Biomolecules

James Benedict S. Perez

 defined as anything that takes up space
Matter and has mass
ELEMENTS COMPOUNDS MATTER
• A substance that • A substance consisting • Composed of
cannot be broken of two or more
down to other different
substances by different elements compounds
chemical combined in a fixed joined together
reactions. ratio.
• Today, chemists
by different
• Table salt, for example, bonds.
recognize 92 is sodium chloride
elements
occurring in (NaCl), a compound
nature; gold, composed of the
copper, carbon, elements sodium (Na)
and oxygen are and chlorine (Cl) in a
examples.
1:1 ratio.
How many elements have we discovered so far?
Do we need all of these elements inside our
bodies?
The Elements of Life
• Of the 92 natural elements,
about 20–25% are essential
elements.
• The essential elements are
similar among organisms, but
there is some variation—for
example, humans need 25
elements, but plants need only
17.
Why do we need to maintain a balanced
amount of these materials?
• Trace elements are required by an Imbalanced
organism in only minute quantities. Diseases
Amounts
• Some trace elements, such as iron
(Fe), are needed by all forms of life
• others are required only by certain
species. For example, in vertebrates Iodine Hypothyroidism
(animals with backbones), the Deficiency
element iodine (I) is an essential
ingredient of a hormone produced
by the thyroid gland.
FORMATION AND FUNCTION OF MOLECULES
DEPEND ON CHEMICAL BONDING BETWEEN
ATOMS
• Covalent Bonds - sharing of a pair
of valence electrons by two
atoms
FORMATION AND FUNCTION OF MOLECULES
DEPEND ON CHEMICAL BONDING BETWEEN
ATOMS
• Ionic Bonds - two atoms are so
unequal in their attraction for
valence electrons that the more
electronegative atom strips an
electron completely away from
its partner.
FORMATION AND FUNCTION OF MOLECULES
DEPEND ON CHEMICAL BONDING BETWEEN
ATOMS
• Weak Chemical Bonds
• Hydrogen bonds - The partial positive
charge on a hydrogen atom that is
covalently bonded to an
electronegative atom allows the
hydrogen to be attracted to a different
electronegative atom nearby.
• Van der Waals – A molecule with
nonpolar covalent bonds may have
positively and negatively charged
regions. Ever-changing regions of
positive and negative charge that
enable all atoms and molecules to
stick to one another.
Chemical reactions make and break chemical
bonds
• Anabolic Chemical Reactions –
Puts together molecules
• Catabolic Chemical Reactions –
Breaks apart large molecules
BIOMOLECULES
• CRITICALLY IMPORTANT LARGE • POLYMERS - long molecule
MOLECULES OF ALL LIVING consisting of many similar or
identical building blocks linked by
THINGS covalent bonds
• MOST ARE SAID TO BE • MONOMERS - smaller molecules
POLYMERS COMPOSED OF ITS which serves as the building blocks
RESPECTIVE MONOMERS of a polymers
The Four Main Classes of Biomolecules

CARBOHYDRATES
PROTEINS
BIOMOLECULES POLYMERS
NUCLEIC ACIDS
LIPIDS
The Synthesis and Breakdown of Polymers
• Enzymes - specialized
macromolecules that speed up
chemical reactions.
• Dehydration Reaction - two
molecules are covalently bonded to
each other, with the loss of a water
molecule
• Hydrolysis Reaction - break using
water. The hydrogen from the
water attaching to one monomer
and the hydroxyl group attaching
to the adjacent monomer.
CARBOHYDRATES
• SERVES AS FUEL AND BUILDING
MATERIAL
• INCLUDE BOTH SUGARS AND
POLYMERS OF SUGARS.
DIFFERENT MONOMERS OF CARBOHYDRATES
• Monosaccharides, or simple
sugars; these are the monomers
from which more complex
carbohydrates are constructed.
• Monosaccharides (from the
Greek monos, single, and
sacchar, sugar) generally have
molecular formulas that are
some multiple of the unit CH2O.
Examples of Monomers ISOMERS
• Glucose
• Fructose HEXOSE
• Galactose
• Ribose
PENTOSE
• Ribulose
• Glyceraldehyde
TRIOSE
• Dihydroxyacetone
Disaccharides (double sugars)
• joined by a glycosidic linkage, a covalent bond formed between two
monosaccharides by a dehydration reaction.
Kinds of Disaccharides
• maltose (Glucose + Glucose)
• Sucrose or table sugar (glucose +
fructose)
• Lactose, the sugar present in milk
(glucose + galactose)
POLYSACCHARIDES
• polymers with a few hundred to
a few thousand monosaccharides
joined by glycosidic linkages
• Serve as storage material or as
building material for structure
Storage Polysaccharides
• Plastids stores starch from
photosynthesis
• Hydrolysis, Breaks the bonds
between the glucose monomers.
• Most animals, including humans,
also have enzymes that can
hydrolyze plant starch, making
glucose available as a nutrient for
cells.
Storage Polysaccharides
• Starch: a plant polysaccharide.
Amylose (unbranched) and
amylopectin (branched) are two
forms of starch
• Glycogen: an animal
polysaccharide. dense clusters of
granules within liver and muscle
cells. Note that glycogen is more
branched than amylopectin
starch.
Structural Polysaccharides
• Cellulose – makes up the plant`s
cell walls
• Chitin – Makes up the
arthropod`s shells
LIPIDS
• ENERGY RESERVE
• SIGNALING
• STRUCTURAL COMPONENTS OF THE
CELL MEMBRANE
LIPIDS ARE A DIVERSE GROUP OF
HYDROPHOBIC MOLECULES
• Does not include true polymers
• Not big enough to be considered
macromolecules.
• The hydrophobic behavior of
lipids is based on their molecular
structure.
Types of lipids
• Fats
• Phospholipids
• Steroids
WHAT ARE FATS?
• Large molecules assembled from
smaller molecules by dehydration
reactions.
• Composed of glycerol and fatty
acids
• Glycerol is an alcohol; each of its
three carbons bears a hydroxyl
group.
• Fatty acid has a long carbon
skeleton, usually 16 or 18 carbon
atoms in length. The carbon at one
end of the skeleton is part of a
carboxyl group.
How do we make Fats?
• Fatty acid molecules are each
joined to glycerol by an ester
linkage.
• The resulting fat is triacylglycerol
(triglyceride) , consisting of three
fatty acids linked to one glycerol
molecule.
SATURATED V.S. UNSATURATED FATS
• SATURATED FATS – FATTY ACID
CHAINS ARE COMPOSED OF
SINGLE BONDS (FOUND IN
ANIMALS)
• UNSATURATED FATS – FATTY ACID
CHAINS ARE COMPOSED OF ONE
OR MORE DOUBLE BONDS
(PLANTS AND FISHES)
TRANS FAT
• UNSATURATED FATS WITH
TRANS FATTY ACID CHAINS
FATS AS FUEL FOR THE BODY
• INSTEAD OF GLYCOLYSIS FATS UNDERGO
A METABOLIC PROCESS CALLED AS
FATTY ACID OXIDATION PATHWAY
Phospholipids
• CONTAINS TWO (2) FATTY ACIDS
ATTACHED TO A GLYCEROL PLUS
A POLAR PHOSPHATE GROUP
• HYDROCARBON CHAINS ARE
HYDROPHOBIC (NON-POLAR)
• PHOSPHATE GROUPS ARE
HYDROPHILIC (POLAR)
STEROIDS
• Consists of four fused rings
• Distinguished by the particular
chemical groups attached to
this ensemble of rings
• Cholesterol is a main
component of animal cell
membranes
• Synthesized in the liver and
obtained from the diet
PROTEINS
• account for more than 50% of
the dry mass of most cells
• Functions
• Speed up chemical reactions
• Defense mechanism
• Storage
• Transport
• Cellular communication
• Movement
• Structural support
PROTEIN FUNCTIONS
• Enzymes (Catalysts)
PROTEIN FUNCTIONS
• Storage Proteins (Stores Amino Acids)
PROTEIN FUNCTIONS
• Hormonal Proteins (Other hormones are made up of proteins)
PROTEIN FUNCTIONS
• Contractile and Motor Proteins (muscle fibers)
PROTEIN FUNCTIONS
• Defensive Proteins (Antibody
and Antigen)
PROTEIN FUNCTIONS
• Transport Proteins (Channeling Proteins)
PROTEIN FUNCTIONS
• Receptor Proteins (receives signals)
PROTEIN FUNCTIONS
• Structural Proteins (Collagen)
MONOMERS OF PROTEINS
• Amino Acids
• Contains an amino group and a
carboxyl group and a variable group
symbolized by R.
• The R group, also called the side
chain, differs with each amino acid.
AMINO ACID POLYMERS
• dehydration reaction (Forms a
peptide bond)
• Repeated over and over to yield
a polypeptide
• a polypeptide of any length has a
single amino end (N-terminus)
and a single carboxyl end (C-
terminus)
Protein Structure and Function
• The specific activities of proteins
result from their intricate three-
dimensional architecture
• Many proteins are roughly
spherical (globular proteins),
while others are shaped like long
fibers (fibrous proteins).
• linked series of amino acids with
a unique sequence

• Dictates secondary and tertiary

structure, due to the chemical
nature of the backbone and the
side chains (R groups) of the
amino acids positioned along the
chain.
• Coiling and folding of the chains
(Hydrogen bonds between the
repeating polypeptide chains)

• α helix, a delicate coil held together by

hydrogen bonding between every
fourth amino acid, shown above

• β pleated sheet. As shown above, in

this structure two or more strands of
the polypeptide chain lying side by side
(called β strands)
• The overall shape of a polypeptide
resulting from interactions between
the side chains (R groups)

• Bounded by hydrophobic interaction as

well as van der Waals interactions help
hold them together

• Covalent bonds called disulfide bridges

(¬S¬S¬) may further reinforce the
shape of a protein
• The overall protein structure that
results from the aggregation of these
polypeptide subunits.
Sickle-Cell Disease: A Change in Primary
Structure
• Caused by the substitution of one
amino acid (valine) for the normal
one (glutamic acid)
• Normal red blood cells are disk-
shaped, but in sickle-cell disease,
the abnormal hemoglobin
molecules tend to crystallize,
deforming some of the cells into a
sickle shape
• A person with the disease has
periodic “sickle-cell crises” when
the angular cells clog tiny blood
vessels, impeding blood flow
Protein Denaturation
• The weak chemical bonds and
interactions within a protein may
be destroyed
• The denatured protein is
biologically inactive
• Causes of protein denaturation
• Different solvents
• Other chemicals that disrupts
chemical bonding
• Excessive heat
• This also explains why excessively
high fevers can be fata
Just how important protein folding is?
• Chaperonins (also called
chaperone proteins), protein
molecules that assist in the
proper folding of other proteins
• Separates the folding protein
from “bad influences” in the
cytoplasmic environment
• Misfolding of polypeptides leads
to diseases (Alzheimer’s,
Parkinson’s, and mad cow
disease)
Nucleic Acids
• store, transmit, and help express
hereditary information
Nucleic Acids
• Gene – a portion in the
chromosome/DNA which is
expressed to form a specific
physical characteristic

• DNA – Nucleic Acids which contains

the genetic information

• RNA – Nucleic Acids which helps in

several processes such as Protein
Synthesis and DNA replication
Components of
Nucleic Acids
• polynucleotides (consists of
monomers called nucleotides)
• composed of three parts:
nitrogenous base, a pentose
sugar, and phosphate groups
Nitrogenous Base
Pairs
• pyrimidines and purines
• pyrimidine has one six-
membered ring of carbon and
nitrogen atoms. (cytosine (C),
thymine (T), and uracil (U))
• Purines are larger, with a six-
membered ring fused to a five-
membered ring. The purines are
adenine (A) and guanine (G)
Nucleotide Polymers
• joined by a phosphodiester
linkage
• One end has a phosphate
attached to a 5 carbon, and the
other end has a hydroxyl group
on a 3 carbon; we refer to these
as the 5 end and the 3 end,
respectively.
 DNA V.S. RNA

HELICAL SHAPE HELICAL

TWO (DOUBLE NO. of STRANDS SINGLE

STRANDED)
A-T,G-C NUCLEOTIDES A-U,G-C

ANTIPARALLEL SEQUENCE SINGLE

DIRECTION
How did we discover the DNA structure?
• James Watson and Francis Crick
(won Nobel Peace Prize)
• Rosalind Franklin utilized X-ray
Crystallography to visualize the
DNA structure
Protein Synthesis
• DNA→RNA →PROTEIN
Protein Synthesis
• Transcription
• DNA to mRNA
• Translation
• mRNA attaches to the ribosomes
and calls for specific tRNA
molecules which carries different
amino Acids
END