Biological Molecule

Most biomolecules can also be called macromolecules, which are polymers

made from single building block called monomers
monomer
pertains to an organic molecule of any class of compounds that can react
with other molecules to form larger molecules or polymers
are repeating units of the same molecules that, when bonded together,
create macromolecules
Polymers (except Lipids) are made up of smaller units of different kinds as
opposed to monomers that repeat themselves.

Built from monomers:

a. Carbohydrates
b. Proteins
c. Nucleic Acids
Lipids are made up of composed of different units, which is why it is not
considered as a monomer.
How these building blocks are formed or broken
down involves two particular processes/chemical reactions:
Dehydration Synthesis/Condensation Reaction
a water molecule is formed as a result of generating a covalent bond
between two monomeric components in a larger polymer
Monosaccharide: 2 molecules of glucose. The hydrogen group of the
other combines with the hydroxyl group of anther sharing electrons to
form covalent bonds.
In this process, water is formed.

Hydrolysis
a water molecule is consumed as a result of breaking the covalent
bond holding together two components of a polymer; the process of
breaking down molecules with the use of water.

Maltose consists of two molecules of glucose, which are linked by an alpha

glycosidic bond. The enzyme maltase efficiently catalyzes the hydrolysis
process of maltose into two glucose molecules.
This process requires a molecule of water and releases stored energy.
 4 classes of organic molecules

carbohydrates
Carbohydrates serve as the primary energy source of the body, mainly in
the form of glucose and can be abundantly found in our diet.

Composed of Carbon (C), Hydrogen (H), & Oxygen (O)

Have a backbone of carbon atoms, with hydrogen and oxygen
attached in the same proportion as they appear in water. Hence the
general formula: CH₂O
This means carbon is hydrated or combined with water.
 There are different kinds of carbohydrates with the simplest one referred
to as monomers. To more complicated monosaccharides primarily for
storage of energy.

Examples:
Glucose - Monosaccharide
Maltose - Disaccharide
 MONOSACCHARIDES
The simplest kind of carbohydrates which has relatively simple structures
consisting of C, H, O, in a 1:2:1 ratio.
Used cellular respiration in order to produce ATP (the molecule of energy)
Carbon skeletons serve as raw material for synthesis of other types of
small organic molecules
Examples: Glucose, Fructose, Galactose, Ribose, Deoxyribose

GLUCOSE
has a mild-sweet flavor
main source of energy of mammalian brain
carbs get digested into glucose and is rapidly absorbed into the body
providing a source of instant energy.
found in every disaccharide and polysaccharide
FRUCTOSE
sweetest sugar
found in fruits and honey
high intake is linked to obesity and diabetes which is mainly because
only liver cells break down fructose (unlike glucose which can be used
by almost every cell in the body)
one of the end products of its breakdown is a triglyceride which is a
form of fat
an isomer of glucose
GALACTOSE
important for early human development
crucial for metabolism and energy delivery in the body
cherry, celery, plums, avocados
 DISACCHARIDES
Two monosaccharides joined by a glycosidic linkage.
Glycosidic linkages can be formed through each hydroxyl of a sugar, and
when multiplied, hydroxyl on a single sugar form glycosidic linkages
resulting in a branch oligosaccharide.
Examples: Sucrose (Gluctose + Fructose), Maltose (Glucose + Glucose),
Lactose (Glucose + Galactose)

MALTOSE
Glucose + Glucose
produced when starch breaks down
not abundant
various models containing syrups are used in the brewing, baking,
softdrink, confectioning, canning, and other forms of food industries.

SUCROSE
Glucose + Fructose (linked in an alpha-glycosidic bond)
aka cane sugar
abundant in the plant world and is commonly known as table sugar

LACTOSE
Glucose + Galactose (also forming a glycosidic linkage)
main carbohydrate in milk
known as milk sugar
Complex Carbohydrates - during dehydration synthesis, thousands of
monosaccharides are joined together into straight or branch chains to
form complex carbohydrates which are known as polysaccharides.
POLYSACCHARIDES
The most important polysaccharide in living organisms consists of long
chains of glucose monosaccharides
Architecture and Function sugar monomers
Energy Storage: Glycogen (Animals) and Starch (Plants)
Structural: Cellulose and Chitin
STARCH
accounts for more than 50%
of our carbohydrate intake
occurs in plants in the form of
granules
polymer of glucose
monomers
joined by 1-4 linkage
within cellular structures
known as plastid
simplest form - amylose
A mixture of two polymers:
Amylose - nonbranched/coiled, easily digestible
Amylopectin - Long and unbranched, not easily digestible
GLYCOGEN
energy reserve carbohydrate in animals
all mammalian cells contain some stored carbohydrates in the form of
glycogen
especially abundant in the liver and skeletal muscles
found as granules in liver and muscle cells
when fasting, animals draw on these glycogen reserves during the
first day without food to obtain the glucose needed to maintain
metabolic balance
CELLULOSE
a fibrous carbohydrate found in all plants
the structural component of plant cell walls
most abundant of all carbohydrates accounting for 50% of all the
carbon found in the vegetable kingdom
CHITIN
second most abundant polysaccharide (next to cellulose)
widely exists in the exoskeleton of shrimps, crabs, and insects
(arthropods), as well as in the cell walls of fungi and algae
Carbohydrates, proteins, and fats are made up of large molecules that
cannot be readily absorbed (or utilized as it is) by the body. This is where the
digestive system is linked as it is involved process of digestion breaks down
large food molecules into smaller food molecules that can be readily
absorbed. Digestion — breakdown and absorption — of food molecules
primarily takes place in the small intestine which is lined with tiny finger-like
projections called villi that possess even larger amounts of microvilli that
constitute the brush border cells. The brush border cells contain the enzymes
that serve as the site of terminal carbohydrate digestion. For example,
sucrose and maltose are readily hydrolyzed by disaccharides.
Digestive System
Carbohydrates, proteins, and fats are made up of large molecules that
cannot be readily absorbed by the body.
Digestion breaks down large food molecules into smaller molecules such
as glucose, amino acids, and fatty acids that can be easily absorbed.

Digestion starts in the mouth

(chewing). Once the food is ready to
be swallowed, it will now pass
through the pharynx, esophagus, and
then go to the stomach. Food will
then go to the small intestine where
digestion and absorption will occur.
How our body absorbs these
molecules?

IN THE SMALL INTESTINE...

The wall of the small intestine is lined with
many tiny finger-like projections called villi.
These are very thin (as little as one cell thick)
and increase the surface area of the small
intestine, both of which increase the speed
of diffusion.
How these molecules are
digested?
CHEMICAL DIGESTION
Lipids: Fats & Oils
LIPIDS
Lipids like carbohydrates are composed of C, H, and O, with the
differences being lipids have a long hydrocarbon chain and has less
oxygen.
A unit of a lipid is composed of glycerol and 3 fatty acids
It can be classified into many groups
Diverse Group: Fats, Phospholipids, and Steroids

FATS
Store twice the amount of
energy compared to
carbohydrates.
They cushion our organs and
insulate our bodies.
There are two types of fat:
Saturated and Unsaturated

SATURATED
composed of a long, straight
chain molecules
are very compact and solid at
room temperature
known to contribute to
cardiovascular diseases
mostly found in animals

UNSATURATED
has bends which results in the
molecules being loose or not
closely packed with each other
liquid at room temperature
found in plants and fish
PHOSPHOLIPIDS
known to have dual characteristics/'personality"
the phosphate (PO4) head is hydrophilic while fatty acid tails are
hydrophobic
Hydrophilic heads on outside - in contact with aqueous solution on the
inside and outside of the cell
Hydrophobic tails on the inside - forms the core
It likes water but also pushes it away! Interaction with H₂O is very
complex and important
 STEROIDS
Common examples are
cholesterol and sex hormones

Important
CHOLESTEROL
cell component of animal cell membranes as it helps the cell
membrane be fluid and flexible
precursor of all other steroids (including vertebrate sex hormones)
high levels in blood may contribute to cardiovascular disease for it may
cause plaque build-up in blood vessels (atherosclerosis)
The total cholesterol of our body is composed of LDL + HDL +
Triglycerides

Low density lipoprotein high density hipoprotein

known as the bad cholesterol known to be the good
because it causes cholesterol to cholesterol for it removes
turn to plaque in our arteries cholesterol from our blood

PROTEINS
Proteins are a diverse group of large and complex polymer molecules,
made up of long chains of amino acids.
They have a wide range of biological roles, including:
Catalytic - all enzymes are proteins, catalyzing biological reactions
Signaling - many hormones and receptors are proteins
Immunological - antibodies are made up of protein so they play in
important role in our immunological response
Structural - proteins are the main component of body tissues such as
muscle, skin, ligaments, and hair
Proteins are made up of amino acids which are monomers
There are 20 amino acids that make up different types of proteins
Proteins can be one or more polypeptide chains folded and bonded
together
Large and complex molecules
Complex 3-D shape
These amino acids form bonds (peptide bonds). These bonds will then
form long chains (polypeptide chain). These chains then fold which result
in formation of complex structures. These structures will then affects the
protein's function.
Examples:
Rubisco - found in plants; enables plants to synthesize glucose
Hemoglobin - found in our blood; aids us in transporting oxygen
Growth hormone
All amino acids have the same general structure; the only difference
between each one is the nature of the R-group. The R-group therefore,
defines the amino acid.
Central Carbon Atom, Hydrogen, Amino Group, Carboxylic Group, R
group
The R-group represents a side chain from the central 'alpha' carbon
atom,
and can be anything from a simple hydrogen atom to a more complex ring
structure
 Classifications: Essential and Non-Essential
ESSENTIAL
one's that body cannot produce which means it we need to get it from
our diet
CONDITIONALLY NON-ESSENTIAL
dependent on the situation of the body
Example:
Arginine is essential to infants, however, infants cannot to produce
arginine, making it essential. Once the infant develops into an
adult, the body can now produce the arginine, making it non-
essential.
NON - ESSENTIAL
the body can produce it on its own
Amino acids can also be grouped according to their chemical structure
They can be...
Non-Polar (Hydrophobic)
Polar (Hydrophilic)
Positively Charged (Basic)
Negatively Charged (Acidic)
The structure of proteins is affected by these different R-group
characteristics.

DIFFERENT STRUCTURES
PRIMARY (1°) STRUCTURE
order of amino acids in chain
based on the amino acid sequence being dictated by our genes/DNA
slight change in this amino acid sequence can affect the protein's
structure and therefore affecting the function of the protein
even one amino acid change can make all the sequence
Example: Lyzosome: Enzyme in tears and mucus that kills bacteria
SECONDARY (2°) STRUCTURE
"Local Folding" - folding along short sections of polypeptide
alpha helix and beta-pleated sheets
interactions between adjacent amino acids
occurs simultaneously - α and β are present within the same
polypeptide. This is because of the interaction of hydrogen
between the r group
 H bonds - weak bonds between R-groups
Forms sections of 3d structure
α-helix
β-pleated sheet
TERTIARY (3°) STRUCTURE
"Whole Molecule Folding"
- interactions between
distant amino acids
This because of other
characteristics such as:
1. Hydrophobic Interactions
non-polar amino acids
cluster away from water
2. Some would from more H-
bonds and ionic bonds
3. Formation of disulfide
bridges
covalent bonds between sulfurs in
sulfhydryls (S-H)
anchors 3-D shape
QUATERNARY (4°) STRUCTURE
more than one polypeptide chain
bonded together
if these don't bond together then
protein will not be functional
Example: Hemoglobin is a
globular that is composed of
four polypeptide chain.
Iron is embedded within these
polypeptide which is efficient in
carrying and transporting oxygen
 Protein Denaturation
UNFOLDING A PROTEIN
Conditions that disrupt H-
bonds, ionic bonds, and disulfide
bridges:
Temperature
pH
Salinity
In Biology, shape doesn't matter
— size does!
Protein loses its shape
Alter 2° and 3° structure
Alter the 3-D shape
Some may return to their functional shape
This in turn alters or destroys (renaturation) after denaturation however,
the protein's functionality many cannot.
ENZYME
Another important protein molecule
Enzymes are protein molecules that are very specific about which
reactions they catalyze. Only molecules with exactly the right shape will
bind with enzyme and react. These are reactant or substrate molecules.
These molecules may be called "loyal molecules" because they only bind or
react with a certain substrate: Only if the shape it right!

The part of the enzyme to which the

reactant binds is called the active
site. This is a very specific shape and
the most important part of the
enzyme.

Enzymes speed up chemical reaction

by lowering the activation energy
(Ea) of a reaction.
The activation energy is needed to start a reaction.
Different reactions have different activation energies.
The rate of enzyme-catalyzed reactions depends on several factors.
 Here are some examples:
Temperature
pH
Enzyme Concentration
Substrate Concentration
Surface Area
Pressure
All enzymes work best at only one particular temperature and pH: this is
called the optimum
Different enzymes have different optimum temperatures and pH values
Like proteins, if the pH and temperature
are not in
the right value, these enzymes could
also lose their function.
If the temperature and pH changes
sufficiently beyond an enzyme's
optimum, the shape of the enzyme
irreversibly changes
When this happens, the enzyme This affects the shape of the active
is denatured site and means that the enzyme will
no longer work
ENZYMES WORK BY ACTIVATING OR DEACTIVATING THEM
ACTIVATORS
COFACTORS
non-protein, small inorganic (absence of carbon) compounds and ions
Mg, K, Ca, Zn, Fe, Cu
bound within enzyme molecule
COENZYMES
non-protein, organic (presence
of carbon) molecule
bind temporarily or permanently
to enzyme near active site
many vitamins
NAD (niacin, B3)
FAD (riboflavin, B2)
Coenzyme A
INHIBITORS
COMPETITIVE INHIBITORS
Are chemicals that resemble an
enzyme's normal substrate and compete
for the active site; blocks the active site
of the enzyme so the substrate cannot
interact with it anymore
NON - COMPETITIVE INHIBITORS
Do not enter the active site but
bind to another part of the
enzyme causing the enzyme to
change its shape which in turn
alters the active site; attach to
the enzyme except to the
active site

Nucleic acid
Our genetic material... CENTRAL DOGMA OF MOLECULAR BIOLOGY
1. Stores Information
genes
blueprint for building proteins
→ →
DNA RNA Proteins
contains all instruction
2. Transfers Information
tells us that DNA contains several instructions on the
blueprint for new cells proteins that our bodies will be making. These instructions
blueprint for next generation will be copied/transcribed by the RNA. The RNA will then
use these instructions and translate them into proteins.

NUCLEOTIDES
3 PARTS
1. Nitrogen Base (C-N ring)
2. Pentose sugar (5C)
ribose in RNA
deoxyribose in DNA
3. Phosphate (PO4) group

ADENOSINE TRIPHOSPHATE
a molecule of energy
modified nucleotide
adenine (AMP) + Pi + Pi
ATP is always replenished
replenished by a variety of means:
creatine phosphate
stored glycogen
aerobic metabolism of glucose,
fatty acids, and other high-
energy molecules
Principle source of energy: ATP
ATP is required for contraction
and relaxation
Muscles require energu to contract and relax which cannot happen without ATP

Several food tests that can tell if certain molecules are

present