- Radiometric dating – technique used to

LESSON 2 – Biomolecules date materials such as rocks, fossils, etc.

Chemistry: A Brief Review Energy

- Organisms are composed of matter, which is
made up of elements
- Element – a substance that cannot be
broken down to other substances by chemical
reactions.
Example: Hydrogen, Oxygen
- Compound – a substance consisting of
two or more elements in a fixed ratio
Example: H2O
– capacity to cause change(Work/Heat)
- Potential energy – the energy that matter has
because of its location or structure
-The electrons of an atom differ in their amounts of
potential energy depending on its energy level.
- Energy Level - an electron’s state of
potential energy is called its energy level or electron
shell

- Of the ~92 natural elements, about 20– 25%
required for life (essential elements)
- Carbon, Hydrogen, Oxygen, and Nitrogen make
up 96% of living matter
- Most of the remaining 4% consists of calcium,
phosphorus, potassium, and sulfur
- Trace elements are required by an organism in
only minute quantities
- Valence electrons - are those in the outermost
shell, or valence shell
• Octet rule – to become stable, atoms
combine to fill the outer valence shell.
• Elements with a full valence shell are
chemically inert (Nobel gases- He, Ne, Ar, Kr, Xe,
Rn)

Atoms
- smallest constituent of ordinary matter
• Proton – a positively charged (+1)
subatomic particle found in the nucleus.
• Electron – a negatively charged (-1)
subatomic particle that orbit the nucleus.
• Neutron – another subatomic particle
found in the nucleus. Has no charge
Note: Neutron mass and proton mass are almost
identical and are measured in Dalton • An orbital is the three-dimensional space
where an electron is found 90% of the time
- Atoms of the various elements differ in • Each electron shell consists of a specific
number of subatomic particles number of orbitals
- Atomic number - number of protons in its
nucleus
- Atomic Charge – number of electrons
- Mass number - sum of protons + neutrons
in the nucleus
- Atomic mass - atom’s total mass, can be
approximated by the mass number

- Isotopes – two atoms of an element

that differ in number of neutrons; two isotopes have
varying atomic mass.
- Radioactive isotopes decay Electronegativity
spontaneously, giving off particles and energy – the tendency of an atom to attract electrons in a
- Half-life – the time required for a quantity bonding pair.
to reduce to half of its initial value. Half- life varies
depending on the isotope
 • The atom that has a higher
electronegativity will attract the e-, making it closer
to them.
- Electrons are not shared evenly
Note: The most electronegative element is
Fluorine.
Types of Bonding
1. Ionic Bond
- This bonding requires the transfer one electron to
the other. Thus, one atom
gains an e- while the other loses it.
- Involves two atoms of opposing charges, a
positive (cation) and a negative (anion) atom.
- Usually involves a metallic and a nonmetallic
atoms.
• Compounds formed by ionic bonds are called
ionic compounds, or salts
Example: NaCl
2. Covalent Bond
- A bond that shares, rather than donates,
an electron to its pair.
• Nonpolar covalent bond – the atoms
share the electron equally
• Polar covalent bond – one atom is more
electronegative, and the atoms do not share the
electron equally
- Due to a slight positivity or negativity of either
atom, the bond will produce a dipole moment
3. Hydrogen Bond
- is a relatively weak bond
- A bond that greatly relies on the element
Hydrogen [H+] for bonding.
- Due to its highly positive nature, H+ can bind to a
highly electronegative atom in a different molecule
(such as O, F, N)
4. Van der Waals
- If electrons are not evenly distributed, they may
accumulate by chance in one part of a molecule
- Individually weak interactions and occur when
atoms or molecules very close to each other
Molecular Shape
• A molecule’s size and shape are key to its function
Example: Morphine binding to natural
Endorphin receptors
• A molecule’s shape is determined by the positions
of its atoms’orbital
Chemical Reactions
- making and breaking of chemical bonds
- The starting molecules of a chemical reaction are
called reactants
- The final molecules of a chemical reaction are
called products
Properties of Water
Water
- transparent, odorless, tasteless, and nearly
colorless substance that covers around 71% of the
Earth’s surface.
- Only 0.3% are available for consumption
- Consists of 2 Hydrogen and 1 Oxygen
atoms
- This substance is crucial to the development
and sustainment of life.
1. Water has a high surface tension
Surface tension – elastic tendency of the
surface of liquids which makes it acquire the least
possible surface area
- Due to the hydrogen bonds created by water;
Two types:
Cohesion – attraction of liquid molecules,
particularly water, to attract each other.
Adhesion – attraction of liquid molecules to
other substances aside from its own.
2. Water has a high temperature range
- Water remains liquid at (0-100oC); it freezes at
0C and boils at 100C
- Due to its hydrogen bond, it requires high energy
to break apart, allowing it to stay liquid, allowing
life to prosper.
 • Play an important role in the formation of the
3. Water has a High Specific heat macromolecules
Specific heat – amount of energy required
to change the temperature of a substance
(compare to heat capacity C)
- Water takes or loses massive amount of energy
before it warms up or cools down, respectively

4. The Density of Water

- Unlike all the other liquids, solid water, (ice) is
less dense than liquid water.
- The lowest density of water is at 4.0C.
- The water freezes from top to bottom, allowing
life to continue below.

Macromolecules
- A very large molecule created by the
polymerization of smaller subunits (monomers).
These are extremely important in the maintenance
of life.
- Monomers can be chemically connected through
dehydration reaction or disassembled through
5. Neutral pH
• Water is neither acidic or basics. In its
purest form, it is neutral; 7
• When substances are introduced, that is when
water can change its pH hydrolysis.
Macromol Monomer Polymer Linkage
• Acids – substances that gives up hydrogen ecule
ions. Has a pH of below 7.0 Carbohydr Monosacch Polysaccha Glycosidic
• Bases – substances that gives hydroxyl ate aride ride bond/linkag
ions. Has a pH of above 7.0 e
pH = - log10([H+]) or log10(1/[H+]) Lipid Fatty acids Not a Ester bonds
and polymer
pOH = - log10([OH-]) or log10(1/[OH-]) glycerols
Protein Amino Polypeptid Peptide
6. It has a high polarity acids e bonds
- Its polarity is due to the oxygen and the two Nucleic Nucleotides Polynucleo Phosphodie
hydrogen atoms in its molecule. Acid tide ster bonds
- Because of this, water can dissolve a high number
of substances. 1. Carbohydrates (C H O)
• Thus, it is called the Universal Solvent • polyhydroxy aldehyde or polyhydroxy ketones or
Rule of thumb: like dissolves like – a polar complex substances which on hydrolysis yield
molecule dissolves a polar molecule while a polyhydroxy aldehyde or polyhydroxy ketone
nonpolar molecule dissolves a nonpolarmolecule o aldehyde(-CHO)
o ketone(-CO-)
Macromolecules: The functional groups - contains C, H, and O, which usually has a formula
• The most important list you need to know in of - Cm(H2O)m
Biochemistry - hence, Hydrated carbon compounds
• A specific group of atoms that have a very
- Carbon atoms are linked to the hydrogen atom and
particular set of characteristics and behavior,
-
regardless of the atoms present a hydroxyl (OH ) group.
- Deoxygenated sugars:
 • Example: Deoxyribose (C H O ) • Carboxyl head(-COOH)
5 10 4
• Hydrocarbon tail
(compare to ribose C5H10O5)
-However, all lipids are hydrophobic due to the
hydrophobic tail being relatively longer than the
A. Types of Carbohydrates
head.
1. Monosaccharides
- The simplest sugars
A. Types of Lipids
- monomer (subunit) for carbohydrates
1. Saturated fatty acids
- Most common types are pentose (5-carbon) and
- These are fatty acids that doesn’t have any
hexose (6-carbon)
double or triple bonds in its fatty acids
- Other Examples: Triose and Tetrose
- solidifies at room temperature
- Examples: Glucose
Galactose
2. Unsaturated fatty acids
Fructose
- These are fatty acids that have double and or
triple bonded carbons
2. Disaccharides
-liquid at room temperature
- two monosaccharides.
- Examples
• Sucrose – Glucose + Fructose
3. Trans-fatty acids
• Lactose – Galactose + Glucose
- are a form of unsaturated fat.
• Maltose – Glucose + Glucose
- formed when a unsaturated fat( normally liquid at
room temp) is hydrogenated
3. Oligosaccharides
Hydrogenation - is a chemical reaction that
- These are carbohydrates that are made-up of three
adds hydrogen to a molecule.
to ten monosaccharides.
- this process removes double/triple bonds. Note:
- Used in many biological processes.
When Double/Triple bonds are removed, this
- Can bound to proteins as Glycoprotein or Lipids
increases the melting point of a fat. Thus, trans fats
as Glycolipids
are unsaturated fats that are solid at room
-Functions for Cell Recognition and Cell Adhesion
temperature.
4. Polysaccharides
- These are long polymers of monosaccharides that
are linked together.
- The nature of polysaccharides are not only
dependent to its composition, but also the way they
are bounded.
- Example: Starch and Cellulose
Glycogen
Chitin
B. Type of Molecular Bond
- Glycosidic bond/linkage – a type of covalent
bond that links carbohydrates from each other
- Dehydration or condensation- linking of the - Cis-trans isomerism
monosaccharides involves the removal of the OH - Happens when a pair of molecules, having the
group of monosaccharide and a hydrogen atom same formula, have different orientation.
from the other (reaction. - Happens when a carbon creates a double-bond to
2. Lipids (C H O)_ another carbon
- Naturally occurring compounds that include fats, - Cis – Same Side
waxes, sterols, fat-soluble vitamins(Vitamins A, - Trans – Opposite side
D, E, K), etc. -Triglycerides
- Monomer: Fatty acids - Free fatty acids are relatively rare, they are
- Has a polar head and a nonpolar tail normally esterified to glycerols
- When bounded to each other, the molecule is
called Triglycerides or triacylglycerides (TAG).
Lipids: Phospholipids
- These are one of the most important lipids in a cell
because they are the major components of the cell
membrane.
• Amphiphilic – a molecule that possesses
both hydrophobic and hydrophilic properties
• Hydrophilic head – due to a phosphate
group
• Two Hydrophobic tail – fatty acids
Phospholipid Aggregation: How are
phospholipid bilayers formed?
Phospholipids
- are the basic components of all present-day
biological membranes, including the plasma
membranes of both prokaryotic and eukaryotic
cells.
- the key characteristic of the phospholipids that
form membranes is that they are amphipathic
molecules, meaning that one portion of the
molecule is soluble in water and another portion is
not.
- long, water-insoluble (hydrophobic) hydrocarbon
chains joined to water-soluble (hydrophilic) head
groups that contain phosphate.
- When placed in water, phospholipids
spontaneously aggregate into a bilayer with their
phosphate-containing head groups on the outside in
contact with water and their hydrocarbon tails in the
interior in contact with each other.
-Such a phospholipid bilayer forms a stable barrier
between two aqueous compartments—for example,
separating the interior of the cell from its external
environment.
Micelle – lipid molecules that arranges itself in a
aqueous solution
Phospholipid bilayer • Cell membrane
Lipids: Waxes
- Complex and varying mixtures of lipids with long
fatty acid tails. These are used as a water repellant,
prevent water loss, or as a lubricant.
Lipids: Steroids
- Lipids with a rigid backbone of four carbon
rings with no fatty acid tails. The functional group
that is attached to the steroid defines if.
- Example: Testosterone and Progesterone
3. Proteins (C, H, O, N for amine group)
- The most diverse macromolecule
- Responsible for numerous bodily or biological
functions
- Proteins are made-up of amino acids, its
monomer.
A. Proteins: Monomer
Amino acids – an organic compound with
an amine group(-NH2) and a carboxyl (-COOH)
group. Variations of amino acids are determined by
its R side chain.
- Naturally, proteins have 20 distinct amino acids.
Each amino acids have different functionality
B. Proteins: Bonding
- Amino acids are linked together by a peptide
bond
Peptide bond – a bond that is formed
between carboxyl group of one molecule (amino
acid) and an amino group of another.
- Continuous bonding will create a polypeptide
 Polypeptide - A linear polymer consisting - Bonding: side chain interactions/intramolecular
of numerous amino acids forces
- Proteins normally consists of a hundred to • Hydrogen bond
thousands of amino acids that are commonly linked • Polarity (hydrophobic interaction)
via peptide bonding • Disulfide bridges
• N terminus – start, NH2 group side • Ionic bond
• C terminus – end, COOH side • VanderWaals

-Protein misfolding at this stage render the protein

useless and sometimes, misfolded proteins cause
diseases
Prion- misfolded protein that causes
C. Proteins: Structure diseases
- The function of the protein is highly Proteopathy – diseases that are caused by
dependent to its structure. misfolded proteins
- The structure of the proteins is -Examples:
determined by the amino acids • Alzheimer’s disease – amyloid β and Tau
• Type 2 Diabetes mellitus – islet amyloid
Four Structural Hierarchy of Proteins polypeptide
1. Primary Amyloid- a protein that is deposited in the
2. Secondary liver, kidneys, spleen, or other tissues in certain
3. Tertiary diseases.
4. Quaternary
4. Quaternary Structure
1. Primary structure - Three dimensional structure of two or more
- Solely refers to the sequence of the amino acids polypeptide chains that operates as a single
in the polypeptide chain functional unit
- Bonding: Peptide bonds
Four Structural Hierarchy of Proteins
2. Secondary structure Protein Structure Linkage
- Highly regular local substructures Primary Peptide bonds
- Bonding: Hydrogen bonds Secondary Hydrogen bonds
- Has two types: Tertiary Side chain
• α- Helix - Repeating helical structures that are interactions
stabilized by hydrogen bonds • Hydrogen bond
• β- Pleated sheets - Sheets of polypeptide that lie • Polarity
in parallel to each other (hydrophobic
interaction)
• Disulfide bridges
• Ionic bond
• Vander Waals

Quaternary Van der Waals

between nonpolar
side chains

3. Tertiary Structure
- These are polypeptides that folds and refolds itself
to assume a three dimensional.
D. Proteins: Enzymes
- REVIEW: Chemical reactions can take years to
perform. To increase the rate, there are three general
ways:
1. Increasing the temperature and pressure
2. Increasing the concentration of the - Always follow a 5’ to 3’ configuration
substances
3. Introduce a catalyst

- Enzymes serves as a Biological

catalysts.
- Like all catalyst, enzymes increase the rate of
reaction by lowering the activation energy

Activation energy – minimum energy required to

start the chemical reaction
- Enzymes are highly specific
- Most enzymes only work on a single set of Numbers 1-5 indicates Carbon no.
reactants (substrate)
- Known as the lock-and-key model Difference between Purines and Pyrimidines
- Every reactant/s will go to the active site to react

4. Nucleic acid (C, H, O, N for nitrogenous base,

P for Phosphate group)
- Account for only 2% of the weight of animals
- Responsible for the storage, expression, and
transmission of genetic information
- Two classes:
• Deoxyribonucleic acid – DNA
- Stores genetic information
• Ribonucleic acid – RNA
- Decoding genetic information into
functional proteins
- are linear polymers of nucleotides that are bonded
through the phosphate group and the 3rd carbon
sugar.
- Linkage via Phosphodiester bond
• Purine bases
– double fused rings of carbon and nitrogen.
- Examples: Adenine and Guanine
• Pyrimidine bases – single ring of carbon and
nitrogen.
- Examples: Cytosine and Thymine
Note:
- Purines are thicker than pyrimidines and this
determines how a DNA arranges itself by following
the “Guanine to Cytosine, Adenine to Thymine”
structure.
- A purine must be bonded to a pyrimidine such as a
pyrimidine is bonded to a purine. Otherwise, the
DNA may become too thick or too thin
- Two purines bonding together would take up too
much space between the two DNA strands, which
would affect the structure and not allow the strands
to be held together properly.

A. Nucleic acid: monomer

Nucleotide - the nucleic acid monomer
- Has three components:
• Phosphate group(-PO4)
• Ribose (C5H10O5)
• A single or double ring of carbon and
nitrogen atoms known as the nitrogenous base

B. Nucleic acid: Deoxyribonucleic acid

- Contains the blueprint of life
- two strands of DNA are connected antiparallel Central Dogma of Molecular Biology
- Consist of two strands coiled around each other to - The overall process of expressing the information
form a double helix stored in the DNA into functional proteins
- Normally found in the nucleus (eukaryotic cell)
- Held together by the by hydrogen bonds between
a purine base and a pyrimidine base
• Guanine to Cytosine
• Adenine to Thymine
- They are connected antiparallel to
each other:
5’ – ATG ATG CCG GAT TAA – 3’
3’ – TAC TAC GGC CTA ATT – 5’

C. Nucleic acid: Ribonucleic acid

- A single stranded molecule that is essential in
various biological processes, especially at the
expression of genes (DNA)
- Like the DNA, it uses the nucleotide bases, in 5’
to 3’ configuration. However, uracil is used in
place of thymine. Replication
- Instead of thiamine, uracil binds to adenine. - A biological process that produces
• Guanine to Cytosine two identical DNA copies.
• Adenine to Uracil
Transcription
D. Nucleic acid: Ribonucleic acid Three major - The process in which the genetic information from
RNA types: the DNA is transferred to the mRNA

a. mRNA – “messenger” Translation

- Convey genetic info from the - The process in which the genetic information from
nucleus towards the ribosomes the mRNA is translated to amino acid sequence

b. tRNA – “transfer”
- Adaptor molecule that links the mRNA to the
amino acid sequence

c. rRNA – “ribosomal”
- RNA component of the ribosomes