02 - Chemistry Text

The Chemical Context of Life
CHAPTER 2
1
Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Takes up space and has mass Exists as elements (pure form) and in chemical combinations called compounds
MATTER
2
Cant 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
ELEMENTS
3
A few other elements Make up the remaining 4% of living matter
OTHER ELEMENTS
4
Table 2.1
(a) Nitrogen deficiency
(b) Iodine deficiency (Goiter)
DEFICIENCIES
Figure 2.3
If there is a deficiency of an essential element, disease results

5
Trace Elements
Trace elements Are required by an organism in only minute quantities Minerals such as Fe and Zn are trace elements
What Are the Elements in the Human Body?

1.Oxygen (65%) 2.Carbon (18%) 3.Hydrogen (10%) 4.Nitrogen (3%) 5.Calcium (1.5%) 6.Phosphorus (1.0%) 7.Potassium (0.35%) 8.Sulfur (0.25%) 9.Sodium (0.15%) 10.Magnesium (0.05%) 11.Copper, Zinc, Selenium, Molybdenum, Fluorine, Chlorine, Iodine, Manganese, Cobalt, Iron (0.70%) 12.Lithium, Strontium, Aluminum, Silicon, Lead, Vanadium, Arsenic, Bromine (trace amounts)
Most of the human body is made up of water, H2O, with cells consisting of 65-90% water by weight. 99% of the mass of the human body is made up of just six elements: oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus.
Compounds
Are substances consisting of two or more elements combined in a fixed ratio Have characteristics different from those of their Figure 2.2 elements
Properties of Matter An elements 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
9
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
10
Subatomic Particle Location
Protons and neutrons

Are found in the atomic nucleus
Electrons
Surround the nucleus in a cloud
11
Simplified models of an Atom

Cloud of negative charge (2 electrons) Nucleus Electrons
Figure 2.4
(a) This model represents the (b) 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 electrons position at one point in time.
In this even more simplified model, the electrons are shown as two small blue spheres on a circle around the nucleus.
12
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)
13
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
14
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)
15
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
16
APPLICATION Scientists use radioactive isotopes to label certain chemical substances, creating tracers that can be used to follow a metabolic process or locate the substance within an organism. In this example, radioactive tracers are being used to determine the effect of temperature on the rate at which cells make copies of their DNA. TECHNIQUE Ingredients including Radioactive tracer Incubators (bright blue) Human cells
10C 25C 40C
15C 30C 45C
2 5
20C 35C 50C
3 6
Ingredients for making DNA are added to human cells. One ingredient is labeled with 3H, a radioactive isotope of hydrogen. Nine dishes of cells are incubated at different temperatures. The cells make new DNA, incorporating the radioactive tracer with 3H. The cells are placed in test tubes, their DNA is isolated, and unused ingredients are removed.
DNA (old and new)

2 3 1 9 4 5 6 7 8
17
A solution called scintillation fluid is added to the test tubes and they are placed in a scintillation counter. As the 3H in the newly made DNA decays, it emits radiation that excites chemicals in the scintillation fluid, causing them to give off light. Flashes of light are recorded by the scintillation counter. The frequency of flashes, which is recorded as counts per minute, RESULTS is proportional to the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment, when the counts per minute are plotted RESULTS against temperature, it is clear that temperature affects the rate of DNA synthesisthe most DNA was made at 35C. 3
Counts per minute (x 1,000) 30 20 10 0 10 20 30 40 50 Temperature (C) Optimum temperature for DNA synthesis
Figure 2.5
18
Other uses Can be used in medicine to treat tumors
Cancerous throat tissue

Figure 2.6
19
Energy Levels of Electrons An atoms electrons Vary in the amount of energy they possess Electrons further from the nucleus have more energy Electrons can absorb energy and become excited Excited electrons gain energy and move to higher energy levels or lose energy and move to lower levels
20
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

21
Electrons and Energy The electrons of an atom

Differ in the amounts of potential energy they possess
(a) A ball bouncing down a flight
Figure 2.7A
of stairs provides an analogy for energy levels of electrons, because the ball can only rest on each step, not between steps.
22
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
23
Electron Configuration and Chemical Properties
The chemical behavior of an atom

Is defined by its electron configuration and distribution K (2e-) L-M (8e-)
24
Question What is the electron configuration of these atoms? Carbon Nitrogen Sulfur
25
Periodic table
Shows the electron distribution for all the elements
Hydrogen 1H First shell Lithium Beryllium 4Be 3Li Second shell Sodium Magnesium Aluminum Silicon Phosphorus Sulfur 13Al 16S 11Na 12Mg 14Si 15P Third shell Figure 2.8 Chlorine 17Cl Argon 18Ar Boron 3B Atomic mass
2 He 4.00
Element symbol
Atomic number Helium 2He
Electron-shell diagram Oxygen Fluorine 8O 9F Neon 10Ne
Carbon 6C
Nitrogen 7N
26
Why do some elements react?

Valence electrons
Are those in the outermost, or valence shell Determine the chemical behavior of an atom
27
Electron Orbitals An orbital

Is the three-dimensional space where an electron is found 90% of the time
28
Electron Orbitals Each electron shell

Consists of a specific number of orbitals
Electron orbitals. Each orbital holds up to two electrons.
1s orbital 2s orbital
x
Z
Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs.
Three 2p orbitals
1s, 2s, and 2p orbitals
Figure 2.9
(a) First shell (maximum 2 electrons)
(b) Second shell (maximum 8 electrons)
(c) Neon, with two filled shells (10 electrons)
29
Covalent Bonds Sharing of a pair of valence electrons Examples: H2

Hydrogen atoms (2 H) 1
In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus.
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.
Figure 2.10
Hydrogen molecule (H2)
30
10
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
Multiple Covalent Bonds

Name (molecular formula) Electronshell diagram Structural formula Spacefilling model
(a) Hydrogen (H2). Two hydrogen atoms can form a single bond.
(b) Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.
Figure 2.11 A, B
32
Compounds & Covalent Bonds

Name (molecular formula) Electronshell diagram Structural formula Spacefilling model
(c) Water (H2O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water.
O H
(d) Methane (CH4). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane.
H H C H H
Figure 2.11 C, D
33
11
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
Covalent Bonding In a nonpolar covalent bond

The atoms have similar electronegativit ies Share the electron equally
35
Covalent Bonding In a polar covalent bond

The atoms have differing electronegativities Share the electrons unequally (H), Because oxygen (O) is more electronegative than hydrogen
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 Figure 2.12 H H2 O H
d+
d+
36
12
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
Ions An anion
Is negatively charged ions
A cation
Is positively charged
38
Ionic Bonding An ionic bond

Is an attraction between anions and cations
1 The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 2
Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions.
Na
Cl
Na
Cl
Figure 2.13
Sodium atom (an uncharged atom)
Na
Cl Chlorine atom (an uncharged atom)
Na+ Sodium on (a cation)
Cl Chloride ion (an anion)
Sodium chloride (NaCl)
39
13
Ionic Substances Ionic compounds

Are often called salts, which may form crystals
Na+ Figure 2.14 Cl
40
Weak Chemical Bonds Several types of weak chemical bonds are important in living systems
41
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+
Water (H2O)
O H d+ d
Ammonia (NH3)
N H d+ H d+ H d+
A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.
Figure 2.15
42
14
Van der Waals Interactions Van der Waals interactions

Occur when transiently positive and negative regions of molecules attract each other
43
Weak Bonds Weak chemical bonds

Reinforce the shapes of large molecules Help molecules adhere to each other
44
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
15
Orbitals & Covalent Bonds In a covalent bond

The s and p orbitals may hybridize, creating specific molecular shapes
Z s orbital
X
Three p orbitals
Four hybrid orbitals
Y
Tetrahedron (a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary Figure 2.16 (a) tetrahedron (outlined in pink).
46
Orbitals & Covalent Bonds

Space-filling model Ball-and-stick model Hybrid-orbital model (with ball-and-stick model superimposed)
Unbonded Electron pair

O
O H H H
H Water (H2O)
104.5
H C H
H C H
H Methane (CH4) Figure 2.16 (b)
(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
47
Shape and Function Molecular shape

Determines how biological molecules recognize and respond to one another with specificity
48
16
Carbon Hydrogen Natural endorphin
Nitrogen Sulfur Oxygen 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
Brain cell
Endorphin receptors
Figure 2.17
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.
49
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
Chemical Reactions Chemical reactions

Convert reactants to products
+
2 H2
O2
2 H2 O Product
Reactants
Reaction
51
17
Chemical Reactions Photosynthesis

Is an example of a chemical reaction
Figure 2.18
52
Chemical Reactions Chemical equilibrium

Is reached when the forward and reverse reaction rates are equal
53
18

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The Chemical Context of Life

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

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

(a) Nitrogen deficiency

(b) Iodine deficiency (Goiter)

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

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

What Are the Elements in the Human Body?

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Subatomic Particle Location

Protons and neutrons

Simplified models of an Atom

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Atomic Number & Atomic Mass

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

15C 30C 45C

20C 35C 50C

DNA (old and new)

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Other uses Can be used in medicine to treat tumors

Cancerous throat tissue

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Potential energy - Is the energy that matter possesses

Kinetic Energy - Is the energy of motion

Electrons and Energy The electrons of an atom

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Energy Levels Are represented by electron shells

Second energy level (shell)

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Electron Configuration and Chemical Properties

The chemical behavior of an atom

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Atomic number Helium 2He

Electron-shell diagram Oxygen Fluorine 8O 9F Neon 10Ne

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Why do some elements react?

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Electron Orbitals An orbital

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Electron Orbitals Each electron shell

1s, 2s, and 2p orbitals

(a) First shell (maximum 2 electrons)

(b) Second shell (maximum 8 electrons)

(c) Neon, with two filled shells (10 electrons)

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Covalent Bonds Sharing of a pair of valence electrons Examples: H2

The two electrons become shared in a covalent bond, forming an H2 molecule.

Hydrogen molecule (H2)

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Covalent Bonding A molecule

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Multiple Covalent Bonds

Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Compounds & Covalent Bonds

The more electronegative an atom