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Chapter 2 The Chemical Context of Life

You will be able to: 1. Identify the four major elements 2. Distinguish between the following pairs

of terms: neutron and proton, atomic number and mass number, atomic weight and mass number

3. Distinguish between and discuss the biological importance of the following: nonpolar covalent bonds, polar covalent bonds, ionic bonds, hydrogen bonds, and van der Waals interactions

Fig. 1-4

The biosphere

Communities

Populations Organisms

Ecosystems

Organs and organ systems

Cells

Cell

Organelles

Atoms

Molecules Tissues

10 m

1 m

50 m

oIn the previous chapter, we discussed the levels of biological organization

oIn Chapter 2, our discussions will be focused at the lowest level of biological organization the chemical components that make up matter

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Concept 2.1: Matter consists of chemical elements in pure form and in

combinations called compounds o Organisms are composed of matter o Matter is anything that takes up space and has

mass

oCopyright 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Elements and Compounds o Matter is made up of elements

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

o A compound is a substance consisting of two or more (2+) elements in a fixed ratio

o A compound has characteristics different from those of its elements o The elements are bound together to become

something new and novel

Fig. 2-3

Sodium Chlorine Sodium chloride

ELEMENT ELEMENT COMPOUND + =

Grey Metal Green Gas White crystal

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Compounds = Total Different Material

Components (elements) of compound cannot be separated, without a Chemical Reaction

+ =

Hydrogen Oxygen

Water

NOT a compound

Compound

o About 25 of the 92 elements are essential to life

o Carbon, Hydrogen, Oxygen, and Nitrogen make up 96% of living matter

o Most of the remaining 4% consists of Calcium, Phosphorus, Potassium, and Sulfur

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

Essential Elements of Life

Table 2-1

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o Each element consists of unique atoms o An atom is the smallest unit of matter that

still retains the properties of an element

Concept 2.2: An elements properties depend on the structure of its atoms

Copyright 2008 Pearson Education, Inc., publishing as Benjamin Cummings

Subatomic Particles

o Atoms are composed of subatomic particles o Relevant subatomic particles include: oNeutrons (no electrical charge) oProtons (positive charge) oElectrons (negative charge)

Behavior of Charges o Opposite charges (positive & negative)

attract each other o Same charges (positive & positive,

negative & negative) repel (push away) each other

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o Neutrons and protons form the atomic nucleus

o Electrons form a cloud around the nucleus o Neutron mass and proton mass are almost

identical and are measured in daltons (electrons are very, very small)

Nucleus

Protons (+ charge) determine element

Neutrons (no charge) determine isotope

Atom

Electrons ( charge) form negative cloud and determine chemical behavior

(Atoms have a lot of empty space)

Atomic Number and Atomic Mass o Atoms of the various elements differ in number

of subatomic particles

o An elements atomic number is the number of protons in its nucleus oDefines an Element

o An elements mass number is the sum of protons + neutrons in the nucleus

o Atomic mass, the atoms total mass, can be approximated by the mass number

Mass Number Atomic Number

1. Protons = 4 Neutrons = 4 Electrons = 4 Atomic # = ? Mass # = ?

2. Protons = 6 Neutrons = 5 Electrons = 6 Atomic # = ? Mass # = ?

3. Protons = 8 Neutrons = 5 Electrons = 8 Atomic # = ? Mass # = ?

# of protons? # of neutrons? # of protons?

# of neutrons?

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1. Protons = 4 Neutrons = 4 Electrons = 4 Atomic # = Mass # =

2. Protons = 6 Neutrons = 5 Electrons = 6 Atomic # = Mass # =

3. Protons = 8 Neutrons = 5 Electrons = 8 Atomic # = Mass # =

# of protons? # of neutrons? # of protons?

# of neutrons?

4 8

6 11

8 13

2 2 3

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Isotopes o All atoms of an element have the same number of

protons (atomic number), but may differ in number of neutrons

o Isotopes are two atoms of an element that differ in number of neutrons, thus different mass numbers oGenerally, behave similarly to each other

Atomic Number Mass Number

o Radioactive isotopes decay spontaneously, giving off particles and energy oSometimes nucleus gets so big, it falls apart

by ejecting particles

o If protons emitted, atomic number can change, and element can change Ex radioactive carbon decays to form nitrogen

o These emissions can be detected and measured

oEmission occurs at characteristic rate, so we can figure out how long it has been and will go on.

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o Some applications of radioactive isotopes in biological research are: oDating fossils o Tracing atoms through metabolic processes oDiagnosing medical disorders

o Energy is the capacity to cause change o Potential energy is the energy that matter has because of

its location or structure (the potential to do work!) o The electrons of an atom differ in their amounts of potential

energy o An electrons state of potential energy is called its energy

level, or electron shell o Electron shells are different distances from the nucleus and

can hold different numbers of electrons

The Energy Levels of Electrons

o Distance = Potential Energy o That is, electrons in the 1st shell closest to the nucleus

have the lowest potential energy o The further out the electrons are from the nucleus, the

greater the potential energy

o First Shell (Closest to Nucleus)-Up to 2 electrons o Second Shell-Up to 8 Electrons o Third Shell Up to 8 electrons

o Electrons fill up inner shells first o If an electron gains extra energy and jumps to higher

shell, it will ~immediately lose that energy and fall back

Electron Shells

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Fig. 2-8 (a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons

Third shell (highest energy level)

Second shell (higher energy level)

Energy absorbed

First shell (lowest energy level)

Atomic nucleus (b)

Energy lost

Electron Distribution and Chemical Properties

o The chemical behavior of an atom is determined by the distribution of electrons in electron shells

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

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Fig. 2-9

Hydrogen 1H

Lithium 3Li

Beryllium 4Be

Boron 5B

Carbon 6C

Nitrogen 7N

Oxygen 8O

Fluorine 9F

Neon 10Ne

Helium 2He

Atomic number

Element symbol Electron- distribution diagram

Atomic mass

2 He

4.00 First shell

Second shell

Third shell

Sodium 11Na

Magnesium 12Mg

Aluminum 13Al

Silicon 14Si

Phosphorus 15P

Sulfur 16S

Chlorine 17Cl

Argon 18Ar

o Valence electrons are those in the outermost shell, or valence shell

o The chemical behavior of an atom & how on element interacts with other elements is mostly determined by the valence electrons

o Elements with a full valence shell are chemically inert (chemically unreactive)

Electron Orbitals An orbital is the three-dimensional space where

an electron is found 90% of the time

Because electrons from bonded atoms will repel each other, orbitals contribute to the shapes of complex molecules

Each electron shell consists of a specific number of orbitals

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Electron-distribution diagram

(a)

(b) Separate electron orbitals

Neon, with two filled shells (10 electrons)

First shell Second shell

1s orbital 2s orbital Three 2p orbitals

x y

z

Fig. 2-10-3

Electron-distribution diagram

(a)

(b) Separate electron orbitals

Neon, with two filled shells (10 electrons)

First shell Second shell

1s orbital 2s orbital Three 2p orbitals

(c) Superimposed electron orbitals

1s, 2s, and 2p orbitals

x y

z

Fig. 2-10-4

The formation and function of molecules depend on chemical

bonding between atoms oValence shells want to be full oAtoms with incomplete valence shells can

share or transfer valence electrons with certain other atoms

oThese interactions usually result in atoms staying close together, held by attractions called chemical bonds oBecome something new with new properties

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Covalent Bonds o A covalent bond is the sharing of a pair of

valence electrons by two atoms

o In a covalent bond, the shared electrons count as part of each atoms valence shell

Hydrogen atoms (2 H)

Hydrogen molecule (H2)

o2 Hydrogen atoms each has 1 electron oThe valence shells can hold 2

oWhen they get close enough, each electron is attracted to the other nucleus (+ and -).

oThe 2 electrons become shared between atoms, orbiting both: a Covalent Bond

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

o A single covalent bond, or single bond, is the sharing of 1 pair of valence electrons

o A double covalent bond, or double bond, is the sharing of 2 pairs of valence electrons

Animation: Covalent Bonds

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o The notation used to represent atoms and bonding is called a structural formula o For example, HH, O=O

o This can be abbreviated further with a molecular formula o For example, H2

o Lewis Dot Structure: Shows outermost, shared electrons

Single covalent bond

Double covalent bond

Fig. 2-12a

(a) Hydrogen (H2)

Name and Molecular Formula

Electron- distribution

Diagram

Lewis Dot Structure and

Structural Formula

Space- filling Model

Fig. 2-12c

(c) Water (H2O)

Name and Molecular Formula

Electron- distribution

Diagram

Lewis Dot Structure and

Structural Formula

Space- filling Model

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

o A compound is a combination of two or more different elements

o Bonding capacity is called the atoms valence o How many electrons it wants, thus how many covalent

bonds it can form (Note: single vs. double) oH atomic number = 1, how many valence electrons?

how many bonds can it form? oO atomic number = 8, valence electrons? bonds? oN atomic number = 7, valence electrons? bonds? oC atomic number = 6, valence electrons? bonds?

o Electronegativity is an atoms attraction for the electrons in a covalent bond

o The more electronegative an atom, the more strongly it pulls shared electrons toward itself, so the electrons spend more time around the more electronegative atom

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

H2

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Fig. 2-12d

(d) Methane (CH4)

Name and Molecular Formula

Electron- distribution

Diagram

Lewis Dot Structure and

Structural Formula

Space- filling Model

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

o Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule G

G+ G+ H H

O

H2O

Water

Protons & Electrons o Protons (usually) = Electrons

oCan ~assume electron # from Atomic Number oKnow Atomic Number# ElectronsElectron

ConfiguationValence

o (+) + (-) = 0 (Neutral) o Lose Proton OR Gain Electron = (-) charged Atom o Gain Proton OR Lose Electron = (+) charged Atom

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Ionic Bonds o Very electronegative atoms sometimes steal

electrons from their bonding partners

o An example is the transfer of an electron from sodium (Na) to chlorine (Cl)

o After the transfer of an electron, both atoms have

charges (Na+ & Cl-)

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

Fig. 2-14-2

Na Cl Na Cl

Na Sodium atom Chlorine atom

Cl Na+ Sodium ion (a cation)

Cl Chloride ion

(an anion)

Sodium chloride (NaCl)

o A cation is a positively charged ion (+) oMore protons than electrons

o An anion is a negatively charged ion (-) oMore electrons than protons

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

o This bond is strong, but fragile, and usually comes apart in water

Animation: Ionic Bonds

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o Compounds formed by ionic bonds are called ionic compounds, or salts

o Salts, such as sodium chloride (table salt), are often found in nature as crystals

Na+ Cl

Weak Chemical Bonds o Most of the strongest bonds in organisms

are covalent bonds that form a cells molecules

o Weak chemical bonds such as ionic bonds and hydrogen bonds are also important

o Weak chemical bonds reinforce shapes of large molecules & help molecules adhere to each other

Fig. 2-16 G G+

G+

G

G+

G+

G+

Water (H2O)

Ammonia (NH3)

Hydrogen bond

Hydrogen Bonds o A hydrogen bond forms when

a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

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

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Van der Waals Interactions o If electrons are distributed

asymmetrically in molecules or atoms, they can result in hot spots of positive or negative charge

o Van der Waals interactions are attractions between molecules that are close together as a result of these charges

o Collectively, such interactions can be strong, as between molecules of a geckos toe hairs and a wall surface

Molecular Shape and Function

o A molecules shape is usually very important to its function

o A molecules shape is determined by the positions of its atoms valence orbitals

o In a covalent bond, the s and p orbitals may merge and change, creating complex molecular shapes

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Fig. 2-17 s orbital Three p

orbitals

(a) Hybridization of orbitals Tetrahedron

Four hybrid orbitals

Space-filling Model

Ball-and-stick Model

Hybrid-orbital Model (with ball-and-stick

model superimposed)

Unbonded electron pair

104.5

Water (H2O)

Methane (CH4) (b) Molecular-shape models

z

x

y

o Biological molecules bind and interact with each other with a specificity based on molecular shape

o Molecules with similar shapes can have similar biological effects

Figure 2.18

Natural endorphin

Morphine

Carbon Hydrogen

Nitrogen Sulfur Oxygen

(a) Structures of endorphin and morphine

(b) Binding to endorphin receptors

Brain cell

Morphine Natural endorphin

Endorphin receptors

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Chemical reactions make and break chemical bonds

o Chemical reactions are the making and breaking of chemical bonds

o The starting molecules of a chemical reaction are called reactants

o The final molecules of a chemical reaction are called products

o Some chemical reactions go to completion: all reactants are converted to products

o All chemical reactions are reversible: products of the forward reaction become reactants for the reverse reaction

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

o Photosynthesis is an important chemical reaction

o The solar energy powered rearrangement of carbon dioxide (from air or water) & water

o Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen o 6 CO2 + 6 H20 C6H12O6 +

6 O2

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Fig. 2-UN9

Example of what type of bonds?

Fig. 2-UN10

Fig. 2-UN11