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..

Ecosystem African savanna

CommunityAll organisms in savanna

PopulationHerd of zebrasOrganism

ZebraOrgan systemCirculatory system

OrganHeart

CellHeart muscle cell

TissueHeart muscletissue

MoleculeDNA

AtomOxygen 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..

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

Nucleus

Cloud of negativecharge (2 electrons)

(a)

(b)

2 Protons

2 Neutrons

2 Electrons

• The number of N and/or e- can change.Isotope = change the number of NIon = change the number of e-

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

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

• Atomic number = sum of P• Atomic mass = sum of P and N

• 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

Firstelectron shell(can hold2 electrons)

Outermostelectron shell(can hold8 electrons)

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8..

Hydrogen (H)Atomic number = 1

• Bonding is accomplished by interactions between two atom’s valence e-.– 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)

Completeouter shells

Sodium ion (Na) Chloride ion (Cl)

Sodium chloride (NaCl)

Ionic Bonds

Covalent AnimationIonic 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)..

(b)

()

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..

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

Water’s Life-Supporting Properties

a. Water’s cohesive nature b. Water’s ability to moderate

temperaturec. Floating iced. Versatility of water as a solvent..

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

i. 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..

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

i. 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..

• Since ice floats, ponds, lakes, and even the oceans do not freeze solid• Marine life could not survive if bodies of water

froze solid..

c. When water molecules get cold, they move apart, forming ice– A chunk of ice has fewer molecules than

an equal volume of liquid water

d. 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..

Ion in solutionSalt crystal

• 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..

Basicsolution

Neutralsolution

Acidicsolution

Oven cleaner

Household bleach

Household ammonia

Milk of magnesia

Seawater

Human bloodPure water

Urine

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)..

Organic Molecules• Composed primarily of H, C, O, & N.• Look at the common functional groups.

Hydroxyl group Carbonyl group Amino group Carboxyl group

Found in alcoholsand sugars Found in sugars

Found in amino acidsand urea in urine (fromprotein breakdown)

Found in amino acids,fatty acids, and somevitamins

Carbohydrates

• Organic molecules that contain carbon, hydrogen and oxygen.– CnH2n0n.

• Monosaccharides = simple sugars.– Structural isomers:

•Glucose, fructose, galactose.

Glucose Fructose

• Disaccharide: 2 monosaccharides joined covalently.– Sucrose (glucose and fructose), lactose (glucose and

galactose), maltose (2 glucose).

(a) Starch

Starch granules inpotato tuber cells

Glucosemonomer

(b) Glycogen

GlycogenGranulesIn muscletissue

(c) Cellulose

Cellulose molecules

Cellulose fibril ina plant cell wall

•Polysaccharide: Numerous mono-saccharides joined covalently.glycogen (repeating glucose joined that are highly branched),starch (thousands of glucose joined), cellulose (thousands of glucose joined)..

• Organic molecules are built by dehydration synthesis:

C6H12O6 + C6H12O6 C12H22O11 + H2O

Glucose Glucose

Maltose

• Organic Molecules are broken down by hydrolysis C12H22O11 + H2O C6H12O6 + C6H12O6

Lipids• 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..

Cholesterol

Testosterone A type of estrogen

Proteins• 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..

Aminogroup

Carboxylgroup

Sidegroup

(a)

Sidegroups

Leucine Serine

(hydrophobic) (hydrophobic)

• The four types of proteins

(a) Structural proteins

(b) Storageproteins

(c) Contractile proteins

(d) Transport 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.

-helix or -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

Amino acid

(a) Primary structure

Hydrogen bond

Alpha helix

(b) Secondary structure

Polypeptide(single subunit)

(c) Tertiary structure

Completeprotein,with fourpolypeptidesubunits

(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)

Phosphategroup

Thymine (T)

Sugar(deoxyribose)

Phosphate

Base

Sugar

• 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..