the chemical context of life chapter 2. life depends on chemistry life is organized into a hierarchy...
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Life depends on Chemistry
Life is organized into a hierarchy of structural levels.
emergent properties appear at each successive level
MatterOrganisms are composed of matter
Matter is anything that takes up space and has mass.
Matter consists of chemical elements in pure form and in combinations called compounds
Element Pure substance made up of one
kind of atom Cannot be broken down into other
substances by chemical means Shown by a short hand symbol Either a capital letter only C, N,
H, O Or a capital and lower case letter
Ca, Na, Mg
Chemical Compound A compound is a substance
consisting of two or more elements in a fixed ratio.
Physical and chemical properties usually very different from those of the elements from which they are formed
Chemical Compound
Table salt (sodium chloride or NaCl) is a compound with equal numbers of chlorine and sodium atoms.
Life Requires 25 Elements More than 100 known , about 25 found in
living organisms Key Element is Carbon 4 make up 96%
C carbon N nitrogen O oxygen H hydrogen Most of the remaining 4% Phosphorus,
Potassium, Sulfur (CHNOPS) Calcium inorganic catalyst Trace elements <0.01% but are essential
Ex: 0.15mg Iodine/day Thyroid function
Chemical PropertiesBased on Structure of Atoms
Atom is the smallest unit of matter that still retains the properties of an element.Atoms composed subatomic
particles. Neutrons and Protons, are packed
together to form a dense core, the atomic nucleus, at the center of an atom.
Electrons form a cloud around the nucleus.
Atoms Protons
positively charged Neutrons no
charge Electron (-),
are in constant motion
Atomic Number # of Protons
Atomic mass # of protons + # of neutrons
Carbon 6P +6N=12 A neutron and a proton almost
identical in mass, 1.7 x 10-24 gram per particle.
The dalton, is used to measure the mass subatomic particles, atoms or molecules
Mass of a neutron or a proton = 1 dalton. The mass of an electron is about 1/200th
that of a neutron or proton. The contribution of electrons when
determining the total mass of an atom is ignored
Isotopes A given element have the same number of
protons, they may differ in the number of neutrons
Two atoms of the same element that differ in the number of neutrons are called isotopes
In nature, an element occurs as a mixture of isotopes 99% of carbon atoms have 6 neutrons (12C). Most of the remaining 1% of carbon atoms have
7 neutrons (13C) while the rarest isotope, with 8 neutrons is 14C.
Radioactive Isotopes The nuclei are unstable and decay
spontaneously, giving off particles and energy
In its decay, an neutron is converted to a proton and electron.This converts 14C to 14N, changing the identity of that atom.
Radioactive isotopes have many applications in biological research.Radioactive decay rates can be used to
date fossils.Radioactive isotopes can be used to trace
atoms in metabolism.
Electrons and Reactivity Electrons in the highest energy level of
an atom determines how the atom reacts
1st / lowest energy level – can hold 2 electrons
2nd / highest energy level – can hold 8 electrons , when there is a partially filled energy level the atoms become chemically reactive, tend to react with other atoms
Bonding Properties Effect of electrons
chemical behavior of an atom depends on its electron arrangement
depends on the number of electrons in its outermost shell, the valence shell How does this
atom behave?
Bonding properties Effect of electrons
chemical behavior of an atom depends on number of electrons in its outermost shell
How does this atom behave? How does this atom behave?
Elements & their valence shells
Elements in the same column have the same valence & similar chemical properties
Elements & their valence shells
Moving from left to right, each element has a sequential addition of electrons (and protons)
Chemical reactivity Atoms tend to
Complete a partially filled outer (valence) electron shell
orEmpty a partially filled outer (valence)
electron shell
This tendency drives chemical reactions
Covalent bonds Two atoms need an electron Share a pair of electrons Strong bond
both atoms holding onto the electrons Forms molecules
example:water = takes energy to separate
Double covalent bonds Two atoms can share more than one
pair of electronsdouble bonds (2 pairs of electrons)triple bonds (3 pairs of electrons)
Very strong bonds
Multiple covalent bonds 1 atom can form covalent bonds with
two or more other atomsforms larger moleculesex. carbon
Polar covalent bonds Pair of electrons not shared
equally by 2 atoms Water = O + H oxygen has stronger
“attraction” for the shared electrons than hydrogen
oxygen has higher electronegativity
Polar Covalent Bonds 2 hydrogens in the water molecule
form an angle Water molecule is polar
oxygen end is –hydrogen end is +
Leads to many interesting properties of water….
Hydrogen bonds
Positive H atom in 1 water molecule is attracted to negative O in another
Can occur wherever an -OH exists in a larger molecule
Weak bonds
Van der Waals interactions Nonpolar covalent bonds can have partially
negative and positive regions. Because electrons are constantly in motion,
there can be periods when they accumulate by chance in one area of a molecule.
This creates ever-changing regions of negative and positive charge within a molecule.
Molecules or atoms in close proximity can be attracted by these fleeting charge differences, creating van der Waals interactions.
While individual bonds (ionic, hydrogen, van der Waals) are weak, collectively they have strength
Weak Bonds H- Bonds bond to electroneg
elements,lasts only 1/109 sec, strength is 1/20 of a H/C covalent bond
Van der Waals large org. mols. Close to each other have transient +/- zones temp interactions
Ionic protiens have =?- charges at diff points holds shapeEx: sickle cell anemia 1 neg charge
disappears deformed, can only bind w/1 oxygen instead of 4 low flow of oxy
Form fits Function Living systems are
very delicate never have ionic bonding use polar covalent and non-polar covalent bonds
The shape of a molecule is related to its biological function
Molecules with similar shapes can interact in similar waysFor example, morphine, heroin, and other
opiate drugs are similar enough in shape that they can bind to the same receptors as natural signal molecules, called endorphins.
Binding to the receptors produces euphoria and relieves pain.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings
Fig. 2.19
Chemical Equilibrium The rate of formation of products is
the same as the rate of breakdown of products (formation of reactants) products and reactants are continually
being formed, but there is no net change in the concentrations of reactants and products.
the concentrations of reactants and products are typically not equal, but their concentrations have stabilized.