Fundamentals of Chemistry Chapter 2

What Are Atoms? Smallest particles that retain properties of an element, smallest particle of a substance Made up of subatomic particles: –Protons (+) –Electrons (-) –Neutrons (0) no charge)

Elements Fundamental forms of matter Can’t be broken apart by normal means 92 occur naturally on Earth

Most Common Elements in Living Organisms Oxygen Hydrogen Carbon Nitrogen

Representing the Hydrogen Atom Shell modelBall model Electron density cloud

Atomic Number and Mass # = Number of protons All atoms of an element have the same atomic number Mass= # of P + # on N Atomic Mass H element symbol Atomic number

Mass Number Number of protons + Number of neutrons Isotopes vary in mass number # of protons = # of electrons

Isotopes Atoms of an element with different numbers of neutrons (different mass numbers) Carbon 12 has 6 protons, 6 neutrons Carbon 14 has 6 protons, 8 neutrons

What Determines whether Atoms Will Interact? The number and arrangement of their electrons

Electrons Carry a negative charge Repel one another Are attracted to protons in the nucleus Move in orbitals - volumes of space that surround the nucleus

Shell Model First shell –Lowest energy –Holds 1 orbital with up to 2 electrons Second shell –4 orbitals hold up to 8 electrons

Chemical Bonds, Molecules, & Compounds Bond is union between electron structures of atoms Atoms bond to form molecules Molecules may contain atoms of only one element - O 2 Molecules of compounds contain more than one element - H 2 O Compound= +/- atoms

Important Bonds in Biological Molecules Ionic Bonds Covalent Bonds Hydrogen Bonds

Ionic Bonding One atom loses electrons, becomes positively charged ion Another atom gains these electrons, becomes negatively charged ion Charge difference attracts the two ions to each other

Covalent Bonding Atoms share a pair or pairs of electrons to fill outermost shell Single covalent bond Double covalent bond Triple covalent bond

Nonpolar Covalent Bonds Atoms share electrons equally Nuclei of atoms have same number of protons Example: Hydrogen gas (H-H)

Polar Covalent Bonds Number of protons in nuclei of participating atoms is not equal Electrons spend more time near nucleus with most protons Water - Electrons more attracted to O nucleus than to H nuclei

Hydrogen Bonding Molecule held together by polar covalent bonds has no net charge However, atoms of the molecule carry different charges Atom in one polar covalent molecule can be attracted to oppositely charged atom in another such molecule

Examples of Hydrogen Bonds hydrogen bond water molecule ammonia molecule

Properties of Water Polarity Temperature-Stabilizing Solvent Cohesive Surface tension

Water Is a Polar Covalent Molecule Molecule has no net charge Oxygen end has a slight negative charge Hydrogen end has a slight positive charge ++ H H O

Water Is a Good Solvent Ions and polar molecules dissolve easily in water When solute dissolves, water molecules cluster around its ions or molecules and keep them separated

Water Cohesion Hydrogen bonding holds molecules in liquid water together Creates surface tension Allows water to move as continuous column upward through stems of plants

Na + Cl – – – – – – – – – – – – Spheres of Hydration

The pH Scale Measures H + concentration of fluid Change of 1 on scale means 10X change in H + concentration Highest H + Lowest H Acidic Neutral Basic

Examples of pH Pure water is neutral with pH of 7.0 Acidic –Stomach acid: pH –Lemon juice: pH 2.3 Basic –Seawater: pH –Baking soda: pH 9.0

The pH Scale

Acids & Bases Acids –Donate H + when dissolved in water –Acidic solutions have pH < 7 Bases –Accept H + when dissolved in water –Acidic solutions have pH > 7

Organic Compounds Hydrogen and other elements covalently bonded to carbon ** The Biomolecules Carbohydrates Lipids Proteins Nucleic Acids

Carbohydrates Monosaccharides (simple sugars) Oligosaccharides (short-chain carbohydrates) Polysaccharides (complex carbohydrates)

Monosaccharides Simplest carbohydrates Most are sweet tasting, water soluble Most have 5- or 6-carbon backbone Glucose (6 C)Fructose (6 C) Ribose (5 C)Deoxyribose (5 C)

Polysaccharides Straight or branched chains of many sugar monomers Most common are composed entirely of glucose –Cellulose –Starch (such as amylose) –Glycogen

Lipids Most include fatty acids –Fats –Phospholipids –Waxes Sterols and their derivatives have no fatty acids Tend to be insoluble in water

Fats Fatty acid(s) attached to glycerol Triglycerides are most common Carboxyl group (-COOH) at one end Carbon backbone (up to 36 C atoms) –Saturated - Single bonds between carbons –Unsaturated - One or more double bonds

Sterols and Derivatives No fatty acids Rigid backbone of four fused-together carbon rings Cholesterol - most common type in animals

Properties of Amino Acids Determined by the “R group” Amino acids may be: –Non-polar –Uncharged, polar –Positively charged, polar –Negatively charged, polar

Primary Structure & Protein Shape Primary structure influences shape in two main ways: –Allows hydrogen bonds to form between different amino acids along length of chain –Puts R groups in positions that allow them to interact

Secondary Structure Hydrogen bonds form between different parts of polypeptide chain These bonds give rise to coiled or extended pattern Helix or pleated sheet Tertiary Structure Folding as a result of interactions between R groups

Quaternary Structure Some proteins are made up of more than one polypeptide chain

Nucleotide Structure Sugar –Ribose or deoxyribose At least one phosphate group Base –Nitrogen-containing –Single or double ring structure

Nucleic Acids Composed of nucleotides Single- or double-stranded Sugar-phosphate backbone

DNA and RNA ** DNA ---Double-stranded Consists of four types of nucleotides A bound to T C bound to G ** RNA --- Usually single strands, Four types of nucleotides Unlike DNA, contains the base uracil in place of thymine Three types are key players in protein synthesis