chemistry of life. general definitions most of the universe consists of matter and energy. energy is...
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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.
• About 25 different chemical elements are essential to life
2.2 Life requires about 25 chemical elements
• Carbon, hydrogen, oxygen, and nitrogen make up the bulk of living matter, but there are other elements necessary for life
• Chemical elements combine in fixed ratios to form compounds
• Example: sodium + chlorine sodium chloride
2.3 Elements can combine to form compounds
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
A. Helium atom
2
2
2
Protons
Neutrons
Electrons
Nucleus
• The nucleus is surrounded by electrons
• Each atom is held together by attractions between the positively charged protons and negatively charged electrons
Figure 2.4B B. Carbon atom
6
6
6
Protons
Neutrons
Electrons
Nucleus
• Neutrons are electrically neutral
• Atoms of each element are distinguished by a specific number of protons
Table 2.4
– The number of neutrons may vary – Variant forms of an element are called isotopes– Some isotopes are radioactive
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 be useful tracers for studying biological processes
• PET scanners use radioactive isotopes to create anatomical images
Radioactive isotopes can help or harm us
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
http://en.wikipedia.org/wiki/Electron-positron_annihilation
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.
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
http://en.wikipedia.org/wiki/Annihilation
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
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
• 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
2.6 Electron arrangement determines the chemical properties of an
atom
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
Figure 2.6
HYDROGEN (H)Atomic number = 1
CARBON (C)Atomic number = 6
NITROGEN (N)Atomic number = 7
OXYGEN (O)Atomic number = 8
Electron
Outermost electron shell (can hold 8 electrons)
First electron shell (can hold 2 electrons)
Where does table salt come from?
• Supermarket?
• Please pass the NaCl…
• 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
Ionic bonds are attractions between ions of opposite charge
Figure 2.7A
NaSodium atom
ClChlorine atom
Na+
Sodium ionCl–
Chloride ion
Sodium chloride (NaCl)
Na Cl Na Cl
+–
• Sodium and chloride ions bond to form sodium chloride, common table salt (cubic structure)
Figure 2.7B
Na+
Cl–
Halite (NaCl)
• Halite, sodium chloride, is found naturally in huge geologic deposits of salt minerals left over from the slow evaporation of ancient seawater.
http://www.science-education.org/classroom_activities/chlorine_compound/nacl.html
"Na" stands for "natrium," the Latin word for sodium.
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
• Some atoms share outer shell electrons with other atoms, forming covalent bonds– Atoms joined together by covalent bonds form
molecules
Covalent bonds, the sharing of electrons, join atoms into 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/GG/garland_PDFs/Panel_2.01a.pdf
• http://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.01b.pdf
• Atoms in a covalently bonded molecule may share electrons equally, creating a nonpolar molecule
• If electrons are shared unequally, a polar molecule is created
Water is a polar moleculeTHE PROPERTIES OF WATER
– 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
• In a water molecule, oxygen exerts a stronger pull on the shared electrons than hydrogen
Figure 2.9
(–)
O
(–)
(+)(+)
H H
Water
Water
• The charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules– This attraction forms
weak bonds called hydrogen bonds
Water’s polarity leads to hydrogen bonding and other unusual properties
Hydrogen bond
• 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
Hydrogen bonds make liquid water cohesive
• 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
Water’s hydrogen bonds moderate temperature
• Molecules in ice are farther apart than those in liquid water
Ice is less dense than liquid water
Hydrogen bond
ICEHydrogen bonds are stable
LIQUID WATERHydrogen 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
• Solutes whose charges or polarity allow them to stick to water molecules dissolve in water– They form
aqueous solutions
Water is a versatile solvent
Figure 2.14
Ions in solution
Salt crystal
Cl–
Na+
Cl–
–
– –
–
–Na+
+
+
+
+
http://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.02b.pdf
• 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 chemistry of life is sensitive to acidic and basic conditions
• The pH scale
Figure 2.15
pH scale
Acidic solution
Neutral solution
Basic solution
Incr
easi
ng
ly A
CID
IC(H
igh
er c
on
cen
trat
ion
of
H+)
Incr
easi
ng
ly B
AS
IC(L
ow
er
con
cen
trat
ion
of
H+)
NEUTRAL[H+] = [OH–]
Lemon juice; gastric juice
Grapefruit juice
Tomato juice
Urine
PURE WATER
Seawater
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
Human blood
H+
OH–
• 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.htmlhttp://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)