Chapter 2 Matter – anything that occupies space and has mass, matter

includes solids, liquids, and gases. 1. All forms of matter are made of one or more fundamental

substances called elements. Elements can not be broken down to substances that have different properties.

2. Common Elements – H, C, N, and O – 95% of human body 3. Atom – smallest unit of matter that is unique to an element.

Subatomic particles include: protons, neutrons & electrons. 4. Protons and neutrons make up the atom’s core or nucleus.

The electrons are outside of the nucleus. Protons have a (+) charge, neutrons are neutral, and electrons have a (-) charge and are attracted to the nucleus.

Periodic Table of the Elements

1. Atomic Number – number of protons in its nucleus and is written as subscript to the left of its atomic symbol

2. Mass Number – sum of the masses of its protons and neutrons (the mass of the electrons is so small it is ignored)

3. Number of Protons = atomic numberNumber of Electrons = equal to the atomic number Number of Neutrons = mass number minus atomic number

4. Isotopes – same atomic number but vary in their mass numbers

Each electron shell can hold a specific number of electrons

1. Shell 1 – can hold 2 electronsShell 2 – can hold 8 electronsShell 3 – can hold 18 electrons

2. When atoms form bonds, the important electrons are those in the outer level.

3. Chemically inert (Noble gases) – outer level is filled to capacity or contains 8 electrons

4. Chemically reactive – outer level contains < 8 electrons

5. The number of electrons that can participate in bonding is limited to 8 electrons. Valence Shell – octet rule – rule of eights

Ionic Bonds – when an atom loses or gains one or moreelectrons, it becomes positively or negatively charged – an ION. A positive ion is called a CATION and a negative ion is called an ANION.

Sodium (Na) has 11 e, only one in the outer shell, so it tends to be an electron DONOR. Chlorine (Cl) has 17 e, and its outer shell has 7 e, so it tends to be an electron ACCEPTOR. When a Na atom and a Cl atom come together, an electron is transferred from the Na atom to the Cl atom. Now both have 8 e in their outer shell.

Covalent Bond – when two atoms share one or more pairs of electrons this called a covalent bond. E.g., H has 1 e in the outer shell so it can accept 1 more e. A H atom can share with another H atom. Because they share the electron pair, each atom has a completed outer shell. H—H or H2.

Oxygen – oxygen has 6 electrons in the outer shell, so atoms share 2 electrons to make a total of 8 electrons. Thus a double covalent bond.

Nitrogen – nitrogen has 5 electrons in the outer shell so atoms share 3 electrons to make a total of 8 electrons. Thus, a triple covalent bond.

Types of Covalent Bonding

There are two types of covalent bonding.

1. Non-polar Covalent Bond – electrons are shared equally. E.g., CH4 Methane Gas; C has 6 protons and H has 4 protons; equal attraction of the electrons. Nonpolar substances are hydrophobic (water fearing).

2. Polar Covalent Bond – electrons are shared unequally, so there is a slight difference in charge. E.g., H2O Water; H has 2 protons and O has 8 protons; O attracts the electrons to a greater extent than H, so O is slightly (-) and H is slightly (+). In general, small atoms with 6 or 7 valence shell electrons, such as O, N, and Cl, are electrohungry and attract electrons very strongly. Polar substances are hydrophilic (water loving).

Hydrogen Bonding

1. Hydrogen bonds form when a hydrogen atom, already covalently linked to one electronegative atom (usually nitrogen or oxygen), is attracted by another electron-hungry atom, and forms a “bridge” between them.

2. Hydrogen bonds are too weak to bind atoms together to form molecules.

Comparison of Ionic, Polar Covalent, and Nonpolar Covalent Bonds

Most chemical reactions exhibit one of three major patterns:

1. Synthesis (Anabolic) – A + B > ABExample: Glucose + Fructose > Sucrose

2. Decomposition (Catabolic) – AB > A + BExample: Protein > Amino Acid + Amino Acid

3. Exchange Reactions – AB + C > AC + BExample: ATP + Glucose > Glucose-phosphate + ADP

4. Oxidation-Reduction (Redox) Reactions – are decomposition reactions and a special type of exchange reaction because electrons are exchanged between the reactants

Oxidation-Reduction Reactions

Oxidation – the reactant losing the electrons is referred to as the electron donor and is said to be oxidized.

Reduction – the reactant taking up the transferred electrons is called the electron acceptor and is said to become reduced.

Redox reactions occur when ionic compounds are formed. E.g., NaCl – Na is oxidized and Cl is reduced

E.g., Cellular Respiration…………

C6H12O6 + 6O2 > 6CO2 + 6H2O + ATP

Glucose + Oxygen > Carbon Dioxide + Water + Energy

Glucose is oxidized to carbon dioxide (loses H atoms) and oxygen is reduced to water (accepts H atoms)

Exergonic Reactions – release energy; reactions yield products that have less energy than the initial reactants but provide energy for other uses.

Endergonic Reactions – energy absorbing; reactions contain more potential energy in their chemical bonds than did the reactants.

Factors Influencing the Rate of Chemical Reactions

1. Temperature – reactions proceed quicker at higher temperatures

2. Particle Size – smaller particles quicker reaction

3. Concentration – high concentration

4. Catalysts - enzymes

Inorganic CompoundsWater

1. High heat capacity – absorbs and releases large amounts of heat before changing in temp. itself

2. High heat of vaporization – liquid to a gas; requires that large amounts of heat be absorbed to break the H bonds that hold water molecules

3. Polar solvent properties – Universal solvent

4. Reactivity – Decomposition reactions = Hydrolysis; Synthesis reactions = Dehydration synthesis

5. Cushioning

Characteristics of Water

• High Surface Tension – hydrogen bonding

Salts – an ionic compound containing cations other than H+ and anions other than the hydroxyl ion (OH-). When salts are dissolved in water, they dissociate into their component ions. E.g., NaCl + water > Na+ and Cl-.

All ions are electrolytes, substances that conduct an electrical current in solution

ACIDS and BASES

Acids – a substance that releases hydrogen ions (H+) and anions when dissolved in water; they are called proton donors; HCL H+ Cl-; H2CO3

- HCO3- + H+

Bases – a substance that releases hydroxyl ions (OH-) and cations when dissolved in water; they are called proton acceptors; NaOH Na+ + OH-

pH: Acid-Base Concentration

The more H+ ions in a solution, the more acidic the solution is.

The more OH- ions, the more basic or alkaline the solution is.

pH units measure the concentration of H+ ions.

The pH scale runs from 0 – 14 and is logarithmic, i.e., each successive change of one pH unit represents a tenfold change in H+ concentration.

Buffers

Homeostasis of acid-base balance is carefully regulated by the kidneys and lungs and by chemical systems called BUFFERS. Buffers help prevent large shifts of pH in the body fluids

Strong Acids – acids that dissociate completely and irreversibly in water and they can change the pH of a solution. E.g., HCl; 100 HCl molecules + 1 ml water > 100 H+ and 100 Cl-

Weak Acids – acids that do not completely dissociate. E.g., H2CO3; 100 H2CO3 + 1 ml water > 90 H2CO3 + 10 H+ + 10 HCO3

Strong Bases – bases that dissociate easily in water and quickly tie up H+

Weak Bases – bases that do not dissociate easily in water and accepts relatively few protons

• Sugars, starches, glycogen and cellulose (plant)

•C, H, O – 1 C atom for each water molecule, hence carbohydrates (= watered carbon)

•Monosaccharides - 3-7 C atoms (e.g., glucose, fructose, galactose)

•Disaccharides – 2 monosaccharides > disaccharide + 1 H20C6H12O6 + C6H12O6 C12H22O11 + H20Glucose + Fructose Sucrose + water(e.g., sucrose, lactose and maltose)

•Polysaccharides – 10’s & 100’s of monosaccharides joined through dehydration synthesis reactions (e.g., glycogen)

• Lipids – C, H, O – amount of oxygen in lipids is usually less than that in carbohydrates, so there are fewer covalent bonds.

• Most lipids are insoluble in polar solvents such as water = hydrophobic

• Triglycerides, phospholipids, steroids, vit. A, E, & K

• Important for efficient transport in blood (since hydrophobic) lipids combine with proteins to form water-soluble lipoproteins

• Triglycerides – solid (FAT) and liquid (OILS) at room temperature; 2X energy per gram as C and P; store triglycerides in fat cells (adipose tissue = adipocytes)

• Building blocks – Glycerol (3 C atoms) and Fatty Acids ( 2 FA)

Neutral Fats

Saturated Fats

• single covalent bond; each carbon bonds to the maximum number of hydrogen atoms; thus each fatty acid is SATURATED with hydrogen atoms

• tend to be solid at room temperature (Animal Tissues) and cocoa butter, palm oil and coconut oil

Monounsaturated Fats

• Fats contain fatty acids with 1 double covalent bond between 2 C atoms and thus are not completely saturated with H atoms, e.g., olive oil, peanut oil

Polyunsaturated Fats

• contain more than 1 double covalent bond between fatty acid carbons; e.g., corn oil, sunflower oil, soybean oil

Phospholipids

• Modified triglycerides; glycerol backbone (3 C) and 2 fatty acids + phosphate group

• The phosphorus-containing group gives phospholipids their distinctive chemical properties…the hydrocarbon tail is nonpolar and only interacts with nonpolar molecules….the phosphate head is polar and attracts other polar or charged particles – molecules that have both polar and nonpolar regions are said to be amphipathic.

Steroids

• flat molecules made of four interlocking hydrocarbon rings

• e.g., cholesterol, found in cell membranes and is the raw material for vit. D, steroid hormones and bile salts ; sex hormones

Eicosanoids

• lipids derived from a 20 C fatty acid found in all cell membranes ; Prostaglandins – important in blood clotting, inflammation and labor contractions

• Amino acids – building blocks of proteins; 20 different amino acids; bonded together by peptide bonds (covalent); dipeptide (2 AA); tripeptide (3 AA); polypeptide (10 AA or more) and polypeptides with 50 or more AA are called proteins.

• Proteins are more complex and a have a larger range of functions than either carbohydrates or lipids

• Structural proteins – cellular building materials; e.g., actin & myosin

• Functional (physiological) – e.g., enzymes (speed up biochemical reactions by increasing the frequency of collisions, lowering the activation energy and properly orienting the colliding molecules)

Structural Levels of ProteinsPrimary – linear sequence of AA composing the polypeptide chain

Secondary – twist or bend upon themselves to form a more complex structure ; alpha or beta

Tertiary – 3d shape of a polypeptide chain; unique for each protein

Quaternary – describes the arrangement of the individual polypeptide chains and how they

bond

Proteins (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• Frequently named for the type of reaction they catalyze• Enzyme names usually end in -ase• Lower activation energy Enzyme binds with substrate• Product is formed at a lower activation energy• Product is released

Enzyme ActionActive site

Amino acids

Enzyme (E)Enzyme-substratecomplex (E-S)

Internal rearrangementsleading to catalysis

Dipeptide product (P)

Free enzyme (E)

Substrates (S)

Peptide bond

H2O

+

Protein Denaturation

In hostile environments (temperature, pH) lose shape (secondary, tertiary and quaternary)

When a protein is subjected to extremes (e.g., pH drops or temperature rises above normal) the protein will unfold and lose their specific 3d structure. The protein is said to have been DENATURED.

In some cases, process is reversible. In extreme cases, the protein is said to have been irreversibly denatured.

Example: egg (albumin is a protein that makes up the “white” of the egg)….uncooked the white is actually clear when you cook the egg (temperature rises above normal) the albumin is denatured (changes the color and the structural arrangement of the protein)

• organic molecules that contain C, H, O, N, and P

• DNA – deoxyribonucleic acid (A,T,C,G); Deoxyribose sugar; found in the nucleus; double-stranded

• RNA – ribonucleic acid (A,U,C,G); Ribose sugar; found outside of the nucleus; single-stranded; mRNA, tRNA, rRNA

• Basic units or building blocks of nucleic acids are called NUCLEOTIDES

• Nucleotides include:

• Nitrogenous Base – Adenine (A), Thymine (T), Cytosine ( C), Guanine (G), Uracil (U)

• Pentose sugar – deoxyribose or ribose

• Phosphate group

Adenosine triphosphate (ATP) – adenine-containing RNA nucleotide which have 2 additional phosphate groups

How ATP drives cellular work