Chemistry of Life and Cells

March 20, 2024

Joni Baumgarten, PhD
BIOL 111
Figures and figure numbers are from Campbell Biology, 12 th ed

Chapter sections (11th ed. of textbook): 3.2, 6.2, 6.5, 6.7, 7.1, 7.2, 7.3, 7.4
Hi, again!
 Active learning!
Research has shown that we
learn when:
• our prior knowledge is
challenged
• we figure out what we know and
don’t know
• we engage in problems/activities
that help us build our skills
• we work in groups – no matter
what your role

From Dale, E. 1954. “Audio-Visual Methods in Teaching”.

The Dryden Press, NY.
Class goals:
• Review the basics that relate to understanding photosynthesis,
ecology, and global climate change
 Atom structure

Atom structure is
fundamental to all
properties of all matter

Figure 2.1
 Atom structure
• Electron orbitals have set levels of
energy
• Potential energy; based on
distance from nucleus
• Where is the lowest energy?

• Atoms “prefer” to have a full

valence shell

Figure 2.6
 Chemical bonds: Covalent bond
• Covalent bonds

• Electrons are shared

• One atom’s electrons complete the

valence shell of the other atom’s
valence shell (and vice versa)

• Strongest kind of chemical bond

Figure 2.9
Chemical bonds: Polar covalent bond
• Atoms in a molecule attract
electrons to varying degrees

• Electronegativity is an atom’s
attraction for the electrons in a
covalent bond

• The more electronegative an

atom, the more strongly it pulls
shared electrons toward itself

Figure 2.11
 Chemical bonds: Ionic bond
• Strong, but dissociate in water

Figure 2.12 and 2.13

 Chemical bonds
• Weak chemical interactions
• Hydrogen bonds
• Van der Waals interaction

Figure 2.14
Four emergent properties of water
• Cohesive behavior
• Ability to moderate temperature
• Versatility as a solvent
• Expansion upon freezing

CAVE

By José Manuel Suárez, CC BY 2.0,

https://commons.wikimedia.org/w/index.php?curid=4602887
 Water is a polar molecule
• 1/20 as strong as a
covalent bond

• Constantly forming
and breaking and
forming bonds with
other adjacent
molecules

Figure 3.2
Draw out the electron cloud for water
• Because of the polarity, the electrons don’t spend equal time at both
atoms; what might that look like?
Draw out the electron cloud for water
• Because of the polarity, the electrons don’t spend equal time at both
atoms

From Jianmin Qu on reaserarchgate.net

 Cohesion and adhesion
• Cohesion to other water molecules

• Adhesion to other types of

molecules (aka other surfaces for
liquid water)

• Surface tension due to water being

more attracted to water than it is to
air

Figure 3.4
 Ability to moderate temperature
• High specific heat

• Water absorbs heat from

warmer air and releases
stored heat to cooler air

• Water can absorb or release a

large amount of heat with
only a slight change in its own
temperature

Figure 3.6
 Ability to moderate temperature
• Heat of vaporization is the heat a liquid
must absorb for 1 g to be converted to
gas
• As a liquid evaporates, its remaining
surface cools, a process called
evaporative cooling

• Heat is absorbed when hydrogen bonds

break

• Heat is released when hydrogen bonds

form
Figure 3.6
 Versatility as a solvent
• Due to the polarity of water
molecule

• Hydration shell

• Solute, solvent, solution,

aqueous solution

• Most chemical reactions in

organisms involve solutes
dissolved in water

Figure 3.8
 Versatility as a solvent
• Water can dissolve compounds
made of nonionic polar molecules,
or large molecules with ionic and
polar regions

• Hydrophobic and hydrophilic:

• A hydrophilic substance is one
that has an affinity for water
• A hydrophobic substance is one
that does not have an affinity
for water

Figure 3.9
 Expansion upon freezing
• Ice floats in liquid water because hydrogen
bonds in ice are more “ordered,” making
ice less dense than water

• Water reaches its greatest density at 4°C

Figure 3.1
 Expansion upon freezing

If ice sank, all bodies of

water would eventually
freeze solid, making life
impossible on Earth
(think: thin layer of life on
top of permafrost)

Figure 3.6 in Campbell Biology, 10th ed.

Draw it out:
• The progression from ice to water to gas
and the corresponding gain or loss of
energy

• How does this relate to hydrogen bonds,

specific heat, and kinetic energy?

By SiliconProphet - Own work, CC BY-SA 4.0,

https://commons.wikimedia.org/w/index.ph
p?curid=104984286
 Animal cell

Figure 6.8
 Plant cell

Figure 6.8
 Surface area to volume

Is there an upper limit

to cell size?

Is there an upper limit

to body size?

Figure 6.7
 Plasma membrane

A selective membrane that

allows the passage of
enough oxygen, nutrients,
and waste to service the
entire cell

Figure 6.6
 The Endosymbiont theory
• Mitochondria and chloroplasts
have similarities with bacteria:
• Enveloped by a double membrane
• Contain free ribosomes and
circular DNA molecules
• Grow and reproduce somewhat
independently
in cells
• These similarities led to the
endosymbiont theory

Figure 6.16
Chloroplasts: Capture light energy via
chlorophyll pigment

Mitochondria:
Chemical energy conversion, synthesize ATP

Figure 6.17 and 6.18

Cell Junctions
• Plant
• Plasmodesmata—channels that connect cells cytoplasm; similar to gap
junctions
• Animal
• Gap junctions—cytoplasmic channels between adjacent cells; allow for
communication
• Desmosomes—rivets made of intermediate filaments that hold cells in strong
sheets
• Tight junctions—Plasma membrane of neighboring cells pushed tightly
together and held by specific proteins; prevent leakage
 Plants: plasmodesmata

Figure 6.29
 Animals:

bind cells to form leak-proof

sheets

rivet cells into strong tissue

allow ions and small molecules

to flow from cell to cell

Figure 6.30
Questions:
• Do animal cells have chloroplasts? Do plant cells have mitochondria?
• What is the major functional difference between mitochondria and
chloroplasts?
• Why do biologists believe that both of these organelles have "double
membranes"?
• Does the cell wall take the place of the cell membrane in plant cells?
Figure 7.1
 Fluid mosaic model
In the fluid mosaic model, the membrane is a mosaic of protein
molecules bobbing in a fluid bilayer of phospholipids
Proteins are not randomly distributed in the membrane

Figure 7.4
 Fluid mosaic model
• Does the role of cholesterol
make sense?

Figure 7.5
Selective permeability
A membrane’s selective permeability:
• It allows some substances to cross more easily than others
• Regulating transport across cellular boundaries is essential
• Form fits function
• Fluid mosaic model helps explain how membranes regulate
substances
 Passive vs active transport
• Diffusion is the tendency for molecules to spread out evenly into the
available space
• Although each molecule moves randomly, diffusion of a population of
molecules may be directional
• At dynamic equilibrium, as many molecules cross the membrane in
one direction as in the other

Figure 7.11
Passive vs active transport
• Substances diffuse down their concentration gradient, the region
along which the density of a chemical substance increases or
decreases
• No work must be done to move substances down the concentration
gradient
• The diffusion of a substance across a biological membrane is passive
transport because no energy is expended by the cell to make it
happen
Doesn’t mean no energy involved, but no ATP
used
(conc. gradient = potential energy
ions diffusing = kinetic energy)
 Energy gradients
• Membrane potential, concentration gradients, electrochemical
gradient

Figure 7.18
 Na-K pump
maintains
concentration
gradients and
membrane
potential

Figure 7.16
 Cotransport and membrane potential
Explain how this makes sense
for the cell

Figure 7.19
 Osmosis
What is going on in this
figure?

Figure 7.12
 Osmosis

Figure 7.13
 Types of transport
What about osmosis?

Figure 7.17
Wrap up:
• Thank you!
• Submit the quiz before class Friday (cut-off on Monday at 10am, just
like Dr. Davis’s assignments)
• The activities from this lecture are due by the 27th)
• For Monday, read Chapter 10