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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

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..


Organ

Heart

Ecosystem African savanna

Community

All organisms in savanna

Population

Herd of zebras

Organism Zebra

Organ system

Circulatory system

Tissue

Heart muscle

tissue

Cell

Heart muscle cell

Molecule

DNA

Atom

Oxygen atom


  • 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..


Nucleus found on the Earth in three physical states

(a)

(b)

Cloud of negative

charge (2 electrons)

2

Protons

Neutrons

2

Electrons

2


  • 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 found on the Earth in three physical statese- 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..


First found on the Earth in three physical states

electron shell

(can hold

2 electrons)

Outermost

electron shell

(can hold

8 electrons)

Electron

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..



Sodium atom (Na)

Chlorine atom (Cl)

Complete

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)..


( molecule and the – end of any other polar molecule or highly electronegative atom (e.g. P, N, O) are called )

Hydrogen bond

()

()

()

()

()

()

()

(b)


  • 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
Water’s Life-Supporting Properties tendency to break apart when the electron from the hydrogen is transferred to the more electronegative atom. This is called

  • 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..


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


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

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


  • 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 to temperature change and water can moderate temperatures.

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..


  • 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 to temperature change and water can moderate temperatures. _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 to temperature change and water can moderate temperatures.

    Household bleach

    Household ammonia

    Milk of magnesia

    Basic

    solution

    Seawater

    Human blood

    Pure water

    Urine

    Neutral

    solution

    Tomato juice

    Grapefruit juice

    Lemon juice;

    gastric juice

    Acidic

    solution

    pH scale


    • A to temperature change and water can moderate temperatures.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)..


    Organic molecules

    Hydroxyl group to temperature change and water can moderate temperatures.

    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

    vitamins

    Found in alcohols

    and sugars

    Found in sugars

    Organic Molecules

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

    • Look at the common functional groups.


    Carbohydrates

    Organic molecules that contain carbon, hydrogen and oxygen. to temperature change and water can moderate temperatures.

    CnH2n0n.

    Monosaccharides = simple sugars.

    Structural isomers:

    Glucose, fructose, galactose.

    Glucose

    Fructose

    Carbohydrates


    Glucose to temperature change and water can moderate temperatures.

    monomer

    Starch granules in

    potato tuber cells

    (a) Starch

    Glycogen

    Granules

    In muscle

    tissue

    (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).


    Glucose to temperature change and water can moderate temperatures.

    Glucose

    Maltose

    • Organic molecules are built by dehydration synthesis:

      C6H12O6 + C6H12O6 C12H22O11 + H2O



    Lipids
    Lipids to temperature change and water can moderate temperatures.

    • 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 to temperature change and water can moderate temperatures.


    • Phospholipids to temperature change and water can moderate temperatures.= 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..


    Cholesterol to temperature change and water can moderate temperatures.

    Testosterone

    A type of estrogen


    Proteins
    Proteins to temperature change and water can moderate temperatures.

    • 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..


    Amino to temperature change and water can moderate temperatures.

    group

    Carboxyl

    group

    Side

    group

    (a)

    Side

    groups

    Serine

    Leucine

    (hydrophobic)

    (hydrophobic)


    (d) Transport proteins to temperature change and water can moderate temperatures.

    (b) Storageproteins

    (a) Structural proteins

    (c) Contractile proteins

    • The four types of proteins


    Protein structure levels
    Protein Structure Levels to temperature change and water can moderate temperatures.

    • 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 to temperature change and water can moderate temperatures. 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 to temperature change and water can moderate temperatures.

    Pleated sheet

    Polypeptide

    (single subunit)

    Amino acid

    (a) Primary structure

    Complete

    protein,

    with four

    polypeptide

    subunits

    Hydrogen bond

    Alpha helix

    (c) Tertiary structure

    (b) Secondary structure

    (d) Quaternary structure



    Nucleic acids
    Nucleic Acids environment

    • 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 environment

    (A,G,C, or T)

    Thymine (T)

    Phosphate

    group

    Sugar

    (deoxyribose)

    Phosphate

    Base

    Sugar



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