fundamentals of chemistry chapter 2. what are atoms? smallest particles that retain properties of an...
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Fundamentals of Chemistry
Chapter 2
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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)
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Elements
• Fundamental forms of matter
• Can’t be broken apart by normal means
• 92 occur naturally on Earth
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Most Common Elements in Living Organisms
Oxygen
Hydrogen
Carbon
Nitrogen
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Representing the Hydrogen Atom
electron
proton
electron
Shell model Ball model Electron density cloud
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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
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Mass Number
Number of protons
+Number of neutrons
Isotopes vary in mass number
# of protons = # of electrons
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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
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What Determines whether Atoms Will Interact?
The number and arrangement of their electrons
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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
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Shell Model
• First shell
– Lowest energy
– Holds 1 orbital
with up to 2
electrons
• Second shell
– 4 orbitals hold
up to 8
electrons HYDROGEN1p+ , 1e-
HELIUM2p+ , 2e-
CARBON6p+ , 6e-
OXYGEN8p+ , 8e-
SODIUM11p+ , 11e-
CHLORINE17p+ , 17e-
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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
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Important Bonds in Biological Molecules
Ionic Bonds
Covalent Bonds
Hydrogen Bonds
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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
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Covalent Bonding
Atoms share a pair or pairs of electrons to fill outermost shell
•Single covalent bond
•Double covalent bond
•Triple covalent bond
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Nonpolar Covalent Bonds
• Atoms share electrons equally
• Nuclei of atoms have same number of protons
• Example: Hydrogen gas (H-H)
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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
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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
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Examples of
Hydrogen Bonds
hydrogenbond
water molecule
ammonia molecule
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Properties of Water
Polarity
Temperature-Stabilizing
Solvent
Cohesive
Surface tension
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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
+ +
HH
O
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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
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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
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Na+
Cl–
– –
––
––
–
––
– –
+ ++
+
+
+
+
+
+
+
+
++ +
+
+
+
+
Spheres of Hydration
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The pH Scale
• Measures H+ concentration of fluid• Change of 1 on scale means 10X
change in H+ concentration
Highest H+ Lowest H+
0---------------------7-------------------14Acidic Neutral Basic
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Examples of pH
• Pure water is neutral with pH of 7.0
• Acidic– Stomach acid: pH 1.0 - 3.0
– Lemon juice: pH 2.3
• Basic– Seawater: pH 7.8 - 8.3
– Baking soda: pH 9.0
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The pH Scale
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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
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Organic CompoundsHydrogen and other elements covalently bonded to carbon
** The Biomolecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids
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Carbohydrates
Monosaccharides(simple sugars)
Oligosaccharides(short-chain carbohydrates)
Polysaccharides(complex carbohydrates)
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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)
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Polysaccharides
• Straight or branched chains of many sugar monomers
• Most common are composed entirely of glucose– Cellulose
– Starch (such as amylose)
– Glycogen
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Lipids
• Most include fatty acids– Fats– Phospholipids– Waxes
• Sterols and their derivatives have no fatty acids
• Tend to be insoluble in water
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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
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Sterols and Derivatives
• No fatty acids
• Rigid backbone of four fused-together
carbon rings
• Cholesterol - most common type in
animals
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Properties of Amino Acids
• Determined by the “R group”
• Amino acids may be:
– Non-polar
– Uncharged, polar
– Positively charged, polar
– Negatively charged, polar
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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
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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
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Quaternary StructureSome proteins are made up of more than one
polypeptide chain
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Nucleotide Structure
• Sugar
– Ribose or deoxyribose
• At least one phosphate group
• Base
– Nitrogen-containing
– Single or double ring structure
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Nucleic Acids
• Composed of nucleotides
• Single- or double-stranded
• Sugar-phosphate backbone
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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