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Chapter 2 & 3 – Chemical Composition of the Body. “Because living things, including humans, are composed only of chemicals , it is absolutely essential for a biology student to have a basic understanding of chemistry.” Sylvia Mader. Organ Heart. Ecosystem African savanna. Community

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Chapter 2 & 3 – Chemical Composition of the Body

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Chapter 2 & 3 – Chemical Composition of the Body

“Because living things, including humans, are composed onlyof chemicals, it is absolutely essential for a biology student to have a basic understanding of chemistry.”

Sylvia Mader..



Ecosystem African savanna


All organisms in savanna


Herd of zebras

Organism Zebra

Organ system

Circulatory system


Heart muscle



Heart muscle cell




Oxygen atom

  • Matter is anything that occupies space and has mass and is found on the Earth in three physical states

    • Solid

    • Liquid

    • Gas

  • Atoms – smallest unit of an element that can undergo a chemical change.

  • Composed of subatomic particles:

    • Protons = (+ charge) found in the nucleus

    • Neutrons = (no charge) found in the nucleus

    • Electrons = (e-,- charge) found orbiting the nucleus in the electron cloud

  • The number of protons determines the atom’s identity, e.g. 6 P = carbon..




Cloud of negative

charge (2 electrons)







  • Atomic number = sum of P

  • Atomic mass = sum of P and N

  • The number of N and/or e- can change.

    • Isotope = change the number of N

    • Ion = change the number of e-

      • cation = positive ion (how does it become positive?)

      • anion = negative ion (how does it become negative?)

  • The position of an atom’s e- is the electron configuration. We will not study configurations except for the outermost level of e- = valence shell

  • The e- found there are the valence e-.

  • The valence e- are the ones involved in ordinary chemical reactions..


electron shell

(can hold

2 electrons)


electron shell

(can hold

8 electrons)


Hydrogen (H)

Atomic number = 1

Carbon (C)

Atomic number = 6

Nitrogen (N)

Atomic number = 7

Oxygen (O)

Atomic number = 8..

  • Bonding is accomplished by interactions between two atom’s valencee-.

    • If e- are shared between two atoms that forms a covalent bond.

      • Single bonds = one shared pair

      • Double bonds = two shared pairs

      • Triple bonds = three shared pairs

    • If e- are transferred from one atom (ion) to another that forms an ionic bond.

  • Hydrogen bonds are special (polar) covalent bonds that are very important to biology..

Covalent Bonds

Sodium atom (Na)

Chlorine atom (Cl)


outer shells

Sodium ion (Na)

Chloride ion (Cl)

Sodium chloride (NaCl)

Ionic Bonds

Covalent Animation

Ionic Animation..

  • Electronegativity is the property that describes an atom’s attraction for a shared pair of e-.

  • If two atoms with different electro-negativity values share e-, i.e. form a covalent bond, one of the atoms will have a “larger share” of the e-.

  • This produces a molecule with differently charged ends (poles). This type of molecule is called polar..

  • Bonds formed between the hydrogen end (+ charged) of a polar molecule and the – end of any other polar molecule or highly electronegative atom (e.g. P, N, O) are called hydrogen bonds.

  • These hydrogen bonds are very important because they alter the physical and chemical properties of many molecules (especially water)..


Hydrogen bond









  • Molecules that are formed by polar covalent bonds have a tendency to break apart when the electron from the hydrogen is transferred to the more electronegative atom. This is called dissociation or ionization.

  • Water ionizes to form equal amounts of hydroxyl (OH-) and hydrogen (hydro-nium, H+) ions..

Water’s Life-Supporting Properties

  • The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties

  • Water’s cohesive nature

  • Water’s ability to moderate temperature

  • Floating ice

  • Versatility of water as a solvent..

  • Water molecules stick together as a result of hydrogen bonding = surface tension

    • Cohesion is vital for water transport in plants

  • Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid..

  • Because of hydrogen bonding, water has a strong resistance to temperature change and water can moderate temperatures.

    • Water can absorb and store large amounts of heat while only changing a few degrees in temperature

  • Earth’s giant water supply causes temperatures to stay within limits that permit life

  • Evaporative cooling removes heat from the Earth and from organisms..

  • When water molecules get cold, they move apart, forming ice

    • A chunk of ice has fewer molecules than an equal volume of liquid water

  • Since ice floats, ponds, lakes, and even the oceans do not freeze solid

    • Marine life could not survive if bodies of water froze solid..

Salt crystal

Ion in solution

  • A solution is a liquid consisting of two or more substances evenly mixed

    • The dissolving agent is called the solvent

    • The dissolved substance is called the solute

    • The polarity of water enhances its ability to act as a solvent.

      • Polar substances are attracted to the polar water molecules and “pulled” out of solution..

  • An acid is a molecule that can release protons (H+).

    • Proton donor.

  • A base is a molecule that can combine with H+ and remove it from solution. Bases are also defined as releasing OH-.

    • Proton acceptor..

    • pH = log _1__ [H+]

      • [H+] = molar concentration of H+.

      • pH inversely related to [H+].

    • Because of logarithmic relationship, a solution with 10 times [H+] of H20 has a pH = 6; solution with 0.1 the [H+] has a pH = 8..

    Oven cleaner

    Household bleach

    Household ammonia

    Milk of magnesia




    Human blood

    Pure water




    Tomato juice

    Grapefruit juice

    Lemon juice;

    gastric juice



    pH scale

    • A buffer is a system of molecules and ions that act to prevent changes in [H+] and stabilizes pH of a solution.

    • In blood:

      • H20 + C02 H2C03 H+ + HC03-

        • Reaction can proceed in either direction (depending upon the concentration of molecules and ions)..

    Hydroxyl group

    Carbonyl group

    Amino group

    Carboxyl group

    Found in amino acids

    and urea in urine (from

    protein breakdown)

    Found in amino acids,

    fatty acids, and some


    Found in alcohols

    and sugars

    Found in sugars

    Organic Molecules

    • Composed primarily of H, C, O, & N.

    • Look at the common functional groups.

    Organic molecules that contain carbon, hydrogen and oxygen.


    Monosaccharides = simple sugars.

    Structural isomers:

    Glucose, fructose, galactose.






    Starch granules in

    potato tuber cells

    (a) Starch



    In muscle


    (b) Glycogen

    Cellulose fibril in

    a plant cell wall

    Cellulose molecules

    (c) Cellulose

    • Polysaccharide: Numerous mono-saccharides joined covalently.

    • glycogen (repeating glucose joined that are highly branched),

    • starch (thousands of glucose joined),

    • cellulose (thousands of glucose joined)..

    • Disaccharide: 2 monosaccharides joined covalently.

      • Sucrose (glucose and fructose), lactose (glucose and galactose), maltose (2 glucose).




    • Organic molecules are built by dehydration synthesis:

      C6H12O6 + C6H12O6 C12H22O11 + H2O

    • Organic Molecules are broken down by hydrolysis

      C12H22O11 + H2O C6H12O6 + C6H12O6


    • Insoluble in water because of nonpolar molecules

      • Triglycerides = 3 fatty acids + glycerol

        • Saturated = joined by only single bonds

        • Unsaturated = joined by at least one double bond

    • Hydrolysis of triglycerides in adipose tissue releases free fatty acids.

      • Free fatty acids can be converted in the liver to ketone bodies.

      • Excess ketone bodies can lower blood pH..

    (b) A triglyceride

    • Phospholipids = phosphate + fatty acid

      • phosphate end is polar = hydrophilic

      • fatty acid end is nonpolar = hydrophobic

    • Steroids = aromatic rings = three 6-carbon rings joined to a 5-carbon ring

      • Steroid hormones are cholesterol derivitaves..



    A type of estrogen


    • Large molecules composed of long chains of amino acids.

      • 20 different amino acids can be used in constructing a given protein.

      • Each amino acid contains an amino group (NH2) at one end and carboxyl group (COOH) at the other end.

    • Differences between amino acids are due to differences in functional groups (“R”).

    • Amino acids are joined by peptide bonds..














    (d) Transport proteins

    (b) Storageproteins

    (a) Structural proteins

    (c) Contractile proteins

    • The four types of proteins

    Protein Structure Levels

    • Primary structure is the sequence of the amino acids in the protein.

    • Secondary structure is produced by weak hydrogen bonds between hydrogen of one amino acid and the and oxygen of a different amino acid nearby.

      • a-helix or b-sheet..

    • Tertiary structure is formed when polypeptide chains bend and fold to produce 3 -dimensional shape.

      • Formed and stabilized by weak chemical bonds between functional groups.

        • Each type of protein has its own own characteristic tertiary structure.

    • Quaternary structure is produced when a number of polypeptide chains covalently linked together..

    Hydrogen bond

    Pleated sheet


    (single subunit)

    Amino acid

    (a) Primary structure



    with four



    Hydrogen bond

    Alpha helix

    (c) Tertiary structure

    (b) Secondary structure

    (d) Quaternary structure

    • A protein’s shape is sensitive to the surrounding environment

      • Unfavorable temperature and pH changes can cause a protein to unravel and lose its shape

      • This is called denaturation..

    Nucleic Acids

    • Include DNA and RNA.

    • Nucleic acids are composed of nucleotides to form long polynucleotide chains.

      • Each nucleotide is composed of 3 smaller units:

        • 5-carbon sugar (deoxyribose or ribose).

        • Phosphate group attached to one end of sugar.

        • Nitrogenous base attached to other end of sugar..

    Nitrogenous base

    (A,G,C, or T)

    Thymine (T)








    • The “backbone” of the nucleic acid is formed by the sugar and phosphate pairs.

    • The “rungs” are formed by paired nitrogenous bases.

      • Nitrogenous bases complementary pair

        • A + T (U)

        • C + G..

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