ap biology 2007-2008 the chemistry of life ap biology fig. 2-1
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AP Biology 2007-2008
The Chemistry of Life
AP Biology
Fig. 2-1
AP Biology
Fig. 2-2EXPERIMENT
RESULTS
Cedrelasapling
Duroiatree Inside,
unprotected Inside,protected
Devil’sgarden
Outside,unprotected
Outside,protected
Insectbarrier
Dea
d le
af t
issu
e (c
m2)
afte
r o
ne
day
Inside,unprotected
Inside,protected
Outside,unprotected
Outside,protected
Cedrela saplings, inside and outside devil’s gardens
0
4
8
12
16
AP Biology
Fig. 2-2a
Cedrelasapling
Duroiatree Inside,
unprotected
Devil’sgarden
Inside,protected
Insectbarrier
Outside,unprotected
Outside,protected
EXPERIMENT
AP Biology
Fig. 2-2b
Dea
d le
af t
issu
e (c
m2 )
afte
r o
ne
day
16
12
8
4
0Inside,
unprotectedInside,
protectedOutside,
unprotectedOutside,protected
Cedrela saplings, inside and outside devil’s gardens
RESULTS
AP Biology
Why are we studying chemistry?Chemistry is the foundation of Biology
AP BiologyProton Neutron Electron
Hydrogen1 proton1 electron
Oxygen8 protons8 neutrons8 electrons
+ 0 –
Everything is made of matter Matter is made of atoms
AP Biology
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
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
AP Biology
Fig. 2-3
Sodium Chlorine Sodiumchloride
How does Sodium Chloride have emergent properties?
AP Biology
The World of Elements
C
Different kinds of atoms = elementsDifferent kinds of atoms = elements
H
ON
P SNa
K
Mg
Ca
AP Biology
Life requires ~25 chemical elements
About 25 elements are essential for life Four elements make up 96% of living
matter:
• _Carbon__ • _Hydrogen___
• _Nitrogen___ • _Oxygen_____
Four elements make up most of remaining 4%:
• phosphorus (P) • calcium (Ca)
• sulfur (S) • potassium (K)
AP Biology
Fig. 2-4a
(a) Nitrogen deficiency
AP Biology
Fig. 2-4b
(b) Iodine deficiency
AP Biology
Concept Check Is a trace element an essential
element? Iron (Fe) is a trace element required for
the proper functioning of hemoglobin, the molecule that carries oxygen in red blood cells. What might be the effects of an iron deficiency?
AP Biology
Bonding properties
Effect of electrons electrons determine
chemical behavior of atom
depends on numberof electrons in atom’s outermost shell valence shell
How does this atom behave?How does this atom behave?
AP Biology
Bonding properties
Effect of electrons chemical behavior of an atom depends on
number of electrons in its valence shell
What’s themagic number?
How does this atom behave?How does this atom behave? How does this atom behave?How does this atom behave?
AP Biology
Elements & their valence shells
Elements in the same row have the same number of shellsElements in the same row have the same number of shells
Moving from left to right, each element has a sequential addition of electrons (& protons)Moving from left to right, each element has a sequential addition of electrons (& protons)
AP Biology
Elements & their valence shells
Elements in the same column have the same valence & similar chemical properties
Elements in the same column have the same valence & similar chemical properties
Remembersome food chains
are built on reducing O to H2O
& some on reducing S to H2S
AP Biology
Concept Check A nitrogen atom has 7 protons, and the most common
isotope of nitrogen has 7 neutrons. A radioactive isotope of nitrogen has 8 neutrons. Write the atomic number and mass number of this radioactive nitrogen.
A lithium atom has 3 protons and 4 neutrons. What is its atomic mass in daltons?
How many electrons does fluorine have? How many electron shells? Name the orbitals that are occupied. How many electorns are needed to fill the valence shell?
AP Biology
–
–
–
Chemical reactivity Atoms tend to
complete a partially filled valence shell
or empty a partially filled valence shell
This tendency drives chemical reactions…This tendency drives chemical reactions…
and creates bondsand creates bonds
AP Biology
–
–
H2 (hydrogen gas)
Covalent bond
BONDS IN BIOLOGYCovalent bonds
sharing electrons
Ionic bondscation and anion (forms salts)
Hydrogen bondshydrogen is attracted to negative charge on
another already bonded atom
Van der Waals interactions
weak attractions occur when 2
atoms are close together and
have charge fluctuations
Hydrogen bond
H2O
H2O
AP Biology
Covalent bonds Why are covalent bonds strong bonds?
two atoms share a pair of electrons both atoms holding onto the electrons very stable
Forms molecules
–
–
H2 (hydrogen gas)H2 (hydrogen gas)
H — H
H2O (water)H2O (water)
H
H
OxygenH
HO
AP Biology
Multiple covalent bonds 2 atoms can share >1 pair of electrons
double bonds 2 pairs of electrons
triple bonds 3 pairs of electrons
Molecular shape
H
H–C–H
H
––
More isbetter!
AP Biology
Nonpolar covalent bond Electrons are shared equally
example: hydrocarbons = CxHx
methane (CH4 )
balanced, stable,good building block
AP Biology
H
H
Oxygen
Polar covalent bonds Electron stays closer to
more electronegative atom.
Example: water = H2O oxygen has stronger
“attraction” for the electrons than hydrogen
oxygen has higher electronegativity
Polarity_______ + vs – poles leads to many interesting
properties of water…
+
+
––
––
AP Biology
Hydrogen bonding Polar water creates molecular attractions
_Between the O and the H of adjacent water molecules.
also can occur wherever an -OH exists in a larger molecule
Let’s go to the videotape!
HO
H
AP Biology
Isotopes
All atoms of an element have the same number of protons but may differ in number of neutrons
Isotopes are two atoms of an element that differ in number of neutrons
Radioactive isotopes decay spontaneously, giving off particles and energy
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
AP Biology
Some applications of radioactive isotopes in biological research are: Dating fossils Tracing atoms through metabolic processes Diagnosing medical disorders
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
AP Biology
Fig. 2-6TECHNIQUE
RESULTS
Compounds includingradioactive tracer(bright blue)
Incubators
1 2 3
4 5 6
7 8 9
10°C 15°C 20°C
25°C 30°C 35°C
40°C 45°C 50°C
1
2
3
Human cells
Humancells areincubatedwith compounds used tomake DNA. One compound is
labeled with 3H.
The cells areplaced in testtubes; their DNA isisolated; andunused labeledcompounds areremoved.
DNA (old and new)
The test tubes are placed in a scintillation counter.
Co
un
ts p
er m
inu
te(
1,0
00)
Optimumtemperaturefor DNAsynthesis
Temperature (ºC)
0
10
10
20
20
30
30 40 50
AP Biology
Fig. 2-6a
Compounds includingradioactive tracer(bright blue)
Human cells
Incubators1 2 3
4 5 6
7 8 950ºC45ºC40ºC
25ºC 30ºC 35ºC
15ºC 20ºC10ºC
Humancells areincubatedwith compounds used tomake DNA. One compound islabeled with 3H.
1
2 The cells areplaced in testtubes; their DNA isisolated; andunused labeledcompounds areremoved.
DNA (old and new)
TECHNIQUE
AP Biology
Fig. 2-6b
TECHNIQUE
The test tubes are placed in a scintillation counter.3
AP Biology
Fig. 2-6c
RESULTSC
ou
nts
per
min
ute
( 1
,000
)
010 20 30 40 50
10
20
30
Temperature (ºC)
Optimumtemperaturefor DNAsynthesis
AP Biology
Fig. 2-7
Cancerousthroattissue
AP Biology
Van der Waals Interactions
If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge
Van der Waals interactions are attractions between molecules that are close together as a result of these charges
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
AP Biology
Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
AP Biology
Molecular Shape and Function
A molecule’s shape is usually very important to its function
A molecule’s shape is determined by the positions of its atoms’ valence orbitals
In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
AP Biology
Biological molecules recognize and interact with each other with a specificity based on molecular shape
Molecules with similar shapes can have similar biological effects
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings
AP Biology
Fig. 2-18
(a) Structures of endorphin and morphine
(b) Binding to endorphin receptors
Naturalendorphin
Endorphinreceptors
Morphine
Brain cell
Morphine
Natural endorphin
KeyCarbonHydrogen
NitrogenSulfurOxygen
AP Biology
Fig. 2-18
(a) Structures of endorphin and morphine
(b) Binding to endorphin receptors
Naturalendorphin
Endorphinreceptors
Morphine
Brain cell
Morphine
Natural endorphin
KeyCarbonHydrogen
NitrogenSulfurOxygen
AP Biology
Fig. 2-18b
Naturalendorphin
EndorphinreceptorsBrain cell
Binding to endorphin receptors
Morphine
(b)
AP Biology
Concept Check Explain what hold together the atoms in
a crystal of magnesium chloride (MgCl2).
If you were a pharmaceutical researcher, shy would you want to learn the three-dimensional shapes of naturally occurring signal molecules?
AP Biology 2007-2008
Chemistry of Life
Properties of Water
AP Biology
More about Water
Why are we studying water?Why are we studying water?
All life occurs in water inside & outside the cell
All life occurs in water inside & outside the cell
AP Biology
Chemistry of water H2O molecules form H-bonds
with each other +H attracted to –O creates a
sticky molecule
AP Biology
Concept Check What is electronegativity and how does
it affect interactions between water molecules?
What would be the effect on the properties of the water molecule if oxygen and hydrogen had equal electronegativity?
AP Biology
Elixir of Life Special properties of water
1. _Cohesion_______________ surface tension, capillary action
2. _The solvent of life ____ many molecules dissolve in H2O hydrophilic_ vs. _hydrophobic__
3. _Expansion upon freezing_____ ice floats!
4. Moderation of temperature________ water stores heat
5. _High specific heat_________ heats & cools slowly
Ice! I could use more ice!
AP Biology
1. Cohesion & Adhesion
Try that with flour…or sugar…
_Cohesion_______________ H bonding between H2O molecules water is “sticky”
surface tension drinking straw
_Adhesion________________ H bonding between H2O & other substances
capillary action meniscus water climbs up
paper towel or cloth
AP Biology
How does H2O get to top of trees?Transpiration is built on cohesion & adhesion
Let’s go to the videotape!
AP Biology
Fig. 3-3
Water-conductingcells
Adhesion
Cohesion
150 µm
Directionof watermovement
AP Biology
2. Water is the solvent of life ____________________________________
polar H2O molecules surround + & – ions solvents dissolve solutes creating solutions
AP Biology
Fig. 3-7
Cl–
Na
Cl–
+
+
+
+
+
+
++
––
–
–
–
–
––
Na+
–
––
+
AP Biology
What dissolves in water? _Hydrophilic______________
substances have attraction to H2Opolar or non-polar?
AP Biology
What doesn’t dissolve in water? _hydrophobic__________
substances that don’t have an attraction to H2O
polar or non-polar?
fat (triglycerol)
Oh, lookhydrocarbons!
AP Biology
3. The special case of ice Most (all?) substances are more dense
when they are solid, but
not water… _Water expands!
H bonds form a crystal
And this hasmade all the difference!
AP Biology
Ice floats
AP Biology
Why is “ice floats” important? Oceans & lakes don’t freeze solid
The ice acts to insulate the 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
Floating ice prevents the water below from freezing. ______________________________________
AP Biology
Fig. 3-6
Hydrogenbond
Liquid waterHydrogen bonds break and re-form
IceHydrogen bonds are stable
AP Biology
4. Specific heat Amount of heat to increase T of 1g by 1°C.
high specific heat takes a lot to heat it up takes a lot to cool it down
H2O moderates temperatures on Earth
AP Biology
Specific heat& climate
AP Biology
5. Heat of vaporizationEvaporative cooling
Organisms rely on heat of vaporization to remove body heat
AP Biology
Concept Check Describe how properties of water contribute to the upward
movement of water in a tree.
Explain the saying, “It’s not the heat, it’s the humidity.”
What if a water strider’s legs are coated with a hydrophobic substance. What might be the benefit? What would happen if the substance were hydrophilic?
AP Biology
Ionization of water & pH Water ionizes
H+ splits off from H2O, leaving OH–
if [H+] = [-OH], water is neutral if [H+] > [-OH], water is acidic if [H+] < [-OH], water is basic
pH scalehow acid or basic solution is1 7 14
H2O H+ + OH–H2O H+ + OH–
AP Biology
pH Scale10–1
H+ IonConcentration
Examples of Solutions
Stomach acid, Lemon juice
1
pH100 Hydrochloric acid0
10–2 2
10–3 Vinegar, cola, beer3
10–4 Tomatoes4
10–5 Black coffee, Rainwater5
10–6 Urine, Saliva6
10–7 Pure water, Blood7
10–8 Seawater8
10–9 Baking soda9
10–10 Great Salt Lake10
10–11 Household ammonia11
10–12 Household bleach12
10–13 Oven cleaner13
10–14 Sodium hydroxide14
tenfold changein H+ ions
pH1 pH210-1 10-2
________________
pH8 pH710-8 10-7
________________
pH10 pH810-10 10-8
________________
AP Biology 1001
2
3
4
5
6
7
8
9
3Amount of base added
Bufferingrange
4 52
pH
Buffers & cellular regulation pH of cells must be kept ~7
pH affects shape of molecules shape of molecules affect function pH affects cellular function
______________________ reservoir of H+
donate H+ when [H+] falls
absorb H+ when [H+] rises
AP Biology
Threats to Water Quality on Earth Acid precipitation refers to rain, snow, or
fog with a pH lower than 5.6 Acid precipitation is caused mainly by the
mixing of different pollutants with water in the air and can fall at some distance from the source of pollutants
Acid precipitation can damage life in lakes and streams
Effects of acid precipitation on soil chemistry are contributing to the decline of some forests
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
AP Biology
Fig. 3-10
Moreacidic
0
AcidrainAcidrain
Normalrain
Morebasic
123456789
1011121314
AP Biology
Human activities such as burning fossil fuels threaten water quality
CO2 is released by fossil fuel combustion and contributes to: A warming of earth called the “greenhouse”
effect Acidification of the oceans; this leads to a
decrease in the ability of corals to form calcified reefs
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
AP Biology
Fig. 3-11
EXPERIMENT
RESULTS
Cal
cif
icat
ion
rat
e(m
mo
l C
aCO
3
per
m2 p
er d
ay)
[CO32–] (µmol/kg)
150 200 250 3000
20
40
AP Biology
Surface tension lab
AP Biology
Fig. 3-UN6
Surface of EarthSurface of Mars
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