Intro to the Chemistry of Life

Chapter 1
FeS2
 Elements of Life

Biological molecules are constructed from a limited number

of elements.

Essential for all organisms:

Most abundant: C, N, O, H, H, P, S
Less abundant: i.e. Na, Mg, K, Ca, Cl
Trace levels: i.e. Mn, Fe, Co, Cu, Zn

Essential for some organisms:

Trace levels:
i.e. V, Cr, Mo, B, Al, Ga, Sn, Si, As, Se, I
Functional Groups and Linkages
Functional Groups and Linkages

O
Ester R
R O
 Functional Groups and Linkages

Certain functional groups and linkages characterize different

types of biomolecules.

The presence of a specific functional group can help predict

the chemical reactivity, solubility, etc.

Understand the chemical behavior and cellular roles.

Alcohols: R−OH (form hydrogen bonds)

Carbonyls: R=O (increase polarity and reactivity of molecules)
Carboxyls: R−COOH (polar and reactive, release H+ atom)
Amines: R−NH2 (form hydrogen bonds)
Phosphates: R−PO42− (reactive, provides energy to reactions*)
 Forming Complex Molecules

During chemical evolution, simple compounds condensed to

form more complex molecules and polymers.

Complementary Molecules Associate

 Forming Complex Molecules

A polymer serves as a template for the assembly of a

complementary molecule.
 Central Dogma of Molecular Biology

The central dogma of

molecular biology explains
the transfer of sequence
information between
information-carrying
biopolymers
 Cellular Architecture

² Cell compartments:
ª Protection from adverse environment
ª Higher local concentrations of biological molecules promote
efficiency
² Metabolic pathways evolved to synthesize molecules and
generate energy.
² Cell types: Prokaryotes and Eukaryotes.
² Three domains of organisms: bacteria, archaea, and
eukarya.
² Evolution occurs as natural selection acts on randomly
occurring variations among individuals.
 Cellular Architecture
Prokaryotic Cells
²  Simple structures
ª  Unicellular
²  Nucleoid
²  Widespread organisms
ª  Highly adaptable metabolisms
²  Cytoplasm packed with micromolecules
ª  Various metabolic functions are carried out
in various regions
²  Basic shapes
ª  Rod-like, spheroidal, or helically coiled
Eukaryotic Cells Relative Prokaryotic Cell Size

²  Complex structures

ª  Uni- and multicellular
²  Membrane-enclosed nucleus
10−100 µm in diameter
ª  Encapsulates DNA
²  Membrane-enclosed organelles
Viruses lack metabolic apparatus to reproduce outside cell host.
 Eukaryotic Cells

1−10 µm ² Inner and outer membrane

² Flagellum, pili
² Various proteins
² Ribosome
Cross-section of E. coli

² DNA
² DNA-binding proteins
² Water
² Small molecules

~1,000,000 ×
Organisms diverse primary because of different monomeric content of the biopolymers
 Prokaryotic Cells

Characterized by numerous membrane-enclosed organelles:

Ribosome site of protein synthesis.
Endoplasmic reticulum synthesis site of many cellular components.
Golgi apparatus modifies some cellular components.
Mitochondria site of aerobic metabolism.

Diagram of a typical Animal Cell

Cell diameter
10-100 µm
 Three domains of organisms
Bacteria Archaea

Eukarya

Based on RNA analysis pioneered by Carl Woese in 1977

Polygenetic relationships are best deduced by comparing

polymeric molecules (RNA, DNA, or protein) from different
organisms.
 Thermodynamics

² Thermo (heat) dynamic (power)

ª Describing and quantifying a particular process, and it can also
help predict spontaneous versus nonspontaneous process.
² Two laws of thermodynamics:
ª First Law: Energy is conserved
ª Second Law: Entropy tends to increase
² A living organism is an open system.
ª It exchanges both matter and energy with its surrounding.
ª It take up chemical fuel, i.e. glucose, and extract energy by
oxidizing it, or it can absorb energy from sunlight.
² Life obeys the laws of thermodynamics
 Energy is Conserved

² The first law of thermodynamics states that energy is

conserved. It can neither be created nor destroyed.
ª Energy (U) is used to do work.
² The energy change (ΔU) of a system is defined by:
ΔU = Ufinal − Uinitial = q − w
Heat Work done by
absorbed by the the system on its
system from its surroundings
surrounding

² Energy takes different forms: Electrical, mechanical,

chemical
 Energy is Conserved

² Most biological processes take place at a

constant pressure, 1 atm. w = PΔV
Energy change of
a system.
² Enthalpy (H): Work done by the
ΔH = ΔU + PΔV system on its
surroundings
ΔH = (q − w) + PΔV Heat absorbed by
ΔH = qat constant pressure the system from its
surrounding

² Change in enthalpy is equivalent to heat.

² In most biomolecules PΔV≈ 0
² Energy change is equal to enthalpy change in biomolecules
(given in units of joules, J).
 Entropy Tends To Increase

•  According to the second law of thermodynamics,

spontaneous processes are characterized by the
conversion of order to disorder
•  Degree of randomness: entropy (S)
S = kB ln(W)
Boltzmann # of energetically ideal gas molecules
constant equivalent ways to
1.3806 ×10−23 JŸK−1 arrange components
within a system

•  Unit of joules (JŸK−1)

Molecules become more random,
•  Experimentally, ΔS ≥ q⁄T and evenly distrusted.
–  Measure heat
 Determining Reaction Spontaneity

Spontaneous process occur without the input of additional

energy from outside the system.
spontaneous? ordered?
Entropy decreases

In 1878, J. Willard Gibbs, true criterion for spontaneity

ΔS ≥ q⁄T = ΔH⁄T re-arrange ΔH − TΔS ≤ 0

Gibbs free energy, G = H −TS

ΔG = ΔH −TΔS <0 spontaneous
 Determining Reaction Spontaneity

Consider a reaction with ΔH = 15kJ and ΔS = 50 JŸK−1.

Is the reaction spontaneous at 10°C or 80°C?
 Determining Reaction Spontaneity
Given that ΔG = ΔH −TΔS, determine the sign of each of the
following terms (is it + or − ?)

1. For a favorable reaction, and spontaneous,

ΔG ? ΔH ? ΔS ?

2. The reaction is spontaneous only when T < ΔH⁄ΔS

ΔG ? ΔH ? ΔS ?

3. The reaction is spontaneous only when T > ΔH⁄ΔS

ΔG ? ΔH ? ΔS ?
 Determining Reaction Spontaneity

2. The reaction is spontaneous only when T < ΔH⁄ΔS

If the temperature is below T= ΔH⁄ΔS

•  ΔS must be large
•  Hence, −TΔS is much larger than ΔH
•  ΔG is negative
•  The reaction is exergonic
Gibbs Free energy and reaction spontaneity is summarized in Table 1-4
 ΔG and [Equilibrium]

ΔG = ΔH −TΔS
S varies with T and concentration.
Hence, ΔG of a chemical reaction must depend on both
[reactants (R)] and [products (P)].

G = G°A + RT ln[A]
Partial molar free energy (chemical potential of A)
at standard state, per mole
 ΔG and [Equilibrium]

G = G°A + RT ln[A] G°A = Partial molar free energy per mole,

at STP

[C]c[D]d
aA + bB cC + dD Kd=
[A]a[B]b

ΔG° = aG°A + bG°B + cG°C+ dG°D

ΔG = ΔG°+ RT ln (Kd)
ΔG = ΔG°+ RT ln (Kd)
 ΔG and [Equilibrium]

[C]c[D]d
aA + bB cC + dD Kd=
[A]a[B]b
ΔG = ΔG°+ RT ln (Kd)
The reaction is at equilibrium, ΔG = 0
ΔG° is a constant term for a specific rxn taking place
RT ln(Kd) is a variable term depending on [R] and [P]

[C]ceq [D]deq
ΔG°= − RT ln (Keq) Keq=
[A]aeq [B]beq