Chapter 2

Biochemistry

Matter

• The “stuff” of the universe• Anything that has mass and takes up

space• States of Matter• Solid: has definite shape and

volume• Liquid: has definite volume but the

shape is changeable.• Gas: has a changeable shape and

volume

Energy

• The capacity to do work (put energy into motion)

• Types of energy– Kinetic: energy in action (moving)– Potential: energy of position: stored

(inactive or at rest)– Chemical: stored in the bonds of

chemical substances

Types of Energy Continued

– Electrical: results from the movement of charged particles

–Mechanical: directly involved in moving matter

– Radiant or electromagnetic: energy traveling in waves (visible light, ultraviolet light, and X-rays)

Law of Conservation of Energy

• This law states that energy is neither created nor destroyed it can only change its form.

• Energy is easily changed from one form to another

• During this conversion some energy may be lost in the form of HEAT.

Composition of Matter

• Elements: unique substances that cannot be broken down by chemical means

• Atoms: more or less identical building blocks for each element

• Atomic Symbol: one or two – letter chemical shorthand for each element

Properties of Elements

• Each element has unique physical and chemical properties

• Physical Properties: Those detected with our senses, (touch, smell, look, etc.)

• Chemical Properties: pertain to the way atoms interact with one another (burn, Explosive)

Elements of the Human Body

• Oxygen (O) 65%• Carbon (C) 18.5%• Hydrogen (H) 9.5%• Nitrogen (N) 3.2• These all make up 96% of the body

Lesser Element

• Calcium (Ca) 1.5%• Phosphorus (P) 1.0%• Potassium (K) .4%• Sulfur (S) .3%• Sodium (Na) .2%• Chlorine (CL) .2%• Magnesium (Mg) .1%• Iodine (I) .1%• Iron (Fe) .1%• These elements make up 3% of the body

Trace Elements

• Trace elements make up less than .01% of the body. These elements are required in minute amounts, and are found as part of enzymes.

• Cr, Co, Cu, F, Mn, Mo, Se, Si, Sn, V, Zn

Atomic Structure

• The nucleus consists of neutrons and protons

• Neutrons: have no charge and a mass of one atomic mass unit (amu)

• Protons: have a positive charge and a mass of (1 amu)

• Electron are found orbiting the nucleus

• Electrons: have a negative charge and 1/2000 the mass of a proton (0 amu)

Models of Atoms

• Planetary Model: electrons move around the nucleus in fixed, circular orbits

• Orbital Model; regions around the nucleus in which electrons are most likely to be found

Models of Atoms

Identification of Elements

• Atomic number: equal to the number of protons

• Mass number: equal to the mass of protons and neutrons

• Atomic weight: average of the mass numbers of all isotopes

• Isotopes: atoms with the same number of protons but a different number of neutrons

• Radioisotopes: atoms that undergo spontaneous decay called radioactivity

Identification of Isotopes

Molecules and Compounds

• Molecules: two or more atoms held together by chemical bond.

• Compound: two or more different kinds of atoms chemically bonded together

Molecules and Compounds

Mixtures and Solutions

• Mixtures: two or more components physically intermixed (not chemically bonded)

• Solution: homogeneous mixtures of components– Solvent: substance present in greatest

amount the one that does the dissolving– Solute: substances present in smaller

amounts the one that is dissolved

Mixture

Solutions

Colloids and Suspensions

• Colloids (emulsions): heterogeneous mixtures whose solutes do not settle out ie: Blood

• Suspensions: heterogeneous mixture with visible solutes that tend to settle out

Colloids

Suspension

Chemical Bonds

• Electron shells, or energy levels, surround the nucleus of an atom

• Bonds are formed using electrons in the outermost energy level

• Valence shell: outermost energy level containing chemically active electrons

• Octet rule: except for the first shell which is full with two electrons, atoms interact in a manner to have eight electrons in their valence shell

Chemically Inert Elements

• Inert elements have their outermost energy level fully occupied by electrons

Chemically Reactive Elements

• Reactive elements do not have their outermost energy level fully occupied by electrons

Types of Chemical Bonds

• Ionic- donating of electrons• Covalent- sharing of electrons• Hydrogen- hydrogen bonded to

selected elements

Ionic Bonds

• Ions are charged atoms resulting from the gaining or losing of an electron– Anion have gained one or more

electrons– Cations have lost one or more electrons

Formation of Ionic Bond

• Ionic bonds form between atoms by transferring one or more electrons

• Ionic compounds form crystals instead of individual molecules

• Example: NaCl (sodium chloride)

Ionic Bond

Covalent Bond

• Covalent Bonds are formed by the sharing of two or more electrons

• Electron sharing produces molecules

Covalent Bond

Hydrogen Bonds

• Too weak to bind atoms together• Common in dipoles such as water• Responsible for surface tension of

water• Important as intermolecular bonds,

giving the molecule a three- dimensional shape

Hydrogen Bonds

Patterns of Chemical Reactions

• Combination reactions: Synthesis reaction which always involve bond formation

• Synthesis means to produce• A + B AB

Decomposition Reaction

• Decomposition reaction: Molecules are broken down into smaller molecules

• AB A +B

Decomposition Reaction

Exchange Reaction

• Exchange Reaction involves both synthesis and decomposition reaction

• During this reaction a switch is made between molecule parts

• AB + C AC + B and AB + CD AD +CB

• This reaction occurs when ATP reacts with glucose and transfers its end phosphate group to glucose, forming glucose-phosphate

a

Exchange Reaction

Factors Influencing Rate of Chemical Reaction

• Temperature: chemical reaction proceed quicker at higher temperature

• Particle size: the smaller the particle the faster the chemical reaction

• Concentration: higher reacting particle concentrations produce faster reactions

• Catalyst: increase the rate of reaction without being chemically changed

• Enzyme: biological catalyst

Biochemistry

• Organic compounds• Contain carbon, are covalently

bonded, and are often large• Carbohydrates, lipids, proteins, DNA,

RNA, Nucleic Acids

Inorganic

• Inorganic compounds• Do not contain carbon• Water, salts, and many acids and

bases

Organic Compounds

Inorganic CompoundsProperties of Water

• High heat capacity: absorbs and releases large amounts of heat before changing temperature

• High heat of vaporization: changing from liquid to a gas requires large amount of heat

• Polar solvent properties: dissolves ionic substances, forms hydration layers around large charged molecules, and serves as the body’s major transport median

Properties of Water

• Reactivity: is an important part of hydrolysis and dehydration synthesis reaction

• Cushioning: resilient cushion around certain body organs

Salts

• Inorganic compounds• Contain cations other than H+ and

anions other than OH- • Electrolytes- they conduct electrical

currents

Acids and Bases

• Acid release H+ and are therefore proton donors

• HCl H+ + Cl- Hydrochloric Acid• Bases release OH- and are proton

acceptors• NaOH Na+ + OH- Sodium

hydroxide• Acid releases H+ ions in a solution• Bases accepts H+ ions in solution

Acid – Base Concentration pH

• Acidic solutions have higher H+ concentration and, therefore, a lower pH

• Alkaline (Base) solution have a lower H+ concentration and, therefore, a higher pH

• Neutral solutions have equal H+ and OH- concentrations

• pH 7.0 distilled water

Acid – Base Concentration pH

• Acidic: pH 0 – 6.99• Basic: pH 7.01 – 14• Neutral: ph 7.00

• Human blood and semen: 7.35 – 7.45

Buffers

• Systems that resist abrupt and large swings in the pH of body fluids

• Carbonic acid – bicarbonate system• Carbonic acid dissociates, reversibly

releasing bicarbonate ions and protons

• The chemical equilibrium between carbonic acid and bicarbonate resists pH changes in the blood.

Organic CompoundCarbon Central Element

• Molecules unique to living systems contain carbon and hence are organic compound

• They include:• Carbohydrates• Lipids• Protein• Nucleic Acid

Carbohydrates

• Contain carbon, hydrogen, and oxygen

• Their major function is to supply a source of cellular food

• Main source of energy for your body• Example:• Monosaccharide, or simple sugar

MonosaccharideGlucose

Fructose

Galactose

Deoxyribose and Ribose

• You also have disaccharides, or double sugars, as well as polysaccharides, or polymers, of simple sugars

Disaccharides

Lipids /Fats• Contain C, H, and O, but the

proportion of oxygen in lipids is less than in carbohydrates.

• Examples:• Neutral Fats, or triglycerides (main fat)

found in subcutaneous tissue and around organs

• Phospholipids found in cell membranes (phospholipid bilayer)

• Steroids; cholesterol, bile salts, vitamin D, sex hormones, adrenal cortical hormone

Function

• Fats are stored form of energy • Insulation: maintain temperature for

body organ• Protection: cushion, shock absorbers• Fat –soluble vitamins: vitamin A, D, E,

and K

Amino Acids

• Building blocks of protein, containing an amino group and a carboxyl group

• Amino group NH2

• Carboxyl groups COOH• 20 amino acids when combined in

different combinations to form between 20 - 30 thousand different proteins

Protein

• Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds

Fibrous and Globular Protein

• Fibrous protein Extended and strand – like Examples: Keratin, elastin, collagen, and certain contractile fibers (Keratin: skin epidermis, hair, nails)• Globular protein Examples: antibodies (helps fight off infection), hormones, and enzymes

Protein Denaturation

• Reversible unfolding of proteins due to drops in pH and/ or increase in temperature

• Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes

• Denatured: –verb (used with object),-tured, -tur·ing. 1. to deprive (something) of its natural character, properties, etc.

• Biochemistry: to treat (a protein or the like) by chemical or physical means so as to alter its original state.

Characteristics of Enzymes

• Most are globular proteins that act as biological catalysts

• Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion)

• Enzymes are chemically specific

Characteristics of Enzymes

• Frequently named for the type of reaction they catalyze

• Enzymes names usually end in –ase• Lower activation energy• Examples of enzymes: amylase,

lipase, hydrolase

Mechanism of Enzyme Action

• Enzyme binds with substrate• Product is formed at a lower

activation energy• Product is released

Nucleic Acids

• Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus

• Their structural unit, the nucleotide, is composed of N – containing base, pentose sugar, and a phosphate group

• Five nitrogen bases contribute to nucleotide structure : adenine (A), guanine (G), cytosine(C), thymine (T), uracil (U)