MOLECULAR STRUCTURE OF LIVING MATTER (MACROMOLECULES)

Macromolecules - are large molecules composed of thousands of covalently connected atoms.

Molecular structure and functions are inseparable.

A polymer is a long molecule consisting of many similar building blocks. These small building-block molecules are called
monomers. Three of the four classes of life’s organic molecules are polymers (Carbohydrates, Proteins, Nucleic acids).

SYNTHESIS AND BREAKDOWN OF POLYMERS

 A dehydration reaction occurs when two monomers bond together through the loss of a water molecule.

 Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the
dehydration reaction.

A. POLYSACCHARIDES

CARBOHYDRATES - sugars or saccharides.

 Most abundant molecules found in nature and are involved in both dynamic and structural roles.
 Are polyhydroxy aldehydes or ketones, or substances that yield such compounds on hydrolysis.
 Simple carbohydrates are called sugars, whereas complex carbohydrates are referred to as glycoconjugates, i.e.,
glycolipids and glycoproteins.

CLASSIFICATIONS

1. MONOSACCHARIDES - Monosaccharides have molecular formulas that are usually multiples of CH2O.
Monosaccharides are the simplest of carbohydrates, since they contain only one polyhydoxy aldehyde or ketone
unit.
Examples: glucose, fructose, ribose
2. DISSACHARIDES - Two monosaccharides bond together using a dehydration reaction to create a disaccharide.
The bond between two monosaccharides is called a glycosidic bond.
Example: Sucrose, Lactose, Maltose.
 Lactose Intolerance - Lack of ability to break down the disaccharide lactose
 Sucrose Intolerance - Lack of ability to break down the disaccharide sucrose
3. OLIGOSACCHARIDES - Contain from 3-10 monosaccharide units.
Example: Raffinose - an oligosaccharide found in peas and beans.
4. POLYSACCHARIDES - Contain very long chains of hundreds or thousands of monosaccharide units, which may be
either in straight or branched unit. Most commonly encountered carbohydrates in nature
Example: cellulose, glycogen, starch
a. STORAGE POLYSACCHARIDES
STARCH - is the main storage polysaccharide of plants and it is the most important dietary source for human
beings. There are two forms of starch: amylose and amylopectin.
i. Starch: AMYLOSE - Consists of long, unbranched chains of glucose(from 100 to 2000 molecules)
connected by ∝ (1 → 4) glycosidic linkages and is a water soluble component which constitutes
about 15-20 percent starch.
ii. Starch: AMYLOPECTIN - Consists of long chains of glucose (up to 1000000) connected by ∝ (1 → 4)
glycosidic linkages, with ∝ (1 → 6) branches every 24 to 30 glucose units along the chain.

80-90 percent of the starch in plants is in this form.

 b. STRUCTURAL POLYSACCHARIDES
CELLULOSE - Occurs exclusively in plants and it is the most abundant organic substance in plant kingdom. It
is the material in plant cell walls that provides strength and rigidity: wood is 50% cellulose

B. LIPIDS - are the one class of large biological molecules that do not form polymers. The unifying feature of lipids is
having little or no affinity for water. Lipids are hydrophobic because they consist mostly of hydrocarbons, which
form nonpolar covalent bonds. Examples are fats, phospholipids, and steroids.

CATEGORIES – Triglycerides, Phospholipids, Steroids, Waxes

1. TRIGLYCERIDES - Includes fats and oils
Fats - solid at room temperature and is used by animals for insulation, protection and long-term energy
storage (e.g, lard and butter).
Oils – liquid at room temperature and is used by plants for long-term energy storage

Two Types of Subunit Molecules:

 Glycerol - three-carbon alcohol with a hydroxyl group attached to each carbon

 Fatty acids - consists of a carboxyl group attached to a long carbon skeleton
2. PHOSPHOLIPIDS - Similar to triglycerides in that they contain glycerol and two fatty acids. What’s different is
that a phosphate group rather than a third fatty acid is attached to the third carbon of glycerol.
- Major component of the plasma membrane of the cell.
3. STEROID - composed of four fused rings of carbon to which different functional groups are attached. One
well known steroid molecule is cholesterol.
a. CHOLESTEROL - Serves as a precursor for the synthesis of other steroids such as testosterone,
estrogen, vitamin D, and cortisone, and is present in plasma membrane where it stabilizes the
membrane.

C. NUCLEIC ACID - Information-carrying molecules—our genetic material

These are macromolecules that store genetic information and enable protein production. These molecules allow
organisms to transfer genetic information from one generation to the next.

There are two types of nucleic acids

 Deoxyribonucleic acid (DNA)

 Ribonucleic acid (RNA)

 DNA provides directions for its own replication.

 DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis.

 Protein synthesis occurs on ribosomes.

1. NUCLEOTIDES - Composed of repeating units or monomers and are building blocks of nucleic acids.
A nucleotide consists of three components:
 Nitrogenous base - A nitrogenous base is simply a nitrogen-containing molecule that has the same chemical
properties as a base.
 There are two types of Nitrogen bases, namely, Purine and Pyrimidine.
 Pyrimidine has a single ring while Purine has two rings.
  Phosphate group - The phosphate group is a molecule containing one atom of phosphorus covalently bound to
four oxygen residues.
 Their electrons, shared among all those oxygen molecules, can store lots of energy, and this is key for
some of their roles in the cell.
 Pentose - Only two 5-carbon sugars are found in nature: ribose and deoxyribose.
 Central molecule in a nucleotide.
2. NUCLEOSIDE - Sugar + Base.
A nucleoside consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) but
without the phosphate group.
TYPES OF NUCLEOTIDES
a. Mononucleotides: only one nucleotide unit (e.g. ATP)
b. Dinucleotides: 2 nucleotides (e.g. NAD)
c. Polynucleotides: repeated condensation of nucleotides (e.g. RNA & DNA)

FUNCTIONS OF NUCLEOTIDE:

• They are the “energy currency” of the cell.

• They are signaling molecules, acting like hormones directly or as transducers of the information.

• They provide the monomers for genetic information in DNA and RNA.

DNA vs RNA

TYPES OF RNA

1. Messenger RNA (mRNA) - carries information for protein synthesis from the DNA in the nucleus to the ribosomes and
it travels to ribosomes, small granular particles in the cytoplasm of a cell where protein synthesis takes place.

2. Transfer RNA (tRNA) - translates the genetic code from the messenger RNA and brings amino acids to the ribosomes
for protein synthesis.

3. Ribosomal RNA (rRNA) – major component of ribosomes.

 D. AMINO ACIDS - Amino acids are the monomers that make up proteins. Specifically, a protein is made up of one
or more linear chains of amino acids, each of which is called a polypeptide. These are compounds containing an
amino group, -NH2, and a carboxylic acid group, -COOH

PROPERTIES:

 High melting points, generally over 200 °C.

 More soluble in water than they are common organic solvents.

 Larger dipole moments than simple amines or simple acids.

 Less acidic than most carboxylic acids and less basic than most amines.

 NH3+ group – acidic part

 COO- group – basic part

 Amphoteric (having both acidic and basic properties).

 There is an internal transfer of a hydrogen ion from the –COOH group to the -NH2 group to leave an ion with
both a negative charge and a positive charge.

 Zwitterion - is a compound with no overall electrical charge, but which contains separate parts which are
positively and negatively charged.

FUNCTIONS:

 When proteins are digested or broken down, amino acids are left. The human body uses amino acids to make
proteins to help the body break down food, grow, repair body tissue perform many other body functions.

 Source of energy by the body

CLASSIFICATION

a. BY ESSENTIALITY (essential and non-essential)

b. BY POLARITY
 PEPTIDE - are "short" proteins. The resulting link between the amino acids is an amide link which biochemists
call a peptide bond. In this reaction, water is released. In a reverse reaction, the peptide bond can be cleaved by
water (hydrolysis). A dipeptide has two amino acid units, a tripeptide has three amino acid units

 The precise order of the amino acids in the peptide is the amino acid sequence.
 The carboxyl group end is referred to as the C terminus while the amino group end is referred to as the N
terminus.

IMPORTANCE: AMINO ACID SEQUENCING

 The sequence of amino acids in a protein can offer insights into its three-dimensional structure and its function,
cellular location, and evolution.

 Understanding cellular functions

 Finding evolutionary history of protein

 Prediction of function related to protein

EDMAN DEGRADATION (Pehr Edman )

 The process of purifying protein by sequentially removing one residue at a time from the amino end of a
peptide.

 Edman degradation is very useful because it does not damage the protein. This allows sequencing of the protein
to be done in less time. Edman sequencing is done best if the composition of the amino acid is known.

E. PROTEIN STRUCTURE AND FUNCTION

o Proteins are very large molecules composed of combinations of 20 different amino acids. The
precise physical shape of a protein is very important for its function.
o Proteins account for more than 50% of the dry mass of most cells.
o Protein functions include structural support, storage, transport, cellular communications,
movement, and defense against foreign substances.

FUNCTIONS OF PROTEINS

a. ENZYMATIC PROTEIN – selective acceleration of chemical reactions

b. STORAGE PROTEINS – storage of amino acids
c. HORMONAL PROTEINS – coordination of an organism’s activities
d. CONTRACTILE AND MOTOR PROTEINS – movement
e. DEFENSIVE PROTEINS – protection against disease
f. TRANSPORT PROTEINS – transport of substances
g. RECEPTOR PROTEINS – response of cell to chemical stimuli
h. STRUCTURAL PROTEINS – support

Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions.
Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life.

POLYPEPTIDES - are unbranched polymers built from the same set of 20 amino acids.

 A protein is a biologically functional molecule that consists of one or more polypeptides.

AMINO ACID MONOMERS

 Amino acids are organic molecules with carboxyl and amino groups.

 Amino acids differ in their properties due to differing side chains, called R groups.

AMINO ACID POLYMERS

 Amino acids are linked by peptide bonds

 A polypeptide is a polymer of amino acids.

 Polypeptides range in length from a few to more than a thousand monomers .

 Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino
end (N-terminus).

PROTEIN STRUCTURE AND FUNCTION - A functional protein consists of one or more polypeptides precisely twisted,
folded, and coiled into a unique shape

FOUR LEVELS OF PROTEIN STRUCTURE

 The primary structure of a protein is its unique sequence of amino acids

 Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word
 Primary structure is determined by inherited genetic information

 Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain

 The coils and folds of secondary structure result from hydrogen bonds between repeating constituents
of the polypeptide backbone

 Typical secondary structures are a coil called an  helix and a folded structure called a  pleated sheet

 Tertiary structure is determined by interactions among various side chains (R groups)

 Tertiary structure is determined by interactions between R groups, rather than interactions between
backbone constituents

 These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions,
and van der Waals interactions

 Strong covalent bonds called disulfide bridges may reinforce the protein’s structure

 Quaternary structure results when a protein consists of multiple polypeptide chains

 Quaternary structure results when two or more polypeptide chains form one macromolecule

 Collagen is a fibrous protein consisting of three polypeptides coiled like a rope

 Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains