BIOLS 102
Dr. Tariq Alalwan
Biology, 10e
Biology
10e
Mader
Lectures by Tariq Alalwan, Ph.D.
Learning Objectives
 Name the principal chemical elements in living things.  Compare the physical properties (mass and charge) and locations of electrons, protons, and neutrons.
 Distinguish between the atomic number and the mass number of an atom.
 Define the terms orbital and electron shell; relate electron shells to principal energy levels.
 Explain how the number of valence electrons of an atom is related to its chemical properties.
Learning Objectives (cont.)
 Distinguish among simplest, molecular, and structural chemical formulas.  Distinguish among covalent bonds, ionic bonds and hydrogen bonds.
hydrogen bonds
 Compare them in terms of the mechanisms by which they form and their relative strengths.
 Explain how hydrogen bonds between adjacent water molecules govern many of the properties of water.
Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
Learning Objectives (cont.)
 Contrast acids and bases, and discuss their properties.
 Convert the hydrogen ion concentration (moles per liter) of a solution to a pH value.
 Describe how buffers help minimize changes in pH.
Chemical Elements  Matter refers to anything that has mass and occupies space
 Only 92 naturally occurring fundamental types of matter –
92 Elements
 Organisms composed primarily (95%) of only six elements
 Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus and Sulfur
 CHNOPS
Elements Composition of Earth’s Crust vs. Organisms
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BIOLS 102
Dr. Tariq Alalwan
Atomic Structure
 Atoms ‐ smallest particles of elements
 Atoms composed of 3 types of subatomic particles
 Protons: positively charged particles within the nucleus
 Neutrons: electrically neutral charged particles also found in nucleus
 Electrons: negatively charged particles orbiting the nucleus
Atomic Symbol
 Each element represented by unique atomic symbol
 One or two letters
Mass
Number
 First letter capitalized
 Superscripted number before:
12
6
Atomic
Number

Represents mass number

Number of protons & neutrons in nucleus
Carbon
Atomic
Symbol
 Subscripted number before:

Represents atomic number

Number of protons in nucleus
C
Periodic Table
 Elements grouped in periodic table based on characteristics
 Vertical columns = groups; chemically similar
 Horizontal rows = periods; larger and larger
I
1 H
Periods
1.008
3
II
4
5
6.941 9.012 10.81
12
2
III IV V VI VII
2 Li Be B
11
VIII
Groups
1
13
6
7
8
9
C
N
O
F
Ne
12.01 14.01 16.00
14
15
16
3 Na Mg Al Si
P
S
22.99 24.31 26.98
19
20
21
He
4.003
10
28.09 30.97 32.07
22
23
24
19.00 20.18
17
18
Cl Ar
35.45 39.95
25
26
4 K Ca Ga Ge As Se Br Kr
39.10 40.08 69.72
Chapter 2: Basic Chemistry
72.59 74.92 78.96
79.90 83.60
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BIOLS 102
Dr. Tariq Alalwan
Isotopes
 Isotopes: Atoms of the same element that differ in the number of neutrons.  Isotopes of an element have the same chemical p p
properties but different weights
g
 Example:
12
6
13
C
Carbon 12
6
14
C
Carbon 13
6
C
Carbon 14
Electron Shells, Orbitals and Energy Levels
 Atoms normally have as many electrons as protons
 Opposite charges balance leaving atom neutral
 Electrons are attracted to the positive nucleus
p
 Revolve around nucleus in 3‐D space orbitals
 Can be pushed into higher orbitals with energy
 Release that energy when they fall back to lower orbital
 Different energy levels referred to as electron shells
The Octet Rule for Distribution of Electrons
 Bohr models show electron shells as concentric circles around nucleus
 Each shell has two or more electron orbitals

I
Innermost shell has 2 orbitals
h ll h bi l

Others have 8 or multiples thereof
 Atoms with fewer than 8 electrons in outermost shell are chemically reactive
 If 3 or less – Tendency is to donate electrons
 If 5 or more – Tendency is to receive electrons
Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
Periodic Table
Elements and Compounds
 Molecule ‐ two or more atoms react or bond together
 If all atoms in molecule are of the same element

Material is still an element (e.g. O2, H2, N2, etc.)
 If at least one atom is from a different element

Material formed is a compound

CO2, H2O, C6H12O6, etc.

Characteristics of compounds dramatically different from constituent elements
Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
Chemical Bonding
 Bonds between atoms are caused by electrons (valence) in outermost shells
 The process of bond formation is called a reaction
 The intensity of simple reactions can be predicted by Th i t it f i l ti
b di t d b the periodic table
 If two elements are horizontally close in the table, they usually react mildly
 If they are horizontally far apart, they usually react vigorously
Types of Bonds: Ionic Bonding
 Octet rule
 Atoms need 8 electrons in outer shell


If have < 4 outers, desire to donate them
If have > 4 outers, desire to receive more
 Consider two elements from opposite ends of periodic table

Element from right side:



Has 7 electrons in outer shell
“Desperately needs” one more (7+1=8)
Element from left side:


Has only 1 electron in outer shell
“Desperately needs” to donate it (1‐1=0=8)
Formation of Sodium Chloride
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BIOLS 102
Dr. Tariq Alalwan
Types of Bonds: Covalent Bonds
 When atoms are horizontally closer together in the periodic table
 The electrons are not permanently transferred from one atom to the other like in NaCl
 A pair of (valence) electrons from the outer shell will “time share” with one atom and then the other
 This also causes the atoms to remain together
 Known as covalent bonding
Covalently Bonded
Molecules
 A double covalent bond is formed when two pairs of electrons are shared (represented by two parallel solid lines)
 Example ‐ O2  A triple covalent bond is formed when three pairs of electrons are shared (represented by three parallel solid lines)
 Example ‐ N2
Nonpolar Covalent Bonds
 Consider two elements that are equidistant from the edges of the periodic table
 Atoms will have about equal affinity for electrons

One will “want” to donate electron(s)

The other will “want” to receive electron(s)
 When bonded covalently:

The bond electrons will spend about equal time with both atoms

Such covalent bonds are said to be nonpolar
Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
Polar Covalent Bonds
 Some atoms attract electrons more strongly than others – electronegativity (a measure of an atom’s attraction for shared electrons in chemical bonds)
 Atoms will have unequal affinity for electrons
q
y
 When bonded covalently:
 The bond electrons will spend more time with one atom than the other

The atom that gets the most time with the electrons will be slightly negative

The other will be slightly positive
 Such covalent bonds are said to be polar
Types of Bonds: Hydrogen Bonds
 Water (H2O or H–O–H) is a polar molecule
 Electrons spend more time with the larger oxygen atom than the smaller hydrogen atom
 H becomes slightly positive and O slightly negative
 When polar molecules are dissolved in water
 The H of water molecules are attracted to the negative parts of the solute molecules
 Results in a weak bond – the hydrogen bond
 Easily broken, but many together can be quite strong
 One of the most important interactions in biological molecules (e.g. proteins, DNA, etc.)
Water Molecule and Hydrogen Bonding
Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
The Chemistry of Water:
Heat Capacity
 Water has a high heat capacity
 Temperature = rate of vibration of molecules
 When water is heated

Hydrogen bonds restrain bouncing

Temperature rises more slowly per unit heat

Thermal inertia – resistance to temperature change
 Because of hydrogen bonding – takes a large heat loss or gain for each 1C change in temperature
 Maintains constant environmental temperatures
Properties of Water:
Heat of Vaporization
 Water has a high heat of vaporization ‐ the energy required to convert 1g of liquid water to a gas
 To raise water from 99 to 100 °C; ~1 calorie
 To raise water from 100 to 101 °C; ~540 calories!
 Large numbers of hydrogen bonds must be broken to evaporate water

This is why sweating (and panting) cools
 Evaporative cooling is best when humidity is low because evaporation occurs rapidly
 Great example is when you get out of the shower!
Temperature and Water
 Calorie (cal)  Amount of heat energy required to raise 1 g of water 1 degree Celsius (C)
 Hydrogen bonds must absorb heat to break, and they release heat when they form Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
Properties of Water:
Water as a Solvent
 Solution ‐ liquid that is a completely homogenous mixture of two or more substances
 Solvent ‐ dissolving agent of a solution
g g
 Solute ‐ substance dissolved in a solution
 Hydrophilic

“Water loving”, property of having an affinity for H2O (polar and ionic molecules)
 Hydrophobic

“Water fearing”, not water‐soluble (nonpolar molecules)
Ionic Compounds Dissociate in Water
Properties of Water:
Cohesion & Adhesion
 Cohesion – Hydrogen bonds hold water molecules tightly together
 Adhesion – Hydrogen bonds for between water and other polar materials
h l i l
 Explains how water makes things wet
 High Surface Tension
 A measure of how difficult it is to stretch or break the surface of a liquid
 Allows small nonpolar objects (e.g. water strider) to sit on top of water
Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
Water as a Transport Medium
 Cohesion & adhesion are both important because combined together they form an event called capillary action  Capillary action defies gravity and helps move water up the plant to its leaves Properties of Water:
Uniqueness of Ice
 Frozen water is less dense than liquid water
y
 The density of water:
 Prevents water from freezing from the bottom up
 Ice forms on the surface first –
the freezing of the water releases heat to the water below creating insulation
 Permits organisms to survive without freezing
pH of Water: Acids
 In pure water, a small number of water molecules dissociate into hydrogen ions (H+) and hydroxide ions (OH−)
HOH ↔ H+ + OH−
 The concentrations of hydrogen ions and hydroxide ions y g
y
in pure water are exactly equal  Acids
 Substances that dissociate in water and release hydrogen ions [H+]
 Hydrochloric acid (stomach acid) is an inorganic acid with symbol HCl

In water, it dissociates into H+ and Cl‐

Dissociation of HCl is almost total, therefore it is a strong acid
Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
pH of Water: Bases  Bases:
 Either take up hydrogen ions [H+] or release hydroxide ions [OH‐]


NaOH NaOH → Na+ + OH‐
OH‐ + H+ → H2O
 Sodium hydroxide is a solid with symbol NaOH

In water, it dissociates into Na+ and OH‐

Dissociation of NaOH is almost total, therefore it is a strong base
 Some bases do not dissociate to yield hydroxide ions directly, example?
pH Scale
 pH scale used to indicate acidity and alkalinity of a solution
 Values range from 0‐14
 Acidic solution (pH <7)

Hydrogen ion concentration is higher than hydroxide ion concentration  Basic solution (pH >7)

Hydrogen ion concentration is lower than hydroxide ion concentration
 Neutral solution (pH 7)

Equal concentrations of hydrogen ions and hydroxide ions (concentration of each is 10−7 mol/L)
The pH Scale
Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
pH Scale (cont.)
 Logarithmic Scale
 Each unit change in pH represents a change of 10 times
 pH of 4 is 10 times as acidic as pH of 5
 pH of 10 is 100 times more basic than pH of 8
H f i i
b i h H f 8
Buffers and pH
 When H+ is added to pure water at pH 7, pH goes down and water becomes acidic
 When OH‐ is added to pure water at pH 7, pH goes up and water becomes alkaline
 Buffers are substances that resist change in pH
 When H+ is added, buffer may absorb, or counter by adding OH‐
 When OH‐ is added, buffer may absorb, or counter by adding H+
 A buffering system includes a weak acid or a weak base
Buffers in Nature
 Biological buffer system
 Human blood normally 7.4 (slightly alkaline)
 Many foods and metabolic processes add or subtract y
p
[H+] or [OH‐] 
Reducing blood pH to 7.0 results in acidosis

Increasing blood pH to 7.8 results in alkalosis

Both life threatening situations
Chapter 2: Basic Chemistry
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BIOLS 102
Dr. Tariq Alalwan
Buffers in Nature (cont.)
 In blood, carbon dioxide reacts with water to form carbonic acid, a weak acid that dissociates to yield H+
and bicarbonate:
CO2 + H2O ↔ H2CO3 ↔ H+ + HCO3–
 Addition of excess hydrogen ions shifts the system to the left, as H+ combine with bicarbonate ions to form carbonic acid
 Addition of hydroxide ions shifts the system to the right
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