Q1. What is bioinformatics and medical-informatics? Why study Bio-informatics?

Relationship between
bio-informatics and Healthcare Informatics

Bio-informatics: Interdisciplinary field that develop methods and software tools for understanding (retrieve,
preprocess, store, analyze and organize) biological data, particularly when data set are large and complex. The
interdisciplinary fields are i) Biology ii) Computer science iii) mathematics iv) Information Engineering and v)
Statistics.
Medical Informatics/Healthcare Informatics: Medical informatics is the sub-discipline of health informatics
that directly impacts the patient–physician relationship. It focuses on the information technology that enables
the effective collection of data using technology tools to develop medical knowledge and to facilitate the delivery
of patient medical care.
Relationship between bio-informatics and Healthcare Informatics

Bio-Informatics Healthcare Informatics

This branch is focused on the whole
This discipline of health informatics
society, to inform epidemiology and
uses computer systems for analyzing
other population-wide medical and managing patient data, with the
phenomena. focus being patient care on an
individual level.
Analyzing problems and finding Managing and using data for
solutions improving patient care.
Creating new processes working Gathering, storing, interpreting, and
with a group of peers managing massive amounts of data

Understanding health-related Analyzing data to help take crucial

information and its various concepts decisions and facilitate action
and models
Developing and applying methods, Developing data-driven solutions for
theories, and processes for the improving the health of patients
storage, retrieval, use, and
management of biomedical data,
information, and knowledge
Providing better biological Designing and implementing tools
knowledge for improving human for measuring data, patient care
health effectiveness, and processes

Q2. Write short notes on Genes, Genomes, Proteomics, Amino Acids.

Genes: In biology, a gene is a sequence of DNA or RNA that codes for a molecule that has a function.
During gene expression, the DNA is first copied into RNA. Gene carries all the information to build and maintain
the cell and pass genetic traits to the generations.
Genomes: A genome is an organism’s complete set of DNA, including all of its genes. Each genome contains all
of the information needed to build and maintain that organism. In humans, a copy of the entire genome—more
than 3 billion deoxyribonucleic acid (DNA) base pairs—is contained in all cells that have a nucleus.
Proteomics: The study of protein structure, function, and interactions produced by a particular cell, tissue, or
organism is called as proteomics.
Amino Acids: Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional
groups, along with a side chain (R group) specific to each amino acid.

Q3. What types of biological data are deal with bioinformatics? Write different types of database of
bioinformatics.
Data types
Primary data Sequence
AATGCGTATAGGC Primary database
DNA
DMPVERILEALAVE amino acid

secondary data secondary protein

Secondary db
"motifs": regular structure
expressions, blocks, e.g., alpha-helices,
profiles, fingerprints beta-strands

tertiary protein
tertiary data structure tertiary db
atomic co-ordinates domains, folding units

Classification of Databases

Database

Nucleotide Protein
Primary, 2ndary, tertiary
Whole Genome
database Sequence Interaction Structure
database
1. Biogird 1. PDB
ENSEMBL
1. EMBL [The European Molecular Biology Laboratory] 1. UniProt
2. STRING 2. CATH
2. PIR
2. GenBank [Protein-protein
3. SCOPE
3. SwissProt interaction]
3. DDBJ [DNA Data Bank of Japan] [All are Primary]
1. Protein Data Bank
2. Class Architecture
Specialized Topology Homology
All together is Under
OMIM-inherited disease database [Online Mendelian 3. Structural
The Database-INSDC Classification Of
Inheritance of Man]
International Nucleotide Protein
Sequence Database Gene expression omnibus-Microarray Database
Array expression Database- Microarray Database
Q4. What is protein? Write down the function of protein.
Proteins are linear polymeric chains made of protein-specific sequences of 20 amino acid residue types.
Protein Functions:
They do most of the work in cells and are required for the structure, function, and regulation of the body's tissues
and organs.

• Structural Support

These proteins provide structure and support for cells. On a larger scale, they also allow the body to move.
Example: Actin, Keratin, Collagen and Elastin.

Keratin: Keratin is a structural protein that is found in your skin, hair and nails.

Collagen: Collagen is the structural protein of your bones, tendons, ligaments and skin.

Elastin: Its high elasticity allows many tissues in your body to return to their original shape after stretching or
contracting, such as your uterus, lungs and arteries.

• Storage of amino acids

Storage proteins serve as biological reserves of metal ions and amino acids, used by organisms. Ferritin
stores iron, a component of heme, which is contained in the transport protein, hemoglobin and
cytochromes.
Example: Milk (amino acids)
Amino acid show the Amino group (ammonia group) and these ammonia are very harmful for the body.
If it is stored in body it will damage the body tissue or organ. Therefore it excess amino acid which is
de-attached with the protein are get converted into urea which is less toxic than ammonia.

• Transport of other substances and Maintains Proper pH

A transport protein (referred to as a transmembrane pump, transporter, acid transport protein, cation
transport protein, or anion transport protein) is a protein that serves the function of moving other materials within
an organism. Transport proteins are vital to the growth and life of all living things.

Maintains Proper pH: Protein plays a vital role in regulating the concentrations of acids and bases in your
blood and other bodily fluids. A constant pH is necessary, as even a slight change in pH can be harmful or
potentially deadly. One way your body regulates pH is with proteins. An example is hemoglobin, a protein that
makes up red blood cells. Hemoglobin binds small amounts of acid, helping to maintain the normal pH value of
your blood.
• Response of cell to chemical stimuli
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme
production, gene expression, etc.) as a result of a chemical stimulus.
• Antibodies: is used to protect against disease. Antibodies bind to specific foreign particles, such as viruses
and bacteria, to help protect the body.
Example: Immunoglobulin G (IgG).
• Selective acceleration of chemical reactions: Enzymes are proteins that aid the thousands of biochemical
reactions that take place within and outside of your cells. The structure of enzymes allows them to combine
 with other molecules inside the cell called substrates, which catalyze reactions that are essential to your
metabolism.
Bodily functions that depend on enzymes include:

• Digestion
• Energy production
• Blood clotting
• Muscle contraction

Lack or improper function of these enzymes can result in disease. Example: Phenylalanine hydroxylase

• Acts as a Messenger
Messenger proteins (hormones) transmit signals to coordinate biological processes between different cells,
tissues, and organs.
They’re made and secreted by endocrine tissues or glands and then transported in your blood to their target tissues
or organs where they bind to protein receptors on the cell surface.
Hormones can be grouped into three main categories:
• Protein and peptides: These are made from chains of amino acids, ranging from a few to several
hundred.
• Steroids: These are made from the fat cholesterol. The sex hormones, testosterone and estrogen, are
steroid-based.
• Amines: These are made from the individual amino acids tryptophan or tyrosine, which help make
hormones related to sleep and metabolism.

Protein and polypeptides make up most of your body’s hormones. Some examples include:

• Insulin: Signals the uptake of glucose or sugar into the cell.

• Glucagon: Signals the breakdown of stored glucose in the liver.
• hGH (human growth hormone): Stimulates the growth of various tissues, including bone.
• ADH (antidiuretic hormone): Signals the kidneys to reabsorb water.
• ACTH (adrenocorticotropic hormone): Stimulates the release of cortisol, a key factor in metabolism.

• Balances Fluids

Proteins regulate body processes to maintain fluid balance. Albumin and globulin are proteins in your blood
that help maintain your body’s fluid balance by attracting and retaining water.

If you don’t eat enough protein, your levels of albumin and globulin eventually decrease. Consequently, these
proteins can no longer keep blood in your blood vessels, and the fluid is forced into the spaces between your cells.
As the fluid continues to build up in the spaces between your cells, swelling or edema occurs, particularly in the
stomach region.

• Transports and Stores Nutrients

Transport proteins carry substances throughout your bloodstream-into cells, out of cells or within cells. For
example, hemoglobin carries oxygen from your lungs to body tissues. Glucose transporters (GLUT) move glucose
to your cells, while lipoproteins transport cholesterol and other fats in your blood.
Protein transporters are specific, meaning they will only bind to specific substances. In other words, a protein
transporter that moves glucose will not move cholesterol.

• Provides Energy

Proteins can supply your body with energy. Protein can serve as a valuable energy source but only in situations
of fasting, exhaustive exercise or inadequate calorie intake.

Q5. What is protein structure? Write down the protein secondary structure prediction algorithm.

Chou-Fasman method: Convert primary sequence to secondary structure.

Rule-1: Helix nucleation (Propagation) law: Randomly find 6 stretch of sequence

>1/3 helix breacker-→not form  − helix >2

<1/2 helix maker→form  − helix <3

Rule-2: Helix termination-

P  100

Stop when 4 such type of amino acid. More Makers, less bracker.

Helix maker is denoted as h  b

p = 1.03

p = 1.05

For β-sheet, there are 5 stretch of amino acid sequence.

Rule-3:

Prolin not to be present in middle, N-terminal/C-terminal. There is some tendency of amino acid to present in
 − helix . Charged amino acid, glutamic acid, aspartic acid are present in N/C terminal.

N--> Negative charged amino acid such as Aspartic acid, glutamic acid.

C--> Positively charged amino acid such as lycin, histidin are present in c terminal.

How to calculate the propensity value

Amino acid has higher propensity value for α, it is allocated to the α-helix. Propensity value is depicted as P /
P .

FA in  - helix
P =
F

F is the frequency of residues to be in α-helix.

Q6. Define motif? What is PROSITE? How PROSITE detect motif?

Motif: A protein sequence motif is an amino-acid sequence short and recurring pattern found in similar
proteins; change of a motif changes the corresponding biological function. Motif found in DNA, repeated
pattern present in DNA or protein which is marking something.

 −  −  : Signature (M1), to identify specific protein families (S1).  − T −  − T : M 2 → S 2

Motif act as designation, Uniqueness, Marker for getting the super families.
a1 − a2 − a3 − a4 → Primary Structure of Protein/ - helix and  - sheet pattern of Amino Acid , how the pattern
is organized is called it motif.

The PROSITE database consists of a large collection of biologically meaningful signatures that are described as
patterns or profiles. PROSITE predict the motif that are presenting in protein. In PROSITE there are some
notation and marking system in amino acid sequence.

Notation/Rules:

1) Name – Single Alphabetic

2) – (linked) Example: (His + Ala)→H-A
3) Any amino acid depicted as X→(His+ Any Amino Acid +Ala)-H-X-A
4) [aaa]→ Any one of them, [AVT]-→Alanine or valine or Threonine
Example: H-X-[AVT]
5) {aaa}→Exception of them
Example: H-X-{AVT}
6) <[aa]>→ Restricted to be present at N or C terminal.
<[p]> → Restricted to be present Proline at N or C terminal
His + Any aa (amino acid) + Na
7) Rules to get the PROSITE: Repetition (4 Alanine) A(4)
[AC]–X-X(4)-{ED} A/C any aa- -V-X-X-X-1
How PROSITE detect motif: by Chou-Fasman method.

Q7. Define homolog. What are the difference between an ortholog and a paralog?

Homology-Homo means same and logy means relationship. At least two individual/organism are compare to
represent the homology/analog. Similar origin that is called homology. Example-Human Arm, Bat Wing and
Mouse forelimb.
Analogy is the similarity in function of two individual/organism but it may differ in origin/structure. Example:
Bat Wing, Butterfly Wing and Bird Wing.

Homolog is divided into two parts: Ortholog and Paralog

Ortholog: Same type of gene in different speciation.
Example-Mouse α, Chick α and frog α
Paralog: Gene duplication (Mouse α+Mouse β) in speciation.
Q8. FASTA vs BLAST.
• Similarity matching of words (3 amino acids,11 bases) But BLAST does not require
identical words.
• In BLAST, If no words are similar, then no alignment. BLAST Will not find matches for
very short sequences.
• BLAST Dose not handle gaps well. “Gapped BLAST” is somewhat better.
Q9. What is multiple .
Multiple Sequence Alignment (MSA)
ATCG
A1
TGGA
A3
ATCG
A2
TCA
Phylogenetic Trees: It is the process for showing genetic, morphological, physiological relatedness and
evolutionary relationship between species. It is the kind of diagram to draw the idea between different species
emerging in different time duration. In order to construct the phylogenetic tree, we can predict/draw the
evolutionary relationship between the living organisms which are more closely related to each other and which
are least related to the organisms.

Software: We can draw Phylogenetic tree from these sequence

S1, S2, S3, S4…………………S6

MSA

Phylogenetic tree

Evolutionary tree

Q10. You are given two DNA sequences ACGTCCTTCATT and GTCTCATG. You have a scoring scheme
where a

• A match gives you +1

• a mismatch gives you −1
• opening a gap costs you −1

Write down the best alignment of the

two sequences.
Q11.

Q12.

Q13.

Q14.
Q15. Describe two main differences between local dynamic programming algorithm (Smith-Waterman
algorithm) and global dynamic programming algorithm (Needleman-Wunsch algorithm).

Q16.