Basic Chemistry ch. 2

Matter and Composition of Matter Definition: Anything that has mass and occupies space Matter is made up of elements –An element cannot be broken down by ordinary chemical means Atoms - are unique building blocks for each element

Atomic Structure Neutrons Protons No charge, In atomic nucleus Mass = 1 atomic mass unit (amu) Protons Positive charge,In atomic nucleus Mass = 1 amu

Atomic Structure Electrons Negative charge ,orbit nucleus Mass = 0 amu Equal in number to protons in atom

Nucleus Nucleus Helium atom Helium atom Proton Neutron Electron cloud Figure 2.1

Definition: Capacity to do work or put matter into motion Energy Definition: Capacity to do work or put matter into motion Types of energy: Kinetic: energy associated with motion Potential: stored (inactive) energy Electrical : results from the movement of charged particles (Na+, K+)

Atoms of different elements contain different numbers of protons Identifying Elements Atoms of different elements contain different numbers of protons Compare hydrogen, helium and lithium

Hydrogen (H) Helium (He) Lithium (Li) Proton Neutron Electron Figure 2.2

Identifying Elements Atomic number = Mass number = Mass numbers of atoms of an element are not all identical Isotopes = atoms of the same element that differ in the # of neutrons they contain

Hydrogen (1H) Deuterium (2H) Tritium (3H) Proton Neutron Electron Figure 2.3

Molecule: two or more atoms bonded together (H2 or C6H12O6) Atoms of Elements can combine Chemically to form Molecules and Compounds Molecule: two or more atoms bonded together (H2 or C6H12O6) Compound:

Chemical Bonds Electrons occupy up to seven electron shells (energy levels) around nucleus Octet rule: Except for the first shell which is full with two electrons, atoms interact in order to have eight electrons in their outermost energy level (valence shell)

Chemically Inert Elements Stable and unreactive Outermost energy level fully occupied or contains eight electrons

(a) Chemically inert elements Valence shell complete 8e 2e 2e Helium (He) Neon (Ne) Figure 2.4a

Chemically Reactive Elements Valence shell not fully occupied by electrons Tend to gain, lose, or share electrons (form bonds) with other atoms to achieve stability

(b) Chemically reactive elements Valence shell incomplete 4e 1e 2e Hydrogen (H) Carbon © 1e 6e 8e 2e 2e Oxygen (O) Sodium (Na) Figure 2.4b

Attraction of opposite charges results in: An ionic bond Ionic Bonds Ions are formed by: Anions (– charge) have gained one or more electrons Cations (+ charge) have lost one or more electrons Attraction of opposite charges results in: An ionic bond

+ – Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na+) Chloride ion (Cl–) Sodium chloride (NaCl) Figure 2.5

Covalent Bonds Formed by sharing of two or more valence shell electrons Allows each atom to fill its valence shell at least part of the time

+ Reacting atoms Resulting molecules or Hydrogen atoms Carbon atom Molecule of methane gas (CH4) (a) Formation of four single covalent bonds: Figure 2.7a

+ Reacting atoms Resulting molecules or Oxygen atom Oxygen atom Molecule of oxygen gas (O2) (b) Formation of a double covalent bond: Figure 2.7b

+ Reacting atoms Resulting molecules or Nitrogen atom Nitrogen atom Molecule of nitrogen gas (N2) (c) Formation of a triple covalent bond:. Figure 2.7c

Sharing of electrons may be equal or unequal Covalent Bonds Sharing of electrons may be equal or unequal Equal sharing produces: Electrically balanced nonpolar molecules

Covalent Bonds Unequal sharing by atoms with different electron-attracting abilities produces: polar covalent bonds H2O

Hydrogen Bonds Attractive force between electropositive hydrogen of one molecule and an electronegative atom of another molecule Important in intramolecular bonds, holding a large molecule in a three-dimensional shape

+ – Hydrogen bond + + – – – + + + – (a) The slightly positive ends (+) of the water molecules become aligned with the slightly negative ends (–) of other water molecules. Figure 2.8

Synthesis Reactions A + B  AB Always involve bond formation Anabolic Endergonic

(a) Synthesis reactions Smaller particles are bonded together to form larger, molecules. Example Amino acids are joined to Form protein. Amino acid molecules Protein molecule Figure 2.9a

Decomposition Reactions AB  A + B Reverse synthesis reactions Involve breaking of bonds Catabolic Exergonic

(b) Decomposition reactions Bonds are broken in larger molecules, resulting in smaller, less complex molecules. Example Glycogen is broken down to release glucose units. Glycogen Glucose molecules Figure 2.9b

Classes of Compounds Inorganic compounds Organic compounds Do not contain carbon (ex. Water, salts, and many acids and bases) Organic compounds Contain carbon, usually large, covalently bonded (ex’s. carbohydrates, fats, proteins, nucleic acids)

Water 60%–80% of the volume of living cells Most important inorganic compound in living organisms because of its properties

Salts Ionic compounds that dissociate into ions in water Ions (electrolytes) conduct electrical currents in solution

Acids : Proton (H+) donors (release H+ in solution) HCl  H+ + Cl–

Bases: Proton acceptors (take up H+ from solution) NaOH  Na+ + OH–

Acid-Base Concentration Acid solutions contain higher amounts of H+ As [H+] increases: acidity increases Basic solutions contain higher concentrations of OH– As [H+] decreases (or as [OH–] increases): alkalinity increases pH = measure of the acidity/bascisity of a solution

Acid-Base Concentration Neutral solutions: pH = 7 Contains equal numbers of H+ and OH– Acidic solutions  [H+],  pH pH = 0–6.99 Basic solutions  [H+],  pH pH= 7.01–14

Sugars and starches whose building blocks = Three classes Carbohydrates Sugars and starches whose building blocks = Three classes Monosaccharides -Simple sugars containing three to seven C atoms (glucose) Disaccharides -Double sugars that are too large to pass through cell membranes Polysaccharides - Three/more simple sugars, e.g., starch and glycogen; not very soluble

Carbohydrates Functions Primary role: Major source of cellular fuel (glucose)

Hexose sugars (the hexoses shown (a) Monosaccharides Monomers of carbohydrates Example Hexose sugars (the hexoses shown here are isomers) Example Pentose sugars Glucose Fructose Galactose Deoxyribose Ribose Figure 2.15a

Animation: Disaccharides (b) Disaccharides Consist of two linked monosaccharides Example Sucrose, maltose, and lactose (these disaccharides are isomers) Glucose Fructose Glucose Glucose Galactose Glucose Sucrose Maltose Lactose PLAY Animation: Disaccharides Figure 2.15b

Animation: Polysaccharides (c) Polysaccharides Long branching chains (polymers) of linked monosaccharides Example This polysaccharide is a simplified representation of glycogen, a polysaccharide formed from glucose units. Glycogen PLAY Animation: Polysaccharides Figure 2.15c

Lipids Insoluble in water Main types: Triglycerides Phospholipids Steroids

Defined as:solid fats and liquid oils Triglycerides Defined as:solid fats and liquid oils Building blocks = three fatty acids bonded to a glycerol molecule Main functions Energy storage Insulation Protection

(a) Triglyceride formation + Glycerol 3 fatty acid chains Triglyceride, or neutral fat 3 water molecules Figure 2.16a

Similar to triglycerides: Phospholipids Similar to triglycerides: Building blocks = Glycerol + two fatty acids and a phosphorus (P)-containing group “Head” and “tail” regions have different properties Important in cell membrane structure

(b) “Typical” structure of a phospholipid molecule Two fatty acid chains and a phosphorus-containing group are attached to the glycerol backbone. Example Phosphatidylcholine Polar “head” Nonpolar “tail” (schematic phospholipid) Phosphorus- containing group (polar “head”) Glycerol backbone 2 fatty acid chains (nonpolar “tail”) Figure 2.16b

Steroids Steroids—interlocking four-ring structure Examples are cholesterol, vitamin D, steroid hormones, and bile salts

Simplified structure of a steroid Four interlocking hydrocarbon rings form a steroid. Example Cholesterol (cholesterol is the basis for all steroids formed in the body) Figure 2.16c

Proteins Building blocks = amino acids After amino acids are linked together they often undergo a natural folding process This folding process results in four different levels of protein structure: primary, secondary, tertiary, quaternary

this amino acid is likely intramolecular bonding. Amine group Acid group (a) Generalized structure of all amino acids. (b) Glycine is the simplest amino acid. (c) Aspartic acid (an acidic amino acid) has an acid group (—COOH) in the R group. (d) Lysine (a basic amino acid) has an amine group (–NH2) in the R group. (e) Cysteine (a basic amino acid) has a sulfhydryl (–SH) group in the R group, which suggests that this amino acid is likely to participate in intramolecular bonding. Figure 2.17

Animation: Primary Structure Amino acid Amino acid Amino acid Amino acid Amino acid (a) Primary structure: The sequence of amino acids forms the polypeptide chain. PLAY Animation: Primary Structure Figure 2.19a

Animation: Secondary Structure a-Helix: b-Sheet: (b) Secondary structure: The primary chain forms spirals (a-helices) and sheets (b-sheets). PLAY Animation: Secondary Structure Figure 2.19b

Animation: Tertiary Structure (c) Tertiary structure: PLAY Animation: Tertiary Structure Figure 2.19c

Animation: Quaternary Structure (d) Quaternary structure: Two or more polypeptide chains, each with its own tertiary structure, combine to form a functional protein. PLAY Animation: Quaternary Structure Figure 2.19d

Protein Denaturation Shape change and disruption of active sites due to environmental changes A denatured protein is nonfunctional

Enzymes Are proteins Biological catalysts Increase the speed of a reaction Allows for millions of reactions/minute

Enzyme Function Substrates + Active site Enzyme

Nucleic Acids DNA and RNA Building blocks = nucleotide, composed of N-containing base, a pentose sugar, and a phosphate group

Deoxyribonucleic Acid (DNA) Four Nitrogen containing bases: adenine (A), guanine (G), cytosine (C), and thymine (T) Double-stranded, helical Replicates before cell division, ensuring genetic continuity Provides instructions for protein synthesis

(c) Computer-generated image of a DNA molecule Sugar: Deoxyribose Base: Adenine (A) Phosphate Thymine (T) Sugar Phosphate Adenine nucleotide Thymine nucleotide Hydrogen bond (a) Deoxyribose sugar Sugar-phosphate backbone Phosphate Adenine (A) Thymine (T) Cytosine (C) Guanine (G) (b) (c) Computer-generated image of a DNA molecule Figure 2.22

Ribonucleic Acid (RNA) Four bases: adenine (A), guanine (G), cytosine (C), and uracil (U) Single-stranded PLAY Animation: DNA and RNA

Adenosine Triphosphate (ATP) Adenine-containing RNA nucleotide with two additional phosphate groups

High-energy phosphate bonds can be hydrolyzed to release energy. Adenine Phosphate groups Ribose Adenosine Adenosine monophosphate (AMP) Adenosine diphosphate (ADP) Adenosine triphosphate (ATP) Figure 2.19

Function of ATP Phosphorylation: The chemical energy contained in the high energy phosphate bonds can be used to perform cellular work

Figure 2.20 Solute + Membrane protein (a) Transport work + Relaxed smooth muscle cell Contracted smooth muscle cell (b) Mechanical work + (c) Chemical work Figure 2.20