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1

Chapter 02

Lecture Outline

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2

Chemistry of Life

3

Points to ponder

• How are living things organized from atoms to molecules?

• What is pH and how is it important to living organisms?

• What are the four macromolecules found in living organisms?

• What are the structure (subunits) and function of these four macromolecules?

• How are proteins organized and how is their shape important to their function?

• How are DNA and RNA similar and how are they different?

4

Building blocks from large to small

• Matter is anything that has mass and takes up

space.

• Elements are the basic building blocks of matter

that cannot be broken down by chemical means.

• Atoms are the smallest units of an element that

retain the element’s physical and chemical

properties. These bond together to form

molecules.

2.1 From Atoms to Molecules

5

Elements • Atomic symbol

• Atomic mass

• Atomic number


Figure 2.1 A portion of the

periodic table of elements.

I

1

H

2

V

3 4 5

B

6

C

7

N

8

O

9

F

P S

K

atomic number

atomic symbol atomic mass

1.008

Li Ne

He

4.003

VIII

II III IV VI VII

10

Be

20.18 19.00 16.00 14.01 12.01 6.941 9.012 10.81

11 18

Na

22.99

19

39.10

24.31

Mg

12

Ar

39.95

17 16 15 14 13

Al Si Cl

35.45 32.07 30.97 28.09 26.98

20 31 32 33 34 35 36

83.60

Kr

79.90

Br

78.96

Se

74.92

As

72.59

Ge

69.72

Ga

40.08

Ca

Peri

od

s

1

2

3

4

Groups

6

Subatomic particles of atoms

• Neutrons are neutral (uncharged).

• Protons are positively charged.

• Neutrons and protons make up the nucleus.

• Electrons are negatively charged and orbit

around the nucleus.



Figure 2.2 The

atomic structure

of select

elements.

Subatomic particles of atoms

0

1

1

1p

hydrogen

H

Subatomic Particles

Atomic Mass Unit

(AMU)

Charge Particle

Proton

Neutron

Electron 0

+1

–1

6p

6n

8p

8n

7p

7n

oxygen

O

carbon

C

nitrogen

N

8

Isotopes

• Isotopes are atoms that have the same atomic number but a different atomic mass because the number of neutrons differ.

• Radioisotopes are useful in dating old objects, imaging body organs and tissues through X-rays, and killing cancer cells.

• Radiation can be harmful by damaging cells and DNA and/or causing cancer.


Isotopes 2.1 From Atoms to Molecules

Figure 2.3 Medical uses for

low-level radiation.

a.

larynx

thyroid gland

trachea

missing

portion

of organ

2.3a: © Biomed Commun./Custom Medical Stock Photo; 2.3b(patient): © National Institutes of Health; 2.3b(scan):

© Mazzlota et al./Science Source

b.

10

Molecules

• Made of atoms that are bonded together

• Can be made of the same atom or

different atoms


11

Ionic bonds

• Atoms in this type of bond donate or take on electrons

• Result in a stable outer shell

• Occur between particles that are charged (ions)


12


Figure 2.5 Formation of an ionic bond.

Ionic bonds

13

• Atoms in this type of bond share electrons

• Result in a stable outer shell


Covalent bonds

14


+

+

b. When two oxygen atoms covalently bond, oxygen gas results.

8p

8n

8p

8n

8p

8n

8p

8n

1p

1p

8p

8n

1p

1p

oxygen

O

2 hydrogen

2H

a. When an oxygen and two hydrogen atoms covalently bond, water results.

water

H2O

oxygen

O2

oxygen gas

O2

oxygen

O2

8p

8n

Figure 2.6 Covalent bonds.

Covalent bonds

15

What are the properties of water?

• Water is liquid at room temperature.

• Liquid water does not change temperature

quickly.

• Water has a high heat of evaporation.

• Frozen water is less dense than liquid water.

• Molecules of water cling together.

• Water is a solvent for polar molecules.

2.2 Water and Life

16

What bond holds water molecules

together?

• Hydrogen bonds

occur between a

hydrogen in a

covalent bond and

a negatively charged

atom.

• These are relatively

weak bonds.

2.2 Water and Life

H H

Hydrogen bonding between water molecules

O

hydrogen

bond

+

+ -

Figure 2.7b Hydrogen bonds and water molecules.

17

Acids and bases

• Acids are substances that dissociate and

release hydrogen ions (H+).

• Bases are substances that take up

hydrogen ions (H+) or release hydroxide

ions (OH-).

2.2 Water and Life

18

What is the pH scale?

• A measure of hydrogen ion (H+) concentration

• Working scale is between 0 and 14 with 7 being

neutral

• A pH below 7 is acidic and above 7 is basic

• The concentration of hydrogen ions between

each whole number changes by a factor of 10

2.2 Water and Life

19

Looking at the pH scale 2.2 Water and Life

H+ OH–

ac

idic

b

as

ic

stomach acid, lemon juice

vinegar, cola, beer

1

0

2

3

4

5

6

7

8

9

H+ Ion

Concentration pH Value Examples

hydrochloric acid

tomatoes

black coffee

urine

pure water

seawater

baking soda

Great Salt Lake

household ammonia

household bleach

sodium hydroxide

10-1 100

10-3

10-4

10-5

10-6

10-7

10-8

10-9

10-10

10-11

10-12

10-13

10-14

10-2

14

13

12

11

10

Figure 2.10

The pH scale.

20

Making and breaking down

organic molecules

• Dehydration reaction – the removal of water

that allows subunits to link together into

larger molecules

• Hydrolysis reaction – the addition of water

that breaks larger molecules into their

subunits

2.3 Molecules of Life

21

How do we build and break down

organic molecules?


subunit subunit

hydrolysis

reaction

subunit subunit

subunit subunit

dehydration

reaction

subunit subunit H

H2O

H2O

b.

a.

OH

OH H

Figure 2.11 The

breakdown and synthesis

of macromolecules.

22

What organic molecules are

found in living organisms?

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids


23

1. What are carbohydrates?

• Made of subunits called monosaccharides

• Made of C, H, and O in which the H and O atoms are in a 2:1 ratio

• Function as short- and long-term energy storage

• Found as simple and complex forms

2.4 Carbohydrates

24

• Monosaccharide –

1 carbon ring as

found in glucose

• Disaccharide –

2 carbon rings as found in maltose

What are simple carbohydrates? 2.4 Carbohydrates

O H

O H

H

H

H

H

H O

C6H12O6

O H

H O

C

C

C

C C

4

5

6

3 2

1

O H H

H

H

CH2OH

H O O

OH HO

OH

CH2OH

maltose

O O

O

C12H22O11

CH2OH CH2OH

Figure 2.12 The synthesis and breakdown of a disaccharide.

25

What are complex carbohydrates?

• Polysaccharides are made of many carbon rings.

• Glycogen is the storage form in animals.

• Starch is the storage form in plants.

2.4 Carbohydrates

O

H

O

O

O H

H

H O H H

starch

granule

cell wall

potato cells

nonbranched

branched

H OH H OH OH H OH H

O O

H O

OH H H

H OH OH H

H O

H H H H H O

CH2OH CH2OH CH2OH CH2OH

© Jeremy Burgess/SPL/Science Source

Figure 2.13 Starch is a plant complex carbohydrate.

26

2. What are lipids?

• Molecules that do not dissolve in water

• Used as energy molecules

• Found in cell membranes

• Found as fats and oils, phospholipids, and

steroids

2.5 Lipids

27

How are fats and oils different?

• Fats • Usually animal origin

• Solid at room temperature

• Function for long-term energy storage, insulation from heat loss, and cushion for organs

• Oils • Usually plant origin

• Liquid at room temperature

2.5 Lipids

28

What is the structure of fats and

oils? • A glycerol molecule and 3 fatty acid tails

2.5 Lipids

C

C

H H H H H H

C

H H H

C C C

H

C

C

H

C

H

H H H H

C

H H

C

H

C

+

C

H

H

3 fatty acids glycerol fat molecule 3 water

molecules

dehydration reaction

OH

OH

OH

H

H

H

H

H C

C

C

H H H H

H C C C C C O

HO

HO

O

HO

O

H H H

H C C C C C

H H H H H

H H H H H H

H C C C C C C +

H

H

H

H

H H H H

H C C C C C C

H H H H H O

H H H H O

H H H H H O H

H C

C

C

O

O

O

3 H2O

H

C

hydrolysis reaction

Figure 2.16 Structure of a triglyceride.

29

• The recommendation for total amount of fat for a

2,000 calorie diet is 65g.

• Be sure to know how many servings there are.

• A % DV of 5% or less is low and 20% or more is

high.

• Try to stay away from trans fats.

• Would you eat the food on the following nutrition

label? Why or why not?

2.5 Lipids

Understanding fats when

reading a nutrition label

30

Understanding fats when

reading a nutrition label

2.5 Lipids

Saturated Fat 3g

Start here.

Limit these

nutrients.

Get enough

of these

nutrients.

18%

15%

10%

20%

10%

0%

4%

2%

20%

4%

Calories from Fat 110 Calories 250

Amount Per Serving

Serving Size 1 cup (228g) Servings Per Container 2

%Daily Value

Iron

Calcium

Vitamin C

Vitamin A

Protein 5g

Sugars 5g

Dietary Fiber 0g

Total Carbohydrate 31g

Sodium 470mg

Cholesterol 30mg

Trans Fat 1.5g

Total Fat 12g

Figure 2.18 Understanding a food label.

31

What is the structure of a

phospholipid?

• The structure is

similar to a

triglyceride.

• One fatty acid is

replaced by a polar

phosphate group.

• Phospholipids are the

primary components

of cellular

membranes.

2.5 Lipids

Figure 2.19 Structure of a phospholipid.

inside cell

outside cell

b. Membrane structure a. Phospholipid structure

nonpolar

tails

polar

head

32

What is a steroid?

• A steroid is a lipid.

• The structure is four

fused carbon rings.

• Examples are

cholesterol and sex

hormones.

2.5 Lipids

Figure 2.20 Examples of steroids.

OH CH3

a. Cholesterol

b. Testosterone c. Estrogen

CH3

CH3

CH3

CH3

HO

HO

OH

O

CH3

H3C

H3C

© Purestock/Superstock RF

33

3. What are proteins?

• Made of subunits called amino acids

• Important for diverse functions in the body

including hormones, enzymes, antibodies,

and transport

• Can denature, undergo a change in shape

that causes loss of function

2.6 Proteins

34

What do amino acids look like? 2.6 Proteins

C

O

C C

C C

C C

H O

C

O

C C

O

cysteine (cys)

(polar)

aspartic acid (asp)

(ionized, polar)

tryptophan (trp)

(nonpolar)

valine (val)

(nonpolar)

lysine (lys)

(ionized, polar)

glutamic acid (glu)

(ionized, polar)

N+H3

CH2

CH2

CH2

H3N+

O

O–

H

CH2

CH2

COO– CH2

CH

H3C

H3N+

H

C C

O

O–

H3N+

H O

O–

H3N+

H

C

CH2

NH CH2 H3N

+

SH

H H3N+

CH2

O–

O–

O–

–O

Figure

2.21 The

structure of

a few

amino

acids.

35

What are the 4 levels of protein

organization?

• Primary – the linear order of amino acids

• Secondary – localized folding into pleated sheets and helices

• Tertiary – the 3-D shape of the entire protein in space

• Quaternary – combination of more than one polypeptide

• All proteins have primary, secondary, and tertiary structure, while only a few have quaternary structure.

2.6 Proteins

36

What do the levels of organization

look like?

2.6 Proteins

Figure 2.23 Levels of protein structure.

hydrogen bond Secondary Structure:

Alpha helix or a pleated sheet

(beta) sheet =

pleated sheet (alpha) helix

Tertiary Structure:

final shape of polypeptide disulfide bond

Quaternary Structure:

two or more associated

polypeptides

peptide bond

H3N+

Primary Structure:

sequence of amino acids

amino acid

COO–

C N

C H

R

C

C H

R

C N

C

C H

R

C

N

C

C H

R

N

C

C H

R

N

C H

R

N

C

N

C H

R

C H

hydrogen bond

37

4. What are nucleic acids?

• Made of nucleotide subunits

• Function in the cell to make proteins

• Include RNA and DNA

2.7 Nucleic Acids

38

What are the 3 parts of a nucleotide?

2.7 Nucleic Acids

nitrogen-

containing

base

sugar

Nucleotide

phosphate P C

5'

4'

3'

1'

2'

S

O

39

What are the 5 bases found in

nucleotides?

• Adenine (A) and guanine (G) are double-ringed purines.

• Cytosine (C), thymine (T), and uracil (U) are single-ringed pyrimidines.

• In DNA, A pairs with T and G pairs with C.

2.7 Nucleic Acids

40

2.7 Nucleic Acids

Figure

2.24 The

structure of

DNA and

RNA.

What are the 5 bases found in

nucleotides?

C

O

U

O N

N

N O

a. DNA structure with base pairs: A with T and G with C b. RNA structure with bases G, U, A, C

Uracil (U) (RNA only)

bases

backbone

Hydrogen bond

Cytosine (C) Guanine (G)

A

T

C

A

G

G

C

T

Adenine (A) Thymine (T)

(DNA only)

P

S

P

S

P

S

S

P

G

U

A

C N

N

H N

H

O

H

H

H

N

N

N

H

H

N

N

N

N

C

N

O

H N

CH3

HN CH

CH

O

N H

C

41

Summary of DNA and RNA

structural differences

• DNA

– Sugar is deoxyribose

– Bases include A, T,

C, and G

– Double-stranded

• RNA

– Sugar is ribose

– Bases include A, U,

C, and G

– Single-stranded

2.7 Nucleic Acids

42

Summary of the macromolecules

S

C

O

P

O H H

H

H

H O O H

H O

C

H

H H H

C

H

C

H

C

H

H

C

H

H

R C

O

H O

C O H H

H

C O H H

C O H H

H

H

C

R

Long-term

energy

storage;

membrane

components

Immediate

energy

and stored

energy;

structural

molecules

Carbohydrates

Lipids

Proteins

Nucleic acids Storage of

genetic

information

Support,

metabolic,

transport,

regulation,

motion

Fatty acid

Glycerol

Monosaccharides,

disaccharides,

polysaccharides

Fats, oils,

phospholipids,

steroids

Structural,

enzymatic,

carrier,

hormonal,

contractile

DNA, RNA

Organic

molecules Examples Monomers Functions

Nucleotide

base phosphate

amino

group

acid

group

COOH

Glucose

Amino acid

group

H2N

CH2OH

OH

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