2.

1: BIOCHEM Introduction

Why study chemistry in an

Anatomy and Physiology class?

- Body functions depend on cellular functions

- Cellular functions result from chemical changes
- Biochemistry helps to explain physiological processes

1
 2.2: Structure of Matter

Matter – anything that has mass and takes up space. It is

composed of elements.

Elements – composed of chemically identical atoms:

• Bulk elements – required by the body in large amounts
• Trace elements - required by the body in small amounts
• Ultratrace elements – required by the body in very
minute amounts

Atoms – smallest particle of an element

2
Table 2.1 Some Particles of Matter

3
 Elements and Atoms
• All matter is composed of elements
•Elements are:
• Bulk elements (C, H, O, N, K, S)
• Trace elements (parts of enzymes)
• Ultratrace elements
• Elements are composed of atoms of the same type
• Compounds are composed of atoms of different types
that are chemically bonded
4
 Atomic Structure
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Atoms - composed of Neutron

subatomic particles: (n0)
-
• Proton – carries a single
positive charge Proton
• Neutron – carries no (p+)
electrical charge
• Electron – carries a single + 0 Electron
negative charge + - (e–)
0 0
0
+
Nucleus
• Central part of atom
• Composed of protons and
neutrons Nucleus
• Electrons move around the -
nucleus
5
Lithium (Li)
 Atomic Number
and 

Atomic Weight

Atomic Number
• Number of protons in the nucleus of one atom
• Each element has a unique atomic number
• Equals the number of electrons in the atom
Atomic Weight
• Approximated by the number of protons plus the number of
neutrons in one atom (since a proton and a neutron each have an
approximate atomic weight of one)
• Electrons do not contribute to the weight of the atom

6
 Isotopes
Isotopes
• Atoms with the same atomic numbers but with
different atomic weights
• Different numbers of neutrons
• Oxygen often forms isotopes (O16, O17, and O18)
• Radioactive isotopes are unstable, releasing energy or
pieces of themselves (atomic radiation)

For an element, the atomic weight is often considered the

average of the atomic weights of its isotopes.

7
 Molecules and Compounds

Molecule – particle formed when two or more atoms

chemically combine

Compound – particle formed when two or more atoms of

different elements chemically combine

Molecular formulas – depict the elements present

and the number of each atom present in the molecule
H2 C6H12O6 H2O

8
 Molecules and Compounds
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

H H H
H

O
H
O O
H
O

H
H
H

H O H
H H H
H H H
O O
H
O H H
O

H
O
O H
H

O
9
 Bonding of Atoms
• Bonds form when atoms combine with other atoms

• Electrons of an atom occupy regions of space called

electron shells which circle the nucleus

• For atoms with atomic numbers of 18 or less, the following

rules apply:
• The first shell can hold up to 2 electrons
• The second shell can hold up to 8 electrons
• The third shell can hold up to 8 electrons

10
 Bonding of Atoms
• Lower shells are filled first
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• If the outermost shell is full, the atom is stable

- - -

+ + 0
+ 0 0 + -
0 0
+ 0
+

- -

Hydrogen (H) Helium (He) Lithium (Li)

11
 Ionic Bonds
Ionic Bonds
• An attraction between a cation and an anion

• Formed when electrons are transferred from one atom to

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

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

Na+
Cl–

+ 11p+
12n0
17p+
18n0 –

Sodium ion (Na+) Chloride ion (Cl–)

Sodium chloride
12
 Bonding of Atoms: Ions
Ion
• An atom that gains or loses electrons to become stable
• An electrically charged atom

Cation
• A positively charged ion 11p+
12n0
17p+
18n0
• Formed when an atom loses electrons

Anion
Sodium atom (Na) Chlorine atom (Cl)
• A negatively charged ion
• Formed when an atom gains

electrons

13
 Covalent Bonds
• Formed when atoms share electrons
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H H H2
- -
-

+ + + +

Hydrogen atom + Hydrogen atom Hydrogen molecule

• Hydrogen atoms form single bonds H―H

• Oxygen atoms form two bonds O=O
• Nitrogen atoms form three bonds N≡N
• Carbon atoms form four bonds O=C=O 14
 Bonding of Atoms:

Structural Formula
• Structural formulas show how atoms bond and are arranged
in various molecules

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

H H
H H O O O O C O

H2 O2 H 2O CO2

15
 Bonding of Atoms:

Polar Molecules
Polar Molecules
• Molecule with a slightly negative end and a slightly positive end
• Results when electrons are not shared equally in covalent bonds
• Water is an important polar molecule
Slightly negative ends

16
(a)
Slightly positive ends
 Hydrogen Bonds
Hydrogen Bonds
• A weak attraction between the positive end of one polar
molecule and the negative end of another polar molecule
• Formed between water molecules
• Important for protein and nucleic acid structure
H H
O

H
Hydrogen bonds
O
H
H
O
H
H O

H H
17
O
H
(b)
 Chemical Reactions
Chemical reactions occur when chemical bonds form or
break among atoms, ions, or molecules

Reactants are the starting materials of the reaction - the

atoms, ions, or molecules

Products are substances formed at the end of the chemical

reaction

NaCl ’ Na+ + Cl-

Reactant Products
18
 Types of Chemical Reactions
Synthesis Reaction – more complex chemical structure is
formed
A + B AB
Decomposition Reaction – chemical bonds are broken to form
a simpler chemical structure
AB A+B

Exchange Reaction – chemical bonds are broken and new bonds

are formed
AB + CD AD + CB
Reversible Reaction – the products can change back to the
reactants
A + B n AB 19
 Acids, Bases, and Salts
Electrolytes – substances that release ions in water
NaCl à Na+ + Cl-
Acids – electrolytes that dissociate to release hydrogen ions
in water
HCl à H+ + Cl-
Bases – substances that release ions that can combine with
hydrogen ions
NaOH à Na+ + OH-
Salts – electrolytes formed by the reaction between an acid
and a base
HCl + NaOH à H2O + NaCl 20
Acids, Bases, and Salts
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Na+
Cl–

Salt crystal

Na+

Ions in
solution
Cl–

21
 Acid and Base Concentration
pH scale - indicates the concentration of hydrogen ions in
solution
Neutral – pH 7;
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indicates equal
 Relative Acidic 6.6 7.4

8.4
Sodium

concentrations of H+
 Amounts H+
of H+ (red)
3.0
4.2
5.3
cabbage
cow’s
 Human
 biocarbonate
milk blood
and OH– tomato 11.5
and OH- (blue) 2.0 apple
gastric juice
juice
8.0
10.5
milk of
Household
ammonia
juice magnesia
7.0 Egg
6.0

Acidic – pH less than


Distilled white Basic
corn water OH–
pH 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
7; indicates a greater Acidic H+ concentration increases Neutral OH– concentration increases Basic (alkaline)

concentration of H+
Basic or alkaline – pH greater than 7;
indicates a greater concentration of OH-

22
 Changes in pH and Buffers

Blood pH
• Normal blood pH is 7.35 – 7.45
• Alkalosis occurs when blood pH rises to 7.5 – 7.8
• Acidosis occurs when blood pH drops to 7.0 – 7.3
• Homeostatic mechanisms help regulate pH
• Buffers are chemicals which act to resist pH changes

23
 2.3: Chemical Constituents 

of Cells
Organic vs. Inorganic Molecules

Organic molecules
• Contain C and H
• Usually larger than inorganic molecules
• Dissolve in water and organic liquids
• Carbohydrates, proteins, lipids, and nucleic acids
Inorganic molecules
• Generally do not contain C and H
• Usually smaller than organic molecules
• Usually dissociate in water, forming ions
• Water, oxygen, carbon dioxide, and inorganic salts
24
 Inorganic Substances
Water
• Most abundant compound in living material
• Two-thirds of the weight of an adult human
• Major component of all body fluids
• Medium for most metabolic reactions
• Important role in transporting chemicals in the body
• Absorbs and transports heat

Oxygen (O2)
• Used by organelles to release energy from nutrients in
order to drive cell’s metabolic activities
• Necessary for survival
25
 Inorganic Substances

Carbon dioxide (CO2)

• Waste product released during metabolic reactions
• Must be removed from the body

Inorganic salts
• Abundant in body fluids
• Sources of necessary ions (Na+, Cl-, K+, Ca+2, etc.)
• Play important roles in metabolism

26
 Organic Substances

Carbohydrates
• Provide energy to cells
• Supply materials to build cell structures
• Water-soluble
• Contain C, H, and O
• Ratio of H to O close to 2:1 (C6H12O6)
• Monosaccharides – glucose, fructose
• Disaccharides – sucrose, lactose
• Polysaccharides – glycogen, cellulose

27
 Organic Substances

Carbohydrates
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H O
C

H C O H Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

H
H O C H
H C O H
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H C
H C
H C
H H
(a) Some glucose molecules
(C6H12O6) have a straight
chain of carbon atoms.
O H C O O
H H
O H H
C
O H H C
O O H
O H C C
O H
(b) More commonly, glucose (c) This shape symbolizes
molecules form a ring structure. the ring structure of a
glucose molecule.
28
 Organic Substances

Carbohydrates
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O O O
O

(a) Monosaccharide (b) Disaccharide

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(c) Polysaccharide

29
 Organic Substances

Lipids
• Soluble in organic solvents; insoluble in water

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H H H H H H H H H H H H H H H
O
H O C C C C C C C C C C C C C C C C H

H H H H H H H H H H H H H H H
(a) Saturated fatty acid

H H H H H H H H H H H
O H H H H
H O C C C C C C C C C C C H H
C C C C C
H H H H H H H H C C H 30
H H
(b) Unsaturated fatty acid H H H
 Organic Substances

Lipids
• Fats (triglycerides)
• Saturated fats contain three saturated fatty acids
• Mostly solid and come from animals
• Unsaturated fats contain at least one unsaturated fatty acid
• Mostly liquid and come from plants

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H O H H H H H H H H H H H H H H H

H C O C C C C C C C C C C C C C C C C H

H H H H H H H H H H H H H H H

O H H H H H H H H H H H H H H H H H

H C O C C C C C C C C C C C C C C C C C C H

H H H H H H H H H H H H H H H H H

O H H H H H H H H H H H H H
H C O C C C C C C C C C C C C C C H
H H H H H H H H H H H H

Glycerol Fatty acid

portion portions
 Organic Substances

Lipids
• Phospholipids
• Building blocks are 1 glycerol, 2 fatty acids, and 1 phosphate per
molecule
• Hydrophilic and hydrophobic
• Major component of cell membranes
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

H H C O Fatty acid

H C O Fatty acid H C O Fatty acid Water-insoluble

(hydrophobic)
H C O Fatty acid “tail”
O H H H
H C O Fatty acid Water-soluble
H C O P O C C N
(hydrophilic)
H H “head”
H O– H H
Glycerol portion
Phosphate portion
(a) A fat molecule (b) A phospholipid molecule (c) Schematic representation
32
(the unshaded portion may vary) of a phospholipid molecule
 Organic Substances 

Lipids
• Steroids
• Four connected rings of carbon
• Widely distributed in the body, various functions
• Component of cell membrane
• Used to synthesize hormones
• Cholesterol
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

CH 3 CH 3
H2 CH3 H
C C CH CH 2 CH2 CH2 CH
H2C C CH 2
CH 3
CH3
H2
C HC CH CH 2
H2C C CH

HO C C CH2
H C C
H2 H

33
(a) General structure of a steroid
(b) Cholesterol
 Organic Substances

Proteins
• Structural material • Protein building blocks are
• Energy source amino acids
• Hormones • Amino acids held
• Receptors together with peptide bonds
• Enzymes
• Antibodies H

C
H C C H
H
H C C H
S C
R H C H H C H
H N C C OH H N C C OH H N C C OH

H H O H H O H H O

34
Organic Substances

Proteins
Four Levels of Protein Structure
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Amino acids

(a) Primary structure—Each

oblong shape in this
polypeptide chain represents
an amino acid molecule. The
whole chain represents a
portion of a protein molecule.

C C R
H H H
H N C O C
C N
C O H N R
H C
O
(b) Secondary structure—The C H H H H H
R C R R
polypeptide chain of a protein N C
N H O C R N C C
molecule is often either pleated O
O C N H C H
or twisted to form a coil. Dotted R R H H O
C C R
lines represent hydrogen bonds. C N H
H H C
R groups (see fig. 2.17) H N C O C N
O H R
are indicated in bold. C O H N O C
H H H
C H H C R
R R N C
N H O C N C
R C O
C H
O C N H HOR
R R H
C C C N H
C
H H C N
H N C O O
H
Pleated C O H N Coiled O
structure H H C structure
C

(c) Tertiary structure—

The pleated and coiled
polypeptide chain of a
protein molecule folds
into a unique three-dimensional
structure.

Three-dimensional
folding

(d) Quaternary structure—Two or more

polypeptide chains may be connected
to form a single protein molecule.

35
Animation: Protein Denaturation

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36
 Organic Substances

Nucleic Acids
• Encode amino acid sequences of proteins
• Building blocks are nucleotides
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P B
S

• DNA (deoxyribonucleic acid) – double polynucleotide

• RNA (ribonucleic acid) – single polynucleotide 37
 Organic Substances

Nucleic Acids
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S
P B P B B P
S S

S
P B P B B
P
S S

S
P B P B B
P
S S

S
P B P B B P
S S

S
P B P B B P
S S

S
P B P B B P
S S 38
(a) (b)