1. The Chemistry of Life

2. Why are we studying chemistry?
Chemistry is the foundation of Biology

3. Everything is made of matter Matter is made of atoms
Hydrogen
1 proton
1 electron
Oxygen
8 protons
8 neutrons
8 electrons
Proton +
Neutron
Electron –

4. The World of Elements H C N O Na Mg P S K Ca
About 25 elements are essential for life
Four elements make up 96% of living matter:
• carbon (C) • hydrogen (H)
• oxygen (O) • nitrogen (N)
Six elements make up most of remaining 4%:
• phosphorus (P) • calcium (Ca)
• sulfur (S) • potassium (K)
• magnesium (Mg) • sodium (Na)

5. 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)

6. 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
How does this atom behave?

7. Bonding properties Effect of electrons
What’s the magic number?
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?
How does this atom behave?

8. Elements & their valence shells
Elements in the same row have the same number of shells
Moving from left to right, each element has a sequential addition of electrons (& protons)

9. Elements & their valence shells
Elements in the same column have the same valence & similar chemical properties
Remember
some food chains are built on reducing O to H2O
& some on
reducing S to H2S
ELECTRONEGATIVITY
Oxygen has medium electronegativity so doesn’t pull electrons all the way off hydrogen whereas chlorine would.
So oxygen forms a polar covalent bond.
Carbon has only a weak electronegativity so forms a nonpolar covalent bond

10. 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
Ionic or Covalent bonds – –

11. Isotopes Differ in number of neutrons Same number of protons
Radioactive isotopes
Spontaneously give off particles of energy
Examples:
H-3 – used as scintillation marker
Attach to organic molecules and quantified by how much light is given off
P-32 – used as radioactive marker
Track mRNA or find nucleic acids
C-14 – used to date fossils
Date organism depending on how much is decayed into N
O-18 – used to make heavy water
Tracked through organism during experimentation
S – used as radioactive marker
Attach to proteins on disulfide bridges of most polypeptides; make proteins coats of viruses radioactive
I – used in cancer treatment
Fight thyroid cancer  binds to thyroid tissue and destroys cells in region during radioactive decay

12. Radioactive Isotope Use in Biology
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.
DNA (old and new)
Ingredients including
Radioactive tracer
(bright blue)
Human cells
Incubators 1 2 3 4 5 6 9 8 7
10°C
15°C
20°C
25°C
30°C
35°C
40°C
45°C
50°C
TECHNIQUE
The cells are placed in test tubes, their DNA is isolated, and unused ingredients are removed.
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.

13. Radioactive Isotope Use in Biology
Temperature (°C)
The frequency of flashes, which is recorded as counts per minute, 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 against temperature, it is clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C. 10 20 30 40 50
Optimum
temperature
for DNA
synthesis
Counts per minute
(x 1,000)
RESULTS 3
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.

14. Radioactive Isotope Use in Biology
Cancerous throat tissue
Figure 2.6

15. Bonds in Biology Weak bonds Strong bonds Hydrogen bond hydrogen bonds
H2O
Weak bonds
hydrogen bonds
attraction between + and –
hydrophobic & hydrophilic interactions
interactions with H2O
van derWaals forces
ionic
Strong bonds
covalent bonds
sharing electrons
H2O
Covalent bond –
H2 (hydrogen gas)

16. Covalent bonds Why are covalent bonds strong bonds? 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)

17. 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
More is better! H
H–C–H –

18. Nonpolar covalent bond
Pair of electrons shared equally by 2 atoms
example: hydrocarbons = CxHx
methane (CH4 )
Lots of energy stored… & released
Pair of electrons shared equally by 2 atoms
strong stable bond
example: hydrocarbons = CxHx
methane (CH4 )
balanced, stable, good building block

19. Polar covalent bonds Pair of electrons shared unequally by 2 atoms
example: water = H2O
oxygen has stronger “attraction” for the electrons than hydrogen
oxygen has higher electronegativity
Attraction of particular kind of atom for the electrons in a covalent bond
water is a polar molecule
+ vs – poles
leads to many interesting properties of water… + H
Oxygen – –
Pair of electrons shared unequally by 2 atoms
strong but interactive bond
example: bonds within water = H2O
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… – – +

20. Hydrogen bonding Polar water creates molecular attractions Weak bond
attraction between positive H in one H2O molecule to negative O in another H2O
also can occur wherever an -OH exists in a larger molecule
Weak bond
but common in biology
H bonds H O
APBio/TOPICS/Biochemistry/MoviesAP/03_02WaterStructure_A.swf
attraction between H+ in one molecule to O- in another molecule
weak bond
example: bonds between water molecules
leads to many interesting properties of water

21. Ionic Bonds Electron transfer between two atoms creates ions Ions
Are atoms with more or fewer electrons than usual
Are charged atoms
Anion - negatively charged ions
Cation - positively charged

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

23. Ionic Bonds Ionic compounds Often called salts  may form crystals
Figure 2.14

24. Van der Waals Interactions
Occur when transiently positive and negative regions of molecules attract each other

25. Weak Chemical Bonds Reinforce the shapes of large molecules
Help molecules adhere to each other

26. Molecular Shape and 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

27. In a Covalent Bond
The s and p orbitals may hybridize, creating specific molecular shapes
s orbital Z
Three p orbitals X Y
Four hybrid orbitals
(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 tetrahedron (outlined in pink).
Tetrahedron
Figure 2.16 (a)

28. Molecular Shape
Determines how biological molecules recognize and respond to one another with specificity

29. Space-filling Ball-and-stick Hybrid-orbital model model
(with ball-and-stick
model superimposed)
Unbonded
Electron pair
104.5° O H
Water (H2O)
Methane (CH4) C
Ball-and-stick
(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
Figure 2.16 (b)

30. Carbon Nitrogen Hydrogen Sulfur Oxygen Natural endorphin 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.
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.
Endorphin
receptors
Brain cell

31. Chemical Reactions Making and breaking of chemical bonds
Leads to changes in the composition of matter
Converts reactants to products
Reactants
Reaction
Product
2 H2 O2
2 H2O +

32. Photosynthesis
Example of a chemical reaction
Figure 2.18

33. Chemical Equilibrium
Reached when the forward and reverse reaction rates are equal