Fundamentals of Chemistry Chapter 2
Dec 22, 2015
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
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 HYDROGEN1p+ , 1e-
HELIUM2p+ , 2e-
CARBON6p+ , 6e-
OXYGEN8p+ , 8e-
SODIUM11p+ , 11e-
CHLORINE17p+ , 17e-
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
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
hydrogenbond
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
+ +
HH
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+
0---------------------7-------------------14Acidic Neutral Basic
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
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 CompoundsHydrogen 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 StructureSome 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