Origin of life, cellular architecture, thermodynamics

1. What are the chemical and three-dimensional structures of biological molecules?

2. How do biological molecules interact with one another?
3. How does the cell synthesize and degrade biological molecules?
4. How is energy conserved and used by the cell?
5. What are the mechanisms for organizing biological molecules and coordinating their
activities?
6. How is genetic information stored, transmitted, and expressed?

Theory of Vitalism
❖ Suggested by Berzelius
❖ one tenet is molecules made from carbon could only be formed by living organisms
❖ This is where “organic” in organic chemistry comes from
➢ OChem is the chemistry of molecules previously thought to need vitalism for
synthesis
❖ Friedrich Wohler proved correct by showing carbon-based molecules could be
synthesized

Organic Elements in Humans

❖ Oxygen, Carbon, Nitrogen, Sulfur and halides are among those found in living things

and organic in nature

 ➢ O,C,H,N, Ca, and P make up 99% of human body
➢ Alkanes ✅, Alkenes ✅, Aromatics ✅, Alkynes ❌

Formation of Life
❖ 4.6 bya – earth formed: H2O, CH4, NH3, and H2, light organic compounds build up
everything
❖ 3.5 bya - cellular life formed: complex structures from starting organic materials
➢ Living organisms form these complex structures out of polymeric materials
known as biological macromolecules
➢ Biological macromolecules are polymeric in nature, formed from small
monomers
 ➢
❖ Polymerization Reactions
➢ Monomers react with each other to form covalent compounds such as
■ Oligomers smaller repeating monomer units
■ Larger polymers
➢ Biopolymers usually form via condensation reaction
■ Water is lost to form a covalent bond
■ Reverse is hydrolysis (breaking with water)
➢
❖ Amide Bond Formation
➢ Proteins are category of Biopolymer
➢ Amino acids condense to form polypeptides via amide bond creation (also known
as the peptide bond)

■
➢ reaction with water breaks it up, creating both the original carboxylic acid and
amine functional groups

Intermolecular Interactions
❖ Biological Macromolecules with themselves/each other, weak nonbonding, central to
macromolecular function
➢ hydrophobic/philic
➢ Electrostatic interactions
➢ Hydrogen bonding
■ Protein-substrate recognition
■ Protein superstructure formation
■ Biological molecule replication
● Nucleic acids
● Prions

●
❖ Molecular Reproduction
➢ In this simple case, a polymer serves as a template for the assembly of a
complementary molecule, which, because of intramolecular complementarity, is
an exact copy of the original.

➢
 Cell Architecture
❖ Cell evolved when membrane-filled vesicles (fluid-filled sacs) formed in the pre-biotic
environment
❖ Prokaryotes: Lack a nucleus that contains genetic information
➢ Eubacteria
➢ Archaea
➢ Bacteria and Archea
■ Typically no membranes/vesicles in cell contents
■ Highly adaptable and numerous
■ Unusual chemistry, esp archae
● Methanogens
● Thermophiles
● Halobacteria
❖ Eukaryotes: Possess a nuclear vesicle, or organelle. Highly specialized and complex. Also
frequently contain endosymbiotic organelles like mitochondria or chloroplasts

➢
❖
■

Thermodynamics and Life

❖ Energy is essential for life
❖ Thermodynamics describes energy
❖ All living organisms are strictly governed by the laws (theories) of thermodynamics.
➢ 1. Energy is conserved, or the change in energy in a system is the sum of the
change in work (done by the system on the surroundings) plus the change in heat
■ ∆𝑈 = Ufin - Uinit = q - w = q - PV
➢ 2. Entropy in the universe is always increasing, everything fights it
■ Ssys + Ssurr = Suniverse > 0
➢ 3. For a pure, crystalline substance, entropy approaches zero
■ S = k logW
❖ Spontaneous vs Nonspontaneous

➢
➢
➢ Spontaneous is reactions without the outside addition of energy (usually
exothermic)
➢ Nonspontaneous occurs without the addition of outside energy (usually
endothermic)
■ Spontaneity & how it is affected by temp. is calculated by Gibbs
■ Δ G = Δ H - T ΔS
● The negative sign in front of the entropy accounts of opposite
spontaneity reaction

■
● Δ H enthalpy (heat)
◆ Energy found in chemical bonds (intra/intermolecular)
◆ Chemical reactions can release heat (exothermic) or take it
up (endothermic)
➢ In exothermic -ΔH (usually spont.), heat moves
from sys → surroundings
➢ In endothermic +ΔH (usually nonspont.), heat
moves from surroundings → sys
● ΔS entropy (disorder)
◆ # of possible physical states
 ◆ Disordered outcomes are more likely, so increases in
entropy are favored
◆ Systems will spontaneously increase entropy without
work
◆ - ΔS nonspontaneous, + ΔS spontaneous
◆ Also increases with temperature (third law)
❖ Equilibrium Constant
➢ When forward/reverse rate is same ratio of concentration products over reactants
is the same Kc

➢
➢ Equilibrium constants and Gibbs free energy
■ ∆𝐺° = −𝑅𝑇 log𝐾
■ e ^ - ∆𝐺°/RT
● Non equilibrium
● ∆𝐺 = ∆𝐺° + 𝑅𝑇 log Q
➢
❖ Finish gibbs spontaneity thermodynamics notes
❖ Make quizlet using review questions
❖ When forward/reverse rate is same ratio of concentration products over reactants is the
same Kc
❖ Convert kilojoules to joules
❖ Name / structure match organic chart

Water and life

● Water and VSEPR theory
● Van der walls interactions
WATER’S STRUCTURE
❖ Polar
❖ Can form hydrogen bonds with other molecules
❖