrophilic molecules are largely polar and are thus very attracted to water molecules.

13. Saturated compounds have all single bonds with the maximum number of hydrogen atoms. One example is animal fat, or lard.

Unsaturated compounds have some type of multiple bonding and less than the maximum number of hydrogen atoms. One example is vegetable oil.

14. Biological membranes are composed largely of phospholipids. This gives them the unique characteristic of one polar end, which will attract to water, and one nonpolar end, which will repel water.

15. DNA is double-stranded; RNA is single-stranded.

DNA contains the sugar deoxyribose; RNA contains the sugar ribose.

DNA has four bases: adenine (A), thymine (T), guanine (G), and cytosine (C); RNA also has four bases: adenine (A), uracil (U), guanine (G), and cytosine (C).

Some students may cite the purpose: DNA carries the genetic code whereas RNA directs the building of proteins

16. Jeff Jones is the biological father. The child has matching second and third bands to the father whereas bands one and four match the mother.

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Biology

BiochemistryExploring Biomolecules

Biochemistry is the study of chemical reactions in living systems. The very name implies a connection between biology and chemistry. There are many types of biomolecules (very big molecules) that play a vital role in living systems.

Purpose

In this activity, you will examine the fundamentals of organic chemistry and relate them to the four main classes of macromolecules.

Materials

Each lab group will need the following:1 set models, organic molecules

1A 8A

1

H 2A 3A 4A 5A 6A 7A

2

He3

Li

4

Be

5

B

6

C

7

N

8

O

9

F

10

Ne11

Na

12

Mg

13

Al

14

Si

15

P

16

S

17

Cl

18

Ar19

K

20

Ca

21

Sc

22

Ti

23

V

24

Cr

25

Mn

26

Fe

27

Co

28

Ni

29

Cu

30

Zn

31

Ga

32

Ge

33

As

34

Se

35

Br

36

Kr37

Rb

38

Sr

39

Y

40

Zr

41

Nb

42

Mo

43

Tc

44

Ru

45

Rh

46

Pd

47

Ag

48

Cd

49

In

50

Sn

51

Sb

52

Te

53

I

54

Xe55

Cs

56

Ba

72

Hf

73

Ta

74

W

75

Re

76

Os

77

Ir

78

Pt

79

Au

80

Hg

81

Tl

82

Pb

83

Bi

84

Po

85

At

86

Rn87

Fr

88

Ra

104

Rf

105

Db

106

Sg

107

Bh

108

Hs

109

Mt

110

Ds

111

Rg

112

Cp

113

Uut

114

Uuq

115

Uup

116

Uuh

57

La

58

Ce

59

Pr

60

Nd

61

Pm

62

Sm

63

Eu

64

Gd

65

Tb

66

Dy

67

Ho

68

Er

69

Tm

70

Yb

71

Lu89

Ac

90

Th

91

Pa

92

U

93

Np

94

Pu

95

Am

96

Cm

97

Bk

98

Cf

99

Es

100

Fm

101

Md

102

No

103

Lr

Figure 1. Basic periodic table.


Student Activity – Biochemistry

Organic Chemistry

Organic chemistry is the study of the chemistry of carbon. When studying bonding, you may remember that carbon has four valence electrons available for bonding. Carbon is unique in that it may form single, double, and triple covalent bonds with other carbon atoms. There exist more organic compounds than inorganic (without carbon) compounds.

Carbon chemistry forms the basis of the chemistry of living things. The molecules that make up living systems are predominantly composed of the elements carbon, oxygen, nitrogen, and hydrogen. The periodic table shown in Figure 1 highlights the elements essential to life on this planet.

As carbon atoms join together and form chains, there are often side chains that form along the carbon backbone. We refer to these clusters of atoms as functional groups. The functional group is the actual building block of the compound that determines the characteristics of that compound. For example, one common functional group is the hydroxyl group, –OH. When this group is found on a carbon chain, it makes the molecule slightly polar like a water molecule.

Long carbon chains without functional groups have little or no attractive forces, and are therefore nonpolar molecules. For example, when crude oil spills into the ocean it does not mix with the water because the water is polar and the oil is nonpolar. An old saying to remember this is, “Like dissolves like.”

The functional groups added to the carbon compounds in living systems are extremely vital because most living organisms are composed largely of water, a polar compound. Although there are many functional groups that exist, three are essential to understanding the structure of the biomolecules that we will study here.

Hydroxyl Group: –OH

This group attaches by taking a hydrogen atom off the carbon chain and replacing it with an –OH group. This action creates something known as an alcohol. Figure 2 shows the structure for ethanol.

C C

O

HH

H

HH

H

Figure 2. Ethanol



Carboxylic Acid Group: –COOH

The carbon atom in this group is double-bonded to one oxygen atom and single-bonded to the hydroxyl group, leaving one bonding site open to attach to the main carbon chain. The compound shown in Figure 3 is ethanoic acid,or more commonly referred to as acetic acid or vinegar.

C C

O

H

H

H

O

H

Figure 3. Ethanoic acid

Amine Group: –NH2

This group attaches to the main carbon chain in much the same way as the hydroxyl group. A hydrogen atom is removed from the main carbon chain, allowing the nitrogen to attach in its place. The “R” in Figure 4 represents “radical,” which is the “rest” of the carbon chain.

N

H

H

R

Figure 4. Amine group

Adding any atom or group of atoms to a carbon chain (like the ones listed here) will change the molecule’s shape, which changes its function, physical properties, and intermolecular attractive forces.

Large carbon molecules are known as macromolecules. These are actually large polymers. A polymer is composed of repeating units of smaller carbon units known as monomers (hence the prefi xes, “mono” = one; “di”= two; “tri” = three; “poly” = many).

The monomers are joined together in a chemical reaction known as a condensation reaction or a dehydration synthesis because water molecules drop out of the chain when the C—C bond forms, linking monomers to form polymers. Breaking a polymer down into monomers occurs by an opposite reaction known as hydrolysis, which means “splitting with water” or adding water to break bonds. Remember that forming bonds releases energy whereas breaking bonds requires energy.



Four main classes of biomolecules or polymers are essential for life: • Proteins • Carbohydrates• Lipids • Nucleic acids

Proteins

Proteins are biomolecules composed of many amino acids that can provide energy to living systems. All amino acids have a carboxyl group, –COOH, and an amine group, –NH2, attached to a central carbon atom. There are 23 amino acids, 20 of which are common to all living organisms.

Look at the structures for the amino acids in Figure 5. The diagram shows how amino acid molecules are joined together; notice that the difference between them is the R group. The amino acids are the monomers, and when joined by a condensation reaction a water molecule drops out and a bond is formed between the amine group of one amino acid and the carboxyl group of the other amino acid. The bond linking the amino acid molecules together is known as a peptide bond.

C

O

OH

H

H

H C

CH 3

C

CH 2 SH

Glycine Alanine Cysteine

Peptide bonds

H2OH2O

CN

H

H

CNH

H O

OH

H

N CH

H

OH

O

C

OH

H

H C

CH 3

C

CH 2 SH

CN

H

H

CN

H O H

N C

H

OH

O

Figure 5. Amino acids and peptide bonds

Proteins are nothing more than chains of amino acids. The 20 amino acids can be joined and rearranged in many ways, much like the 26 letters of the alphabet. Most proteins are series of hundreds of amino acids. The sequence of these amino acids determines the protein’s structure and function. Even the slightest change in the amino acid sequence will change the protein. For example, the difference between normal hemoglobin and hemoglobin in individuals with sickle-cell anemia is only two amino acids.



Some examples of common materials composed of proteins include: • Hair • Tendons • Ligaments• Silk• Hormones – These proteins transport substances throughout the body and fi ght infection.

Insulin is a hormone produced in the pancreas.• Enzymes – These proteins control the body’s chemical reactions. Pepsin is a common

digestive enzyme.

There are many levels of structure to most proteins. The primary structure is the basic amino acid sequence—the order in which they are joined. However, the R groups attached to the amino acid often form intermolecular attractive forces with other proteins or with themselves, which leads to folding, bending, or joining of many proteins together for some very complex structures.

The two most common types of intermolecular attractions that exist within and between proteins are disulfi de bridges between two adjacent sulfur atoms and hydrogen bonding between the hydrogen on one molecule and the fl uorine, oxygen, or nitrogen on an adjacent molecule. Remember that even though they are called “hydrogen bonds” these are merely an attractive force, not a true bond.

These intermolecular attractions often cause twisting and folding of the protein. Two common structures are shown here: the α-helix (like a spring, Figure 6) and the β-pleated sheet (like a paper fan, Figure 7). The shape of the protein is easily altered by a change in temperature or pH. We call this alteration of shape denaturing the protein. When an egg is boiled, the clear liquid of the egg turns white—cooking is a denaturing of the protein.

Figure 6. α-helix Figure 7. β-pleated sheet



Carbohydrates

Carbohydrates have the general chemical formula of Cn(H2O)n, and thus the name is appropriate: hydrated (water) carbons. Like proteins, carbohydrates also provide energy to living systems. Carbohydrates exist as monosaccharides, disaccharides, and polysaccharides.

The monomer unit of a carbohydrate is a monosaccharide, or simple sugar. Glucose and fructose are examples of monosaccharides that you may already know. Most naturally occurring carbohydrates contain more than one monosaccharide unit. Monosaccharides link together in much the same way that amino acid molecules link in proteins—by condensation or dehydration synthesis reactions.

The bond formed between two monosaccharides is known as a glycosidic bond. Sucrose, common table sugar, is a disaccharide formed by linking the two monosaccharides glucose and fructose (Figure 8).

Three important polysaccharides that are made from glucose monomers are: • Glycogen – The way animals store energy in the liver and muscles, using branched chains• Starch – Used by plants to form glucose• Cellulose – Probably the most common organic compound on Earth, composed of straight

chains linked together to form all types of fi bers (like cotton)

OO

CH 2 OH

HH

HOOH

H

H

OH

H

OH

CH 2 OH

HO

H

OH

HO

H

H

CH 2 OH

H2OGlucose Fructose

Glucose -α (1-2) - Fructose

Sucrose

O O

CH 2 OH

HH

HOOH

H

H

OH

H

CH 2 OH

H

OH

HO

H

H

CH 2 OH

O

Figure 8. Glycosidic bond between sugars



Lipids

Lipids are large organic molecules that are nonpolar, and thus not very soluble in water. Like proteins and carbohydrates, lipids serve as energy for living systems. Lipids are very effi cient energy-storage molecules, storing about two times the amount of energy as proteins or carbohydrates. The simplest lipids are known as fatty acids. A fatty acid is composed of a long, straight carbon chain with a carboxyl group, –COOH, at one end.

The two ends of the fatty acid have very different properties. The long, straight carbon chain is nonpolar and will repel water (hydrophobic, or “water-fearing”) whereas the carboxyl group on the opposite end is polar and is very attracted to water (hydrophilic, or“water-loving”). Figure 9 shows the diagrams of a glycerol and afatty acid.

C C C C C C C C C C C C C C C CHO

H

H

H

H

H H H H H H H H H H H HH

H H H H H H H H H H H H HH

O

C

C

H OH

C

H

H

OH

H

H OH

Glycerol Fatty acid

Figure 9. Glycerol and fatty acid

This unique structure of one polar end and one nonpolar end allows the fatty acid to form membranes when dropped into water—one end attracts the water while the other end repels the water. This property is what gives soaps and detergents their cleaning power (Figure 10).

Figure 10. Fatty acid forming a membrane

(Water)

(Water)

Hydrocarbonchains

Phosphategroup



Fatty acids may be saturated or unsaturated fats. Saturated fats contain all single bonds between carbons—they are said to be “saturated” with hydrogen. Unsaturated fats contain some multiple bonding. The multiple bonds replace some of the hydrogen atoms.

Lipids may be divided into three basic categories according to their structure: • Triglycerides – As the name implies, three fatty acids are joined to a glycerol. Saturated

triglycerides are usually solids at room temperature whereas unsaturated triglycerides are usually liquids at room temperature. Shortening, animal fats, and oils belong in this category.

• Phospholipids – Two molecules of fatty acid joined to a glycerol and a phosphate group, PO4

3- (Figure 11). Cell membranes are composed of two layers of phospholipids, making a lipid bilayer.

• Waxes – A long fatty acid chain joined to a long alcohol chain. These compounds are highly waterproof and form protective coatings on plants and animals. For example, earwax helps prevent bacteria from entering into the middle ear.

CCH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH 3

O

C

CH 2

H

C

H

H O

CCH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH 3

O

O

O -

OH

H

H

H

H

CH 3

CH 3

H3C

Polar head

Nonpolar tails

OPHOCCN+

Figure 11. Phospholipid



Steroids are a special class of lipids composed of four fused carbon rings with various functional groups attached to them. One of the most familiar steroids is cholesterol, which is necessary for nerve cells and other body cells to function normally. The male hormone, testosterone, and the female hormone, estrogen, also belong to this category. Some typical steroids are shown in Figure 12.

CH3

CH3

CH3

CH3

CH3

HO

CH3

CH3

O

OHCCH OH2

OHO

O

CH3

CH3CCH3

O

O

CH3

CH3OH

CH3

HO Estradiol

OH

Cholesterol

CH3

CH3

CH3

CH3

CH3

HO

TestosteroneCortisol

ProgesteroneCholecalciferol

Figure 12. Common steroids



Nucleic Acids

Nucleic acids are the group of biomolecules that transmit genetic information. The two nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA contains the information necessary to pass on the genetic code from generation to generation.

The monomer in DNA is a nucleotide. A nucleotide consists of a sugar (deoxyribose), a phosphate group, and a base (Figure 13).

Only four bases exist in DNA,which are sequenced in different orders to code for everything living, past or present. Human DNA consists of almost 3 billion base pairs. The four bases are adenine, thymine, guanine, and cytosine.

POCH2

HH H

H

HO

O

C C

C CBase

HO O

POCH2

HH H

H

HO

O

C C

C CBase

HO O

CH2

HH H

H

H

O

C C

C CBase

PO

HO O

Repeatingunits alongDNA chain

POCH2

HH H

H

HO

O

C C

C CBase

O

O O- -

H

Figure 13. DNA and its nucleotides



Deoxyribonucleic acid (DNA) is a double-stranded, helically shaped molecule (Figure 14). The strands are held together by intermolecular attractions known as hydrogen bonds. DNA is found in the nucleus of every cell.

Figure 14. Double helix of DNA

Ribonucleic acid (RNA) is single-stranded and also composed of monomers known as nucleotides. DNA in the nucleus provides the code for creating RNA. The two main differences between the DNA and the RNA nucleotides are that RNA has a different sugar: DNA has deoxyribose whereas RNA has ribose (Figure 15).

C C

C

O

CH H

OH H

H

CH 2 OH

H

OH

C C

C

O

CH H

OH OH

H

CH 2 OH

H

OH

Deoxyribose Ribose

Figure 15. Sugars of DNA and RNA



The four bases for RNA are adenine, uracil (instead of thymine), guanine, and cytosine. RNA is responsible for carrying the genetic code from the nucleus to the cytoplasm of the cell, where it codes for protein synthesis. The bases in DNA and RNA are shown in Figure 16.

Figure 16. Bases of DNA and RNA

Much has been learned about DNA in the past century. One really useful tool that is in widespread use is DNA fi ngerprinting. With only a small sample of blood, hair, skin, or other tissue, crimes have been solved and parents have been identifi ed. How does this work? 1. Enzymes cut the DNA into fragments. Enzymes recognize specifi c base sequences, so they

know where to cut. The fragments will be of different lengths for different people.

2. These fragments are loaded into a gel and subjected to an electric fi eld. DNA is negatively charged, so it is attracted to the positive terminal of the fi eld.

3. Heavy fragments move slowly through the matrix of the gel and do not travel as far as smaller fragments.

If a person’s DNA fragments are loaded in one part of the gel and a sample from the crime scene or the potential parent is loaded onto the same gel, comparisons can easily be made. If the fragments match, the samples most likely came from the same person. There is only about a 1 in 5 billion chance that matching DNA comes from two different sources—nearly impossible considering there are about 7 billion people on our planet.



Conclusion Questions

1. Organic chemistry is the study of carbon compounds. What unique bonding characteristics does the carbon atom have that allows for so many organic compounds to exist?

2. List four elements that compose most of the molecules in living systems.

3. List fi ve other elements that are essential to life on this planet. (Hint: Use the periodic table given in the notes—there are many more than fi ve.)

4. Defi ne functional group. Name and draw three functional groups that are common in biomolecules.

5. What is a polymer?



Conclusion Questions (continued)

6. How are polymers formed? How are they broken apart?

7. Name the monomer unit for each of the following biomolecules:

a. Proteins

b. Carbohydrates

c. Nucleic acids

8. Describe how a peptide bond is formed. What is meant by the term dipeptide?




9. Discuss and describe the four levels of structural organization within a protein.

10. Explain the term disaccharide. Give one common example, and tell how it is formed.

11. Glucose monomers are responsible for many carbohydrate polymers. List three glucose monomers and describe each of their functions.

12. Distinguish between the terms hydrophobic and hydrophilic. Structurally, how do molecules of these two groups differ?

13. Describe what is meant when a lipid is described as saturated or unsaturated. Give one common example for each category.




14. Explain why biological membranes are composed largely of lipids.

15. Describe three differences between DNA and RNA.

16. Examine the DNA fi ngerprint analysis in Figure 17. “M” is the mother, Jennifer Jones. “C” is the child, George Jones. “AF” is the alleged father, Jeff Jones.

Is Jeff Jones the biological father of George or not? Justify your answer. Remember that to conclude the alleged father is truly the biological father, every band in the child’s DNA fi ngerprint that does not match the mother’s DNA fi ngerprint must match the father’s.

Figure 17. DNA comparison for paternity

Biochemistry Exploring Biomolecules - biogenius -...

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