Matter and Energy

Matteranything that occupies space and has mass (weight)

Matter may exist as one of three states:
o Solid: definite shape and volume
o Liquid: definite volume; shape of container
o Gaseous: neither a definite shape nor volume
Matter may be changed
o Physically - Changes do not alter the basic nature of a substance
o Chemically - Changes alter the chemical composition of a substance
Matter and Energy
Energythe ability to do work.
o Has no mass and does not take up space
o Kinetic energy: energy is doing work
o Potential energy: energy is inactive or stored
Forms of energy
o Chemical energy is stored in chemical bonds of substances
o Electrical energy results from movement of charged particles
o Mechanical energy is energy directly involved in moving matter
o Radiant energy travels in waves
Energy form conversions
o ATP (adenosine triphosphate) traps the chemical energy of food in its bonds
Composition of Matter
Elementsfundamental units of matter
o 96 percent of the body is made from four elements:
1. Oxygen (O)
2. Carbon (C)
3. Hydrogen (H)
4. Nitrogen (N)
Periodic table contains a complete listing of elements
Atoms
o Building blocks of elements
o Atoms of elements differ from one another
o Atomic symbol is chemical shorthand for each element
o Indivisible (incapable of being divided)
Subatomic Particles
Nucleus
o Protons (p+) are positively charged
o Neutrons (n0) are uncharged or neutral
Orbiting the nucleus
o Electrons (e) are negatively charged
Atoms are electrically neutral
o Number of protons equals numbers of electrons in an atom
o Positive and negative charges cancel each other out
Ions are atoms that have lost or gained electrons
Planetary model
o Portrays the atom as a miniature solar system

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 o Protons and neutrons are in the nucleus
o Electrons are in orbitals
Orbital model
o More modern
o Predicts chemical behavior of atoms
o Electrons are depicted by an electron cloud, a haze of negative charge, outside
the nucleus
Electrons determine an atoms chemical behavior
Although outdated, the planetary model is simple and easy to understand and use
Identifying Elements
Atomic numberequal to the number of protons that the atom contains
o Unique to atoms of a particular element
o Indirectly tells the number of electrons in an atom
Atomic mass numbersum of the protons and neutrons contained in an atoms nucleus
Isotopes and Atomic Weight
Isotopes
o Atoms of the same element with the same number of protons and the same
atomic number
o Vary in number of neutrons
Atomic weight
o Close to mass number of most abundant isotope
o Atomic weight reflects natural isotope variation
Radioactivity
Radioisotope
o Heavy isotope of certain atoms
o Tends to be unstable
o Decomposes to more stable isotope
Radioactivityprocess of spontaneous atomic decay
Molecules and Compounds
Moleculetwo or more atoms of the same elements combined chemically
Example of a chemical reaction resulting in a molecule:
H (atom) + H (atom) H2 (molecule)
o The reactants are the atoms on the left
o The product is the molecule on the right represented by a molecular formula
Compoundtwo or more atoms of different elements combined chemically to form a
molecule of a compound
Example of a chemical reaction resulting in a compound:
4H + C CH4 (methane)
Chemical Reactions
Chemical reactions occur when atoms combine with or dissociate from other atoms
o Atoms are united by chemical bonds
o Atoms dissociate from other atoms when chemical bonds are broken
Electrons and Bonding
Electrons occupy energy levels called electron shells (levels)
Electrons closest to the nucleus are most strongly attracted
Each shell has distinct properties

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 o The number of electrons has an upper limit
o Shells closest to the nucleus fill first
Bonding involves only interactions between electrons in the outer (valence) shell
Atoms with full valence shells do not form bonds
Inert Elements
Atoms are stable (inert) when the outermost (valence) shell is complete
How to fill the atoms shells
o Shell 1 can hold a maximum of 2 electrons
o Shell 2 can hold a maximum of 8 electrons
o Shell 3 can hold a maximum of 18 electrons
Rule of eights
o Atoms are considered stable when their outermost orbital has 8 electrons
o The exception to this rule of eights is shell 1, which can hold only 2 electrons
Reactive Elements
Outermost valence shell is incomplete
Atoms will gain, lose, or share electrons to complete their outermost orbitals
o Atoms reach a stable state
o Bond formation produces a stable valence shell
Chemical Bonds
Ionic bonds
o Form when electrons are completely transferred from one atom to another
o Allow atoms to achieve stability through the transfer of electrons
Ions
o Result from the loss or gain of electrons
Anions have negative charge due to gain of electron(s)
Cations have positive charge due to loss of electron(s)
o Tend to stay close together because opposite charges attract
Covalent bonds
o Atoms become stable through shared electrons
o Electrons are shared in pairs
o Single covalent bonds share one pair of electrons
o Double covalent bonds share two pairs of electrons
Covalent bonds are either nonpolar or polar
o Nonpolar
Electrons are shared equally between the atoms of the molecule
Electrically neutral as a molecule
Example: carbon dioxide
o Polar
Electrons are not shared equally between the atoms of the molecule
Molecule has a positive and negative side, or pole
Example: water
Hydrogen Bonds
Hydrogen bonds
o Weak chemical bonds
o Hydrogen is attracted to the negative portion of a polar molecule
o Provides attraction between molecules

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 o Responsible for the surface tension of water
o Important for forming intramolecular bonds, as in protein structure
Patterns of Chemical Reactions
Synthesis reaction (A + B AB)
o Atoms or molecules combine
o Energy is absorbed for bond formation
o Underlies all anabolic activities in the body
Decomposition reaction (AB A + B)
o Molecule is broken down
o Chemical energy is released
o Underlies all catabolic activities in the body
Exchange reaction (AB + C AC + B and AB + CD AD + CB)
o Involves both synthesis and decomposition reactions as bonds are both made
and broken
o Switch is made between molecule parts, and different molecules are made

Most chemical reactions are reversible

Reversibility is indicated by a double arrow
o When arrows differ in length, the longer arrow indicates the more rapid reaction or
major direction of progress
Factors influencing the rate of chemical reactions are shown in Table 2.4
Biochemistry: Essentials for Life
Inorganic compounds: - Lack carbon - Tend to be small, simple molecules - Include water,
salts, and some acids and bases
Organic compounds: - Contain carbon - All are large, covalently bonded molecules - Include
carbohydrates, lipids, proteins, and nucleic acids
Important Inorganic Compounds
Water - Most abundant inorganic compound in the body
o Vital properties
High heat capacity
Polarity/solvent properties
Chemical reactivity
Cushioning
High heat capacity: water absorbs and releases a large amount of heat before it changes
temperature - Prevents sudden changes in body temperature
Polarity/solvent properties: water is often called the universal solvent
o Solvents are liquids or gases that dissolve smaller amounts of solutes
o Solutes are solids, liquids, or gases that are dissolved or suspended by solvents
o Solution forms when solutes are very tiny
o Colloid forms when solutes of intermediate size form a translucent mixture
Chemical reactivity
o Water is an important reactant in some chemical reactions
o Reactions that require water are known as hydrolysis reactions
o Example: water helps digest food or break down biological molecules
Cushioning
o Water serves a protective function

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 o Examples: cerebrospinal fluid protects the brain from physical trauma, and
amniotic fluid protects a developing fetus
Important Inorganic Compounds
Salts
o Contain cations other than H+ and anions other than OH
o Easily dissociate (break apart) into ions in the presence of water
o Vital to many body functions
Example: sodium and potassium ions are essential for nerve impulses
o All salts are electrolytes
o Electrolytes are ions that conduct electrical currents
Acids
o Release hydrogen ions (H+) when dissolved in water
o Are proton donors, since hydrogen ions are essentially a hydrogen nucleus
o Example: HCl H+ + Cl
o Strong acids ionize completely and liberate all their protons
o Weak acids ionize incompletely
Bases
o Release hydroxyl ions (OH) when dissolved in water
o Are proton acceptors
o Example: NaOH Na+ + OH
o Strong bases seek hydrogen ions
Important Inorganic Compounds
Neutralization reaction
o Type of exchange reaction in which acids and bases react to form water and a salt
o Example: NaOH + HCl H2O + NaCl
pH
Measures relative concentration of hydrogen ions
Based on the number of protons in a solution, expressed in terms of moles per liter
Each successive change on the pH scale represents a tenfold change in H concentration
+

pH 7 = neutral
o Number of hydrogen ions exactly equals the number of hydroxyl ions
pH below 7 = acidic
pH above 7 = basic
Bufferschemicals that can regulate pH change
Chemical Reactions
Polymer: chainlike molecules made of many similar or repeating units (monomers)
Many biological molecules are polymers, such as carbohydrates and proteins
Dehydration synthesismonomers are joined to form polymers through the removal of
water molecules
o A hydrogen ion is removed from one monomer while a hydroxyl group is removed
from the monomer it is to be joined with
o Monomers unite, and water is released
Hydrolysispolymers are broken down into monomers through the addition of water
molecules
o As a water molecule is added to each bond, the bond is broken, and the
monomers are released

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Important Organic Compounds
Carbohydrates contain carbon, hydrogen, and oxygen
o Include sugars and starches
o Classified according to size
Monosaccharidessimple sugars
Disaccharidestwo simple sugars joined by dehydration synthesis
Polysaccharideslong-branching chains of linked simple sugars
Carbohydrates
Monosaccharidessimple sugars
o Single chain or single-ring structures
o Contain 3 to 7 carbon atoms
o Examples: glucose (blood sugar), fructose, galactose, ribose, deoxyribose
Disaccharidestwo simple sugars joined by dehydration synthesis
o Examples include sucrose, lactose, and maltose
Polysaccharides: long, branching chains of linked simple sugars
o Large, insoluble molecules
o Function as storage products
o Examples include starch and glycogen
Important Organic Compounds
Lipids
o Most abundant are the triglycerides, phospholipids, and steroids
o Contain carbon, hydrogen, and oxygen
Carbon and hydrogen outnumber oxygen
o Insoluble in water, but soluble in other lipids
Common lipids in the human body
o Neutral fats (triglycerides)
Found in fat deposits
Source of stored energy
Composed of three fatty acids and one glycerol molecule
Saturated fatty acids
Unsaturated fatty acids
Saturated fats
o Contain only single covalent bonds
o Chains are straight
o Exist as solids at room temperature since molecules pack closely together
Unsaturated fats
o Contain one or more double covalent bonds causing chains to kink
o Exist as liquid oils at room temperature
o Heart healthy
Trans fats
o Oils that have been solidified by the addition of hydrogen atoms at double bond
sites
o Increase risk of heart disease
Omega-3 fatty acids
o Found in cold-water fish and plant sources, including flax, pumpkin, and chia
seeds; walnuts and soy foods

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 o Appears to decrease risk of heart disease
Lipids
Common lipids in the human body (continued)
o Phospholipids
Contain two fatty acids rather than three
Phosphorus-containing head carries an electrical charge and is polar
Charged region interacts with water and ions while the fatty acid chains
(tails) do not
Form cell membranes
o Steroids
o Formed of four interlocking rings
o Include cholesterol, bile salts, vitamin D, and some hormones
o Some cholesterol is ingested from animal products. The liver also makes
cholesterol
o Cholesterol is the basis for all steroids made in the body
Important Organic Compounds
Proteins
o Account for over half of the bodys organic matter
Provide for construction materials for body tissues
Play a vital role in cell function
Act as enzymes, hormones, and antibodies
o Contain carbon, oxygen, hydrogen, nitrogen, and sometimes sulfur
o Built from amino acids
Proteins
Amino acid structure
o Contain an amine group (NH2)
o Contain an acid group (COOH)
o Vary only by R groups
Protein structure
o Polypeptides contain fewer than 50 amino acids
o Large proteins may have 50 to thousands of amino acids
o Sequence of amino acids produces a variety of proteins
Structural levels of proteins
o Primary structure
o Secondary structure
Alpha helix
Beta-pleated sheet
o Tertiary structure
o Quaternary structure
Fibrous (structural) proteins
o Appear in body structures
o Exhibit secondary, tertiary, or even quaternary structure
o Bind structures together and exist in body tissues
o Stable proteins
o Examples include collagen and keratin
Globular (functional) proteins

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 o Function as antibodies, hormones, or enzymes
o Exhibit at least tertiary structure
o Can be denatured and no longer perform physiological roles
o Active sites fit and interact chemically with other molecules
Enzymes
Act as biological catalysts, increase the rate of chemical reactions, bind to substrates at an
active site to catalyze reactions
Recognize enzymes by their ase suffix examples: Hydrolase & Oxidase
Important Organic Compounds
Nucleic acids make up genes, are composed of carbon, oxygen, hydrogen, nitrogen, and
phosphorus atoms and are largest biological molecules in the body
Nucleic Acids
Built from nucleotides containing three parts:
1. A nitrogenous base
A = Adenine
G = Guanine
C = Cytosine
T = Thymine
U = Uracil
2. Pentose (five-carbon) sugar
3. A phosphate group
Deoxyribonucleic acid (DNA)
o The genetic material found within the cells nucleus
o Provides instructions for every protein in the body
o Organized by complimentary bases to form a double-stranded helix
o Contains the sugar deoxyribose and the bases adenine, thymine, cytosine, and
guanine
o Replicates before cell division
Ribonucleic acid (RNA)
o Carries out DNAs instructions for protein synthesis
o Created from a template of DNA
o Organized by complementary bases to form a single-stranded helix
o Contains the sugar ribose and the bases adenine, uracil, cytosine, and guanine
o Three varieties are messenger, transfer, and ribosomal RNA
Adenosine triphosphate (ATP)
o Composed of a nucleotide built from ribose sugar, adenine base, and three
phosphate groups
o Chemical energy used by all cells
o Energy is released by breaking high-energy phosphate bond
o ATP is replenished by oxidation of food fuels
ADP (adenosine diphosphate) accumulates as ATP is used for energy
Three examples of how ATP drives cellular work are shown next

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