RA # 4

BIOMOLECULES

GALLANOSA, Andre Bryan

CON – 1E

Prof. Cyda O. Meimban

Introduction

A major goal of biochemistry is to study the cellular processes of

living organisms and how these processes relate to the functioning of
the organism. Research in the area of biochemistry has been
extremely successful over the last century; we now know the atoms
and biomolecules that make up living organisms, the central dogma
around which biological information is transferred and how this
information results in a greater understanding of ourselves and the
world in which we live. One of the most important results from research
in biochemistry is that all organisms are uniform at the molecular level
and the diversity we see today is a result of evolution.

Course considers biomolecules—proteins, sugars, lipids—and

transformations among them (metabolism), with emphasis on proteins
(enzymes) and their role in catalyzing metabolic reactions.
Biomolecules

Biomolecule, also called biological molecule, any of numerous

substances that are produced by cells and living organisms.
Biomolecules have a wide range of sizes and structures and perform
a vast array of functions. The four major types of biomolecules are
carbohydrates, lipids, nucleic acids, and proteins.

Among biomolecules, nucleic acids, namely DNA and RNA, have

the unique function of storing an organism’s genetic code—the
sequence of nucleotides that determines the amino acid sequence
of proteins, which are of critical importance to life on Earth. There are
20 different amino acids that can occur within a protein; the order in
which they occur plays a fundamental role in determining protein
structure and function. Proteins themselves are major structural
elements of cells. They also serve as transporters, moving nutrients and
other molecules in and out of cells, and as enzymes and catalysts for
the vast majority of chemical reactions that take place in living
organisms. Proteins also form antibodies and hormones, and they
influence gene activity.

Likewise, carbohydrates, which are made up primarily of molecules

containing atoms of carbon, hydrogen, and oxygen, are essential
energy sources and structural components of all life, and they are
among the most abundant biomolecules on Earth. They are built from
four types of sugar units—monosaccharides, disaccharides,
oligosaccharides, and polysaccharides. Lipids, another key
biomolecule of living organisms, fulfill a variety of roles, including
serving as a source of stored energy and acting as chemical
messengers. They also form membranes, which separate cells from
their environments and compartmentalize the cell interior, giving rise
to organelles, such as the nucleus and the mitochondrion, in higher
(more complex) organisms.

All biomolecules share in common a fundamental relationship

between structure and function, which is influenced by factors such
as the environment in which a given biomolecule occurs. Lipids, for
example, are hydrophobic (“water-fearing”); in water, many
spontaneously arrange themselves in such a way that the
hydrophobic ends of the molecules are protected from the water,
while the hydrophilic ends are exposed to the water. This arrangement
gives rise to lipid bilayers, or two layers of phospholipid molecules,
which form the membranes of cells and organelles. In another
example, DNA, which is a very long molecule—in humans, the
combined length of all the DNA molecules in a single cell stretched
end to end would be about 1.8 metres (6 feet), whereas the cell
nucleus is about 6 μm (6 10-6 metre) in diameter—has a highly flexible
helical structure that allows the molecule to become tightly coiled
and looped. This structural feature plays a key role in enabling DNA to
fit in the cell nucleus, where it carries out its function in coding genetic
traits.
 Biology and its subfields of biochemistry and molecular biology
study biomolecules and their reactions. Most biomolecules are
organic compounds, and just four elements—oxygen, carbon,
hydrogen, and nitrogen—make up 96% of the human body's mass.
But many other elements, such as the various biometals, are present
in small amounts.

The uniformity of both specific types of molecules (the

biomolecules) and of certain metabolic pathways are invariant
features among the wide diversity of life forms; thus these
biomolecules and metabolic pathways are referred to as
"biochemical universals" or "theory of material unity of the living
beings", a unifying concept in biology, along with cell theory and
evolution theory.
Types of biomolecules
A diverse range of biomolecules exist, including:

 Small molecules:
o Lipids, fatty acids, glycolipids, sterols, monosaccharides
o Vitamins
o Hormones, neurotransmitters
o Metabolites
 Monomers, oligomers and polymers:

Covalent
Polymerization proc bond name
Biomonomers Bio-oligo Biopolymers
ess between
monomers

Polypeptides,
Amino acids Oligopeptides proteins Polycondensation Peptide bond
(hemoglobin...)

Monosaccharid Oligosaccharid Polysaccharides Glycosidic

Polycondensation
es es (cellulose...) bond

Polyterpenes: cis-
1,4-
polyisoprene natural
Isoprene Terpenes Polyaddition
rubber and trans-1,4-
polyisoprene gutta-
percha

Polynucleotides, nucl
Oligonucleotide Phosphodiest
Nucleotides eic
s er bond
acids (DNA, RNA)
Nucleosides and Nucleotides

Nucleosides are molecules formed by attaching a nucleobase to

a ribose or deoxyribose ring. Examples of these include cytidine (C),
uridine (U), adenosine (A), guanosine (G), and thymidine (T).

Nucleosides can be phosphorylated by specific kinases in the cell,

producing nucleotides. Both DNA and RNA are polymers, consisting of
long, linear molecules assembled by polymerase enzymes from
repeating structural units, or monomers, of mononucleotides. DNA
uses the deoxynucleotides C, G, A, and T, while RNA uses the
ribonucleotides (which have an extra hydroxyl(OH) group on the
pentose ring) C, G, A, and U. Modified bases are fairly common (such
as with methyl groups on the base ring), as found in ribosomal RNA or
transfer RNAs or for discriminating the new from old strands of DNA
after replication.

Each nucleotide is made of an acyclic nitrogenous base, a

pentose and one to three phosphate groups. They contain carbon,
nitrogen, oxygen, hydrogen and phosphorus. They serve as sources of
chemical energy (adenosine triphosphate and guanosine
triphosphate), participate in cellular signaling (cyclic guanosine
monophosphate and cyclic adenosine monophosphate), and are
incorporated into important cofactors of enzymatic reactions
(coenzyme A, flavin adenine dinucleotide, flavin mononucleotide,
and nicotinamide adenine dinucleotide phosphate).

DNA and RNA structure

DNA structure is dominated by the well-known double helix formed

by Watson-Crick base-pairing of C with G and A with T. This is known
as B-form DNA, and is overwhelmingly the most favorable and
common state of DNA; its highly specific and stable base-pairing is the
basis of reliable genetic information storage. DNA can sometimes
occur as single strands (often needing to be stabilized by single-strand
binding proteins) or as A-form or Z-form helices, and occasionally in
more complex 3D structures such as the crossover at Holliday junctions
during DNA replication.

Stereo 3D image of a group I intron ribozyme ; gray lines show base

pairs; ribbon arrows show double-helix regions, blue to red from 5' to
3' end; white ribbon is an RNA product.
 RNA, in contrast, forms large and complex 3D tertiary structures
reminiscent of proteins, as well as the loose single strands with locally
folded regions that constitute messenger RNA molecules. Those RNA
structures contain many stretches of A-form double helix, connected
into definite 3D arrangements by single-stranded loops, bulges, and
junctions. Examples are tRNA, ribosomes, ribozymes, and riboswitches.
These complex structures are facilitated by the fact that RNA
backbone has less local flexibility than DNA but a large set of distinct
conformations, apparently because of both positive and negative
interactions of the extra OH on the ribose. Structured RNA molecules
can do highly specific binding of other molecules and can themselves
be recognized specifically; in addition, they can perform enzymatic
catalysis (when they are known as "ribozymes", as initially discovered
by Tom Cech and colleagues).

Saccharides

Monosaccharides are the simplest form of carbohydrates with only

one simple sugar. They essentially contain an aldehyde or ketone
group in their structure. The presence of an aldehyde group in a
monosaccharide is indicated by the prefix aldo-. Similarly, a ketone
group is denoted by the prefix keto-. Examples of monosaccharides
are the hexoses, glucose, fructose, Trioses, Tetroses, Heptoses,
galactose, pentoses, ribose, and deoxyribose. Consumed fructose
and glucose have different rates of gastric emptying, are differentially
absorbed and have different metabolic fates, providing multiple
opportunities for 2 different saccharides to differentially affect food
intake. Most saccharides eventually provide fuel for cellular
respiration.
 Disaccharides are formed when two monosaccharides, or two
single simple sugars, form a bond with removal of water. They can be
hydrolyzed to yield their saccharin building blocks by boiling with
dilute acid or reacting them with appropriate enzymes. Examples of
disaccharides include sucrose, maltose, and lactose.

Polysaccharides are polymerized monosaccharides, or complex

carbohydrates. They have multiple simple sugars. Examples are
starch, cellulose, and glycogen. They are generally large and often
have a complex branched connectivity. Because of their size,
polysaccharides are not water-soluble, but their many hydroxy groups
become hydrated individually when exposed to water, and some
polysaccharides form thick colloidal dispersions when heated in
water. Shorter polysaccharides, with 3 - 10 monomers, are called
oligosaccharides. A fluorescent indicator-displacement molecular
imprinting sensor was developed for discriminating saccharides. It
successfully discriminated three brands of orange juice beverage. The
change in fluorescence intensity of the sensing films resulting is directly
related to the saccharide concentration.

Lignin

Lignin is a complex polyphenolic macromolecule composed

mainly of beta-O4-aryl linkages. After cellulose, lignin is the second
most abundant biopolymer and is one of the primary structural
components of most plants. It contains subunits derived from p-
coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol and is
unusual among biomolecules in that it is racemic. The lack of optical
activity is due to the polymerization of lignin which occurs via free
radical coupling reactions in which there is no preference for either
configuration at a chiral center.

Lipids

Lipids (oleaginous) are chiefly fatty acid esters, and are the basic
building blocks of biological membranes. Another biological role is
energy storage (e.g., triglycerides). Most lipids consist of a polar or
hydrophilic head (typically glycerol) and one to three nonpolar or
hydrophobic fatty acid tails, and therefore they are amphiphilic. Fatty
acids consist of unbranched chains of carbon atoms that are
connected by single bonds alone (saturated fatty acids) or by both
single and double bonds (unsaturated fatty acids). The chains are
usually 14-24 carbon groups long, but it is always an even number.

For lipids present in biological membranes, the hydrophilic head is

from one of three classes:

 Glycolipids, whose heads contain an oligosaccharide with 1-15

saccharide residues.
 Phospholipids, whose heads contain a positively charged group
that is linked to the tail by a negatively charged phosphate
group.
 Sterols, whose heads contain a planar steroid ring, for example,
cholesterol.
Other lipids include prostaglandins and leukotrienes which are both
20-carbon fatty acyl units synthesized from arachidonic acid. They are
also known as fatty acids
Amino Acids

Amino acids contain both amino and carboxylic acid functional

groups. (In biochemistry, the term amino acid is used when referring
to those amino acids in which the amino and carboxylate
functionalities are attached to the same carbon, plus proline which is
not actually an amino acid).

Modified amino acids are sometimes observed in proteins; this is

usually the result of enzymatic modification after translation (protein
synthesis). For example, phosphorylation of serine by kinases and
dephosphorylation by phosphatases is an important control
mechanism in the cell cycle. Only two amino acids other than the
standard twenty are known to be incorporated into proteins during
translation, in certain organisms:

 Selenocysteine is incorporated into some proteins at a UGA

codon, which is normally a stop codon.
 Pyrrolysine is incorporated into some proteins at a UAG codon.
For instance, in some methanogens in enzymes that are used to
produce methane.

Besides those used in protein synthesis, other biologically important

amino acids include carnitine (used in lipid transport within a cell),
ornithine, GABA and taurine.
Protein Structure

The particular series of amino acids that form a protein is known as

that protein's primary structure. This sequence is determined by the
genetic makeup of the individual. It specifies the order of side-chain
groups along the linear polypeptide "backbone".

Proteins have two types of well-classified, frequently occurring

elements of local structure defined by a particular pattern of
hydrogen bonds along the backbone: alpha helix and beta sheet.
Their number and arrangement is called the secondary structure of
the protein. Alpha helices are regular spirals stabilized by hydrogen
bonds between the backbone CO group (carbonyl) of one amino
acid residue and the backbone NH group (amide) of the i+4 residue.
The spiral has about 3.6 amino acids per turn, and the amino acid side
chains stick out from the cylinder of the helix. Beta pleated sheets are
formed by backbone hydrogen bonds between individual beta
strands each of which is in an "extended", or fully stretched-out,
conformation. The strands may lie parallel or antiparallel to each
other, and the side-chain direction alternates above and below the
sheet. Hemoglobin contains only helices, natural silk is formed of beta
pleated sheets, and many enzymes have a pattern of alternating
helices and beta-strands. The secondary-structure elements are
connected by "loop" or "coil" regions of non-repetitive conformation,
which are sometimes quite mobile or disordered but usually adopt a
well-defined, stable arrangement.
Apoenzymes

An apoenzyme (or, generally, an apoprotein) is the protein without

any small-molecule cofactors, substrates, or inhibitors bound. It is often
important as an inactive storage, transport, or secretory form of a
protein. This is required, for instance, to protect the secretory cell from
the activity of that protein. Apoenzymes become active enzymes on
addition of a cofactor. Cofactors can be either inorganic (e.g., metal
ions and iron-sulfur clusters) or organic compounds, (e.g., [Flavin
group|flavin] and heme). Organic cofactors can be either prosthetic
groups, which are tightly bound to an enzyme, or coenzymes, which
are released from the enzyme's active site during the reaction.

Isoenzymes

Isoenzymes, or isozymes, are multiple forms of an enzyme, with

slightly different protein sequence and closely similar but usually not
identical functions. They are either products of different genes, or else
different products of alternative splicing. They may either be
produced in different organs or cell types to perform the same
function, or several isoenzymes may be produced in the same cell
type under differential regulation to suit the needs of changing
development or environment. LDH (lactate dehydrogenase) has
multiple isozymes, while fetal hemoglobin is an example of a
developmentally regulated isoform of a non-enzymatic protein. The
relative levels of isoenzymes in blood can be used to diagnose
problems in the organ of secretion.
Summary

The molecules which are produced by living animals are known as

biomolecules this includes large Macromolecules like protein, lipids,
polysaccharides, and nucleic acids and small molecules like metabolites , and
natural products. These molecules are also known as biogenic substances.

The biomolecules are basically divided into two types small molecules and
polymers. Small molecules are lipids, glycolipids, polysaccharides, sterols,
glycerolipids, vitamins, metabolites and neurotransmitters, hormones. The most
important biomolecule is nucleosides and nucleotides. The DNA is made up of
these nucleotides. Nucleoside are molecules which are formed by attachment of
Nucleobase to ribose or deoxyribose ring. These are cytidine, uridine, adenosine,
thymidine , Guanosine, thymidine and inosine. The enzymes kinases
phosphorylate nucleosides within the cell and results in production of nucleotides.
DNA and RNA are made up of repeated structural units , monomers of
mononucleotides.

The other form of biomolecules are Saccharides. Commonly known as the

sugars. Monosaccharides are the simplest form of carbohydrates which contains
simple sugar. These contains ketone or aldehyde group in their structure.
Aldehyde group presence is known by aldo prefix and ketone group is known by
prefix keto. Fructose, glucose, hexose are monosaccharide. When two
monosaccharides combine they form disaccharides. Or two single simple sugars
formed by bond with removal of water molecules. Lactose, maltose and sucrose
are disaccharides.

The complex form of monosaccharides are known as polysaccharides which

are polymerized Monosaccharides. They have multiple simple form of sugars.
Glycogen, Cellulose and starch are examples of polysaccharides.
Oligosaccharides are shorter polysaccharides with 3-10 monomers. The complex
polyphenolic macromolecule composed of beta-O4-aryl linkage are known as
lignins.

The fatty acid esters are known as Lipids. These are the basic building blocks of
biological membranes. Lipids are amphiphilic. Fatty acids consist of unbranched
chain of carbon atom connected with single bonds or double bonds and known
as saturated fatty acids and unsaturated fatty acids respectively. The lipids which
are present in biological membranes with hydrophilic head are of three classes.
These are Glycolipids, Phospholipids and Sterol (e.g. Cholesterol).

The molecule which has both carboxylic acid functional group and amino group
is known as amino acids. Amino acids are the building blocks of proteins. During
protein synthesis only two amino acids other than twenty are known to be
involved during translation. These are selenocysteine and Pyrrolysine.

Proteins are known as particular series of amino acids and attached by linear
polypeptide backbone. There are different types of proteins. They are globular or
filamentous proteins. Many enzymes are proteins. But it does not mean all proteins
are enzymes. Many a time's statements are made in study and are asked to justify.
It is "All enzymes are proteins but all proteins are not enzymes" The difference in
type is related with their form or structures. The hydrogen bond is either alpha helix
or beta sheet. The secondary structure of protein is known by their number
arrangement. Thus when two or more number of polypeptide chains clusters, they
form protein. This is known as quaternary structure of protein. Hemoglobin is
protein which has two alpha and two beta polypeptide chains. Hemoglobin are
integral part of blood and this is very important in oxygen transport though out
the body.Vitamins are not synthesized by a given organism. Coenzyme is one
such example but it is very vital for the survival or health. Vitamins are vital amines.
Another biomolecule is Apoenzyme which is a protein but without cofactors,
substrates or inhibitor bound to it. It is inactive form of storage, transport or
secretary form of protein. When cofactor is added to Apoenzyme , it becomes
activated enzymes. Inorganic Cofactors are metals ions, iron sulfur cluster and
organic cofactors are flavin and heme.

Isoenzymes or isozymes are multiple form of enzyme. They have slightly different
protein sequence but usually not identical functions. It has been found in research
that different genes are responsible for its production.
Personal Reaction

Bibliography
©2019 Encyclopædia Britannica, Inc.

1. Bunge, M. (1979). Treatise on Basic Philosophy, vol. 4. Ontology II: A World of Systems, p. 61-2. link.
2. ^ endogeny. (2011) Segen's Medical Dictionary. The Free Dictionary by Farlex. Farlex, Inc. Accessed
June 27, 2019.
3. ^ Green, D. E.; Goldberger, R. (1967). Molecular Insights into the Living Process. New York:
Academic Press – via Google Books.
4. ^ Gayon, J. (1998). "La philosophie et la biologie". In Mattéi, J. F. (ed.). Encyclopédie philosophique
universelle. vol. IV, Le Discours philosophique. Presses Universitaires de France. pp. 2152–2171 –
via Google Books.
5. ^ Jump up to:a b c d Slabaugh, Michael R. & Seager, Spencer L. (2007). Organic and Biochemistry for
Today (6th ed.). Pacific Grove: Brooks Cole. ISBN 0-495-11280-1.
6. ^ Jump up to:a b Alberts B, Johnson A, Lewis J, Raff M, Roberts K & Wlater P (2002). Molecular biology
of the cell (4th ed.). New York: Garland Science. pp. 120–1. ISBN 0-8153-3218-1.
7. ^ Saenger W (1984). Principles of Nucleic Acid Structure. Springer-Verlag. ISBN 0387907629.
8. ^ Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC,
Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM
(2008). "RNA Backbone: Consensus all-angle conformers and modular string
nomenclature". RNA. 14: 465–481. doi:10.1261/rna.657708. PMC 2248255. PMID 18192612.
9. ^ Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (1982). "Self-splicing RNA:
autoexcision and autocyclization of the ribosomal RNA intervening sequence of
Tetrahymena". Cell. 31: 147–157. doi:10.1016/0092-8674(82)90414-7. PMID 6297745.
10. ^ Jump up to:a b Peng, Bo & Yu Qin (June 2009). "Fructose and Satiety". Journal of Nutrition: 6137–42.