copyright 2005 pearson education, inc. publishing as benjamin cummings living things abide by...

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Living things abide by chemical laws

• Chemistry abides by physical laws

• These rules govern how living things work

• Physics = forces in/placed on the body (kinesiology, sports medicine, blood pressure, nerve conduction, etc.)

• Chemistry = how the processes/uses matter (physiology, pharmacy, anesthesia, growth and repair, etc.)

Chapter 2: The Chemical Context of Life


Outline:

1) The chemical makeup of life

1) Matter, elements and compounds

2) Atoms and their structure

3) Radioactive isotopes of elements

2) Electrons – what make elements able to bind to and react with each other

1) Electron shells and orbitals

3) Formation of molecules and compounds from elements

1) Covalent Bonds

2) Ionic Bonds

3) Weak chemical bonds (hydrogen bonds, van der Waals interactions)

4) Molecular shape and function


Matter consists of chemical elements in pure form and in combinations called compounds

Organisms are composed of matter

•Matter - anything that takes up space and has mass

•Matter is made up of elements

•An element is a substance that cannot be broken down to other substances by chemical reactions

•A compound is a substance consisting of two or more elements in a fixed ratio

Sodium Chlorine Sodium chloride

Which of these are matter? elements? compounds?


Essential Elements of Life

• About 25 of the 92 naturally occurring elements are essential for life

• Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter

• Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur

• Trace elements are those required by an organism in minute quantities


Deficiencies of different types of elements

(a) Nitrogen deficiency (b) Iodine deficiency


An element’s propertiesdepend on the structure of its atoms

• Each element consists of unique atoms

• An atom is the smallest unit of matter that still retains the properties of an element

• Atoms are composed of subatomic particles

• Relevant subatomic particles include:

– Neutrons (no electrical charge)

– Protons (positive charge)

– Electrons (negative charge)

• Neutrons and protons form the atomic nucleus

• Electrons form a cloud around the nucleus

Nucleus

ElectronsCloud of negativecharge (2 electrons)

Simplified views of a Helium atom


Atomic Number and Atomic Mass

• Atoms of the various elements differ in the number of subatomic particles contained within the core atom structure

• An element’s atomic number is the number of protons present in one atom

• An element’s mass number is the sum of protons plus neutrons in the nucleus of one atom

• Atomic mass, the atom’s total mass, can be approximated by the mass number


Isotopes

• Atoms of an element ALWAYS have the same number of protons but may differ in number of neutrons. If an atom of a specific element loses or gains a proton, that atom is transformed into an atom of a different element.

• Isotopes are two atoms of an element that differ in number of neutrons. Remember, they MUST have the same number of protons.

• Most isotopes are stable, but some are radioactive, giving off particles and energy.

• When these isotopes undergo radioactive decay, they lose different particles, depending on the type of radioactive decay, and the atoms are often changed into a different element.


• Most of the time, we think of radiation as a bad thing (carcinogenic)

• What good are isotopes in biology?

Isotopes

Cancerousthroattissue

Radioactivity can be used to locate tumors in the body


The Energy Levels of Electrons

• Energy is the capacity to cause some kind of change

• Potential energy is the energy that matter has because of its location or structure. It is simply the stored energy present in a system that can be used to accomplish something.

• The electrons of an atom differ in their amounts of potential energy

• An electron’s state of potential energy is called its energy levelA ball bouncing down a flightof stairs provides an analogy forenergy levels of electrons. Electrons,like the ball, can only stop on a stepof energy, not between steps, just likea ball.

Third energy level (shell)

Second energy level (shell)

First energy level (shell)

Atomicnucleus

Energyabsorbed

Energylost

Representation of the energy gained or lost by an electron

when it moves between two different energy levels.


Electron Configuration and Chemical Properties• The chemical behavior of an atom is determined by the

distribution of its electrons in electron shells

• The periodic table of the elements shows the electron distribution for each element

Firstshell

Hydrogen1H

Lithium3Li

Secondshell

Thirdshell

Sodium11Na

Beryllium4Be

Magnesium12Mg

Boron5B

Aluminum12Al

Silicon14Si

Carbon6C

Nitrogen7N

Phosphorus15P

Oxygen8O

Sulfur16S

Chlorine17Cl

Fluorine9F

Neon10Ne

Argon18Ar

Helium2He

Atomic number

Element symbol

Electron-shelldiagram

Atomic mass

2He4.00

Electron shell diagrams are often used to represent the number of electrons in an atom (and therefore the

charge)


• Valence electrons are those in the outermost shell, or valence shell of an atom.

• The chemical behavior of an atom is mostly determined by the valence electrons

– Often determines charge

– Determines bonding

What electrons in an atom make the atom of an element able to react with other atoms?


Electron Orbitals• An orbital is the three-dimensional space where an electron is

found 90% of the time – with each electron shell consisting of a SPECIFIC number of orbitals

Electronorbitals

Electron-shelldiagrams

1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals

First shell(maximum2 electrons)

Second shell(maximum8 electrons)

Neon, with twofilled shells(10 electrons)

x

z

y


How do two atoms come together to form molecules and compounds?

• The formation and function of molecules depends on chemical bonding between two atoms

• Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms

• These interactions usually result in atoms staying close together, held by attractions called chemical bonds

Ionic Bond Covalent Bond


Covalent Bonds

• A covalent bond is the sharing of a pair of valence electrons by two atoms

• In a covalent bond, the shared electrons count as part of each atom’s valence shell

• Two atoms are then joined together by virtue of sharing these two electrons to form a molecule

Hydrogen atoms (2 H)

Hydrogenmolecule (H2)


• A molecule consists of two or more atoms held together by covalent bonds

• A double covalent bond, or double bond, is the sharing of two pairs of valence electrons

• Covalent bonds can form between atoms of the same element or atoms of different elements

What do covalent bonds do?


A single covalent bond, or single bond, is the sharingof one pair of electrons between two atoms

Oxygen (O2)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

A double covalent bond, or double bond, is the sharingof two pairs of electrons between two atoms

Covalent bonds can form between atoms of the sameelement, or from different elements.

Methane (CH4)

Water (H2O)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel


• Electronegativity is an atom’s attraction for the electrons in a covalent bond

• The more electronegative an atom, the more strongly it pulls shared electrons toward itself, thus giving it a slightly more negative charge, while the other atom involved in the bond gains a slight positive charge.

• In a nonpolar covalent bond, the atoms share the electron equally

• In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally

Covalent bonds can actually give the atoms somewhat of a charge

H

O

H

H2O+ +

–

The covalent bonds in water are polar covalent bonds.


Ionic Bonds

• Atoms sometimes strip electrons from their bonding partners

• An example is the transfer of an electron from sodium to chlorine

• After the transfer of an electron, both atoms have charges

• A charged atom (or molecule) is called an ion

– An anion is a negatively charged ion

– A cation is a positively charged ion

• An ionic bond is an attraction between an anion and a cation

NaSodium atom(an uncharged

atom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium ion(a cation)

Cl–

Chlorine ion(an anion)

Sodium chloride (NaCl)

•Compounds formed by ionic bonds are called ionic compounds, or salts•Salts, such as sodium chloride (table salt), are often found in nature as crystals

Ionic BondsIonic Bonds

Na+

Cl–

What is the molecular structureof a crystal?

They are very organized andcontain regularly spaced atoms.


Weak Chemical Bonds

• Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules

• Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important

• Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other


Hydrogen Bonds

• A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

• In living cells, the electronegative partners are usually oxygen or nitrogen atoms

• This attraction will weakly hold the two different atoms together and thus, hold the compound these elements are in loosely together.

• DNA is held together as a double strand by hydrogen bonds.

–

++

–

+

+

+

Hydrogen bonds holdwater moleculestogether (cohesion)

Hydrogen bond

–

+

+–

Water(H2O)

–

–+

+

Hydrogen bond

Water(H2O)

Water(H2O)


van der Waals Interactions

• Molecules or atoms that are very close together can be attracted by fleeting charge differences

• These weak attractions are called van der Waals interactions

• Individually, a van der Waals interaction is VERY weak. Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface


The shape of a molecule dramatically affects its function

• A molecule’s shape is determined by the positions of its atoms’ valence orbitals

• In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes

• Biological molecules recognize and interact with each other with a specificity based on molecular shape

• Molecules with similar shapes can have similar biological effects

Naturalendorphin

Morphine

CarbonHydrogen

NitrogenSulfurOxygen

Structures of endorphin and morphine

Molecules with similar shapes can have similar biological effects

Naturalendorphin Morphine

Brain cell

Endorphinreceptors

Binding to endorphin receptors

Molecules with similar shapes can bind to the same cellularreceptor


Chemical reactions make and break chemical bonds

• Chemical reactions lead to new arrangements of atoms

• The starting molecules of a chemical reaction are called reactants

• The final molecules of a chemical reaction are called products

Reactants Reaction Products 2 H2OO22 H2


Why Does This Matter to Living Things?

• Get together with a partner

• Name at least two chemical reactions in your body (in which new compounds are created)

copyright 2005 pearson education, inc. publishing as benjamin cummings living things abide by...

Documents