Mapua Institute of Technology Introduction to Bioelectronics and Bioinformation Engineering

School of Chemical Engineering and Chemistry The Biological Cell and the Biomolecules

BIOELECTRONICS is the discipline resulting from the convergence of biology and electronics. It has the
potential to significantly impact many areas important to the nation’s economy and well-being, including
healthcare and medicine, homeland security, forensics, and protecting the environment and the food
(1)
supply. Not only can advances in electronics impact biology and medicine, but conversely
understanding molecular biology may provide powerful insights into efficient assembly processes,
devices, and architectures for nanoelectronics technologies, as physical limits of existing technologies are
(1)
approached.
Interdisciplinary fields of Bioelectronics and Bioinformation Engineering

A. BIOLOGY: Review of the Cells

Prokaryotic cell e.g. bacterium Eukaryotic cells: Plant and Animal cells

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Mapua Institute of Technology Introduction to Bioelectronics and Bioinformation Engineering
School of Chemical Engineering and Chemistry The Biological Cell and the Biomolecules

Biomolecular Components of the Cell

 Carbohydrates
 Lipids
 Proteins
 Nucleic acids: DNA and RNA

Carbohydrates – serve as energy source and for energy storage, and as structural components of cells,
e.g. starch, glycogen and cellulose

Lipids – are structural component and energy storage, e.g. fats stored in fat cells, cell membrane, waxes
and oils

Proteins – are macromolecules consisting of polymers of amino acids, polypeptides. Proteins perform a
vast of functions including catalysis, responding to stimuli and transporting molecules.

Nucleic acids – are polymers of nucleotides, responsible for carrying and expressing genetic information

PROTEIN
Proteins are biopolymers (called polypeptides) of L-amino acids.
Only L-amino acids are used to make proteins (rare exceptions of proteins in bacterial cell wall, which
contain some D-amino acids)
The process of putting amino acids together to make proteins is called translation. Translation relies on
the genetic code, in which three nucleotides in mRNA specify one amino acid in protein.
The difference between a polypeptide and a protein is that the term polypeptide refers simply to a chain of
amino acids. The term protein refers to the chain of amino acids after it folds properly and is (in some
cases) modified. Proteins may consist of more than one polypeptide chain.
Proteins are sometimes described as the "workhorses" of the cell because they do so many things -
catalyze reactions, provide structural integrity, transport molecules, provide movement, bind molecules,
and others.

AMINO ACIDS
Amino acids are the building blocks of proteins. An amino acid consists of an asymmetric carbon (-
carbon) at the center with four different groups attached to it: an amino group, a carboxyl group, a
hydrogen atom and a variable group, R (except for glycine). Thus amino acids have chiral centers.

Stereoisomer of alanine

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Mapua Institute of Technology Introduction to Bioelectronics and Bioinformation Engineering
School of Chemical Engineering and Chemistry The Biological Cell and the Biomolecules

Essential amino acids Non-essential amino acids

Threonine, Thr (T) Alanine, Ala (A)
Valine, Val (V) Asparagine, Asn (N)
Methionine, Met (M) Aspartic acid, Asp (D)
Isoleucine, Ile (I) Cysteine, Cys (C)
Leucine, Leu (L) Glutamic acid, Glu (E)
Lysine, Lys (K) Glutamine, Gln (Q)
Phenylalanine, Phe (F) Glycine, Gly (G)
Tryptophan, Trp (W) Proline, Pro (P)
Histidine, His (H) Serine, Ser (S)
Arginine, Arg (R) Tyrosine, Tyr (Y)

Essential amino acids are those the body cannot make and must be obtained from dietary sources.

PEPTIDES AND POLYPEPTIDES

Peptides are chains of amino acids joined by a peptide bond. The linkage of two amino acids is a
dipeptide and the reaction is an example of condensation reaction. When few amino acids are joined,
they are called oligopeptide, and thousands of it, they are called polypeptide.

Peptides are named from sequence of their constituent amino acids, beginning from the amino terminal
residue at the left proceeding toward the carboxyl terminus at the right.

Peptides undergo characteristic chemical reactions:

a. Hydrolysis by boiling with either strong acid or base
b. Hydrolysis by certain enzymes (proteases)

Some biologically important peptides have only few amino acid residues like the commercially
synthesized L-Aspartyl-L-phenylalanyl methyl ester or better known as aspartame.

STRUCTURE OF PROTEINS
The order or sequence of amino acids distinguishes different proteins from each other. The sequence of
amino acids determines the 3-dimensional shape of the protein. Alterations to the amino acid sequence of
a protein changes its 3D shape.

Primary structure is the most basic level of protein structure. It is the linear sequence of amino acids.
The primary structure of a protein is specified by the order of bases in the genomic DNA. Different
sequences of the acids along a chain, however, affect the structure of a protein molecule in different
ways.

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Mapua Institute of Technology Introduction to Bioelectronics and Bioinformation Engineering
School of Chemical Engineering and Chemistry The Biological Cell and the Biomolecules

Secondary structures are stable and occur widely in

proteins (globular and fibrous). Most prominent are the
-helix and -conformation. The simplest arrangement
the polypeptide chain could assume with its rigid
peptide bonds is a helical structure that is right-
handed. -Helical structure (right-handed) is
predominant in -keratin. Secondary structures are
stabilized by favorable hydrogen bonding between
residues and have been brought into close
juxtaposition by folding or coiling of the primary
structure. In the -conformation, the backbone of the
polypeptide chain is extended into a zigzag manner
(-pleated sheets) and the hydrogen bonding can
either be intrachain or interchain between peptide
linkages of adjacent polypeptide chains.

-keratin – right-handed helix; rich in Phe, Ile, Val,

Met, and Ala.
collagen – left-handed helix; rich in Gly, Ala, Pro and
Hyp

Structure-properties of fibrous proteins:

-helix cross-linked by disulfide bonds – tough, insoluble protective structures of varying hardness and
flexibility ex. -keratin of hair, feathers and nails
-Conformation – soft, flexible filaments ex. Fibrion of silk
Collagen triple helix – high tensile strength, without stretch ex. Collagen of tendons, bone matrix

Myoglobin Hemoglobin

Tertiary structure (three dimensional arrangement of atoms in protein) is formed when forces cause the
molecule to become even more compact, as in globular proteins. Each molecule of a particular protein
has the same conformation and this differs from molecules of other proteins.

Myoglobin contains a single polypeptide chain folded about a prosthetic group, the heme, which contains
the oxygen binding site. The heme in myoglobin is in the form of an iron complexed with protoporphyrin
IX. Myoglobin, by contrast with hemoglobin, is an oxygen storage protein. Oxygen transported to tissues
must be released for utilization. In tissues, such as muscle, with high oxygen demands, myoglobin
provides large oxygen reserves.

Quaternary protein structure refers to the interaction between subunits of oligomeric protein or large
protein assemblies as in hemoglobin and some enzymes. Four subunits of hemoglobin exhibit
cooperative interactions on oxygen-binding.

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 Mapua Institute of Technology Introduction to Bioelectronics and Bioinformation Engineering
School of Chemical Engineering and Chemistry The Biological Cell and the Biomolecules

FUNCTIONS OF PROTEINS
a. Transport
b. Nutrient and storage
c. Contraction
d. Structure or support
e. Defense
f. Regulation of cellular or physiological activity
g. Biological Catalyst

ENZYMES
- Most enzymes are proteins.
- They function as catalyst in biological reactions.
- Enzymes are globular proteins - their molecules are round in shape.
- Each enzyme has a specific catalytic action.
- Their normal activity depends on their environment.
- Abnormal conditions cause reduced activity

NUCLEIC ACIDS
Nucleic acids are complex structures composed of nucleotide chains that are used to maintain genetic
information.

Component structures of nucleotide:

 Pyrimidine and purine bases
 Sugar
 Phosphate

Pyrimidine bases Purine bases

NH2 O O H 2N O

CH3 N N
N HN HN HN HN

O N O N O N N N H2N N N
H H H H H

CYTOSINE (C) URACIL (U) THYMINE (T) ADENINE (A) GUANINE (G)

Nucleosides: Pyrimidine + sugar

NH2 O NH2
O O

CH3 N
N HN N C N
HN HN C
CH
CH
HC C
N O N O N C C
O N N N
H2N N
HO HO HO
O O HO HO
O O O

OH OH OH OH OH OH OH OH OH OH
CYTIDINE URIDINE THYMIDINE ADENOSINE GUANOSINE

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Mapua Institute of Technology Introduction to Bioelectronics and Bioinformation Engineering
School of Chemical Engineering and Chemistry The Biological Cell and the Biomolecules

Nucleotides: Nucleoside + Phosphate

C
P U T A G
O P P P P
O O O O

OH OH
OH OH OH OH OH OH OH OH
Cytidine Uridine Thymidine Adenosine Guanosine
monophosphate monophosphate monophosphate monophosphate monophosphate

Two common Nucleic Acids:

1. RNA – Ribonucleic acid
RNAs are single-stranded polynucleotides that are used to express genetic information.
Three types of RNAs:
rRNA – ribosomal RNA
mRNA – messenger RNA
tRNA – transfer RNA

2. DNA – Deoxyribonucleic acid

DNAs are double-stranded polynucleotide helix that carries the genetic information.

Differences in the structure of RNA and DNA

RNA DNA
A, G, C, U type of bases used A G, C, T
ribose sugar used Deoxyribose
single polynucleotide strand double

 Nucleic acids are formed through linkage of one nucleotide with another by forming a covalent
bond called 3’,5’-phosphodiester bond. The next nucleotide to be attached to the growing
polynucleotide chain is always added at the 3’-end.

 Nucleic acids are constructed starting from the 5’-end going to the 3’-end
Example: 5’- ATG CCC GGG AAA GCG TTT CCG……….-3’

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Mapua Institute of Technology Introduction to Bioelectronics and Bioinformation Engineering
School of Chemical Engineering and Chemistry The Biological Cell and the Biomolecules

James Watson and Francis Crick’s model of the DNA

The DNA molecule consists of 2 strands of polynucleotide held together through hydrogen bonding
interaction of the bases contained in the 2 strands. This pairing of bases is called complimentary base
pairs: A=T and CG

The orientation of the 2 strands is anti-parallel to each other.

Cytosine Guanine Thymine Adenine

Parameters A Form B Form Z Form

Direction of Right Right Left
helical
rotation
Residues 11 BP 10 BP 12 BP
per turn of
helix
Occurence Favored at Favored at high Favored at high
dehydrated water salt concentration
condition concentration

B-Form DNA

A-form DNA Z-form DNA

References:

(1) Walker, G., et al. (2009) A Framework for BIOELECTRONICS: Discovery and Innovation, Report for
Semiconductor Electronics Division, NIST.
(2) Starr and Taggart (2004). Biology. The Unity and Diversity of Life, 10th edition, Wadsworth Group,
Thomson Learning, Inc., California
(3) Matthews, van Holde and Ahern, Biochemistry 3rd edition
nd
(4) Lehninger, Nelson and Cox (1993). Principles of Biochemistry, 2 edition, Worth Publishers, New
York
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