bio 310 chapt 02

7/30/2019 Bio 310 Chapt 02

1/76

1

Eric P. WidmaierBoston University

Hershel RaffMedical College of Wisconsin

Kevin T. Strang

University of Wisconsin - Madison

*See PowerPoint Image Slides for all

figures and tables pre-inserted into

PowerPoint without notes.

Chapter 02Lecture Outline*

Chemical Composition

of the Body

Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

7/30/2019 Bio 310 Chapt 02

2/76

2

Atoms: the Subunits of Elements

Atoms are made of protons, neutrons, andelectrons.

Each element has an atomic number.

Equal to the number of protons containedin the atom

Each element has an atomic weight.

Hydrogen, oxygen, carbon, nitrogen account

for >99% of the atoms in the human body.

7/30/2019 Bio 310 Chapt 02

3/76

3

7/30/2019 Bio 310 Chapt 02

4/76

4

Components of Atoms

The chemical properties of atoms can be

described in terms of three subatomic

particlesprotons, neutrons, and electrons.

The protons and neutrons are confined to a

very small volume at the center of an atom

called the atomic nucleus.

The electrons revolve in orbitals at various

distances from the nucleus.

7/30/2019 Bio 310 Chapt 02

5/76

5

Figure 2-1

7/30/2019 Bio 310 Chapt 02

6/76

6

Atomic Number

Each chemical element contains a specific

number of protons, and it is this number that is

known as the atomic number.

Example: hydrogen has an atomic number of 1,

so it has a single proton.

Because an atom is electrically neutral, the

atomic number is also equal to the number of

electrons in the atom.

7/30/2019 Bio 310 Chapt 02

7/76

7

Atomic Weight

Usually, the number of neutrons in the nucleus of an atom is

equal to the number of protons.

However, many chemical elements can exist in multiple forms,

called isotopes, which differ in the number of neutrons they

contain.

For example, the most abundant form of the carbon atom, 12C,

contains 6 protons and 6 neutrons, and has an atomic number

of 6 and an atomic weight of 12.

The radioactive carbon isotope 14C contains 6 protons and 8

neutrons, giving it an atomic number of 6 but an atomic weight

of 14.

7/30/2019 Bio 310 Chapt 02

8/76

8

Atomic Weight

One gram atomic mass of a chemical element

is the amount of the element, in grams, equal

to the numerical value of its atomic weight.

Thus, 12 g of carbon is 1 gram atomic mass of

carbon.

One gram atomic mass of any element

contains the same number of atoms (6 x1023;

Avogadros constant).

7/30/2019 Bio 310 Chapt 02

9/76

9

Atomic Weight

The atomic weight scale indicates an atoms

mass relative to the mass of other atoms.

(comparison done to carbon)

Because the atomic weight scale is a ratio of

atomic masses, it has no absolute units. The

unit of atomic mass is known as a dalton.

7/30/2019 Bio 310 Chapt 02

10/76

10

Ions If an atom gains or loses one or more electrons, it acquires a net electric

charge and becomes an ion.

Hydrogen atoms and most mineral and trace element atoms readily form

ions.

Ions that have a net positive charge are called cations.

Examples: Ca2+,Na+

Ions that have a net negative charge are called anions.

Example: Cl-

Because of their charge, ions are able to conduct electricity when

dissolved in water; consequently, the ionic forms of mineral elements are

collectively referred to as electrolytes.

7/30/2019 Bio 310 Chapt 02

11/76

11

Table 2-2

7/30/2019 Bio 310 Chapt 02

12/76

12

Molecules

Two or more atoms bonded together forma molecule.

Molecules can be represented by theircomponent atoms.

Example: C6H12O6

7/30/2019 Bio 310 Chapt 02

13/76

13

Chemical Bonds

Chemical bonds between atoms in a molecule form

when electrons transfer from the outer energy shell

of one atom to that of another, or when two atoms

with partially unfilled electron orbitals share

electrons.

7/30/2019 Bio 310 Chapt 02

14/76

14

Covalent Bonds are the Strongest

Chemical Bonds

Fig. 2-2

7/30/2019 Bio 310 Chapt 02

15/76

15

Polar Covalent Bonds

Electrons are not always shared equally

between two atoms, but instead reside close to

one atom of the pair.

This atom thus acquires a slight negative

charge, while the other atom becomes slightly

positive.

Such bonds are known as polar covalent bonds.

7/30/2019 Bio 310 Chapt 02

16/76

16

Polar Covalent Bonds

For example, the bond between hydrogen and oxygen in a hydroxyl group

(

OH) is a polar covalent bond in which the oxygen is slightly negative andthe hydrogen slightly positive.

Atoms of oxygen, nitrogen and sulfur, which have a relatively strong

attraction for electrons, form polar bonds with hydrogen atoms (Table 2-3).

One of the characteristics of polar bonds is that molecules that contain such

bonds tend to be more soluble in water than molecules containing the other

major type of covalent bond.

Consequently, these polar molecules readily dissolve in the blood, interstitial

fluid, and intracellular fluid. Indeed, water itself is the classic example of a

polar molecule, with a partially negatively charged oxygen atom and two

partially positively charged hydrogen atoms.

7/30/2019 Bio 310 Chapt 02

17/76

17

7/30/2019 Bio 310 Chapt 02

18/76

18

Nonpolar Covalent Bonds

In contrast to polar covalent bonds, bonds between atoms with similar

electronegativities are said to be nonpolar covalent bonds. In such bonds,the electrons are equally or nearly equally shared by the two atoms.

Bonds between carbon and hydrogen atoms and between two carbon atoms

are electrically neutral, nonpolar covalent bonds (see Table 23).

Molecules that contain high proportions of nonpolar covalent bonds are

called nonpolar molecules; they tend to be less soluble in water than those

with polar covalent bonds.

Consequently, such molecules are often found in the lipid bilayers of the

membranes of cells and intracellular organelles. When present in body

fluids such as the blood, they may associate with a polar molecule that

serves as a sort ofcarrier to prevent the nonpolar molecule from coming

out of solution.

7/30/2019 Bio 310 Chapt 02

19/76

19

Hydrogen Bonds When two polar molecules are in close contact, an electrical attraction may

form between them. For example, the hydrogen atom in a polar bond in one

molecule and an oxygen or nitrogen atom in a polar bond of anothermolecule attract each other, forming a type of bond called a hydrogen

bond. Such bonds may also form between atoms within the same molecule.

Hydrogen bonds are very weak, having only about 4 percent of the strength

of the polar bonds between the hydrogen and oxygen atoms in a singlemolecule of water. Although hydrogen bonds are weak individually, when

present in large numbers, they play an extremely important role in

molecular interactions and in determining the shape of large molecules.

Remember that the shape of large molecules often determines their

functions and their ability to interact with other molecules. For example,

some molecules interact with a lock-and-key arrangement that can only

occur if both molecules have the correct shape.

Fi 2 3

7/30/2019 Bio 310 Chapt 02

20/76

20

Hydrogen Bonds Link

Adjacent Water Molecules

Fig. 2-3

Fi 2 5

7/30/2019 Bio 310 Chapt 02

21/76

21

Molecular Shape

Rotation aroundchemical bonds

allows different

molecular shapes.

Figure 2-5

7/30/2019 Bio 310 Chapt 02

22/76

22

Ionic Molecules

The process of ion formation (ionization) occurs in single atoms and atoms that are

covalently linked in molecules. Within molecules, two commonly encounteredgroups of atoms that undergo ionization are the carboxyl group (COOH) and the

amino group (NH2).

The shorthand formula for only a portion of a molecule can be written as R

COOH or RNH2. The carboxyl group ionizes when the oxygen linked to the

hydrogen captures the hydrogens only electron to form a carboxyl ion (RCOO),releasing a hydrogen ion (H+): RCOOH 12 RCOO + H+.

The amino group can bind a hydrogen ion to form an ionized amino group (R

NH3+): RNH2 + H

+ 12 RNH3+.

The ionization of each of these groups can be reversed.

7/30/2019 Bio 310 Chapt 02

23/76

23

Free Radicals Free radicals are atoms or molecules with unpaired electrons in an outermost

orbital. Free radicals are unstable and highly reactive.

Free radicals are formed by the actions of certain enzymes in some cells,

such as types of white blood cells that destroy pathogens.

Free radicals are produced in the body following exposure to radiation or

toxin ingestion. These free radicals can do considerable harm to the cells of

the body. For example, oxidation due to long-term buildup of free radicals

has been proposed as one cause of several different human diseases, notably

eye, cardiovascular, and neural diseases associated with aging.

Examples of biologically important free radicals are superoxide anion,

O2; hydroxyl radical, OH ; and nitric oxide, NO .

7/30/2019 Bio 310 Chapt 02

24/76

24

Solutions

Substances dissolved in a liquid are known as solutes.

The liquid in which solutes are dissolved is the

solvent.

Solutes dissolve in a solvent to form a solution.

Water is the most abundant solvent in the body,

accounting for approximately 60 percent of total body

weight.

However, not all molecules dissolve in water.

N Cl di l i Fi 2 6

7/30/2019 Bio 310 Chapt 02

25/76

25

NaCl dissolves in water

In this example, Na+ & Cl- are the solutes andwater is the solvent.

Fig. 2-6

7/30/2019 Bio 310 Chapt 02

26/76

26

Solubility in Water

Molecules with ionic or polar covalent bonds

have an electrical attraction to water

molecules.

These molecules are able to dissolve in water

and are called hydrophilic (water loving).

Molecules with nonpolar covalent bonds are

not able to dissolve in water and are called

hydrophobic (water fearing).

7/30/2019 Bio 310 Chapt 02

27/76

27

Amphipathic Molecules

Amphipathic molecules are a special class of molecules that have a polar or

ionized region at one end and a nonpolar region at the opposite end.

When mixed with water, amphipathic molecules form clusters, with their

polar (hydrophilic) regions at the surface of the cluster where they are

attracted to the surrounding water molecules. The nonpolar (hydrophobic)

ends are oriented toward the interior of the cluster.

This arrangement provides the maximal interaction between water

molecules and the polar ends of the amphipathic molecules. Nonpolar

molecules can dissolve in the central nonpolar regions of these clusters and

thus exist in aqueous solutions in far higher amounts than would otherwisebe possible based on their low solubility in water.

The orientation of amphipathic molecules plays an important role in plasma

membrane structure.

7/30/2019 Bio 310 Chapt 02

28/76

28

Amphipathic Molecules

Fig. 2-7

7/30/2019 Bio 310 Chapt 02

29/76

29

Concentration

Concentration is expressed as the amount

of solute (based on its molecular weight)

dissolved per liter of solution.

The molecular weight in grams = 1 mole

1 M solution = 1 mole/Liter

7/30/2019 Bio 310 Chapt 02

30/76

30

Acids and Bases

Acids increase the concentration of H+ in

a solution.

Bases decrease the concentration of H+ ina solution.

The amount of H+ in a solution is

expressed as pH.

pH = -log[H+

]

7/30/2019 Bio 310 Chapt 02

31/76

31

7/30/2019 Bio 310 Chapt 02

32/76

32

Types of Special Water Reactions

Hydrolysis is the breakdown of a large

molecule into a small molecule by using water.

Other types of reactions are:

Dehydration

Condensation

7/30/2019 Bio 310 Chapt 02

33/76

33

Osmosis

Water moves between fluid compartments by

the process of osmosis (covered more in

Chapter 4).

In osmosis, water moves from regions of low

solute concentrations to regions of high solute

concentrations, regardless of the specific type

of solute.

7/30/2019 Bio 310 Chapt 02

34/76

34

Terminology

Organic chemistry is the study of carbon-

containing molecules.

Inorganic chemistry is the study of noncarbon-

containing molecules.

Biochemistry is the chemistry of livingorganisms. (can be considered part of organic

chemistry)

Cl f O i M l l

7/30/2019 Bio 310 Chapt 02

35/76

35

Classes of Organic Molecules

Carbohydrates Monosaccharides

Disaccharide

Polysaccharides

Lipids Fatty Acids

Triglycerides

Phospholipids

Steroids

Proteins

Amino Acid Subunits Polypeptides

Nucleic Acids DNA

RNA

7/30/2019 Bio 310 Chapt 02

36/76

36Fig. 2-8

7/30/2019 Bio 310 Chapt 02

37/76

37

Carbohydrates

Monosaccharides are the simplest carbohydrates.

Fig. 2-9

7/30/2019 Bio 310 Chapt 02

38/76

38

Disaccharide Formation

Fig. 2-10

7/30/2019 Bio 310 Chapt 02

39/76

39

Glycogen: a Polysaccharide

Fig. 2-11

7/30/2019 Bio 310 Chapt 02

40/76

40

How the Body Uses Sugars

Glycogen exists in the body as a reservoir of available energy

that is stored in the chemical bonds within individual glucosemonomers.

Hydrolysis of glycogen, as occurs during periods of fasting,

leads to release of the glucose monomers into the blood,thereby preventing blood glucose from decreasing to

dangerously low levels.

Glucose is often called blood sugar because it is the majormonosaccharide found in the blood.

7/30/2019 Bio 310 Chapt 02

41/76

41

Lipids Lipids are molecules composed predominantly (but not

exclusively) of hydrogen and carbon atoms.

These atoms are linked by nonpolar covalent bonds. Thus,

lipids are nonpolar and have a very low solubility in water.

Lipids can be divided into four subclasses: fatty acids,

triglycerides, phospholipids, and steroids.

Lipids are important in physiology partly because some ofthem provide a valuable source of energy. Other lipids are a

major component of all cellular membranes, and still others

are important signaling molecules.

Li id

7/30/2019 Bio 310 Chapt 02

42/76

42

Lipids

Fig. 2-11

F tt A id

7/30/2019 Bio 310 Chapt 02

43/76

43

Fatty Acids Fatty acids consist of a chain of carbon and hydrogen atoms

with an acidic carboxyl group at one end.

When all the carbons in a fatty acid are linked by single

covalent bonds, the fatty acid is said to be a saturated fatty

acid.

Some fatty acids contain one or more double bonds between

carbon atoms, and these are known as unsaturated fatty acids.

If one double bond is present, the fatty acid is

monounsaturated, and if there is more than one double bond, it

is polyunsaturated.

Triglycerides

7/30/2019 Bio 310 Chapt 02

44/76

44

Triglycerides

Triglycerides (also known as triacylglycerols) constitute the

majority of the lipids in the body.

Triglycerides form when glycerol, a three-carbon alcohol,

bonds to three fatty acids.

Triglycerides are found in all cells and comprise part of

cellular membranes, including those of intracellular organelles.

They are also stored in great quantities in adipose tissue, where

they serve to supply energy to the cells of the body,

particularly during times when a person is fasting or requires

additional energy (maintained exercise, for example).

7/30/2019 Bio 310 Chapt 02

45/76

45Fig. 2-12A

7/30/2019 Bio 310 Chapt 02

46/76

46Fig. 2-12B

7/30/2019 Bio 310 Chapt 02

47/76

47Fig. 2-12C

Ch l t l

7/30/2019 Bio 310 Chapt 02

48/76

48

Cholesterol

Fig. 2-13

Ph h li id

7/30/2019 Bio 310 Chapt 02

49/76

49

Phospholipids

Phospholipids are similar in overall structure to triglycerides,

but the third hydroxyl group of glycerol is linked to phosphate.

In addition, a small polar or ionized nitrogen-containing

molecule is usually attached to this phosphate.

These groups constitute a polar (hydrophilic) region at one end

of the phospholipid, whereas the fatty acid chains provide a

nonpolar (hydrophobic) region at the opposite end.

Therefore, phospholipids are amphipathic. It is this property of

phospholipids that permits them to form the lipid bilayers of

cellular membranes.

St id

7/30/2019 Bio 310 Chapt 02

50/76

50

Steroids

Steroids have a distinctly different structure from those of the

other subclasses of lipid molecules.

Four interconnected rings of carbon atoms form the skeleton

of every steroid.

Steroids are NOT water-soluble.

Examples of steroids are cholesterol, cortisol from the adrenal

glands, and female (estrogen) and male (testosterone) sex

hormones secreted by the gonads.

Proteins

7/30/2019 Bio 310 Chapt 02

51/76

51

Proteins

Proteins account for about 50 percent of the

organic material in the body (17 percent of the

body weight), and they play critical roles in

almost every physiological process.

Proteins are composed of carbon, hydrogen,

oxygen, nitrogen, and small amounts of other

elements, notably sulfur. They aremacromolecules, often containing thousands of

atoms.

Amino Acids

7/30/2019 Bio 310 Chapt 02

52/76

52

Amino Acids

The subunit monomers of proteins are amino acids.

Every amino acid except proline has an amino (NH2) and a

carboxyl (COOH) group bound to the terminal carbon atom in the

molecule.

The proteins of all living organisms are composed of the same set of

20 different amino acids, corresponding to 20 different side chains.

The side chains may be nonpolar (8 amino acids), polar (7 amino

acids), or ionized (5 amino acids).

The human body can synthesize many amino acids, but several must

be obtained in the diet; these are known as essential amino acids.

Proteins are Made of Amino Acids

7/30/2019 Bio 310 Chapt 02

53/76

53

Proteins are Made of Amino Acids

Fig. 2-14

Peptide Bonds

7/30/2019 Bio 310 Chapt 02

54/76

54

Peptide Bonds

Fig. 2-15

7/30/2019 Bio 310 Chapt 02

55/76

55Fig. 2-16

Protein Structures

7/30/2019 Bio 310 Chapt 02

56/76

56

Protein Structures

Primary Protein Structure

Secondary Protein Structure

Tertiary Protein Structure

Quaternary Protein Structure


7/30/2019 Bio 310 Chapt 02

57/76

57


Two variables determine the primary structureof a protein:

(1) The number of amino acids in the chain

(2) The specific type of amino acid at each

position along the chain

A polypeptide in the primary protein structure

is analogous to a linear string of beads, each

bead representing one amino acid.

Conformation

7/30/2019 Bio 310 Chapt 02

58/76

58

Conformation

Proteins do not appear in nature like a linear

string of beads on a chain.

Interactions between side groups of each

amino acid lead to bending, twisting, and

folding of the chain into a more compact

structure.

The final shape of a protein is known as its

conformation.

Secondary Protein Structure

7/30/2019 Bio 310 Chapt 02

59/76

59

Secondary Protein Structure The attractions between various regions along a polypeptide chain creates

secondary structure in a protein.

Because peptide bonds occur at regular intervals along a polypeptide chain, the

hydrogen bonds between them tend to force the chain into a coiled conformation

known as an alpha helix.

Hydrogen bonds can also form between peptide bonds when extended regions of a

polypeptide chain run approximately parallel to each other, forming a relatively

straight, extended region known as a beta pleated sheet.

The sizes of the side chains and the presence of ionic bonds between side chains

with opposite charges can interfere with the repetitive hydrogen bonding required to

produce these alpha and beta shapes and result in irregular regions called randomcoil conformations. These occur in regions linking the more regular helical and

beta pleated sheet patterns.

Beta pleated sheets and alpha helices tend to impart upon a protein the ability to

anchor itself into a lipid bilayer.


7/30/2019 Bio 310 Chapt 02

60/76

60


Once secondary structure has been formed,

associations between additional amino acid

side chains become possible.

These interactions fold the polypeptide into its

final three-dimensional conformation, making

it a functional protein.

Factors that Determine Tertiary Structure

7/30/2019 Bio 310 Chapt 02

61/76

61

Factors that Determine Tertiary Structure

Five major factors determine the tertiary structure of a

polypeptide chain once the amino acid sequence (primarystructure) has been formed:

1. Hydrogen bonds between portions of the chain or with

surrounding water molecules

2. Ionic bonds between polar and ionized regions along thechain

3. Attraction between nonpolar (hydrophobic) regions

4. Covalent disulfide bonds linking the sulfur-containing side

chains of two cysteine amino acids5. van der Waals forces


7/30/2019 Bio 310 Chapt 02

62/76

62


Some proteins are composed of more than one polypeptide

chain and are said to have quaternary structure.

They are known as multimeric (many parts) proteins.

The same factors that influence the conformation of a single

polypeptide also determine the interactions between the

polypeptides in a multimeric protein.

Therefore, the chains can be held together by interactions

between various ionized, polar, and nonpolar side chains, as

well as by disulfide covalent bonds between the chains.

Polypeptides: Conformations

7/30/2019 Bio 310 Chapt 02

63/76

63

Polypeptides: Conformations

Fig. 2-17

Amino acid interactions

7/30/2019 Bio 310 Chapt 02

64/76

64

Amino acid interactions

Fig. 2-18

Multimeric example

7/30/2019 Bio 310 Chapt 02

65/76

65

Multimeric example The polypeptide chains in a multimeric protein may be identical or

different.

For example, hemoglobin, the protein that transports oxygen in the

blood, is a multimeric protein with four polypeptide chains; two of

one kind and two of another.

Even a single amino acid change resulting from a mutation may

have devastating consequences. An example of this is when a molecule of valine replaces a molecule

of glutamic acid in the b chains of hemoglobin. The result of this

change is a serious disease calledsickle cell anemia.

When red blood cells in a person with this disease are exposed to

low oxygen levels, their hemoglobin precipitates. This contorts the

red blood cells into a crescent shape, which makes the cells fragile

and unable to function normally.

Hemoglobin

7/30/2019 Bio 310 Chapt 02

66/76

66Fig. 2-19

g

Nucleic Acids

7/30/2019 Bio 310 Chapt 02

67/76

67

Nucleic Acids

Nucleic acids are extremely important because they

are responsible for the storage, expression, andtransmission of genetic information.

There are two classes of nucleic acids, deoxyribo-

nucleic acid (DNA) and ribonucleic acid (RNA).

DNA molecules store genetic information coded in

the sequence of their genes, whereas RNA moleculesare involved in decoding this information into

instructions for linking together a specific sequence

of amino acids to form a specific polypeptide chain.

Nucleotides

7/30/2019 Bio 310 Chapt 02

68/76

68

Nucleotides

Fig. 2-20

Bases

7/30/2019 Bio 310 Chapt 02

69/76

69Fig. 2-21

DNA

7/30/2019 Bio 310 Chapt 02

70/76

70

DNA Four different nucleotides are present in DNA,

corresponding to the four different bases thatcan be bound to deoxyribose. These bases are

divided into two classes:

1. The purine bases: adenine (A) and guanine(G), which have double rings of nitrogen

and carbon atoms

2. The pyrimidine bases, cytosine (C) and

thymine (T), which have only a single ring

DNA

7/30/2019 Bio 310 Chapt 02

71/76

71

DNA A DNA molecule consists of two chains of

nucleotides coiled around each other in the form of a

double helix.

The two chains are held together by hydrogen bonds

between a purine base on one chain and a pyrimidinebase on the opposite chain.

Specificity is imposed on the base pairings by thelocation of the hydrogen-bonding groups in the four

bases. G is always paired with C, and A with T.

Deoxyribonucleic acid (DNA)

7/30/2019 Bio 310 Chapt 02

72/76

72

Deoxyribonucleic acid (DNA)

Fig. 2-22 Fig. 2-23

RNA

7/30/2019 Bio 310 Chapt 02

73/76

73

RNA molecules differ in only a few respects from

DNA:

1. RNA consists of a single chain of nucleotides.

2. In RNA, the sugar in each nucleotide is ribose

rather than deoxyribose.3. The pyrimidine base thymine in DNA is replaced

in RNA by the pyrimidine base uracil (U).

(AU pairing)

The other three bases, adenine, guanine, and cytosine,

are the same in both DNA and RNA.

7/30/2019 Bio 310 Chapt 02

74/76

74

ATP

7/30/2019 Bio 310 Chapt 02

75/76

75

The purine bases are important not only in

DNA and RNA synthesis, but also in amolecule that serves as the molecular energy

source for all cells.

In all cells, from bacterial to human, adenosine

triphosphate (ATP) is the primary molecule

that receives the transfer of energy from thebreakdown of fuel moleculescarbohydrates,

fats, and proteins.

ATP

7/30/2019 Bio 310 Chapt 02

76/76

ATP

bio 310 chapt 02

Documents