STRENGTH“Do not pray for easy lives. Pray to be stronger men! Do not pray for tasks equal to your powers. Pray for power equal to your tasks."

-Phillips Brooks

CHAPTER 2

The Chemical basis of Life

Matter

• Anything that occupies space and has mass. • Can exist as:

• Gas• Liquid• Solid

• Is composed of elements• What are examples of each type

of matter?

Elements

• Element- any of 112 known substances that can not be separated into smaller substances. • 92 of the 112 occur in nature• 2 additional elements are hypothetical

(114, 116)• And 2 more are not known to exist (113,

115)• Are referred to by a chemical symbol and

are organized in the Periodic Table of Elements.

• Nitrogen (N), Oxygen (O), Hydrogen (H), and Carbon (C) make up 96% of the matter found in all living organisms

Elements in Animal Body

• Major Elements• Oxygen (O)

• Necessary for cellular energy• Carbon (C)

• Primary component of organic molecules• Hydrogen (H)

• Component of water and organic molecules, necessary for energy transfer and respiration

• Nitrogen (N)• Component of all proteins and nucleic acid

Elements• Minor Elements

• Calcium (Ca)• Bones, teeth, muscle contraction, nerve impulse

transmission• Phosphorus (P)

• Energy transfer• Potassium (K)

• Important in nerve function. Principle positive ion within cells

• Sulfur (S)• Component for most proteins

• Sodium (Na)• Ion in extracellular fluid, important in nerve function.

• Chlorine (Cl)• Most abundant neg ion in extracellular fluid

• Magnesium (Mg)• Component of energy-transferring enzymes

Elements• Trace Elements

• Silicone (Si)• Aluminum (Al)• Iron (Fe)• Manganese (Mn)• Fluorine (F)• Vanadium (V)• Chromium (Cr)• Copper (Cu)• Boron (B)• Cobalt (Co)• Zinc (Zn)• Selenium (Se)• Molybdenum (Mo)• Tin (Sn)• Iodine (I)

Atoms

• The smallest unit of an element that retains the unique properties of that element.

• Composed of:• Protons• Neutrons• Electrons

More about atoms-Protons and Neutrons

• Protons and Neutrons are found in the nucleus.

• Each proton and neutron has an atomic mass of 1.

• Together protons and neutrons determine the atomic weight of the atom.

• Protons have positive charge.• Neutrons have no electrical charge and

are considered neutral.• Net charge of atoms are neutral because

have equal numbers of protons and electrons.

Electrons

• Tiny particles that remain in constant motion around the nucleus.

• So tiny that their mass does not contribute to the atomic weight of the atom.

• Have negative charge.• Orbit around nucleus but not necessarily in

a planetary manner, more in an orbital manner so that electrons exist in a cloud and they can move closer to one side of the atom or the other.

Atoms continued

• The number of protons gives an atom its atomic number.

• If an atom loses or gains an electron, then it becomes positively or negatively charged, thereby becoming an ion.

• If an atom has a different number of neutrons, then they are called isotopes of the element

Atomic Number

Isotopes

Ions

Na atom11 e, 11 p

e-

Na+ ion10 e, 11 p

Atoms that gain or lose an electron giving it a positive or negative charge.

Rate of Decay

• The time rate of disintegration of radioactive material, generally accompanied by emission of particles or gamma radiation.

• C-14’s can be measured in rocks and fossils.

Electron Shell

• Area around the nucleus where the electrons are most likely to be.

• Electron’s energy level determines which electron shell it will inhabit.

• Lower energy electrons will be closer to nucleus in lower shells.

• If shells are not full, then atoms will be more active.

• Helium and Neon have full electron shells so are chemically inert.

How the Shells work.• First shell can contain 2 electrons.• Second shell on can contain 8 electrons.

Let’s Look at CarbonCarbon has:6 Protons6 Electrons6 Neutrons

Atomic Mass = 6 p+ + 6 n = 12

Molecules and Compounds

• Molecules- when atoms are joined together by chemical bonds. Are the smallest particle of a substance that retains the properties of the substance.

• Molecule of the element- when two or more atoms of the same element are joined together.

• Bonds- how atoms are attached to one another.

• Compounds- A substance made up of two or more elements.

Chemical Bonds

• Means that the atoms are sharing or transferring electrons between them.

• Trying to fill their shells or give up extra electrons to another atom.

• Remember that atoms are constantly trying to become more stable.

• Types of chemical bonds:• Covalent• Ionic• Hydrogen

Covalent Bonds

• Bonds formed when atoms share electrons.

• O2

• Electrons spend part of time in outer electron shell of each atom.

• Classified depending on how many electrons are being shared.• single covalent bond — one electron is shared

• double covalent bond — two electrons are shared

• triple covalent bond — three electrons are shared

• May be shared equally (nonpolar) or unequally (polar).

Polar Water Molecule• Shared electrons in a covalently bonded molecule may spend more time

near one atom than the other• Shared electrons in water molecule spend more time near O atom than H

atoms• Created ‘poles’

• Gives molecule a slight positive charge on H side of molecule and slight negative charge on O side of molecule

http://www.youtube.com/watch?v=qmgE0w6E6ZI

Ionic Bonds

• Formed when electrons are transferred from one atom to another.

• Formed most often between two different types of atoms.• Usually between with fewer than 2

electrons in outer shell and those that are nearly full.

• Transfer causes a positive charge on one atom and a negative charge on the other. Keeps attraction to one another called electrostatic attraction.

Ionic Bonds

Electron transferred

Attraction betweenopposite charges

Types of Ions

• Cations- Ions with a net positive charge.• Na+

• Anions- Ions with a net negative charge• Cl-

• Ions are important in contraction of muscle fibers, transmission of nerve impulses, and maintenance of water balance.

Hydrogen Bonds

• A specific type of a weak ionic bond.• Weaker than ionic or covalent bonds.• Bond between hydrogen atoms already

covalently bonded in a molecule to oppositely charged particles.

• Since Hydrogen wants to “donate” electron, will have outer electron going toward other nucleus.

• This will make Hydrogen have an overall positive charge.

• Positive charge will cause electrostatic attraction to a negative molecule.

• Found in water or DNA to stabilize shape.

Hydrogen Bonds

+ charged hydrogen atom of one H2O molecule is attracted to the – charged atom of another H2O molecule.

Chemical Reactions

• The formation and breaking of chemical bonds.

• Require energy input or release of energy.• Chemical Equation- reaction is described

in written form.• X + Y → Z

(reactants) (products)• Arrow indicates direction of the reaction

Types of Chemical Reactions

Synthesis Reaction

• New and more complex molecule is made from simpler chemicals.• X+Y→XY• O + O = O2

• Synthesis reactions require energy.• Type of reaction that occurs during

digestion.

Chemical Reactions – Decomposition

Single complex chemical is broken down into multiple, simpler, chemicals.• XY→X+Y• 2H20→2H2 + O2

• Decomposition reactions expend or release energy.

Chemical Reactions - Exchange• Certain atoms are exchanged between

molecules. • Combination of synthesis and

decomposition reaction. • WX + YZ → WY + XZ• NaHCO3 + HCl → NaCl + H20 + C02

• Sodium Bicarbonate (indigestion relief, Tums) with stomach acid.

• Exchange reactions have no net energy requirements.

• Energy released from decomposition portion, helps with synthesis portion.

Chemical Reactions Continued

• Factors that influence reaction rates• Concentration of reactants• Temperature of environment

• Increased molecular movement• Activation energy- the energy required for the

reaction to happen.• Some reactions require presence of a catalyst or

enzyme• Catalyst = protein that holds reactants together

so they can interact• Reaction speed is increased when catalyst

protein (ENZYME) is present

Chemical Components of Living Organisms: Organic and Inorganic Compounds

• Inorganic compounds- do not contain hydrocarbon groups (H and C bonded together) and often have ionic bonding.

• Water

• Salts

• Acids and Bases

• Organic compounds- contain hydrocarbon groups and are usually covalently bonded

• Carbohydrates

• Lipids

• Proteins

• Nucleic Acids

Water – The Universal Solvent• Solvent – substance in which another substance

is dissolved• Solutes- chemicals added to water• Solution- resulting chemical and water mixture• Hydrophilic (water loving)- chemicals that

dissolve well or mix with water.• Hydrophobic (water hating)- chemicals or

molecules that do not mix well with water. • Water is an ideal transport medium

• Blanketing power allows molecules in water to move around and be cushioned from one another.

• Blood• Urine

• Water has a high heat capacity and a high heat of vaporization• Easily able to absorb heat.• Won’t evaporate easily.

• Water is used for lubrication.

Salts• Mineral compounds that have ionic bonds• Principal form of minerals that enter and

are stored in the body. • In ionic form are called electrolytes-

substances that have ability to transmit an electrical charge.

Acids and Bases

• Acids- ionically bonded substances that when added to water freely release hydrogen ions (H+).• Called H+ donors or proton donors

• Bases- alkaline in nature release a hydroxyl ion (OH-).• Called proton acceptors

• Acids and Bases are also electrolytes as they can transmit electricity when ionized in water.

The pH Scale

• Ranges from 1(most acidic) – 14(most basic).

• Lower numbers are the most acidic, higher numbers are more alkaline.

• 7.0 is neutral PH• Animal body – 7.4

Buffers

• A substance that minimizes the change of the acidity of a solution when an acid or base is added to the solution.

• By not allowing excessive hydrogen or hydroxyl ions to accumulate, buffers help cell maintain a neutral pH.

H2CO3 <-> H+ + HCO3-

• In this case carbonic acid ionizes when placed in water to yield hydrogen ions and the weak base, bicarbonate.

Organic Molecules• Molecules that contain carbon.

• Why carbon?• 4 outer electrons in outer shell, trying to share this to complete

outer shell. Is most stable when has four covalent bonds with other atoms.

• Divided into 4 groups:• Carbohydrates

• Glycogen• Ribose

• Lipids• Triglycerides• Phospholipids• Steroids• Prostaglandins

• Proteins• Globular• Fibrous

• Nucleic Acids• DNA• RNA• Adenosine triphosphate (ATP)

Carbohydrates

• Used for energy, storage of energy, and cellular structures.• Made up of C, H and O• Glucose, table sugar, starch, cellulose

• Monosaccharides - Simple Sugars• Glucose and Fructose

• Disaccharide - two monosaccharides are joined together in synthesis reaction.

• Polysaccharides- combinations of many monosaccharides.• Glycogen and cellulose• Cellulose is the most abundant organic

molecule in the biosphere

Carbohydrate Terminology• Dehydration Synthesis – the process of joining

multiple simple sugars to form one or more complex materials by removing water.

• Anabolism- process of building molecules needed for cellular functioning via synthesis reactions.

• Hydrolysis – process of using water to break down a molecule in a reaction, • ex. Sucrose Glucose + Fructose

• Catabolism- Decomposition of nutrients. • Glycoprotein- when a macromolecule is formed

out of a carbohydrate attached to a protein.

Lipids

• Used for energy and stored in fat for future energy needs.

• Serve as chemical messengers in the form of some hormones.

• Made up of C, H, O (lower)• Sometimes contain Phosphorus• 4 classes of Lipids:

• 1. Neutral fats• 2. Phospholipids• 3. Steroids• 4. Eicosanoids

Lipids continued..• Neutral Fats

• Also called triglycerides or fats.• Contains three fatty acids (tri) and a glycerol

molecule.• Fatty acid – chain of carbon atoms with one or two

hydrogen atoms attached to each C by single or double bonds

• Saturated fatty acids- all bonds in the hydrocarbon chain are single bonds. Ex. Animal fats -> lard

• Unsaturated fatty acids- when there are some double bonds between the carbon and hydrogen atoms. Plant origin -> Corn/olive oil

• Lipoproteins- macromolecule composed of proteins and lipids

• Hydrolysis- when triglycerides are decomposed.

Saturated vs. Unsaturated Fatty Acids

Phospholipids• Have a glycerol backbone

• Two fatty acids and a Phosphate (PO4) group

• Have a lipid bilayer when placed in water. • Hydrophilic (phosphate side) are facing water,

while hydrophobic tails line up with one another.• Main Component of cell membranes

Steroids• Lipids that take the form of four interlocking

hydrocarbon rings.

• Are hydrophobic, non-polar, with very little O2

• Examples include:

• Cholesterol – used to aid in fat digestion, used by adrenal glands, testes, ovaries and creation of steroid hormones

• Cortisol, estrogen, progesterone, testosterone

Eicosanoids• Lipids formed from a 20 carbon fatty acid

and ring structure. (hairpin structure)• Include:

• Prostaglandins- mediate inflammation• Thrombaxone- meidateplatelet function• Leukotrienes- mediate

bronchoconstriction and increased mucus production.

Proteins – Worker Molecules

• Most abundant organic molecules in the body.

• Have widest variety of functions.

• Catalyze- speed up reactions occurring in the body.

• Transport ions and other molecules into and out of the cell and around the body.

• Made chiefly of carbon, oxygen, hydrogen, and nitrogen.

• Composed of amino acids, which are the building blocks of proteins.

• Each protein is a unique sequence of amino acids

Amino Acids• 20 different Amino Acids in the body

• Building blocks for proteins (> 100 AA chain)

• Cells DNA orders specific combination

• Basic structure:

• Central Carbon attached to a Hydrogen

• Amino Group – NH2

• Carboxyl Group – COOH

• Side Chain (R) – unique and defines AA

• Peptide Bond – bond that holds two AA together carboxyl group of one AA and the amino group of the other AA.

Structure of Proteins• Shape of protein directly determines its function.

• Antibodies- fit together like puzzle to foreign invaders.• Structure is described in four layers:

• Primary Structure- sequence and number of amino acids that link together to form the peptide chain.

• Secondary Structure- the natural bend of parts of the peptide chain as it is formed in three dimensions.

• Amino and carboxyl groups form weak H bonds.• Alpha helix and beta pleated.

• Tertiary Structure- overall shape of a single protein molecule.

• Quaternary Structure- when two or more protein chains join to form a complex macromolecule. H bonds again!

• http://www.youtube.com/watch?v=Oz2x_yxPXww&feature=related

Structural Proteins

• Stable, rigid, water-insoluble proteins that are used for adding strength to tissues or cells.

• May also be called Fibrous proteins.• Important in structural framework and

physical movement.• Examples include:

• Collagen• Keratin• Cartilage• Actin and Myosin

Functional Proteins

• Generally are water-soluble, have a flexible, three-dimensional shape, which can change under different circumstances

• May also be called Globular proteins.• Function in chemical reactions, transport of

molecules, regulation of metabolism, and immune system.

• Include:• Hormones• Hemoglobin• Antibodies• Protein-based hormones• Enzymes

Enzymes• Proteins that catalyze or speed up chemical

reactions.• Specific to reactions they catalyze and the

substrates• Substrates – the substance that the enzyme

acts upon. • Will end in –ase• Are essential in the body for catalyzing

(speeding up) chemical reactions without being destroyed themselves during the process.

Enzymes

Nucleic Acids• Largest molecule of body composed of Carbon,

Oxygen, Hydrogen, Nitrogen, and Phosphorus.• 2 classes of Nucleic Acids

• DNA (deoxyribonucleic acid)• Exists mainly in the nucleus but also

mitochondria.• Contains all instructions needed by cell to

build proteins.• Coded in segments called genes.

• RNA (ribonucleic acid)• Transfers the instructions out of the nucleus

and into the cytoplasm and builds proteins.• Exists as mRNA, tRNA, and rRNA.

Nucleotides

• The molecular building blocks of nucleic acids.

• Are 5 different nucleotides, but all have the same structure. • Are all composed of a 5-Carbon

pentose sugar plus a phosphate group• Sugar in DNA is deoxyribose.• Sugar in RNA is ribose. • Nucleotides are named for their

nitrogen base.

Structure of a nucleotide

Nucleotides• Adenine-both DNA and RNA• Guanine-both DNA and RNA• Cytosine-both DNA and RNA• Thymine-Only in DNA• Uracil- Only in RNA

Nucleic Acid Formation

• Occurs when sugar and phosphate groups join in a long chain with nitrogenous base open for metabolic activity.

• Information needed to produce proteins is based on order of the nucleotides.

• C-G-T makes amino acid alanine.• Chromosomes-long chains of genes

combined with proteins.

DNA• Consists of two parallel strands of

nucleotides adenine, guanine, cytosine and thymine.

• Connected by hydrogen bonds between specific pairings of nucleotides.• Adenine and Thymine• Guanine and Cytosine

• Once bound, these two strands twist around one another to form a double helix.

• Order of nucleotides is what makes unique genetic code of each individual.

Structure of DNA

RNA

• Consists of only one strand of nucleotides.• Does not have thymine, but instead has uracil.• Pairings are:

• Guanine and Cytosine• Adenine and Uracil

• Exists in three forms:• tRNA- Transfer RNA

• Copies information in the DNA molecule• mRNA- Messenger RNA

• Carries information out of the nucleus• rRNA-Ribosomal RNA

• Creates the proteins needed by the body

ATP

• Adenosine Triphosphate- energy of the cells. • Cells need ATP to fuel or carry out any work. • Cellular Respiration- when the cells use up the

nutrients• ATP is a RNA nucleotide containing adenine with

two additional phosphate groups attached. • When bonds (high energy bonds) between

phosphate groups are broken, energy is released. • When phosphate group is lost, resulting molecule

is adenosine diphosphate (ADP).

Why is it so important?• Since we know how these bonds work, we

can understand how certain things such as drugs and chemical reactions in the body occur.

• Will help us later on in digestion of food, growth of the body, cellular signaling, and transmission of nerve impulses.