BIOPLS 210 Jan Smalle jsmalleuky'edu Website: Smalle Lab

1
BIO/PLS 210Jan Smallejsmalle_at_uky.eduWebsite
Smalle Lab
2
The Chemistry of Life

• Chapter 2

3
Photosynthesis and Respiration

• Photosynthesis
• 6CO2 6H2O energy ? C6H12O6 6O2

Respiration C6H12O6 6O2 ? 6CO2 6H2O energy
4
Overall Photosynthesis Reaction

• 6CO2 6H2O energy ? C6H12O6 6O2

Oxygen
Carbon dioxide
Water
Glucose
H
C
O
H
H
H
H
H
C
O
O
C
H
O
C
H
H
O
O
C
C
O
H
C
O
H
O
H
O
H
H
O
Oxygen
Water
Carbon dioxide
Glucose
5
Overall Photosynthesis Reaction

• 6CO2 6H2O energy ? C6H12O6 6O2

7 C-O bonds 5 C-C bonds 7 C-H bonds 5 H-O
bonds 12 O-O bonds 36 covalent bonds
24 C-O bonds 12 H-O bonds 36 covalent bonds
6
Overall Respiration Reaction

• C6H12O6 6O2 ? 6CO2 6H2O energy

7 C-O bonds 5 C-C bonds 7 C-H bonds 5 H-O
bonds 12 O-O bonds 36 covalent bonds
24 C-O bonds 12 H-O bonds 36 covalent bonds
7
Twelve Most Common Elements in Living Organisms
8
Atoms

• Smallest unit of matter to enter into chemical
  reactions
• Formed from three types of particles
• Protons
• Neutrons
• Electrons

9
Atomic Particles
10
Electrons

• Negative charge
• Almost no mass
• Move around nucleus in orbitals
• Number of electrons number of protons in
  electrically neutral atom
• Electrons are used by organisms to store energy
• An electron that has more energy is located at a
  further distance from the nucleus

11
Electron Orbitals

• Represent energy levels
• Atom most stable with two electrons in each
  orbital
• Inner shell
• Lowest energy level
• Outer shell
• Highest energy level

12
hydrogen
carbon

• Hydrogen has one proton and one electron located
  in one orbital surrounding the nucleus.
• Carbon has six protons and (thus) six electrons.
  One electron pair is located in the inner
  orbital. The other four are distributed over four
  outer orbitals organized in a tetrahedron
  structure.

13
hydrogen
carbon

• Carbon has six protons and (thus) six electrons.
  One electron pair is located in the inner
  orbital. The other four are distributed over four
  outer orbitals organized in a tetrahedron
  structure.
• Electrons of the Carbon atom are distributed over
  two energetically different electron shells.

14
Chemical Bonding

• Types of bonds
• Ionic
• Covalent

15
sodium atom 11 protons 11 electrons
sodium ion 11 protons 10 electrons
a sodium chloride crystal (table salt), held
together by ionic bonds
Na
Na
Cl
Cl
chloride ion 17 protons 18 electrons
chloride atom 17 protons 17 electrons
Fig. 2-2, p. 16
16
Covalent Bonds

• Single bond
• Atoms share two electrons
• Represented by single line (-) in structural
  formula

H
H - C - H
H
Methane
17
Covalent Bonds

• Double bond
• Share four electrons
• Represented by double line () in structural
  formula

H
H
C C
H
H
Ethylene
18
Overall Photosynthesis Reaction

• 6CO2 6H2O energy ? C6H12O6 6O2

7 C-O bonds 5 C-C bonds 7 C-H bonds 5 H-O
bonds 12 O-O bonds 36 covalent bonds
24 C-O bonds 12 H-O bonds 36 covalent bonds
19
Electron energy levels
Carbon (C)
Oxygen (O)
Nitrogen(N)
Inner shell (Low potential energy)
Outer shell (high potential energy)
Nucleus
Electron
Carbon six protons and six electrons Nitrogen
seven protons and seven electrons Oxygen eight
protons and eight electrons
20
Carbon (C)
Carbon (C)
Inner shell (Low potential energy)
Outer shell (high potential energy)
C-C bond
21
Carbon (C)
Carbon (C)
C-C bond
22
Electron energy levels
Carbon (C)
Oxygen (O)
Inner shell (Low potential energy)
Outer shell (high potential energy)
Oxygen has 8 protons in its nucleus. The result
is a higher positive charge that exerts a
stronger attraction force on the electrons of the
outer shell. On average, these electrons will be
located closer to the nucleus (compared to
Carbon).
23
Carbon (C)
Oxygen (O)
Inner shell (Low potential energy)
Outer shell (high potential energy)
C-O bond
24
Carbon (C)
Oxygen (O)
C-O bond?
No !
Yes !
25
C-O bond?
C O
No !
Yes !

• Oxygen has a higher electronegativity than
  Carbon (Oxygen nucleus has 8 protons compared to
  6 in the carbon nucleus. The higher proton number
  results in a higher positive charge).
• Electron pair is pulled towards the O nucleus
• Bonding electron pair contains a lower level of
  potential energy compared to when it is in the
  middle between nuclei (see waterfall analogy).

26
Waterfall analogy
RIVER
High potential energy
Low potential energy
LAKE
C
C
Gravitational force
Electrical force
High potential energy
Low potential energy
Electrical force
Earth center
O
C
27
Carbon-Carbon bonds contain useful energy

• Bonding electron pair of C-C contains more energy
  than C-O pair

28
Hydrogen (H)
Carbon (C)
Inner shell (Low potential energy)
Outer shell (high potential energy)
H-C bond
29
Hydrogen (H)
Carbon (C)
Inner shell (Low potential energy)
Outer shell (high potential energy)
The potential energy of the bonding electron pair
of a H-C bond is defined by the distance to the C
nucleus. The distance to the H nucleus is in
this case irrelevant since the single electron
orbital of the H atom already defines the lowest
possible energy state of an electron (or electron
pair).
30
H-C bond
H-O bond
The potential energy of the bonding electron pair
of a H-C or H-O bond is defined by the distance
to the C or O nucleus. The distance to the H
nucleus is in this case irrelevant since the
single electron orbital of the H atom already
defines the lowest possible energy state of an
electron (or electron pair).
31
Carbon-hydrogen bonds contain useful energy
H
H
O
C

• Bonding electron pair of C-H contains more energy
  than H-O pair

32
Basis of photosynthesis Light energy is used to
transform C-O and H-O bonds into C-C and H-C
bonds
H
Energy


Increased potential energy
O
Basis of respiration Energy is liberated by
transforming C-C and C-H bonds into C-O and H-O
bonds
H
Energy


Decreased potential energy
O
33
Why do we need to know this?
34
Fossil fuels constitute up to 80 of our present
day energy consumption (Source U.S. DOE).
35
Some interesting calculations(source Jeffey
Dukes, Climatic Change 61 31-44, 2003)

• One gallon of gasoline (3.26 kilograms)
  represents 98 tons of prehistoric buried plant
  material.
• The amount of fossil fuel burned in 1997 equals
  400 times all the plant matter that grows in the
  world in a year.
• The amount of plants that went into the fossil
  fuels we have burned since the industrial
  revolution began (1751) is equal to all the
  plants grown on earth over 13,300 years.

36
Photosynthesis and fossil fuels

• All the energy (C-C and C-H bonds) in oil, gas
  and coal originally came from photosynthesis.
• In the same way that we burn wood to release
  energy that trees capture from the sun, we burn
  fossil fuels to release energy that ancient
  plants captured from the sun. This fossil fuel
  energy has been deposited in a solar power bank
  account over millions of years.
• Sustainability wood compared to fossil fuels.
• We are withdrawing energy from our solar power
  bank account without making any significant
  deposits. Fossil fuels are not renewable within a
  human life span (or within the life span of a
  civilization).

37
Alternatives to fossil fuels?
38
Understanding Photosynthesis to improve our
ability to harvest and store solar energy.

• Photosynthesis involves light harvest and energy
  storage.
• Future possibilities to increase/maintain
  available energy
• 1) Mimicking of plant light harvest to generate
  electricity or to produce H2.
• 2) Improving energy storage by plants by
  improving enzymatic efficiencies.

39
Types of Biological Molecules
40
Energy storage compoundsEnergy carrier
compounds
41
Energy carrier compounds1) ATPand2) NADH
and NADPH
42
Uphill and downhill reactions. Only the downhill
reaction will go forward spontaneously. Uphill
reactions require an input of free energy from
some other source. Any uphill reaction needs
to be combined with a downhill reaction to
provide the energy needed.
products have more energy than reactants did
C D
substrates
Free energy
Free energy
substrate
A B
products have less energy than reactant did
Fig. 8-8, p. 129
Progress of reaction
43
Down hill Reactions That Run Most of the Cells
Machinery

• Hydrolysis of ATP
• Oxidation of NADH and NADPH

44
Energy storage versus energy carrier compounds

• To release the energy contained in a glucose
  molecule, we need to first add energy. Glucose is
  an energy storage compound. Enzymes cannot
  directly use glucose to power their enzymatic
  reactions.
• ATP is an energy carrier compound. Enzymes
  directly use ATP to power enzymatic reactions.
  Binding of ATP to enzymes leads to its hydrolysis
  with the concomitant release of the energy
  contained in the pyrophosphate bond.

45
ATP

• ATP H2O ADP Pi energy
• ADP Pi energy ATP H2O
• ATP is ideally suited as energy currency
• The amount of energy released is twice as much as
  is needed to drive most cellular reactions.
• ATP does not cross cell membrane and is short
  lived.
• The third phosphate bond of ATP is weak,
  unstable, breaks easily.

46
Fig. 8-9, p. 130
47
Proteins can bind ATP

• Most proteins (enzymes) that catalyze uphill
  reactions bind ATP and use its energy.

ATP
ATP
ADP Pi
48
NADH and NADPH carriers of high energy electrons

• NADH nicotinamide adenine dinucleotide
• NADPH nicotinamide adenine dinucleotide
  phosphate
• Both are coenzymes
• Reactive part of molecule is nicotinamide
  functional group
• Humans obtain this from food because we cannot
  synthesize nicotinamide (niacin)

49
The oxidation of nicotinamide adenine
dinucleotide by oxygen The NADH loses one H and
one chemical bond between H and C, which
represents two electrons. The electrons may be
transferred to a series of compounds before they
reach oxygen.
50
NADH and NADPH

• NADH is used predominantly to make ATP during
  respiration
• NADPH is predominantly used during photosynthesis
  (formation of energy storage compounds)