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Chemical Level of Organization Chapter 2 Atoms, Molecules and Bonds 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 P and S Representing the Hydrogen Atom electron proton electron Shell model Ball 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 1.0079 ----- Atomic Mass H element symbol 1 --- 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 SODIUM 11p+ , 11e- CHLORINE 17p+ , 17e- CARBON 6p+ , 6e- OXYGEN 8p+ , 8e- HYDROGEN 1p+ , 1e- HELIUM 2p+ , 2e- 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 - O2 • Molecules of compounds contain more than one element - H2O • 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 Formation of NaCl • Sodium atom (Na) – Outer shell has one electron • Chlorine atom (Cl) – Outer shell has seven electrons • Na transfers electron to Cl forming Na+ and Cl• Ions remain together as NaCl Covalent Bonding Atoms share a pair or pairs of electrons to fill outermost shell •Single covalent bond •Double covalent bond •Triple covalent bond 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 hydrogen bond Examples of Hydrogen Bonds water molecule ammonia molecule 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 O H + H + 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 Glycogen • Sugar storage form in animals • Large stores in muscle and liver cells • When blood sugar decreases, liver cells degrade glycogen, release glucose 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 Protein Synthesis • Protein is a chain of amino acids linked by peptide bonds • Peptide bond – Type of covalent bond – Links amino group of one amino acid with carboxyl group of next – Forms through condensation reaction Protein Shapes • Fibrous proteins – Polypeptide chains arranged as strands or sheets • Globular proteins – Polypeptide chains folded into compact, rounded shapes 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 Polypeptides with Attached Organic Compounds • Lipoproteins – Proteins combined with cholesterol, triglycerides, phospholipids • Glycoproteins – Proteins combined with oligosaccharides 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 • • • • 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