Chemistry of Life

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Chemistry of Life
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General Definitions

• Most of the Universe consists of matter and
  energy.
• Energy is the capacity to do work
• All matter is composed of basic elements that
  cannot be broken down to substances with
  different chemical or physical properties.
• Elements are substances consisting of one type of
  atom
• Atoms are the smallest particle into which an
  element can be divided.

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2.2 Life requires about 25 chemical elements

• About 25 different chemical elements are
  essential to life

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• Carbon, hydrogen, oxygen, and nitrogen make up
  the bulk of living matter, but there are other
  elements necessary for life

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2.3 Elements can combine to form compounds

• Chemical elements combine in fixed ratios to form
  compounds
• Example sodium chlorine ? sodium chloride

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General Definitions

• Subatomic particles
• The proton is located in the center (or nucleus)
  of an atom, each atom has at least one proton.
• Protons have a charge of 1
• The neutron also is located in the atomic nucleus
  (except in Hydrogen).
• The neutron has no charge
• The electron is a very small particle located
  outside the nucleus. It determines the chemical
  behavior of an atom.
• The charge on an electron is -1
• The number of protons in the atomic nucleus gives
  the atomic number.(H has 1, C has 6)

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• An atom is made up of protons and neutrons
  located in a central nucleus

• The nucleus is surrounded by electrons

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Protons
Nucleus
2
Neutrons
2
Electrons
A. Helium atom
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• Each atom is held together by attractions between
  the positively charged protons and negatively
  charged electrons

• Neutrons are electrically neutral

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Protons
Nucleus
6
Neutrons
6
Electrons
B. Carbon atom
Figure 2.4B
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• Atoms of each element are distinguished by a
  specific number of protons

• The number of neutrons may vary
• Variant forms of an element are called isotopes
• Some isotopes are radioactive

Table 2.4
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Nuclear Decay

• If a nucleus has too few or too many neutrons it
  may be unstable, and will decay after some period
  of time.
• For example, nitrogen-16 atoms (7 protons, 9
  neutrons) beta decay to oxygen-16 atoms (8
  protons, 8 neutrons) within a few seconds of
  being created.
• In this decay a neutron in the nitrogen nucleus
  is turned into a proton and an electron by the
  weak nuclear force. The element of the atom
  changes because while it previously had seven
  protons (which makes it nitrogen) it now has
  eight (which makes it oxygen). Many elements have
  multiple isotopes which are stable for weeks,
  years, or even billions of years.

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Radioactive isotopes can help or harm us

• Radioactive isotopes can be useful tracers for
  studying biological processes
• PET scanners use radioactive isotopes to create
  anatomical images

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PET SCAN

• Positron emission tomography, also called PET
  imaging or a PET scan, is a diagnostic
  examination that involves the acquisition of
  physiologic images based on the detection of
  radiation from the emission of positrons.
• Positrons are tiny particles emitted from a
  radioactive substance administered to the
  patient.

The positron is the antiparticle or the
antimatter counterpart of the electron. The
positron has an electric charge of 1, a spin of
1/2, and the same mass as an electron.
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Positron Emission

• Positron emission is a type of beta decay,
  sometimes referred to as "beta plus" (ß). In
  beta plus decay, a proton is converted, via the
  weak force, to a neutron, a beta plus particle (a
  positron) and a neutrino. Isotopes which emit
  positrons include Carbon-11, Nitrogen-13,
  Oxygen-15 and Fluorine-18
• for example these isotopes are used in positron
  emission tomography, a technique used for medical
  imaging.

http//en.wikipedia.org/wiki/Nuclear_decay
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Electron-positron Collision
Image of the "annihilation" process known in
elementary physics. It shows how a positron (e)
is emitted from the atomic nucleus together with
a neutrino (v). The positron moves then randomly
through the surrounding matter where it hits
several different electrons (e-) until it finally
loses enough energy that it interacts with a
single electron. This process is called an
"annihilation" and results in two diametrically
emitted photons with a typical energy of 511 keV
each.
http//en.wikipedia.org/wiki/Electron-positron_ann
ihilation
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How the procedure work?

• A radioactive substance is produced in a machine
  called a cyclotron and attached, or tagged, to a
  natural body compound, most commonly glucose, but
  sometimes water or ammonia.
• Once this substance is administered to the
  patient, the radioactivity localizes in the
  appropriate areas of the body and is detected by
  the PET scanner.

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PET SCAN EQUIPMENT

• PET scanner has a hole in the middle and looks
  like a large doughnut.
• Within this machine are multiple rings of
  detectors that record the emission of energy from
  the radioactive substance in the body and permit
  an image to be obtained.

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Inside the PET scanner
During the annihilation process two photons are
emitted in diametrically opposing directions.
These photons are registered by the PET as soon
as they arrive at the detector ring. After the
registration, the data is forwarded to a
processing unit
http//en.wikipedia.org/wiki/Annihilation
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How to separate healthy tissue from cancerous?

• Different colors or degrees of brightness on a
  PET image represent different levels of tissue or
  organ function.
• For example, because healthy tissue uses glucose
  for energy, it accumulates some of the tagged
  glucose, which will show up on the PET images.
  However, cancerous tissue, which uses more
  glucose than normal tissue, will accumulate more
  of the substance and appear brighter than normal
  tissue on the PET images.

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Computed Tomography PET
Image fusion readily localized tumor location in
the spleen (arrow) in this patient with
lymphoma(green arrowheads indicate normal
physiologic activity in the bowel and kidney).
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Unified Image
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2.6 Electron arrangement determines the chemical
properties of an atom

• Electrons are arranged in shells
• The outermost shell determines the chemical
  properties of an atom
• In most atoms, a full outer shell holds eight
  electrons

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Electrons and energy
From Life The Science of Biology, 4th Edition,
by Sinauer Associates
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• Atoms whose shells are not full tend to interact
  with other atoms and gain, lose, or share
  electrons

Outermost electron shell (can hold 8 electrons)
Electron
First electron shell (can hold 2 electrons)
HYDROGEN (H) Atomic number 1
CARBON (C) Atomic number 6
NITROGEN (N) Atomic number 7
OXYGEN (O) Atomic number 8
Figure 2.6
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Where does table salt come from?

• Supermarket?
• Please pass the NaCl

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Ionic bonds are attractions between ions of
opposite charge

• When atoms gain or lose electrons, charged atoms
  called ions are created
• An electrical attraction between ions with
  opposite charges results in an ionic bond

Na
Cl
Na
Cl
Na Sodium atom
Cl Chlorine atom
Na Sodium ion
Cl Chloride ion
Figure 2.7A
Sodium chloride (NaCl)
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• Sodium and chloride ions bond to form sodium
  chloride, common table salt (cubic structure)

Na
Cl
Figure 2.7B
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Halite (NaCl)

• Halite, sodium chloride, is found naturally in
  huge geologic deposits of salt minerals left over
  from the slow evaporation of ancient seawater.

"Na" stands for "natrium," the Latin word for
sodium.
http//www.science-education.org/classroom_activit
ies/chlorine_compound/nacl.html
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Halophytes

• True halophytes are plants that thrive when given
  water having greater than 0.5 NaCl.
• They are salt-resistant!

Sabal palmetto shows remarkable tolerance of
salt, even being able to grow where washed by sea
water at high tide
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Covalent bonds, the sharing of electrons, join
atoms into molecules

• Some atoms share outer shell electrons with other
  atoms, forming covalent bonds
• Atoms joined together by covalent bonds form
  molecules

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Formation of covalent bonds
Methane CH4
From Life The Science of Biology, 4th Edition,
by Sinauer Associates
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• Molecules can be represented in many ways

Table 2.8
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Bonds
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Molecules

• http//www.accessexcellence.org/RC/VL/GG/garland_P
  DFs/Panel_2.01a.pdf
• http//www.accessexcellence.org/RC/VL/GG/garland_P
  DFs/Panel_2.01b.pdf

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Water is a polar molecule
THE PROPERTIES OF WATER

• Atoms in a covalently bonded molecule may share
  electrons equally, creating a nonpolar molecule
• If electrons are shared unequally, a polar
  molecule is created

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• In a water molecule, oxygen exerts a stronger
  pull on the shared electrons than hydrogen

• This makes the oxygen end of the molecule
  slightly negatively charged
• The hydrogen end of the molecule is slightly
  positively charged
• Water is therefore a polar molecule

()
()
O
H
H
()
()
Figure 2.9
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Water
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Water
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Waters polarity leads to hydrogen bonding and
other unusual properties

• The charged regions on water molecules are
  attracted to the oppositely charged regions on
  nearby molecules
• This attraction forms weak bonds called hydrogen
  bonds

Hydrogen bond
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Hydrogen bonds make liquid water cohesive

• Due to hydrogen bonding, water molecules can move
  from a plants roots to its leaves
• Insects can walk on water due to surface tension
  created by cohesive water molecules

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Waters hydrogen bonds moderate temperature

• It takes a lot of energy to disrupt hydrogen
  bonds
• Therefore water is able to absorb a great deal of
  heat energy without a large increase in
  temperature
• As water cools, a slight drop in temperature
  releases a large amount of heat

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Ice is less dense than liquid water

• Molecules in ice are farther apart than those in
  liquid water

Hydrogen bond
ICE Hydrogen bonds are stable
LIQUID WATER Hydrogen bonds constantly break and
re-form
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• Ice is therefore less dense than liquid water,
  which causes it to float

• If ice sank, it would seldom have a chance to
  thaw
• Ponds, lakes, and oceans would eventually freeze
  solid

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Water is a versatile solvent

• Solutes whose charges or polarity allow them to
  stick to water molecules dissolve in water
• They form aqueous solutions

Na


Na


Cl
Cl





Ions in solution
Salt crystal
Figure 2.14
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http//www.accessexcellence.org/RC/VL/GG/garland_P
DFs/Panel_2.02b.pdf
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The chemistry of life is sensitive to acidic and
basic conditions

• A compound that releases H ions in solution is
  an acid, and one that accepts H ions in solution
  is a base
• Acidity is measured on the pH scale
• 0-7 is acidic
• 8-14 is basic
• Pure water and solutions that are neither basic
  nor acidic are neutral, with a pH of 7

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pH scale

• The pH scale

H
OH
Lemon juice gastric juice
Increasingly ACIDIC (Higher concentration of H)
Grapefruit juice
Acidic solution
Tomato juice
Urine
NEUTRAL H OH
PURE WATER
Human blood
Seawater
Neutral solution
Increasingly BASIC (Lower concentration of H)
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
Basic solution
Figure 2.15
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• Cells are kept close to pH 7 by buffers

• Buffers are substances that resist pH change
• They accept H ions when they are in excess and
  donate H ions when they are depleted
• Buffers are not foolproof

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Common Buffers Used in Biology
http//www.stolaf.edu/people/giannini/flashanimat/
water/weakacid.swf
http//www.stolaf.edu/people/giannini/biological2
0anamations.html
http//www.chembio.uoguelph.ca/educmat/chm19104/ch
emtoons/chemtoons.htm
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Cells composition

• Water
• Inorganic ions
• Organic ions

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Inorganic ions

• Na
• K
• Mg
• Ca
• Cl
• HPO4
• HCO3

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Organic ions

• formed by the actions of living things and have
  a carbon backbone.
• carbon can make covalent bonds with another
  carbon atom, carbon chains and rings that serve
  as the backbones of organic molecules are
  possible.

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Organic ions

• Chemical bonds store energy. The C-C covalent
  bond has 83.1 Kcal (kilocalories) per mole, while
  the CC double covalent bond has 147 Kcal/mole.
• Each organic molecule group has small molecules
  (monomers) that are linked to form a larger
  organic molecule (macromolecule). Monomers can be
  joined together to form polymers that are the
  large macromolecules made of three to millions of
  monomer subunits.

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Macromolecules

• Carbohydrates (simple sugar)
• Lipids (fatty acids)
• Proteins (amino acids)
• Nucleic acids (nucleotides)