Download Lecture 2 - The Chemistry of Life

Lecture 2: The Chemistry of Life
In this lecture:
• Matter, atoms, and the periodic table
• Chemical bonding
– Ionic vs. covalent bonds
– Hydrogen bonds and Van der Waals forces
• Polarity
• Electronegativity
What is “stuff” made of?
• Matter
– Anything that takes up space and has mass (or
weight)
– Makes up everything we see, touch, feel, and hear
in the universe
– (Dark matter is another thing entirely)
What is “matter” made of?
Matter is made up of elements.
An element is “a substance that cannot be broken down to
other substances by chemical reactions”
Potassium, hydrogen, carbon, phosphorus
Compounds are substances made of two or more elements
The properties of a compound are not related to the
properties of its elements
The periodic table is very carefully arranged. We shall see why soon…
Matter = atoms = elements
Compounds = 2+ elements
The elements of life
• About 20-25% of the elements are necessary to life
• Carbon, hydrogen, nitrogen, and oxygen make up
96% of living beings
• Phosphorus, calcium, potassium, and sulfur make up
most of the other 4%
• There are some trace elements that are necessary for
life, but needed in very minute amounts
– Zinc in DNA regulation, silicon in shell formation, iron
in blood
What is matter made of?
• Matter is made of atoms
• An atom is the smallest unit of matter that still
retains the properties of an element
– Atom means “indivisible” in Greek
What are atoms made of?
• Three subatomic particles go into an atom
– Proton (positive charge)
– Neutron (neutral/no charge)
– Electron (negative charge)
• Neutrons and protons form the atomic
nucleus
• Electrons form a cloud around the nucleus
• Neutron mass and proton mass are almost
identical and are measured in daltons
A helium atom
Is this what an atom really looks like?
Atomic Number and Atomic Mass
• Atoms of the various elements differ in number of
subatomic particles
• An element’s atomic number is the number of
protons in its nucleus
• Atomic mass, the atom’s total mass is the sum of
protons plus neutrons in the nucleus
Electron positions
• Electrons are arranged in “shells” around the
nucleus
• 2 electrons in the innermost shell, 8 in all the
subsequent shells
• The number of electrons an atom has is equal
to the number of protons
– (7 positive protons + 7 negative electrons =
neutral charge)
– Neutrons just hang out
Figure 2.9
Hydrogen
1H
Mass number
First
shell
2
He
4.00
Atomic number
Helium
2He
Element symbol
Electron
distribution
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Sodium
11Na
Third
shell
Magnesium Aluminum
12Mg
13Al
Valence electrons
• Valence electrons are those in the outermost
shell
• The chemical behavior of an atom is mostly
determined by the valence electrons
• Elements with a full valence shell are
chemically inert
Diagram of valence electrons
Let’s draw a sulfur atom
•
•
•
•
•
What is the atomic number of sulfur?
How many protons?
How many neutrons?
How many electrons?
Where do the electrons go?
Solution: A sulfur atom
Isotopes
• All atoms of an element have the same
number of protons but may differ in number
of neutrons
• Isotopes are two atoms of an element that
differ in number of neutrons
• Radioactive isotopes decay spontaneously,
giving off particles and energy
Radioactive decay of isotopes
• Half-life is the time it takes half of the
isotopes in a compound to decay into normal
atoms
• The ratio of carbon-14 to carbon-12 can be
used to date biological samples
• Some applications of radioactive isotopes in
biological research are
– Dating fossils
– Tracing atoms through metabolic processes
– Diagnosing medical disorders
Summary of an atom
Chemical Bonds
• Atoms with incomplete valence shells (<8)
“want” to have filled shells
• Atoms will bond with each other to fill their
shells, forming a chemical bond
Figure 2.11-3
Hydrogen atoms (2 H)
Hydrogen has one proton
and one valence electron
It wants two to completely
fill its inner shell, and so
will bond
Hydrogen molecule (H2)
Bonding
• A molecule consists of two or more atoms
held together by covalent bonds
• Four types of bonds: covalent, ionic, metallic,
hydrogen (sometimes)
• Covalent and hydrogen most common in biology
Ionic Bonding
• Ionic bonding – electron is donated
Ionic Bonding
• Atoms sometimes strip electrons from their
bonding partners
• An example is the transfer of an electron from
sodium to chlorine
• After the transfer of an electron, both atoms
have charges
• A charged atom (or molecule) is called an ion
• A cation is a positively charged ion
• An anion is a negatively charged ion
• An ionic bond is an attraction between an
anion and a cation
Covalent Bonding
• Covalent bonding – electron is shared
• Some examples
of covalent
bonds
Bonding in covalent bonds
• A single bond is the sharing of one pair of
valence electrons
• A double bond is the sharing of two pairs of
valence electrons
Polarity in covalent bonds
• In a nonpolar covalent bond, the atoms share the
electron equally
• In a polar covalent bond, one atom is more
electronegative, and the atoms do not share the
electron equally
• Unequal sharing of electrons causes a partial positive
or negative charge for each atom or molecule
Electronegativity
• Atoms in a molecule attract electrons to varying
degrees
• Electronegativity is an atom’s attraction for the
electrons
• The more electronegative an atom, the more
strongly it pulls shared electrons toward itself
Electronegativity
Electronegativity increases in this direction
Weak Chemical Bonds
• Most of the strongest bonds in organisms are
covalent bonds that form a cell’s molecules
• Weak chemical bonds, such as ionic bonds
and hydrogen bonds, are also important
• Weak chemical bonds reinforce shapes of
large molecules and help molecules adhere to
each other
Weak Chemical Bonds – Hydrogen Bonds
• A hydrogen atom covalently bonded to one
electronegative atom is also attracted to another
electronegative atom
• In living cells, the electronegative partners are
usually oxygen or nitrogen atoms
Weak Chemical Bonds: Van der Waals force
• Polar molecules have “hot spots” of negative or
positive charge where electrons are unevenly
distributed
• Van der Waals interactions are attractions between
molecules that are close together as a result of these
charges
“This force comes from fluctuations in charge distributions between
neighboring molecules, which need not be polar; their charge
fluctuations naturally fall into synch, creating an attractive force.”
How Geckos stick on der Waals
• Geckos use Van der Waals interactions
between their toe hairs and a wall to ‘stick’
Chemical Reactions: making and breaking
bonds
• The starting molecules of a chemical reaction are
called reactants
• The final molecules of a chemical reaction are called
products
Photosynthesis, a chemical reaction
• Plants use sunlight to create
an essential building block
• Sunlight powers the
conversion of carbon dioxide
and water to glucose and
oxygen
6 CO2 + 6 H20 → C6H12O6 + 6 O2
What do my multivitamins do in the body?
• The FDA officially recognizes 12 ‘essential’
minerals: calcium, magnesium, zinc, selenium, copper, manganese,
chromium, molybdenum, and chloride
• Silicon, boron, nickel, vanadium, and lead may
play a biological role, but aren’t ‘essential’
– The role of these hasn’t been well defined
– For a lot of these, we don’t know exactly what
they do, so the FDA is hands-off
Biological organisms and elements
Mono Lake, CA:
The ‘Aliens’ of Mono Lake
• Mono Lake has no natural outlets
– Chemicals enter, but don’t leave
– HUGE buildup of toxic waste chemicals and salt
– No fish, only brine shrimp can live there
• In December 2010 NASA announced the
discovery of a bacteria that can use arsenic
– Arsenic is normally VERY toxic to living things!!
– It replaces phosphorus in biochemical reactions, but is
far less stable
– Anything that accidentally includes arsenic (DNA, ATP,
etc.) tends to break down very fast
• These bacteria can stably integrate arsenic in place
of phosphorus into their DNA
• Use large storage vacuoles to isolate arseniccontaining molecules away from important cellular
machinery
Controversey
• 2012 – scientists begin refuting NASA’s
findings
• NASA scientists fed the bacteria salts that
contained trace amounts of phosphorus,
which may have allowed the bacteria to live
• No arsenic found in the DNA after all
http://www.scientificamerican.com/article.cfm?id=study-fails-to-confirm-existence
Vocabulary
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•
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•
•
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Matter
Element
Compound
Atom
Molecule
Protons, neutrons,
electrons
• Nucleus
• Atomic number
• Isotope
• Potential energy, kinetic
energy
• Valence electrons
• Electron shells
• Electronegativity
• Covalent bond, ionic bond
• Hydrogen bond, Van der
Waals force
• Products, reactants
• Polarity