Transcript Lecture 2 - Faculty of Science at Bilkent University

Chemistry of Life
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.
2.2 Life requires about 25 chemical elements
• About 25 different chemical elements are
essential to life
• Carbon,
hydrogen,
oxygen, and
nitrogen make
up the bulk of
living matter,
but there are
other elements
necessary for
life
2.3 Elements can combine to form compounds
• Chemical elements combine in fixed ratios to
form compounds
• Example: sodium + chlorine  sodium chloride
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)
• An atom is made up of protons and neutrons
located in a central nucleus
• The nucleus is surrounded by electrons
2
Protons
Nucleus
2
Neutrons
2
Electrons
A. Helium atom
• Each atom is held together by attractions
between the positively charged protons and
negatively charged electrons
• Neutrons are electrically neutral
6
Protons
Nucleus
Figure 2.4B
6
Neutrons
6
Electrons
B. Carbon atom
• 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
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.
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
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.
Positron Emission
• Positron emission is a type of beta decay,
sometimes referred to as "beta plus" (β+). 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
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_annihilation
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.
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.
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
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.
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).
Unified Image
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
Electrons and energy
From: Life: The Science of Biology, 4th
Edition, by Sinauer Associates
• 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
HYDROGEN (H)
Atomic number = 1
Figure 2.6
First electron shell (can hold 2 electrons)
CARBON (C)
Atomic number = 6
NITROGEN (N)
Atomic number = 7
OXYGEN (O)
Atomic number = 8
Where does table salt come from?
• Supermarket?
• Please pass the NaCl…
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
Sodium atom
Cl
Chlorine atom
Figure 2.7A
Na
Na+
Sodium ion
–
Cl
Cl–
Chloride ion
Sodium chloride (NaCl)
• Sodium and chloride ions bond to form sodium
chloride, common table salt (cubic structure)
Na+
Cl–
Figure 2.7B
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_activities/chlorine_compound/nacl.html
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
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
Formation of covalent bonds
Methane
CH4
From: Life: The Science of Biology, 4th
Edition, by Sinauer Associates
• Molecules can be
represented in
many ways
Table 2.8
Bonds
Molecules
• http://www.accessexcellence.org/RC/VL/G
G/garland_PDFs/Panel_2.01a.pdf
• http://www.accessexcellence.org/RC/VL/G
G/garland_PDFs/Panel_2.01b.pdf
THE PROPERTIES OF WATER
Water is a polar molecule
• Atoms in a covalently bonded molecule may
share electrons equally, creating a nonpolar
molecule
• If electrons are shared unequally, a polar
molecule is created
• 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
Water
Water
Water’s 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
Hydrogen bonds make liquid water cohesive
• Due to hydrogen
bonding, water
molecules can move
from a plant’s roots to
its leaves
• Insects can walk on
water due to surface
tension created by
cohesive water
molecules
Water’s 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
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
– 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
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
Figure 2.14
Salt
crystal
http://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.02b.pdf
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
• The pH
scale
H+
OH–
Acidic solution
Increasingly ACIDIC
(Higher concentration of
H+)
pH scale
Neutral solution
Figure 2.15
Basic solution
Increasingly BASIC
(Lower concentration of
H+)
NEUTRAL
[H+] = [OH–]
Lemon juice; gastric juice
Grapefruit juice
Tomato juice
Urine
PURE WATER
Human blood
Seawater
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
• 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
Common Buffers Used in Biology
http://www.stolaf.edu/people/giannini/flashanimat/water/weakacid.swf
http://www.stolaf.edu/people/giannini/biological%20anamations.html
http://www.chembio.uoguelph.ca/educmat/chm19104/chemtoons/chemtoons.htm
Cell’s composition
• Water
• Inorganic ions
• Organic ions
Inorganic ions
•
•
•
•
•
•
•
Na
K
Mg
Ca
Cl
HPO4
HCO3
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.
Organic ions
• Chemical bonds store energy. The C-C covalent
bond has 83.1 Kcal (kilocalories) per mole, while
the C=C 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.
Macromolecules
• Carbohydrates (simple sugar)
• Lipids (fatty acids)
• Proteins (amino acids)
• Nucleic acids (nucleotides)