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.p
hp?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
independentlyin 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