You need to know this for the Chemistry Quiz
Atoms
Chapter 2:
Fundamentals of Chemistry
Building blocks of matter
Dr. Amy Rogers
Made up of subatomic particles
Invisible but not indivisible:
Bio 139 Microbiology
Some figures courtesy of
Biology: A Guide to the Natural World by Krogh
The main subatomic particles
Charge
Location
• Proton
Positive
Nucleus
Mass
• Neutron
Neutral
Nucleus
Mass
• Electron
Negative
Orbital “shell” Space/Volume
Can only be broken down by extraordinary means
(for example, particle accelerators)
Atomic Model
If drawn to scale, electrons would be 1/3 mile away!
Atomic Number = # of protons
This defines an element
Isotopes
Same element, different number of Neutrons
– Hydrogen: one proton (+ one electron)
– Gold: 79 protons (+79 electrons)
Atomic Weight:
sum of protons & neutrons
Mole (also called gram molecular weight):
the weight of a substance in grams equal to total atomic
weight of all the atoms in a molecule of the substance
e.g. Glucose (C6H12O6) molecular weight = 180
1 Mole glucose = 180 grams
Some isotopes are unstable and undergo radioactive decay
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Interactions between atoms:
Chemical Bonding
Stable energy states
• Energy always seeks its lowest state
• Matter is transformed from pure elements into
everything else by joining atoms together
• Bonding converts the atoms to a lower, more
stable energy state
• This is called Chemical Bonding
• Stable energy state = Filled outer electron shell
• Electrons are responsible for atoms
bonding together
Outer Shells
• Electrons move within defined “energy levels”
outside the nucleus
• The volume of each energy level, or shell, fits a
specific number of electrons
• First shell:
Second shell:
Third shell:
2 electrons
8 electrons
8 electrons
Stable atoms:
Largely inert
Outer electron shells
are full
Unstable atoms:
Highly reactive
Outer electron
shells are unfilled
(fewer than 2 or 8
valence
electrons)
Ionic Bonding:
Give and Take
Electrons are given from one atom to another,
leading to a net transfer of charge.
This charge separation creates ions, which are
attracted to one another electrostatically.
Cation:
(2 or 8 valence
electrons)
positively charged ion;
lost electron(s)
ex. Na+
Anion:
negatively charged ion;
gained electron(s)
ex. Cl-
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Covalent Bonding:
Polar Covalent Bonding:
Share and share alike
Sharing of the electrons is unequal, leading to
slight charge separation (polarity).
Electrons are NOT transferred, but shared.
Oxygen has greater electronegativity
Carbon more electronegative but
molecule is symmetric
Hydrogen Bonds:
A special kind of weak electrostatic attraction that
results from polar covalent bonds involving
hydrogen
• Hydrogen bonds are WEAK but MANY
of them together are a significant force
• Critically important for
biology
• Hydrogen bonds form
from attraction between
partial + and - charges of
polar molecules
Metabolism:
Forming & Breaking chemical bonds
Catabolism:
X—Y
breaking of bonds (digestion)
X + Y + energy
exergonic reaction
• Hydrogen bonds are very important for:
– Protein folding
– DNA base pairing
– Receptor/ligand interactions
– Properties of water
Metabolism:
Forming & Breaking chemical bonds
Anabolism:
synthesis (bond creation)
X + Y + energy
X—Y
endergonic reaction
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Some Biologically Important
Properties of Water
• Solvent: for Polar & charged solutes (hydrophilic)
• Specific Heat: high
• Reactant in biochemical reactions
Water as a Solvent:
Water is polar & forms hydrogen bonds
Solubility:
The solution to many problems
Solute
Solvent
Solution
Hydrophobic molecules
(with itself and with solutes)
•Do not dissolve in water
•Crucial for maintaining
biological “compartments”
•Nonpolar molecules
Hydrophilic:
“water loving”
interacts with
or dissolves in water
•Hydrocarbons, lipids
Polar or Ionic Solutes
Specific Heat:
The amount of energy required to raise the
temperature of a substance by 1o C
Heat buffering
by water maintains (relatively) stable
temperatures on planet earth
and in animals’ bodies
Specific Heat of Water:
Why so high?
• Heat is the kinetic energy of moving
molecules
• It takes a lot of energy to get water
molecules moving because:
Hydrogen Bonds must be broken
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Water as a reactant
• Most biochemical reactions take place in water
• Water is often not only a solvent, but also a reactant
X—H + HO—Y
Æ
X—Y + H2O
Dehydration synthesis
X—Y + H2O
Æ
X—H + HO—Y
Hydrolysis
(often endergonic)
(ex. anabolic formation of organic polymers
such as complex carbohydrates, some lipids, and proteins)
(often exergonic)
(ex. catabolism of complex carbohydrates, lipids, proteins
to simple sugars, fats, amino acids)
Acids & Bases:
All things in moderation
• Opposite of acidic is alkaline (basic)
• Alkaline/Basic = low [H+] or high [OH-]
• Low [H+] = high pH
-
• OH (hydroxide ion) is a strong base:
It accepts H+ to yield water
• pH is a measure of concentration of hydrogen ions (H+,
or protons) in a solution
• More hydrogen ions = more acidic
• High acidity = low pH
pH
• On the pH scale, 7 is neutral
OH- + H+
H2O
Carbon:
The primary ingredient of life
– 0 is highly acidic
– 14 is highly basic/alkaline
• Logarithmic scale:
one change in pH unit = 10x change in [H+]
e.g., pH 5 = 100 times more acidic than pH 7
•Organisms use buffers to maintain appropriate pH (usually 6-8)
•pH extremes can denature proteins & disrupt membranes
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Carbon
Carbon Structures:
Hydrocarbons
• Atomic number = 6
• 4 valence electrons; wants 8
• Most stable with 4 covalent bonds per carbon
Propane
C3 H8
• Stability, Variety, Complexity of organic molecules
Hydrocarbons are reduced: saturated with hydrogen, no oxygen atoms present
Lots of energy stored in these bonds; can be released by oxidation
Functional Groups
drastically alter chemical properties
Functional Groups
Change Everything
Ethane
(hydrocarbon gas)
Ethanol
(liquid alcohol)
Nonpolar
Polar
Won’t dissolve in water
Water soluble
Complex organic molecules:
Carbohydrates
•Main energy source for most living things
•Monosaccharides (simple sugars):
•carbon ring with several alcohol groups
(+ one aldehyde or ketone)
•Some are isomers (same molecular formula but different structures)
•e.g., glucose & fructose (C6H12O6)
Most common
monosaccharide:
Glucose
Groups of atoms that confer a special property on a carbon-based molecule
Other examples: ribose & deoxyribose
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Disaccharides e.g., lactose, maltose, sucrose (table sugar)
two monosaccharides connected by the removal of water
and the formation of a glycosidic bond
Polysaccharides (complex carbohydrates)
• Starch
• Glycogen
• Cellulose
energy storage in plants
energy storage in animals
structural role (cell walls)
These 3 examples are all
very long (thousands of subunits)
polymers of glucose
Example of dehydration synthesis!
Polymers
large molecules made up of
many similar or identical chemical subunits
Polymer
Monomer Subunits
Polysaccharides &
Complex carbohydrates
Monosaccharides
or simple sugars
Proteins
Amino acids
Nucleic acids
Nucleotides
Lipids
Fatty acids:
Long hydrocarbon chains with carboxyl group at end
• Diverse category including
fats, phospholipids, steroids
• Relatively more hydrogen & less oxygen than
carbohydrates; therefore more energy-rich
• Hydrophobic
• Many important functions including
– Energy storage
– Cell membranes
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Saturated fatty acid:
•maximum hydrogen content;
all single bonds between
carbons.
Fats
3 carbon glycerol “head” + 1 to 3 fatty acid “tails”
•Usually solid at room temp.
Unsaturated fatty acid:
•one or more double bonds;
not “saturated” with hydrogen;
“kink” in chain.
•Often liquid at room temp,
esp. if polyunsaturated
(more than one double bond)
+
If:
3 fatty acids: triacylglycerol (or triglyceride)
2 fatty acids: diacylglycerol
1 fatty acid: monoacylglycerol
Formation of triacylglycerols
Phospholipids
Diacylglycerols (glycerol head + 2 fatty acids tails)
+ a charged phosphate group
R = long hydrocarbon chain
(do NOT need to be all the same)
Dehydration synthesis forming three ester bonds
Phospholipids
In an aqueous environment, phospholipids
will spontaneously form structures to “hide” their
hydrophobic parts
Hydrophobic end (nonpolar fatty acid tails)
Hydrophilic end (charged phosphate group)
VERY IMPORTANT property
Principle component of all cell membranes
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Lipids: Steroids
e.g. cholesterol, steroid hormones, vitamin D
Basic structure of all steroids:
Four carbon rings
Proteins are polymers of
Amino Acids
Specific steroids have various
side chains, bond arrangements.
Here:
cholesterol
Proteins begin as polypeptide chains
Peptide bonds form between
Amino acids differ in the structure
of their side chain (R group)
Examples at left
(do NOT memorize)
carboxyl group of one amino acid
and
amino group of another amino acid
Note similarity of basic structure
despite variety of R groups
This tremendous chemical diversity is
linked like letters of the alphabet into
protein “words”
Dehydration synthesis again!
• Polypeptides fold into complex shapes
Protein folding: Telephone cord analogy
• Final protein has a very specific 3-D
conformation critical to its function
• Most folding is mediated by hydrogen bonds
• At high temperature or extreme pH, these bonds
are broken and the protein unfolds or
denatures
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Nucleotides:
DNA & RNA: polymers of nucleotides
Subunits of nucleic acids
Energy carriers
3 components:
Phosphate(s)
Sugar
(ribose or deoxyribose)
Base (ATGCU)
ATP: adenosine triphosphate
High energy bonds between 2 outer phosphate groups
DNA
RNA
Double stranded
Single stranded
Deoxyribose
Ribose
Bases:
Bases:
Adenine
Guanine
Cytosine
Thymine
Adenine
Guanine
Cystosine
Uracil
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