Fundamentals of Bioinformatics | Bioinformatics #1

5 min readNov 2, 2023

Basic Terms and Concepts

Science: “a systematically organized body of knowledge on a particular subject”
Technology: “the application of scientific knowledge for practical purposes”
Biology: “the comprehensive (kapsayıcı) the study of living organisms”
Informatics: “the study (i.e. collection, classification, storage, retrieval, and dissemination (yayma)) of recorded knowledge”
Bioinformatics & Computational biology (theoretical): “conceptualizing biology in terms of bio-entities and then applying informatics techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these entities, on a large-scale” (Luscombe et al., 2001)
Computational biology (practical): “Computational analysis of biological data for scientific inference”
Bioinformatics (practical): “Developing methods, tools and services for biological data analysis”
Computational Molecular Biology: Subset of computational biology that focuses on proteins, DNA, RNA
Computational Genomics: Subset of computational biology that focuses on genomes or proteomes (genes or proteins in the context of an entire organism)
Computational Structural Biology: Subset of computational biology that focuses on properties of structures of molecules

The rise of computation in biology came due to the need to analyze the flow and content of this information in order to understand it and to manipulate and ultimately control life.

The Cell

Living organisms (on Earth) require ability to

Separate inside from outside (lipids)
Build 3D machinery to perform biological functions (proteins)
Store information on how to build machinery (DNA)

All cells have some common features: Membrane, cytoplasm.

Organisms — Eukaryotes and Prokaryotes

Prokaryotic cells are simpler than eukaryotic cells
Prokaryotes are (mostly) single cellular organisms
Eukaryotic cell has a nucleus(çekirdek), separated from the rest of the cell by a membrane
Eukaryotes can be single cellular (Yeast) or multicellular (animals, plants)
Prokaryotes include Archaea and Bacteria.
Eukaryotes include fungi, certain algae, plants, and animals.

Structure of Eukaryotic Cells

Nucleus contains chromosomes, which are the carrier of the genetic material
Organelles like mitochondria, lysosomes, golgi complexes are enclosed compartments within the cell and are responsible for particular biological processes
Area inside the cell membrane and outside of the organelles is called the cytoplasm
Cell membrane: Cell membranes consist of two layers of lipid molecules with hydrophobic ends facing in (keeps water out)

Nucleus: Contain genetic material. Separated from the rest of the cell by a nuclear membrane.

Signaling, Control, and Gene Activity

Cells make decisions through complex networks of chemical reactions, called pathways

Synthesizing new materials
Breaking material down for spare parts
Signals to eat, die, or divide
Signals to one another to communicate

Central Dogma of Molecular Biology

Information flows from DNA through RNA to synthesize proteins in cells

DNA:
• Holds information on how the cell works

RNA:
• Acts to transfer short pieces of information to different parts of the cell • Provides templates to synthesize proteins

Proteins:
• Form enzymes that send signals to other cells and regulate gene activity • Form the body’s major components (hair, skin, etc)
• Often referred to as the workhorses of the cell

DNA

Genes & Genome

Gene: Contiguous subparts of single strand DNA
Genome: The set of all genes in a given organism

The genes consist of short coding sequences or exons are interrupted by a longer intervening noncoding sequence or introns (although a few genes in the human genome have no introns).

RNA (Ribonucleic acid)

DNA → RNA (Transcription / Gene Expression) RNA polymerase(enzyme):

Finds gene initiation marker (codon) on DNA strand
Reads DNA strand containing marker
Builds (complementary) strand of messenger RNA (mRNA)
Stops when gene end marker (codon) found

There are several forms of RNA:

mRNA (messenger RNA) — carries a gene’s information out of nucleus
tRNA (transfer RNA) — transfer’s mRNA’s information onto a protein chain of amino acids
rRNA (ribosomal RNA) — part of the ribosome, where proteins are synthesized

Gene Expression

Gene expression; is the process of producing a biologically functional molecule of either protein or RNA (gene product)

Transcription: RNA polymerase makes a copy of information in the gene (complementary RNA). Transcription refers to the process of copying a piece of the DNA onto mRNA.

Translation: Occurs on ribosomes, messenger RNA is decoded or translated to determine the sequence of amino acids in the protein being synthesized. Uses mRNA as template to make proteins. One codon corresponds to one amino acid. (From mRNA to Proteins)

Genes and Proteins

One gene encodes one* protein.
Like a program, it starts with start codon (e.g.ATG), then each three code one amino acid. Then a stop codon (e.g. TGA) signifies end of the gene.

Sometimes,in the middle of a (eukaryotic) gene, there are introns that are spliced out (as junk) during transcription. Good parts are called exons.

Proteins

Huge proportion of cell (after water)
Many functions: Structure (e.g. collagen in bone), Enzymes, Transmembrane receptors, Hormones
Four levels of structure