Chapter 2

Basic Chemistry

Chapter 2 Objectives
Describe an atom Compare the ways in which atoms combine to form

molecules and compounds Distinguish among the three major types of chemical reactions that are important for studying physiology Describe the crucial role of enzymes in metabolism Distinguish between organic and inorganic compounds Explain the chemical properties of water that make life possible Describe the pH scale and the role of buffers in body fluids Discuss the structures and functions of carbohydrates, lipids, proteins, nucleic acids

What are these structures? And why do we care?

Matter and Energy

O Matteranything that occupies space and

has mass (weight) O Energythe ability to do work

O Chemical
O Electrical O Mechanical O Radiant

Atoms
Element cannot be changed or

broken down into simpler substances

Atom smallest, stable unit of matter

Atoms join together to form chemicals with different characteristics

Chemical characteristics determine physiology at the molecular and cellular levels

Figure 2.4

Nucleus

Nucleus

Helium atom 2 protons (p+) 2 neutrons (n0) 2 electrons (e) (a) Planetary model KEY: = Proton = Neutron = Electron

Helium atom 2 protons (p+) 2 neutrons (n0) 2 electrons (e) (b) Orbital model

= Electron cloud

Table 2.2 Subatomic Particles

Atomic Structure
Atomic Structure

Atomic number:
Number of protons All atoms contain protons and electrons,

normally in equal numbers (if not it is called an ION)

Nucleus:
Contains protons and neutrons

Atomic structure Q:

What is the charge of an atom when protons and electrons are equal? What is the charge of an atom with more protons than electrons? What is the charge of an atom with more electrons than protons?

Electron Shells
OElectrons and Energy Levels
O Electrons in the electron cloud determine the

reactivity of an atom
O The electron cloud contains shells, or energy

levels that hold a maximum number of electrons:

O Lower shells fill first (2 electrons)

O Outermost shell is the valence shell, and it

determines bonding (8 electrons Rule of 8!)

Figure 2.5a

Figure 2.6

Chemical Bonds:
How Can an Atom fill its shell
Ionic Bonds bonds created by the

electrical attraction between anions and cations (e- donated and accepted).

What is an ion, anion, cation?

How is an ion formed?

Why are ions important in A & P?

Chemical Bonds: How Can an Atom fill its shell

Covalent Bonds atoms obtain the rule

of 8 by SHARING electrons with other atoms

What is the difference between single and double covalent bonds?

What does nonpolar and polar mean?

Where is the difference between polar and nonpolar important?

Figure 2.7a

Figure 2.7b

Figure 2.7c

Figure 2.8b

Weaker Bonds
Hydrogen bonds the attraction

between a slight positive charge on the hydrogen and the slight negative charge on the oxygen of a polar covalent bond
Very weak, but alters molecular

shapes and can pull molecules together

What does hydrogen bonding

cause in water?

+ H O Hydrogen bonds + H O H H O (a) + H (b) H + H

+ +

Figure 2.9

Types of reactions

Patterns of Chemical Reactions

O Synthesis reaction (A + BAB)
O Atoms or molecules combine O Energy is absorbed for bond formation

O Decomposition reaction (ABA + B)

O Molecule is broken down O Chemical energy is released

Critical thinking: Find a Physiological

Example of each
What reaction is What reaction is

this?

this ?

Figure 2.10a

Figure 2.10b

Patterns of Chemical Reactions

O Exchange reaction (AB + CAC + B)
O Involves both synthesis and decomposition

reactions O Switch is made between molecule parts and different molecules are made

Figure 2.10c

Inorganic Versus Organic Compounds

OInorganic
O Molecules not based on carbon and hydrogen O Carbon dioxide, oxygen, water, and inorganic acids,

bases, and salts

OOrganic
O Molecules based on carbon and hydrogen O Carbohydrates, proteins, lipids, nucleic acids

Importance of Water
O Water
O Most abundant inorganic compound in the body O Vital properties
O High heat capacity
O Polarity/solvent properties O Chemical reactivity O Cushioning

Important Inorganic Compounds

O Salts
O Easily dissociate into ions in the presence

of water O Vital to many body functions O Include electrolytes which conduct electrical currents

H O H

Water molecule

Na+

Na+

Cl

Cl

Salt crystal

Ions in solution

Figure 2.11

Important Inorganic Compounds

O Acids
O Release hydrogen ions (H+) O Are proton donors

O Bases
O Release hydroxyl ions (OH) O Are proton acceptors

O Neutralization reaction
O Acids and bases react to form water and a salt

pH
O Measures relative concentration of

hydrogen ions
O pH 7 = neutral

O pH below 7 = acidic
O pH above 7 = basic O Bufferschemicals that can regulate pH

change

Figure 2.12

Buffers and pH
OBuffers
O Weak acid/salt compounds
O Neutralizes either strong acid or strong base O Sodium bicarbonate is very important in humans

O What do the following do?

What are we talking about here?

What does this train represent?

Figure 2.14d

Carbohydrates
O Carbohydrates contain carbon, hydrogen, and

oxygen in a 1:2:1 ratio

O Monosaccharides:
O Simple sugars with three to seven carbon atoms O Glucose, fructose

O Disaccharides:
O Two simple sugars condensed by dehydration synthesis O Sucrose, Lactose, maltose

O Polysaccharides:
O Many monosaccharides condensed by dehydration

synthesis O Glycogen, Cellulose, Starch O Where are they found?

Lipids
Mainly hydrophobic molecules such as fats, oils, and

waxes
Made mostly of carbon and hydrogen atoms no ratio Includes
Fatty acids Triglycerides Phospholipids Cholesterol

Lipids
O Common lipids in the human body
O Neutral fats (triglycerides)
O Found in fat deposits O Source of stored energy O Composed of three fatty acids and one glycerol molecule
O Saturated fatty acids contain only single covalent bonds O Unsaturated fatty acids contain one or more double covalent bonds

Glycerol

3 fatty acid chains

Triglyceride, or neutral fat

(a) Formation of a triglyceride

3 water molecules

Figure 2.15a

Figure 2.16a

Figure 2.16b

Lipids
O Common lipids in the human body

(continued)
O Phospholipids
O Contain two fatty acids rather than three
O Form cell membranes

Polar head

Nonpolar tail

Phosphorus-containing group (polar end)

Glycerol backbone

2 fatty acid chains (nonpolar end)

(b) Phospholipid molecule (phosphatidylcholine)

Figure 2.15b

Lipids
O Common lipids in the human body

(continued)
O Steroids
O Include cholesterol, bile salts, vitamin D, and

some hormones O Cholesterol is the basis for all steroids made in the body

Figure 2.15c

Proteins
O Proteins are the most abundant and important

organic molecules
O Contain basic elements
O Carbon (C), hydrogen (H), oxygen (O), and nitrogen

(N)
O Basic building blocks
O 20 amino acids

O What are some functions of proteins:

Amine group

Acid group

(a) Generalized structure of all amino acids

(b) Glycine (the simplest amino acid)

(c) Aspartic acid (an acidic amino acid)

(d) Lysine (a basic amino acid

(e) Cysteine
(a sulfurcontaining amino acid)

Figure 2.17a-e

(a) Primary structure. A proteins primary structure is the unique sequence of amino acids in the Amino polypeptide chain. acids

Hydrogen bonds Amino acids (b) Secondary structure. Two types of secondary structure are named alpha-helix and betapleated sheet. Secondary structure is reinforced by hydrogen bonds. Dashed lines represent the hydrogen bonds in this figure. Alphahelix -pleated sheet

Figure 2.18a-b

Figure 2.18c-d

Figure 2.19a

Heme group

Globin protein

(b) Hemoglobin molecule composed of the protein globin and attached heme groups. (Globin is a globular or functional protein.)
Figure 2.19b

Enzymes
O Act as biological catalysts O Increase the rate of chemical reactions by

lowering the activation energy required O Bind to substrates at an active site

Substrates (S) e.g., amino acids +

Energy is Water is absorbed; released. bond is H2O formed.

Product (P) e.g., dipeptide

Peptide bond

Active site

Enzyme-substrate complex (E-S) Enzyme (E) 1 Substrates bind to active site. Enzyme changes shape to hold substrates in proper position. 2 Structural changes occur, resulting in the product. Enzyme (E) 3 Product is released. Enzyme returns to original shape, ready to catalyze another reaction.

Figure 2.20

O Nucleic Acids

Important Organic Compounds

O Built from nucleotides

O Pentose (5 carbon) sugar O A phosphate group O A nitrogenous base
O A = Adenine O G = Guanine O C = Cytosine O T = Thymine O U = Uracil.

Hydrogen bond

Deoxyribose sugar Phosphate

(d) Diagram of a DNA molecule KEY: Thymine (T) Cytosine (C)

Adenine (A)

Guanine (G) Figure 2.21c-d

Structure of Nucleic Acids

Important Organic Compounds

O Adenosine triphosphate (ATP)
O Composed of a nucleotide built from ribose

sugar, adenine base, and three phosphate groups O Chemical energy used by all cells O Energy is released by breaking high energy phosphate bond O ATP is replenished by oxidation of food fuels

Adenine High energy bonds

Ribose Phosphates

(a) Adenosine triphosphate (ATP)

Adenosine diphosphate (ADP) (b) Hydrolysis of ATP Figure 2.22a-b

(a) Chemical work. ATP provides the energy needed to drive energyabsorbing chemical reactions. Solute

Membrane protein (b) Transport work. ATP drives the transport of certain solutes (amino acids, for example) across cell membranes.

Relaxed smooth muscle cell

Contracted smooth muscle cell

(c) Mechanical work. ATP activates contractile proteins in muscle cells so that the cells can shorten and perform mechanical work.

Figure 2.23a-c