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
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
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
hydrogen
bond
Examples
of
Hydrogen
Bonds
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
O
H
+
H
+
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
Spheres of Hydration
–
–
+
+
+
+
Na+
–
–
–
–
–
–
–
–
–
+
+
+
+
+
Cl–
+
+
+
+
+
+
+
+
+
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-------------------14
Acidic
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 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