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Chapter 2. The Chemical Context of Life. 1. Matter. · Takes up space and has mass · Exists as elements (pure form) and in chemical combinations called compounds. 2. Elements. · Can’t be broken down into simpler substances by chemical reaction ·Composed of atoms

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slide1

Chapter 2

The Chemical Context of Life

1

slide2

Matter

·Takes up space and has mass

·Exists as elements (pure form) and in chemical combinations called compounds

2

slide3

Elements

·Can’t be broken down into simpler substances by chemical reaction

·Composed of atoms

·Essential elements in living things include carbon C, hydrogen H, oxygen O, and nitrogen N making up 96% of an organism

3

slide4

Other Elements

·A few other elements Make up the remaining 4% of living matter

4

Table 2.1

slide5

Deficiencies

·If there is a deficiency of an essential element, disease results

Figure 2.3

(b) Iodine deficiency (Goiter)

(a) Nitrogen deficiency

5

slide6

Trace Elements

·Trace elements are required by an organism in only minute quantities

·Minerals such as Fe and Zn are trace elements

6

slide7

Compounds

·Are substances consisting of two or more elements combined in a fixed ratio

·Have characteristics different from those of their elements

+

Figure 2.2

Sodium

Chloride

Sodium Chloride

7

slide8

Properties of Matter

·An element’s properties depend on the structure of its atoms

·Each element consists of a certain kind of atom that is different from those of other elements

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

8

slide9

Subatomic Particles

·Atoms of each element Are composed of even smaller parts called subatomic particles

·Neutrons, which have no electrical charge

·Protons, which are positively charged

·Electrons, which are negatively charged

9

slide10

Subatomic Particle Location

·Protons and neutrons

·Are found in the atomic nucleus

·Electrons

·Surround the nucleus in a “cloud”

10

slide11

Simplified models of an Atom

Cloud of negative

charge (2 electrons)

Electrons

Nucleus

Figure 2.4

This model represents the

electrons as a cloud of

negative charge, as if we had

taken many snapshots of the 2

electrons over time, with each

dot representing an electron‘s

position at one point in time.

(a)

In this even more simplified

model, the electrons are

shown as two small blue

spheres on a circle around the

nucleus.

(b)

11

slide12

Atomic Number & Atomic Mass

·Atoms of the various elements differ in their number of subatomic particles

·The number of protons in the nucleus = atomic number

·The number of protons + neutrons = atomic mass

·Neutral atoms have equal numbers of protons & electrons (+ and – charges)

12

slide13

Atomic Number

·Is unique to each element and is used to arrange atoms on the Periodic table

·Carbon = 12

·Oxygen = 16

·Hydrogen = 1

·Nitrogen = 17

13

slide14

Atomic Mass

·Is an approximation of the atomic mass of an atom

·It is the average of the mass of all isotopes of that particular element

·Can be used to find the number of neutrons (Subtract atomic number from atomic mass)

14

slide15

Isotopes

·Different forms of the same element

·Have the same number of protons, but different number of neutrons

·May be radioactive spontaneously giving off particles and energy

·May be used to date fossils or as medical tracers

15

slide17

Other uses

·Can be used in medicine to treat tumors

Cancerous throat tissue

Figure 2.6

18

slide18

Energy Levels of Electrons

·An atom’s electrons Vary in the amount of energy they possess

·Electrons further from the nucleus have more energy

·Electron’s can absorb energy and become “excited”

·Excited electrons gain energy and move to higher energy levels or lose energy and move to lower levels

19

slide19

Energy

·Energy

·Is defined as the capacity to cause change

·Potential energy

- Is the energy that matter possesses because of its location or structure

·Kinetic Energy

- Is the energy of motion

20

slide20

Electrons and Energy

·The electrons of an atom

·Differ in the amounts of potential energy they possess

(a)

A ball bouncing down a flight

of stairs provides an analogy

for energy levels of electrons,

because the ball can only rest

on each step, not between

steps.

Figure 2.7A

21

slide21

Energy Levels

·Are represented by electron shells

Third energy level (shell)

Second energy level (shell)

Energy

absorbed

First energy level (shell)

Energy

lost

Atomic

nucleus

(b)

An electron can move from one level to another only if the energy

it gains or loses is exactly equal to the difference in energy between

the two levels. Arrows indicate some of the step-wise changes in

potential energy that are possible.

Figure 2.7B

22

slide22

Electron Configuration and Chemical Properties

·The chemical behavior of an atom

·Is defined by its electron configuration and distribution

·K (2e-)

·L-M (8e-)

23

slide23

Periodic table

·Shows the electron distribution for all the elements

Helium

2He

Atomic number

2

He

4.00

Hydrogen

1H

Element symbol

Atomic mass

First

shell

Electron-shell

diagram

Lithium

3Li

Beryllium

4Be

Boron

3B

Carbon

6C

Nitrogen

7N

Oxygen

8O

Fluorine

9F

Neon

10Ne

Second

shell

Aluminum

13Al

Chlorine

17Cl

Argon

18Ar

Sodium

11Na

Magnesium

12Mg

Silicon

14Si

Phosphorus

15P

Sulfur

16S

Third

shell

Figure 2.8

25

slide24

Why do some elements react?

·Valence electrons

·Are those in the outermost, or valence shell

·Determine the chemical behavior of an atom

26

slide25

Covalent Bonds

·Sharing of a pair of valence electrons

·Examples: H2

Hydrogen atoms (2 H)

In each hydrogen

atom, the single electron

is held in its orbital by

its attraction to the

proton in the nucleus.

1

+

+

2

When two hydrogen

atoms approach each

other, the electron of

each atom is also

attracted to the proton

in the other nucleus.

+

+

The two electrons

become shared in a

covalent bond,

forming an H2

molecule.

3

+

+

Hydrogen

molecule (H2)

Figure 2.10

30

slide26

Covalent Bonding

·A molecule

·Consists of two or more atoms held together by covalent bonds

·A single bond

·Is the sharing of one pair of valence electrons

·A double bond

·Is the sharing of two pairs of valence electrons

31

slide27

Multiple Covalent Bonds

Name

(molecular

formula)

Electron-

shell

diagram

Space-

filling

model

Structural

formula

(a)

Hydrogen (H2).

Two hydrogen

atoms can form a

single bond.

H

H

(b)

Oxygen (O2).

Two oxygen atoms

share two pairs of

electrons to form

a double bond.

O

O

Figure 2.11 A, B

32

slide28

Compounds & Covalent Bonds

Name

(molecular

formula)

Electron-

shell

diagram

Space-

filling

model

Structural

formula

(c)

Water (H2O).

Two hydrogen

atoms and one

oxygen atom are

joined by covalent

bonds to produce a

molecule of water.

H

O

H

(d)

Methane (CH4).

Four hydrogen

atoms can satisfy

the valence of

one carbon

atom, forming

methane.

H

H

H

C

H

Figure 2.11 C, D

33

slide29

Covalent Bonding

·Electronegativity

·Is the attraction of a particular kind of atom for the electrons in a covalent bond

·The more electronegative an atom

·The more strongly it pulls shared electrons toward itself

34

slide30

Covalent Bonding

·In a nonpolar covalent bond

·The atoms have similar electronegativities

·Share the electron equally

35

slide31

Covalent Bonding

·In a polar covalent bond

·The atoms have differing electronegativities

·Share the electrons unequally

Because oxygen (O) is more electronegative than hydrogen (H),

shared electrons are pulled more toward oxygen.

d

This results in a

partial negative

charge on the

oxygen and a

partial positive

charge on

the hydrogens.

O

H

H

Figure 2.12

d+

d+

H2O

36

slide32

Ionic Bonds

·In some cases, atoms strip electrons away from their bonding partners

·Electron transfer between two atoms creates ions

·Ions

·Are atoms with more or fewer electrons than usual

·Are charged atoms

37

slide33

Ions

·An anion

·Is negatively charged ions

·A cation

·Is positively charged

38

slide34

Ionic Bonding

·An ionic bond

·Is an attraction between anions and cations

2

1

Each resulting ion has a completed

valence shell. An ionic bond can form

between the oppositely charged ions.

The lone valence electron of a sodium

atom is transferred to join the 7 valence

electrons of a chlorine atom.

+

Cl

Na

Na

Cl

Cl–

Chloride ion

(an anion)

Na+

Sodium on

(a cation)

Na

Sodium atom

(an uncharged

atom)

Cl

Chlorine atom

(an uncharged

atom)

Figure 2.13

Sodium chloride (NaCl)

39

slide35

Ionic Substances

·Ionic compounds

·Are often called salts, which may form crystals

Na+

Cl–

Figure 2.14

40

slide36

Weak Chemical Bonds

·Several types of weak chemical bonds are important in living systems

41

slide37

Hydrogen Bonds

·A hydrogen bond

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

d

d +

d +

42

slide38

Van der Waals Interactions

·Van der Waals interactions

·Occur when transiently positive and negative regions of molecules attract each other

43

slide39

Weak Bonds

·Weak chemical bonds

·Reinforce the shapes of large molecules

·Help molecules adhere to each other

44

slide40

Molecular Shape and Function

·Structure determines Function!

·The precise shape of a molecule

·Is usually very important to its function in the living cell

·Is determined by the positions of its atoms’ valence orbitals

45

slide41

Orbitals & Covalent Bonds

Hybrid-orbital model

(with ball-and-stick

model superimposed)

Ball-and-stick

model

Space-filling

model

Unbonded

Electron pair

O

O

H

H

H

H

104.5°

Water (H2O)

H

H

C

C

H

H

H

H

H

H

Methane (CH4)

(b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the molecules

Figure 2.16 (b)

47

slide42

Shape and Function

·Molecular shape

·Determines how biological molecules recognize and respond to one another with specificity

48

slide43

Nitrogen

Carbon

Hydrogen

Sulfur

Oxygen

Natural

endorphin

Morphine

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to

receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

Natural

endorphin

Morphine

Endorphin

receptors

Brain cell

(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.

Figure 2.17

49

slide44

Chemical Reactions

·Chemical reactions make and break chemical bonds

·A Chemical reaction

·Is the making and breaking of chemical bonds

·Leads to changes in the composition of matter

50

slide45

Chemical Reactions

·Chemical reactions

·Convert reactants to products

+

2 H2O

2 H2

+

O2

Reactants

Reaction

Product

51

slide46

Chemical Reactions

·Photosynthesis

·Is an example of a chemical reaction

Figure 2.18

52

slide47

Chemical Reactions

·Chemical equilibrium

·Is reached when the forward and reverse reaction rates are equal

53

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