1. Why are we studying chemistry?
Atoms are ordered into molecules and these molecules interact with each other within cells. We need to begin by considering the chemical components that make up all matter. Vital processes of life should be considered chemical reactions. Chemistry is the basis for thinking about disease – central to medicine and the pharmaceutical industry.

2. Life requires ~25 chemical elements
About 25 elements are essential for life
Four elements make up 96% of living matter:
• carbon (C) • hydrogen (H)
• oxygen (O) • nitrogen (N)
Four elements make up most of remaining 4%:
• phosphorus (P) • calcium (Ca)
• sulfur (S) • potassium (K)
Elements are the basic chemical units that cannot be broken apart by typical chemical processes

3. Elements and Compounds
Matter is made up of elements
An element is a substance that cannot be broken down to other substances by chemical reactions
A compound is a substance consisting of two or more elements in a fixed ratio
A compound has characteristics different from those of its elements
Sodium
Chlorine
Sodium
chloride

5. How does this atom behave?
Bonding properties
Effect of electrons
electrons determine chemical behavior of atom
depends on number of electrons in atom’s outermost shell
valence shell
Outer shell can hold 8 electrons. Argon has a full valence shell so it is inert, meaning chemically unreactive.
How does this atom behave?

6. How does this atom behave?
Bonding properties
Effect of electrons
chemical behavior of an atom depends on number of electrons in its valence shell
Sulfur on the LEFT
Magnesium on the RIGHT
How does this atom behave?

7. This tendency drives chemical reactions…
Chemical reactivity
Atoms tend to
complete a partially filled valence shell or
empty a partially filled valence shell
This tendency drives chemical reactions…
and creates bonds – –

8. Bonds in Biology Hydrogen bond Covalent bond Weak bonds Strong bonds
H2O
Weak bonds
hydrogen bonds
attraction between + and –
hydrophobic & hydrophilic interactions
van derWaals forces
(ionic)
Strong bonds
covalent bonds –
H2 (hydrogen gas)
Covalent bond
Van derWaals- gecko example where the gecko is able to climb because of the millions of tiny hairs on its feet- each creates a weak force with a surface, but together are strong enough to hold its weight.

9. Covalent bonds H H H — H O Why is this a strong bond? Forms molecules
two atoms share a pair of electrons
both atoms holding onto the electrons
very stable
Forms molecules H
Oxygen – H O
H — H
H2 (hydrogen gas)
H2O (water)

10. Multiple covalent bonds
2 atoms can share >1 pair of electrons
double bonds
2 pairs of electrons
triple bonds
3 pairs of electrons
Very strong bonds
Hydrogen, Oxygen, water, methane
More is better! H
H–C–H –

11. Polar covalent bonds + – H – – – +
Pair of electrons shared unequally by 2 atoms
Water = O + H
oxygen has stronger “attraction” for the electrons than hydrogen
oxygen has higher electronegativity
water is a polar molecule
+ vs – poles
leads to many interesting properties of water… H
Oxygen + – – – – +

12. Hydrogen bonding Polar water creates molecular attractions Weak bond
positive H atom in one H2O molecule attracted to negative O in another H2O
also can occur wherever an -OH exists in a larger molecule
Weak bond
APBio/TOPICS/Biochemistry/MoviesAP/03_02WaterStructure_A.swf

13. Ionic bonds are attractions between ions of opposite charge
LE 2-7a-1
Ionic bonds are attractions between ions of opposite charge
Transfer of
electron
Na readily gives up its electron to become stable; likewise chlorine readily accepts an electron to become stable. Na
Sodium atom Cl
Chlorine atom

14. Sodium chloride (NaCl)
NaCl is known as a compound
Na+
Sodium ion
Cl-
Chloride ion
Sodium chloride (NaCl)

15. LE 2-7b
Sodium chloride
crystal
Na+
Cl-

16. Ionic attractions are weak, so salts dissolve easily in water.

18. CHAPTER 3 WATER AND LIFE

19. Why are we studying water?
More about Water
Why are we studying water?
All life occurs in water
inside & outside the cell

20. Water is a polar molecule- the opposite ends have opposite charges
H2O molecules form H-bonds with each other
+ attracted to –
creates a sticky molecule
APBio/TOPICS/Biochemistry/Movies AP/hydrogenbonds-Thinkwell.swf
The water molecule is a polar molecule: the opposite ends have opposite charges
Polarity allows water molecules to form hydrogen bonds with each other

21. Elixir of Life Special properties of water cohesion & adhesion
surface tension, capillary action
good solvent
many molecules dissolve in H2O
hydrophilic vs. hydrophobic
lower density as a solid
ice floats!
high specific heat
water stores heat
Surface tension is a measure of how hard it is to break the surface of a liquid
Surface tension is related to cohesion

22. Cohesion & Adhesion H bonding between H2O molecules is cohesion
water is “sticky”
surface tension
drinking straw
H bonding between H2O & other substances is adhesion
capillary action
meniscus
water climbs up paper towel or cloth
Cohesion
Is the bonding of a high percentage of the molecules to neighboring molecules
Is due to hydrogen bonding
Helps pull water up through the microscopic vessels of plants
Surface tension
Is a measure of how hard it is to break the surface of a liquid
Is related to cohesion

23. How does H2O get to top of trees?
Transpiration built on cohesion & adhesion
APBio/TOPICS/04Biochemistry/MoviesAP/03_03WaterTransport_A.swf

24. Water is the solvent of life
Polarity makes H2O a good solvent
polar H2O molecules surround + & – ions
solvents dissolve solutes creating solutions
What dissolves in water easily?
polar or non-polar molecules?
How about Oxygen? Does that dissolve in H2O?
When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell

25. Do you dissolve in water?
Hydrophilic
substances have attraction to H2O
polar or non-polar?
What dissolves in water easily?
polar or non-polar molecules?
How about Oxygen? Does that dissolve in H2O?

26. Hydrophobic Or don’t you?
substances that don’t have an attraction to H2O
polar or non-polar?
What dissolves in water easily?
polar or non-polar molecules?
How about Oxygen? Does that dissolve in H2O?
fat (triglycerol)

27. Hydrophilic and Hydrophobic

28. The special case of ice
Most (all?) substances are more dense when they are solid, but
Not water…
Ice floats!
H bonds form a crystal
At warm temperatures, water molecules have a lot of energy and are able to move past and mix with each other despite the attractions between the hydrogen atoms and unbonded electron pairs.
As water is cooled down, however, the molecules have less energy and hydrogen bonding takes over.  The molecules form a ordered crystal through hydrogen bonding that spaces the molecules farther apart than when they were in a liquid.  This makes ice less dense than water allowing it to float.

29. Ice floats
Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense

30. Specific heat H2O resists changes in temperature
high specific heat
Water absorbs heat from warmer air and releases stored heat to cooler air
H2O moderates temperatures on Earth
Santa Barbara 73
San Bernardino
100
Riverside 96
Pacific Ocean 68
Burbank
90
Santa Ana
84
Palm Springs
106
Los Angeles
(Airport) 75
San Diego 72
40 miles
70s (F)
80s
90s
100s
Heat must be absorbed to break the hydrogen bonds (then water molecules can begin moving faster- having a higher kinetic energy); heat will be released when bonds form- when the temp drops slightly many additional bonds form releasing energy in the form of heat. In organisms, presence of water shields them from fluctuations in environmental temperature. Water resists changes in temperature.

31. Water Hydroxide Hydrogen
Water Ionizes
The covalent bond within a water molecule breaks spontaneously
This produces two ions in a process called ionization
because of the great strength of covalent bonds, this does not occur too often
H2O  OH H+
Water Hydroxide Hydrogen
Helps to explain pH (Power of Hydrogen). The concept of p[H] was first introduced by Danish chemist Soren Peder Sorenson in 1909 and revised to the modern pH in 1924

32. Gastric juice, lemon juice Inside of small intestine
pH Scale
pH Scale
Battery acid
Gastric juice, lemon juice
Vinegar, wine,
cola
Beer
Tomato juice
Black coffee
Rainwater
Urine
Saliva
Pure water
Human blood, tears
Seawater
Inside of small intestine
Milk of magnesia
Household ammonia
Household
bleach
Oven cleaner
Basic
solution
Neutral
Acidic 1 2 3 4 5 6 7 8 9 10
[H+] = [OH]
Increasingly Basic
[H+] < [OH]
Increasingly Acidic
[H+] > [OH] H+
OH 11 12 13 14
It is the concentration of respective H+ or OH- that determines the extent to which a solution is acidic or basic. In pure water only 1 water molecule in every 554 million is dissociated. So the concentration of H+ in pure water is 1.0 x 10-7 M.

33. Buffers & cellular regulation
pH of cells must be kept ~7
pH affects shape of molecules
shape of molecules affect function
pH affects cellular function
Buffers minimize changes in concentrations of H+ and OH- in a solution
reservoir of H+
donate H+ when [H+] falls
absorb H+ when [H+] rises 1 2 3 4 5 6 7 8 9
Amount of base added
Buffering
range pH
Exercise = acidic in muscles
CO2 = carbonic acid
lactic acid
body uses buffers that contain a weak acid and a corresponding base to counter act this

34. [CO32−] (mol/kg of seawater)
Ocean Acidification
CO2
CO2  H2O  H2CO3
H2CO3  H  HCO3−
H  CO32−  HCO3−
CO32−  Ca2  CaCO3
Atmospheric CO2 from human activities and its fate in the ocean
[CO32−] (mol/kg of seawater)
(mmol CaCO3/m2  day)
Calcification rate
220
280
260
240 20 10
Figure 2.24 Atmospheric CO2 from human activities and its fate in the ocean
Human activities such as burning fossil fuels threaten water quality
CO2 is the main product of fossil fuel combustion
About 25% of human-generated CO2 is absorbed by the oceans
How does this graph relate to ocean acidification? Data taken from a study reported in 2000, Langdon et al used an artificial coral reef system to test the effect of carbonate concentration on the rate of calcification by reef organisms.
As seawater acidifies, H ions combine with CO32− ions to form bicarbonate ions (HCO3–)
It is predicted that carbonate ion concentrations will decline by 40% by the year 2100
This is a concern because organisms that build coral reefs or shells require carbonate ions
CO2 dissolved in seawater forms carbonic acid; this causes ocean acidification 34

35. GHOSTS

36. Properties of Water Powerful Solvent
* able to dissolve most chemical compounds, can carry important nutrients in living organisms
High Specific Heat and Heat of Vaporization
* can absorb large amounts of heat energy before getting hot, releases heat energy slowly as cools helps to moderate climate, allows organisms to regulate their body temperature
Strong Cohesion
* occurs because of hydrogen bonding between water molecules  high surface tension
Organizes Nonpolar Molecules
* able to form maximum number of hydrogen bonds by excluding nonpolar molecules from disrupting bonding
Water expands as it freezes, becoming less dense than its liquid form
Combine this with other slides

37. Why is “ice floats” important?
Oceans & lakes don’t freeze solid
surface ice insulates water below
allowing life to survive the winter
if ice sank…
ponds, lakes & even oceans would freeze solid
in summer, only upper few inches would thaw
seasonal turnover of lakes
cycling nutrients in autumn