Transcript Chapter 2 The Chemical Basis of Life: Atoms, Molecules and Water Biology • Based on the principles of chemistry and physics • All living organisms.

Chapter 2
The Chemical Basis of Life:
Atoms, Molecules and Water
Biology
• Based on the principles of chemistry and
physics
• All living organisms are a collection of
atoms and molecules
• All life forms are composed of matter
– Anything that contains mass and occupies
space
2
Atoms
• Smallest functional units of matter that
form all chemical substances
• Cannot be further broken down into other
substances by ordinary chemical or
physical means
• Each specific type of atom is a chemical
element
3
Atoms
• Three subatomic particles
– Protons- positive, found in nucleus, same
number as electrons
– Neutrons- neutral, found in nucleus, number
can vary
– Electrons- negative, found in orbitals, same
number as protons
• Entire atom has no net electric charge
4
Electrons occupy orbitals
• Scientists initially visualized
an atom as a mini solar
system
– This is an oversimplified but
convenient image
• Electrons travel within
regions surrounding the
nucleus (orbitals) in which
the probability is high of
finding that electron
• Can be depicted as a cloud
5
6
Orbitals vs Shells
Orbitals
• s orbitals are spherical
• p orbitals are propeller or dumbbell shaped
• Each orbital can hold only 2 electrons
– An atom with more than 2 electrons has more than 1
orbital
Shells
• Atoms with progressively more electrons have orbitals
within electron shells that are at greater and greater
distances from the center of the nucleus
– 1st shell - 1 spherical orbital (1s) - holds 2 electrons
– 2nd shell - 1 spherical orbital (2s) and 3 dumbbellshaped orbitals (2p) – can hold 4 pairs of electrons
7
Nitrogen Atom
• A nitrogen atom has seven
protons and seven
electrons
• 2 electrons fill 1st shell
• 5 electrons in 2nd shell
– 2 fill 2s orbital
– 1 each in the 2p orbitals
• Outer 2nd shell is not full
– Electrons in the outer
shell that are available
to combine with other
atoms are called the
valence electrons
8
Characteristics of Elements
Atomic number – number of protons
Atomic weight (mass) – average of
the mass numbers of all element’s
isotopic forms
Electron orbitals – volumes of
space surrounding the atomic nucleus
where electrons are likely
to be found
9
Periodic table
Period
Groups
1
Hydrogen
1
H
1
1+
1.0079
2
3
Element name
Atomic number
Symbol
atomic mass
4
5
6
7
8
Helium
2
Element name
Atomic number
Symbol
He
atomic mass
(average mass of all isotopes)
2+
(average mass of
all isotopes)
4.0026
Lithium
3
Beryllium
4
Boron
5
Carbon
6
Nitrogen
7
Oxygen
8
Fluorine
9
Neon
10
Li
Be
B
C
N
O
F
Ne
3+
4+
5+
6+
7+
8+
9+
10+
6.941
9.0122
10.811
12.011
14.007
15.999
18.998
20.180
Aluminum
13
Sillicon
14
Phosphorus
15
Sulfur
16
Chlorine
17
Argon
18
Sodium
11
3
2
Magnesium
12
Na
Mg
Al
Si
P
S
Cl
Ar
11+
12+
13+
14+
15+
16+
17+
18+
22.990
24.305
26.982
28.086
30.974
32.065
35.453
39.948
10
How are Elements,
Isotopes and Ions
different?
It depends on which
subatomic particle is
changed in number.
Change in
Proton number  new element
Neutron number  isotope
Electron number  ion
11
11
Carbon, Hydrogen, Oxygen, and Nitrogen
• “CHON” typically make up about 95% of
the atoms in living organisms
– Hydrogen and oxygen occur primarily in water
– Nitrogen is found in proteins
– Carbon is the building block of all living matter
• Mineral elements - less than 1%
– Ca, Cl, Mg, P, K, Na, S
• Trace elements - less than 0.01%
– Essential for normal growth and function
– I, Fe, Zn and others
12
(a) Nitrogen deficiency
(b) Iodine deficiency
13
Matter, Elements & Compounds
• Matter is anything that takes
Sodium
Chloride
up space and has mass
• An element has all the same
kind of atoms
• A compound has two or
more elements in a fixed ratio
NaCl
• A compound has
characteristics different from
those of its elements
14
Types of Chemical Bonding
between Atoms
• Atoms with incomplete valence shells can share or
transfer valence electrons with certain other atoms
• These interactions usually result in atoms staying close
together, held by attractions called chemical bonds
• Chemical bonds – when 2 or more atoms share,
donate or accept electrons to form molecules and
compounds
15
Three Types of Chemical Bonds
1. Covalent bonds – electrons are shared
among atoms
– Non-polar covalent bonds – equal sharing
– polar covalent bonds – unequal sharing
2. Ionic bonds – electrons are transferred to
one atom forming positively charged
cations and negatively charged anions
3. Hydrogen bonds – weak bonds between
hydrogen and other atoms
16
What about Van der Waals
Interactions?
• If electrons are distributed asymmetrically in
molecules or atoms, they can result in “hot spots”
of positive or negative charge
• Van der Waals interactions are
attractions between molecules
that are close together as a
result of these charges
17
All bonds are not equal in strength
For molecules in solution
•
•
•
•
•
Nonpolar Covalent
Polar Covalent
Ionic
Hydrogen
van der Waals Forces
18
Non-polar Covalent bonds
•
•
•
Atoms share
electrons equally
Most prevalent in
organic
compounds
Non-polar = no
charge
19
Polar Covalent Bonds
•
•
•
•
Unequal sharing of
electrons
Results in slightly
positive and negative
poles
Found in H2O
Makes hydrogen
bonds possible
20
Ionic Bonds
•
Complete
transfer of
one or more
electrons
from one
atom to
another
•
form ions
(cations and
anions)
when they
dissociate
Na+
Cl
21
Hydrogen Bonds
•
Electrical attraction
between hydrogen
in one polarized
bond and oxygen
or nitrogen on
another, or in the
same, molecule
22
Chemical Reactions
• Occur when one or more substances are
changed into other substances
– Reactants converted to products
• Share many properties
– All require a source of energy
– Reactions in living organisms often require catalysts
(enzymes)
– Tend to proceed in a particular direction but will
eventually reach equilibrium
23
– Occur in liquid environment - water
Symbolism
• → implies all reactants are converted to products
• All chemical reactions are reversible: products of the
forward reaction become reactants for the reverse reaction
•
implies a reversible reaction
• Chemical equilibrium is reached when the forward and
reverse reaction rates are equal
• In biological systems, products of the forward reaction may
be used in the next reaction in a pathway
24
Properties of water
• A solution is made up of the
– Solvent - liquid
– Solutes - substances dissolved in solvent
• Aqueous solution- water is the solvent
• Hydrophillic substances - “water-loving”
– Readily dissolve in water
– Molecules that contain ionic and/or polar covalent bonds
• Hydrophobic substances - “water-fearing”
– Do not readily dissolve in water
– Non-polar molecules like hydrocarbons
• Amphipathic molecule
– Have both polar/ionized and nonpolar regions
– May form spherical aggregates (micelles) in water
• Colloid – suspension of fine particles in water
25
When your professor asks questions,
choose from these answers:
1. Water
2. NaCl
3. Na+and Cl4. Hydrophobic
5. Hydrophilic
26
Amphipathic molecules form Micelles
•
•
Polar
(hydrophilic)
regions at the
surface of the
micelle
Nonpolar
(hydrophobic)
ends are
oriented toward
the interior of the
micelle
27
The Amazing Molecule: Water
• Water is the biological medium on Earth
• All living organisms require water more than
any other substance
• Most cells are surrounded by water, and cells
themselves are about 70–95% water
• The abundance of water is the main reason
the Earth is habitable
• Water acts as a solvent and fills many other
roles crucial to the survival of living things
28
What occurs between H20
molecules?
29
Hydrogen Bonds
• Hold water molecules together
• Each water molecule can form a maximum
of 4 hydrogen bonds
• The hydrogen bonds joining water molecules
are weak, about 1/20th as strong as covalent
bonds.
• They form, break, and reform with great
frequency
30
Hydrogen Bonds
• Extraordinary Properties of water that are a result of
hydrogen bonding
– Cohesive behavior: H2O molecules associating with
other H2O molecules
– Adhesive behavior: H2O molecules associating with
other types of molecules
– Resistance to temperature change (high specific heat)
– High heat of vaporization
– Expands upon freezing
– Versatile solvent
31
Cohesion and Adhesion
Cohesion makes Surface
Tension possible!
Cohesion and Adhesion are
essential for movement of water
from roots to leaves in plants
32
High specific heat & High heat of vaporization
• Specific heat = amount of heat that must be absorbed or lost for
one gram of a substance to change its temperature by 1oC
• Heat of vaporization = amount of energy required to transform a
given quantity of a substance into a gas
• Water’s high specific heat makes it an effective temperature
regulator, both within and outside living organisms
• Water’s high heat of vaporization makes it an effective
evaporative cooling agent
33
33
Water Expands Upon Freezing
Density is greatest at 4oC
When water reaches 0oC,
molecules become locked
into a crystalline lattice with
each molecule bonded to
four partners with maximum
spacing between them.
As ice starts to melt, some of
the hydrogen bonds break
and some water molecules
can slip closer together than
they can while in the ice
state.
Ice floats because it is ~10% less
dense than water.
34
Water is the Universal Solvent of Life
A hydration shell or
sphere forms around
ions, sugars, and
amino acids
35
Concentration of a Solution
• Molecular weight – sum of the weights of all atoms in a
molecule (daltons)
• Mole – amount of a substance that has a mass in grams
numerically equivalent to its molecular weight in daltons.
• Avogadro’s number – 6.02 X 1023
– A mole of one substance has the same number of
molecules as a mole of any other substance.
36
Molarity
The concentration of a material in solution is called its molarity
or M.
A one molar solution has one mole of a substance
dissolved in one liter of solvent, typically water.
Let's calculate a one molar solution of sucrose, C12H22O11.
C = 12 daltons
12 x12 = 144
H = 1 dalton
1 x 22 = 22
O = 16 daltons
16 x 11 = 176
For a 2 M solution?
For a 0.05 M solution?
For a 0.2 M solution?
342g of sucrose in
1L of water will give
a 1M solution
342
Try these on your own
37
Acids, Bases and the pH Scale
• In solution, some water molecules ionize into
hydronium and hydroxide ions
• We can simplify this to: H2O
H+ + OH• Other dissolved substances may lead to an
increase in H+ or OH-, leading to acidic or
basic solution
• Acids donate H+, bases accept H+
• pH is a measure of [H+] ie pH = -log10[H+]
38
The pH Scale
39
39
Buffers Are a Combination of a Weak Acid
and Base and prevent pH shifts
Ex. H2CO3
carbonic acid
HCO-3 + H+
bicarbonate
40
Threats to Water Quality on Earth
• Acid precipitation
refers to rain, snow, or
fog with a pH lower
than 5.6
• Occurs when sulfur
oxides and nitrogen
oxides react with water
in the atmosphere
• Can damage
– Forests
– Organisms in lakes and
streams
– Coral reefs
41