The Chemical Context of Life

Chapter 2

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.

Pure sodium metal, chlorine gas, combination forms an edible compound.

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

Attraction between (+) Proton & (-) Electron keep the electrons in the vicinity of the nucleus.

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 row have the same number of shells

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

Ionic bonds-Transfer of an electron Forms + & - ions

+ = cation– = anion

Weak bond

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 Reactions Bonds are made or broken

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.