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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