Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chemical Foundations of Biology Biology is a multidisciplinary science Living

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

Chemical Foundations of Biology

• Biology is a multidisciplinary science

• Living organisms are subject to basic laws of physics and chemistry

• Many organisms use chemistry to defend themselves

• Snakes use venom

• Skunks STINK

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? Which are elements?

Which are 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.


• Some applications of radioactive isotopes in biological research:

– Dating fossils

– Tracing atoms through metabolic processes

– Diagnosing medical disorders

Radioactive isotopes have MANY productive uses in both science and medicine

Ingredients includingradioactive tracer(bright blue)

Incubators

Human cells

DNA (old and new)

1 2 3

4 5 6

7 8 9

10°C

25°C

40°C

15°C

30°C

45°C

20°C

35°C

50°C

TECHNIQUEUses of radioactivity in science research

GOAL: learn theoptimal temperaturefor DNA synthesisin growing humancells.

Experiment: Add aradioactive ‘tracer,’which is a radioactivelylabeled substrate.Here, it is a labeled basethat makes up DNA.

Grow the cells at differenttemperatures and see wheremore of your ‘tracer’ isincorporated into new DNA.

After isolating DNA, you use a machine capable of measuringthe amount of radioactivity present in your DNA samples.

Optimumtemperaturefor DNAsynthesis

RESULTSC

ou

nts

per

min

ute

(x 1

,000

)

30

20

10

010 20 30 40 50

Temperature (°C)

DNA is synthesized best at 37 ºC Would you have expected this result?

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 level

A ball bouncing down a flight

of stairs provides an analogy for

energy levels of electrons. Electrons,

like the ball, can only stop on a step

of energy, not between steps, just like

a 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

Hydrogen

1H

Lithium

3Li

Secondshell

Thirdshell

Sodium

11Na

Beryllium

4Be

Magnesium

12Mg

Boron

5B

Aluminum

12AlSilicon

14Si

Carbon

6CNitrogen

7N

Phosphorus

15P

Oxygen

8O

Sulfur

16SChlorine

17Cl

Fluorine

9FNeon

10Ne

Argon

18Ar

Helium

2HeAtomic number

Element symbol

Electron-shelldiagram

Atomic mass

2He4.00

Electron shell diagrams are often used to represent the amount of potential energy that a given electron

possesses


• 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

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 of either the same type, or different types

• 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


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

Na

Sodium atom(an uncharged

atom)

Cl

Chlorine 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.

–

Water(H2O)

Ammonia(NH3)

Hydrogen bond

+

+

–

+

+

+

A hydrogen bond holdsa molecule of waterand a molecule ofAmmonia together.


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

Space-fillingmodel

Ball-and-stickmodel

Hybrid-orbital model(with ball-and-stick

model superimposed)

Unbondedelectronpair

Water (H2O)

Methane (CH4)

Molecular shape models

104.5°

Naturalendorphin

Morphine

Carbon

Hydrogen

Nitrogen

Sulfur

Oxygen

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


• Some chemical reactions go to completion: All reactants are converted to products

• Most chemical reactions are reversible: Products of the forward reaction become reactants for the reverse reaction

• Chemical equilibrium is reached when the forward and reverse reaction rates are equal

How do chemical reactions behave in vivo?

Documents

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chemical Foundations of Biology Biology is a multidisciplinary science Living