GENERAL BIOLOGY I & II

. LESSON 1: CHEMISTRY OF BIOLOGY .

BIOLOGY . 3. Energy and Matter
➢The scientific study of life that have 5 unifying ➔ Life requires the transfer and
themes: organization, information, energy transformation of energy and matter
and matter, interactions, and evolution ➔ Energy comes from the sun, making life
================================================ possible.
CHARACTERISTICS OF LIFE ➔ Energy flows one-way [ light to heat ], but
● Order chemical is cycled
● Homeostasis 4. Interactions
● Adaptation ➔ From molecules to ecosystems,
● Metabolism interactions are important in biosystems.
● Reproduction ➔ The environment affects the organism, and
● Response to Stimuli the organisms affect the environment.
● Growth and Development ● Feedback Regulation - the output or
================================================ product of a process regulates that very
Themes in Studying Biology . process.
○ Positive Feedback Loop - rarely happens,
1. Organization
the end product speeds up its own
➔ Life operates in biological organization.
production.
➔ This reveals the principle of reductionism. ○ Negative Feedback Loop - a loop in which
➔ As the complexity of life increases, the response reduces the initial stimulus.
emergent properties arise due to the 5. Evolution
interaction of different parts. ➔ The proposed core theme of biology.
◆ Systems biology is a field of life science that studies ● Evolution - a process of biological change
the interaction of biological systems in which species accumulate differences
➔ This complexity arises due to a series of from their ancestors as they adapt to
natural selection. different environments over time.
Level of Biological Organization: ➔ Evolution accounts for the unity (shared
Atom > Molecule > Macromolecule > Organelle > traits) and diversity (differences) of life.
Cell > Tissue > Organ > Organ System > Organism > ★ According to Theodosius Dobzhansky, a
Population > Community > Ecosystem > Biosphere
founder of modern evolutionary biology,
★ According to Cell Theory, developed in the “Nothing in biology makes sense except in the
1800s, the cell is the basic unit of life. light of evolution.”
○ Prokaryotic Cells lack membrane-bound
★ According to Charles Darwin, in his book On
organelle and nucleus
the Origin of Species by Means of Natural
○ Eukaryotic Cells have those qualities
Selection:
2. Information 1. Evolution is Descent with
➔ Life’s processes involve the expression Modification: Species accumulate
and transmission of genetic information. differences from ancestors
➔ Chromosomes are structures containing 2. Natural Selection causes Evolution:
genetic material in the form of DNA individuals with inherited traits that are
➔ A particular section of the DNA is called a better adapted are more likely to
gene that are the basic unit of inheritance survive and reproduce than less
➔ They encode the necessary information to adapted individuals.
build whatever the organism needs, and ★ Descent with modification implies that
they inherit characteristics from their common traits descend from one generation to
parents. the next, inheriting those characteristics.
➔ The sequences of genes serve as a ★ Fossils and other evidence corroborate
blueprint for making a protein. anatomical unity in supporting this view of
➔ The sequence of genes in one organism descent from a common ancestor.
essentially results in the same thing in
On the right is a
another.
phylogenetic tree that
● Genomics - a branch of biology that highlights the evolutionary
applies systems biology approach — it is relationships. A
the large-scale analysis of DNA sequence. phylogenetic tree is
○ Genome - the entire library of genetic composed of nodes and
instructions that an organism inherits. branches. The internal
○ Genome Sequence - the entire sequence nodes represent ancestors
of nucleotides for a representative member and are points in evolution
of a species when, based on scientific
● Proteomics - studies organism’s sets of evidence, an ancestor is
proteins and their properties thought to have diverged
○ Proteome - the entire library of proteins to form two new species.
that an organism expresses.
 GENERAL BIOLOGY I & II
WATER .
➢ Has many emergent properties
➢ Composed of 2 molecules of Hydrogen and 1
molecule of Oxygen
➢ Bent tetrahedral shape, shaped like V
➢ O is more electronegative than H, thus
attracting more electrons than H.
➢ A partial positive (𝝳+) charge forms in the
regions of hydrogen, partial negative (𝝳-)
charge in the regions of oxygen.
➢ Hydrogen bonds cause their interactions— the
reason for these emergent properties.
Properties of Water Contributing to Life Suitability .
1. Cohesion of Water Molecules
➔ Cohesion : Due to
hydrogen bonding, water
molecules are attracted to
each other.
➔ Surface Tension : Due to
cohesion, this results and the surface of the
liquid becomes hard to break or stretch.
★ The spider takes advantage of surface tension
to walk above water.
➔ It also contributes to the transport of
nutrients against gravity — capillary action
➔ Adhesion : water can hydrogen bond
extrinsically with other molecules. This
helps to transport nutrients in the body.
2. Thermoregulation Properties
● Kinetic Energy - energy acquired from
any movement of an object.
○ Thermal Energy - sum of kinetic energies
due to random atomic motions.
○ Temperature - average kinetic energies
due to random atomic motions.
● Heat - transfer of thermal energy in order
to reach equilibrium (m: calorie = 4.184 J).
➔ Specific heat is defined as the energy
required to raise the temperature of 1g of a
𝑐𝑎𝑙
substance by 1°C, in the case of water, 1 𝑔 · °𝐶
◆ It can be thought as how well a substance resists
temperature changes
➔ Water has relatively high specific heat.
➔ This allows the thermoregulation and
stabilization of environmental conditions
for marine life. Also, this is responsible for
sea and land breeze phenomena.
➔ At any temperature, some of the atoms in
liquids evaporate. Eventually, they will
vaporize completely.
● Heat of Vaporization - energy required to
convert 1g of a liquid into gas.
➔ By the same token, water has a relatively
high heat of vaporization, manifested thru:
a. Climate Moderation: high heat is
needed to evaporate surface water,
released, then condensed.
b. Steam Burns: steam can cause burns
when heat energy is released to the
skin when it condenses.
c. Evaporative Cooling: likewise, as heat
evaporates, it absorbs heat, leaving a
cold air and cools the environment.
3. Floating of Ice on Liquid
➔ Water is densest at 4°C, less dense as a
solid than a liquid.
➔ Due to hydrogen bonding, water expands
when cooled rather than heated.
➔ At 0°C, the molecules form crystalline
lattice structure, each water molecule
hydrogen bonded to four partners.
➔ Only a few inches are thawed, insulating
the water below and providing habitat for
both fishes, polar bears, etc.
➔ If this weren’t the case, all bodies of water
would eventually freeze.
4. Water: The Universal Solvent
➔ Because of water’s
polarity, water is a versatile
solvent.
➔ Oxygens are attracted
to the cation, while
hydrogens are attracted to
the anion.
➔ Water forms a shield
around the ions called
hydration shell, causing it
to be dissolved.
➔ If this weren’t the case, all bodies of water
would eventually freeze.
★ A material doesn’t need to be water-soluble to
be hydrophilic. It also has to do with atom size.
2 H2O ⇌ H3O + OH
★ The reaction shows the dissociation of Water
into hydronium and hydroxide.
★ It is in dynamic equilibrium and it is reversible.
★ In life, the concentrations of OH and H ions are
extremely important — changes can drastically
affect the conditions of chemistry.
● Acids - increase concentrations of H+ ions.
They have pH of <7
● Bases - reduces concentrations of H+ ions.
They have pH of >7
★ Once the concentrations of OH and H are equal
in a solution, they are said to be neutral.
★ Weak acids are acids that reversibly release
and accept back hydrogen ions, like:
2 H2CO3 ⇌ HCO3 + H
 GENERAL BIOLOGY I & II
The pH Scale .
➔ In any aqueous solution at
25°C, the product of the H+
and OH- concentrations is
constant at 10-14.

+ − −14
[𝐻 ][𝑂𝐻 ] = 10

➔ Particularly,
+ − −7
[𝐻 ], [𝑂𝐻 ] = 10 for neutral
solutions.

➔ If enough acid is added to a

solution to increase [H+] to 10-5 M, then the [OH-]
declines by 10-9 M.
➔ Similarly, if enough baseis added to a solution to
increase [OH-] to 10-4 M, then the [OH-] declines by
10-10 M.

+
𝑝𝐻 = − 𝑙𝑜𝑔[𝐻 ]

Buffers .
❖ The internal pH of most cells are close to 7
(blood pH is 7.4, which is slightly basic)
❖ If 0.01 mol of a strong acid is added to a liter of
pure water, the pH drops from 7.0 to 2.0.
❖ If the same amount of acid is added to a liter of
blood, however, the pH decrease is only from
7.4 to 7.3 due to existence of BUFFERS.
★ This is of great concern because carbonate ions
are required for calcification, the production of
calcium carbonate (CaCO3) by many marine
organisms, including reef-building corals and
animals that build shells.

BUFFERS .
➢ A substance that minimizes changes in the
concentrations of H+ and OH- in a solution.
➢ It does so by accepting hydrogen ions from
the solution when they are in excess and
donating hydrogen ions to the solution when
they have been depleted.
➢ Most buffer solutions contain:
○ A weak acid — serves as H+ donor
○ A base, — serves as H+ acceptor which
combines reversibly with hydrogen ions

2 H2CO3 (carbonic acid) ⇌ HCO3 (bicarbonate) + H

● Right reaction reduces pH, more acidic, > H+
● Left reaction increases pH, more basic, < H+
★ In the ocean, CO2 dissolves in water, forming
carbonic acid, making the pH more acidic.
★ This is called ocean acidification, fluctuating
the pH of the ocean and causing detrimental
effects to marine life.
 GENERAL BIOLOGY I & II
Characteristics of Carbon .
❖ Has 4 valence electrons Functional Group Properties Structure
❖ Has many allotropes and other forms Group
❖ Highly unreactive under normal conditions Hydroxyl (-OH) ● Polar
❖ Has ability to bond with multiple elements, ● Ampotheric
commonly with Hydrogen, Oxygen, and (can be both act
Nitrogen as acid / base)
● Forms Alcohols
★ The properties of a carbon-containing
molecule depend on the arrangement of its Carbonyl ● Polar
● Acidic
carbon skeleton and on its chemical groups. ● Can form either
Ketone,
Organic Chemistry is the Key to the Origin of Life . Aldehyde
❖ Compounds containing carbon are called
organic compounds (with a few exception) Carboxyl ● Polar
and their study is called organic chemistry. ● Acidic
STANLEY MILLER (1953) . ● Forms
Carboxylic
➔ Grad student under Harold Urey at
Acids
University of Chicago.
➔ Designed an experiment on the abiotic
synthesis of organic compounds — Amino ● Polar
compounds necessary for life’s existence ● Basic
➔ In his results, he ● Forms Amines
identified a variety of or Amides
organic molecules
common to
organisms Sulfhydryl ● Slightly Polar
● Basic
➔ He concluded that ● Forms Thiols
organic molecules are
the first step to the
origin of life, which
may have abiotically
been spontaneously Phosphate ● Ionic, Anion
synthesized in early ● [Strongly] Basic
Earth’s atmosphere ● Forms Organic
Phosphates
➔ Although results
● Releases
are viable, his
energy upon
replication was later reaction with
disproved since he fail water
to account for other (hydrolysis).
factors in the primeval
atmosphere.
➔ The overall
percentages of major
elements of life [ C, H, N , O , P , S] are quite uniform,
reflecting a common evolutionary origin of all life.

HYDROCARBONS .
➢ refers to an organic chemical compound that
is composed exclusively of hydrogen and
carbon.
FUNCTIONAL GROUPS .
➢ are specific groupings of atoms within
molecules that have their own characteristic
properties, regardless of the other atoms
present in a molecule.