1. Chapter 2
Atoms, Molecules, and Life

2. What Are Atoms? Smallest unit of an element
Atoms are the fundamental structural units of matter and are composed of three types of particles
(a) Hydrogen (H)
electron
shell
atomic
nucleus e p
(b) Helium (He) n
In the central atomic nucleus, there are positively charged protons and uncharged neutrons
In orbit around the nucleus are negatively charged particles called electrons
-Atoms are electrically neutral because their number of positive protons and negative electrons is equal
Nucleus is very stable.
Electrons can capture or release energy and may form bonds with other atoms.

3. What Are Atoms? Elements
An element is a substance that cannot be broken down by ordinary chemical reactions
All atoms belong to one of 92 types of naturally occurring elements

4. What Are Atoms?
The atomic mass of an element is the total mass of its protons, neutrons, and electrons
Atomic number - The number of protons in the nucleus of an atom
is the defining value for an element
All atoms of an element have the same atomic number
For example, carbon has six protons, nitrogen has seven
The mass of electrons is negligible. Each proton and neutron have a mass of 1.
See the periodic table.

5. Table 2-1

6. What Are Atoms? Isotopes
Atoms of an element with different numbers of neutrons
Different mass number
Some isotopes are radioactive (meaning that they spontaneously break apart, forming different atoms and releasing energy) and are used in research
At room temperature, elements may occur as solids, liquids, or gases
Radioactive Carbon-14 vs. carbon-12
Release particles with enough energy to damage DNA

7. What Are Atoms? Electron shells
Electrons are distributed around the nucleus of an atom in electron shells
The first shell, or energy level, holds two electrons
Subsequent shells holds up to eight
Larger atoms can accommodate more electrons than smaller ones can
Carbon (C)
Oxygen (O)
Phosphorus (P)
Calcium (Ca) Ca O C P
4e
6e
5e
2e
8e
6p
8p
15p
20p 6n 8n
16n
20n
Electrons fill the first, nearest shells to the nucleus first.

8. What Are Atoms? Energy capture and release
Life depends on electrons capturing and releasing energy
Electron shells correspond to energy levels
heat energy
light  
An electron
absorbs energy
The energy boosts
the electron to a
higher-energy shell
The electron drops
back into lower-energy
shell, releasing energy
as light 1 2 3
Switching on a light bulb

9. How Do Atoms Interact to Form Molecules?
Interaction between atoms
Atoms will not react with other atoms if the outermost shell is completely empty or full (such atoms are considered inert)
Example: Neon, with eight electrons in its outermost shell is full
Atoms will react with other atoms if the outermost shell is partially full (such atoms are considered reactive)
Example: Oxygen, with six electrons in its outermost shell, can hold two more electrons, and so is susceptible to reacting

10. How Do Atoms Interact to Form Molecules?
Chemical bonds hold atoms together in molecules
the force of attraction between neighboring atoms that holds them together within a molecule
Reactive atoms gain stability through electron interactions (chemical reactions)
A chemical reaction is a process by which new chemical bonds are formed or existing bonds are broken, converting one substance into another
Three major types of chemical bonds: ionic, covalent, and hydrogen
1. Molecules consist of two or more atoms
2. Reactions between atoms depend upon the configuration of electrons in the outermost electron shell

11. Chemical Bonds Ions and ionic bonds
Electron transferred
Na
Cl
(b) Ions
(c) An ionic compound: NaCl
Attraction between
opposite charges –
11p
11n
17p
18n
Sodium ion ()
Chloride ion (–)
(a) Neutral atoms
Sodium atom (neutral)
Chlorine atom (neutral)
Ions and ionic bonds
Atoms that have lost or gained electrons, thereby altering the balance between protons and electrons, are charged, and are called ions
Oppositely charged ions that are attracted to each other are bound into a molecule by ionic bonds
Salt crystals are formed by a repeated, orderly arrangement of sodium (Na+) and chloride (Cl-) ions
Atoms that have lost electrons become positively charged ions (e.g., sodium: Na+)
Atoms that have gained electrons become negatively charged ions (e.g., chlorine: Cl–)

12. Chemical Bonds Covalent bonds
form between uncharged atoms that share electrons
An atom with a partially full outermost electron shell can become stable
found in H2 (single bond), O2 (double bond), N2 (triple bond), and H2O
stronger than ionic bonds but vary in their stability
Two electrons (one from each atom), when shared, form a covalent bond
Water easily breaks down ionic bonds.
Because biological molecules must function in a watery environment, the atoms in most biological molecules, such as those found in proteins, sugars, and fats, are joined by covalent bonds

13. Chemical Bonds Nonpolar or polar covalent bonds
Nonpolar covalent bond – both atoms exert the same pulling force on bond electrons (H2)
Polar covalent bonds - molecules where atoms of different elements are involved (H2O), the electrons are not always equally shared
H2O is a polar molecule
Slightly positively charged pole is around each hydrogen
Slightly negatively charged pole is around the oxygen

14. Covalent Bonds Involve Shared Electrons
(b) Polar covalent bonding in water (H2O) +
(+)
(oxygen: slightly negative)
(–)
(hydrogens:
slightly positive)
8p 8n _
(a) Nonpolar covalent bonding in hydrogen
gas (H2)
(hydrogens: uncharged)
Electrons spend
equal time near
each nucleus
Same charge on
both nuclei
Larger positive
charge
more time near
the larger nucleus
Smaller positive
Fig. 2-6

15. How Do Atoms Interact to Form Molecules?
Free radicals
Some cellular reactions produce free radicals
A free radical is a molecule in which atoms have one or more unpaired electrons in their outer shells
Free radicals are highly unstable and reactive
Free radicals steal electrons, destroying other molecules
Cell death can occur from free radical attack
These reactions are essential for life, over time, the stress from free radicals can contribute to aging and eventually death.
Free radicals are implicated in heart disease, Alzheimer’s, cancer, and aging
Antioxidants react with free radicals and render them harmless.

16. Chemical Bonds Hydrogen bonds
are attractive forces between polar molecules
Hydrogen bonds form when partial opposite charges in different molecules attract each other
The partially positive hydrogen atoms of one water molecule are attracted to the partially negative oxygen on another
Polar biological molecules can form hydrogen bonds with water, each other, or even within the same molecule
Hydrogen bonds are comparatively weak but, collectively, can be quite strong

17. Why Is Water So Important to Life?
Water molecules attract one another
Cohesion is the tendency of the molecules of a substance to stick together
Hydrogen bonding between water molecules
Cohesion of water molecules along a surface produces surface tension
tendency for a water surface to resist being broken
Cohesion – square dancers breaking and re-forming bonds allowing flow.
Water cohesion explains how water molecules can form a chain in delivering moisture from the roots to the top of a tree.
the bonds are stronger than the weight of water so the chain doesn’t break.
Spiders and water striders rely on surface tension to move across the surface of ponds

18. Why Is Water So Important to Life?
Water interacts with many other molecules
Water is an excellent solvent (completely surrounds and disperses individual atoms)
A wide range of substances dissolve in water to form solutions
Water is excellent because it’s polar
Solution – a solvent containing one or more dissolved substances
Positively charged hydrogen poles of water are attracted to Cl-
Negatively charged oxygen to Na+
Poles surround each ion completely preventing them from interacting with other Na+ or Cl- ions.

19. Why Is Water So Important to Life?
Water interacts with many other molecules
Water-soluble molecules are hydrophilic
Water molecules are attracted to and can surround
Dissolve readily in water
Water-insoluble molecules are hydrophobic
repel and drive together uncharged and nonpolar molecules like fats and oils
The “clumping” of nonpolar molecules is called hydrophobic interaction
ions or polar molecules, such as sugars and amino acids

20. Why Is Water So Important to Life?
Water moderates the effects of temperature change
The energy required to heat 1 gram of a substance by 1°C is called its specific heat
It takes a lot of energy to heat water
Temperature reflects the speed of molecular motion
It requires 1 calorie of energy to raise the temperature of 1g of water 1°C (the specific heat of water), which is a very slow process
All because water is polar and has hydrogen bonds.
2. Water has a very high specific heat.
atoms in constant motion. More heat, more motion.
water uses the heat energy to break the hydrogen bonds which is then NOT available to raise the temperature.
helps prevent overheating when organisms bodies are mostly water.

21. Why Is Water So Important to Life?
Water moderates the effects of temperature change
The heat of vaporization is the amount of heat needed to cause a substance such as water to evaporate (to change from a liquid to a vapor)
Evaporating water uses up heat from its surroundings, cooling the nearby environment (as occurs during sweating)
It takes a lot of energy to cause water to evaporate
Because the human body is mostly water, a sunbather can absorb a lot of heat energy without sending her/his body temperature soaring
Requires energy to break the hydrogen bonds to allow evaporation.
Evaporation has a cooling effect because the fastest-moving (warmest) molecules are those that vaporize, leaving cooler molecules behind.

22. Why Is Water So Important to Life?
Water forms an unusual solid: ice
Most substances become denser when they solidify from a liquid
Ice is unusual because it is less dense than liquid water
Water molecules spread apart slightly during the freezing process
3. When water freezes, each molecule forms stable hydrogen bonds with four other water molecules, creating an open, hexagonal arrangement.
Ice floats in liquid water
Ponds and lakes freeze from the top (creating an insulating layer) down and never freeze completely to the bottom
Many plants and fish are therefore saved from freezing

23. Why Is Water So Important to Life?
Water-based solutions can be acidic, basic, or neutral
A small fraction of water molecules are ionized:
H2O  OH– + H+
hydrogen ion
(H)
hydroxide ion
(OH)
water
(H2O) 
(  )
(  ) O H
Pure water contains equal concentrations of OH- and H+.

24. Why Is Water So Important to Life?
Water-based solutions can be acidic, basic, or neutral
Solutions where H+ > OH– are acidic
Substance that releases H+ into solution
For example, hydrochloric acid ionizes in water:
HCl  H+ + Cl–
Lemon juice and vinegar are naturally occurring acids

25. Why Is Water So Important to Life?
Water-based solutions can be acidic, basic, or neutral
Solutions where OH– > H+ are basic
Substance that removes H+ from solution
For example, sodium hydroxide ionizes in water:
NaOH  Na+ + OH–
Baking soda, chlorine bleach, and ammonia are basic
OH combines with H to make water molecules.

26. The degree of acidity of a solution is measured using the pH scale
1 molar hydrochloric
acid (HCI)
stomach acid (2)
lemon juice (2.3)
"acid rain" (2.5–5.5)
beer (4.1)
tomatoes (4.5)
black coffee (5.0)
normal rain (5.6)
milk (6.4)
pure water (7.0)
seawater (7.8–8.3)
baking soda (8.4)
antacid (10)
washing soda (12)
oven cleaner (13.0)
hydroxide (NaOH)
1 molar sodium 1 2 3 4 5 6 7 8 9 10 11 12 13 14
pH value
H concentration in moles/liter
100
10–1
10–2
10–3
10–4
10–5
10–6
10–7
10–8
10–9
10–10
10–11
10–12
10–13
10–14
neutral
(H  OH)
(H  OH)
(H < OH)
vinegar, cola (3.0)
urine (5.7)
blood, sweat (7.4)
chlorine bleach (12.6)
drain cleaner (14.0)
orange (3.5)
increasingly acidic
increasingly basic
household ammonia (11.9)

27. Why Is Water So Important to Life?
A buffer helps maintain a relatively constant pH in a solution
A buffer is a compound that accepts or releases H+ in response to a pH change
If the solution becomes too acidic, a buffer accepts (and absorbs) H+ which creates an acidic molecule
If the solution becomes too basic, an acidic molecule liberates hydrogen ions to combine with OH– to form water
2. HCO3– H  H2CO3
bicarbonate hydrogen ion carbonic acid
3. H2CO OH–  HCO3– H2O
carbonic acid hydroxide ion bicarbonate water
Even small fluctuations in pH can drastically change the structure and function of a cell/molecules.