Chemical Foundations
for Cells
Chapter 6
Chemical Benefits and Costs
• Understanding of chemistry
provides fertilizers, medicines,
etc.
• Chemical pollutants damage
ecosystems
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 = 65%
Hydrogen = 9.5%
Carbon = 18.5%
Nitrogen = 3.3%
What Are Atoms?
• Smallest particles that retain properties
of an element
• Made up of subatomic particles:
– Protons (+)
– Electrons (-)
– Neutrons (no charge)
Hydrogen and Helium Atoms
electron
proton
neutron
HYDROGEN
HELIUM
Atomic Number
• Number of protons
• All atoms of an element have the same
atomic number
• Atomic number of hydrogen = 1
• Atomic number of carbon = 6
Mass Number
Number of protons
+
Number of neutrons
Isotopes vary in mass number
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
Atoms seek to be more stable – complete
orbitals
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
y
Z
X
When all p orbitals are full
Electron Orbitals
• Orbitals can hold up to two
electrons
• Atoms differ in the number of
occupied orbitals
• Orbitals closest to nucleus are
lower energy and are filled first
Shell Model
• First shell
– Lowest energy
– Holds 1 orbital with up
to 2 electrons
• Second shell
– 4 orbitals hold up to 8
electrons
CALCIUM
20p+ , 20e-
Electron Vacancies
• Unfilled shells make
atoms likely to react
• Hydrogen, carbon,
oxygen, and
nitrogen all have
vacancies in their
outer shells
CARBON
6p+ , 6e-
NITROGEN
7p+ , 7e-
HYDROGEN
1p+ , 1e-
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
Chemical Bookkeeping
• Use symbols for elements when writing
formulas
• Formula for glucose is C6H12O6
– 6 carbon atoms
– 12 hydrogen atoms
– 6 oxygen atoms
Chemical Bookkeeping
• Chemical equation shows reaction
Reactants ---> Products
• Equation for photosynthesis:
6CO2 + 6H2O ---> + C6H12O12 + 6H2O
Important Bonds in Biological
Molecules
Ionic Bonds
Covalent Bonds
Hydrogen Bonds
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
Ion Formation
• Atom has equal number of
electrons and protons - no net
charge
• Atom loses electron(s), becomes
positively charged ion
• Atom gains electron(s), becomes
negatively charged ion
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
Formation of NaCl
7mm
electron transfer
SODIUM
ATOM
11 p+
11 e-
CHLORINE
ATOM
17 p+
17 e-
SODIUM
ION
11 p+
10 e-
CHLORINE
ION
17 p+
18 eFig. 2.10a, p. 26
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
one
large
molecule
another
large
molecule
a large
molecule
twisted
back
on
itself
Fig. 2.12, p. 27
Hydrogen Ions: H+
• Unbound protons
• Have important biological effects
• Form when water ionizes
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
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
Properties of Water
Polarity
Temperature-Stabilizing
Cohesive
Solvent
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
Liquid Water
H +
+
_
O
H +
H
+
+
_
O
H
+
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
Temperature-Stabilizing
Effects
• Liquid water can absorb much heat
before its temperature rises
• Why?
• Much of the added energy disrupts
hydrogen bonding rather than
increasing the movement of molecules
Why Ice Floats
• In ice, hydrogen bonds lock molecules
in a lattice
• Water molecules in lattice are spaced
farther apart then those in liquid water
• Ice is less dense than water
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
Spheres of Hydration
Diffusion
• Brownian motion – molecules
are in constant motion
• Diffusion – movement from
area of high concentration to
area of low concentration
– Affected by
• Concentration
• Temperature or agitation
• Pressure
Dynamic Equilibrium
• Molecules are still in motion
• No net gain or loss of molecules
• Living systems seek to achieve
Organic Compounds
Hydrogen and other elements
covalently bonded to carbon
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbon’s Bonding Behavior
• Outer shell of
carbon has 4
electrons; can
hold 8
• Each carbon atom
can form covalent
bonds with up to
four atoms
Bonding Arrangements
• Carbon atoms can
form chains or rings
• Other atoms project
from the carbon
backbone
Condensation Reactions
• Form polymers from subunits
• Enzymes remove -OH from one
molecule, H from another, form bond
between two molecules
• Discarded atoms can join to form water
CONDENSATION
enzyme action at functional groups
Fig. 3.4a, p. 37
Hydrolysis
• A type of cleavage reaction
• Breaks polymers into smaller units
• Enzymes split molecules into two or
more parts
• An -OH group and an H atom derived
from water are attached at exposed
sites
HYDROLYSIS
enzyme action at functional groups
Fig. 3.4b, p. 37
Carbohydrates – energy source
Monosaccharides
(simple sugars)
Disaccharides
(two simple sugars)
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)
Two Monosaccharides
glucose
fructose
Disaccharides
• Two
monosaccharides
covalently bonded
• Formed by
condensation reaction
glucose
fructose
+ H2O
sucrose
Polysaccharides
•
Straight or branched chains of many saccharides
•
Most common are composed entirely of glucose
– Cellulose
• tough, indigestible
• structural material in plants
– Starch
• easily digested
• storage form in plants
– Glycogen
• sugar storage form in animals
– Chitin
• structural material for hard parts of invertebrates
• cell walls of many fungi
Lipids
• Most include fatty acids
– Fats
– Phospholipids
– Waxes
• Tend to be insoluble in water
• Energy source, insulation & protection
Fatty Acids
• Carboxyl group (-COOH) at one end
• Carbon backbone (up to 36 C atoms)
– Saturated - Single bonds between carbons
– Unsaturated - One or more double bonds
Three Fatty Acids
What difference does the double bond make?
stearic acid
oleic acid
linolenic acid
Fats
• Fatty acid(s)
attached to
glycerol
• Triglycerides are
most common
Proteins
• Carbon, hydrogen, oxygen, nitrogen &
sulfur
• Amino acid building blocks
• AA linked by peptide bonds
• Enzymes
• Build tissue
Enzymes
• Protein
• Act as catalyst
– Helps reaction happen faster or at lower
temperatures
• Substrate specific shapes
– Lock & key system
– Recycled; not used up
Denaturation
• Disruption of threedimensional shape
• Breakage of weak bonds
• Causes of denaturation:
– pH
– Temperature
• Destroying protein shape
disrupts function
Nucleic Acids
• Carbon, hydrogen,
oxygen, nitrogen &
phosphorus
• Nucleotides – building
blocks
• DNA, RNA
• Genetic information