Introduction to Computational Biology Flashcards

These flashcards cover the historical perspective of cell theory, distinctions between cell types, key cellular organelles, DNA replication mechanisms, cell division stages, and computational biology analogies including Genetic Algorithms.

Francis Janssen and Zacharias Janssen

Constructed the first compound microscope in 1590, providing $10-30\times$ magnification and enabling the observation of small organisms like fleas.

Robert Hooke

Examined thin cork slices in 1665 and coined the term "cell" from the Latin word cella, meaning hollow space.

Anton van Leeuwenhoek

Perfected lens polishing to reach up to $300\times$ magnification, discovering bacteria, protozoa, and other living microorganisms.

Schleiden and Schwann

Botanist and Zoologist pair who established in 1838-1839 that all living organisms are composed of cells as the fundamental units of structure and function.

Rudolf Virchow

Pathologist who declared in 1855 that all cells arise from pre-existing cells, forming the basis of life continuity.

Prokaryotes

Unicellular organisms belonging to bacteria or archaea domains that lack a nucleus and store DNA in a circular molecule within the nucleoid region.

Eukaryotes

Cells characterized by a true nucleus, multiple linear chromosomes associated with histones, and a variety of membrane-bound organelles.

Binary Fission

The specific mode of cell division observed in prokaryotes such as bacteria.

Plasma Membrane (Fluid Mosaic Model)

Structure proposed by Singer and Nicolson in 1972, consisting of a phospholipid bilayer with hydrophilic heads and hydrophobic tails where proteins move laterally.

Nucleolus

A region within the nucleus that synthesizes rRNA and assembles ribosomal subunits.

Cytoskeleton

An internal framework composed of microtubules, microfilaments, and intermediate filaments that provides shape, mechanical support, and facilitates transport.

Rough Endoplasmic Reticulum (RER)

A network of flattened sacs (cisternae) studded with ribosomes that synthesizes and processes proteins for secretion or membrane insertion.

Smooth Endoplasmic Reticulum (SER)

A network of tubules lacking ribosomes that synthesizes lipids, phospholipids, and steroid hormones, while also detoxifying drugs.

Ribosomes

Non-membrane-bound organelles composed of rRNA and proteins that translate mRNA into polypeptide chains.

Mitochondria

Double membrane-bound organelles with an inner membrane folded into cristae; known as the powerhouse of the cell for producing ATP through cellular respiration.

Golgi Apparatus

A stack of flattened sacs (cisternae) that modifies, sorts, and packages proteins and lipids received from the endoplasmic reticulum.

Lysosomes

Single membrane-bound organelles containing hydrolytic enzymes, often called "suicidal bags" or "recycling centers" for their role in intracellular digestion.

Vacuoles

Fluid-filled sacs surrounded by a membrane called the tonoplast; they maintain turgor pressure and store water, nutrients, and waste.

Cell Wall

A rigid outer covering made of cellulose (plants), chitin (fungi), or peptidoglycan (bacteria) that protects the cell and prevents osmotic bursting.

Chloroplasts

Green, double membrane-bound organelles in plants containing thylakoids (grana) and stroma where photosynthesis occurs.

DNA Replication

The process by which a cell copies its DNA, occurring via a semi-conservative mechanism where each new molecule has one parental and one new strand.

Helicase

An enzyme that unwinds the DNA double helix by breaking hydrogen bonds, creating a replication fork.

DNA Polymerase

An enzyme that adds complementary nucleotides to template strands in the $5' \rightarrow 3'$ direction during DNA synthesis.

Topoisomerase

An enzyme that prevents DNA from becoming tangled or over-coiled as it unwinds during replication.

Interphase

The period of the cell cycle between divisions, subdivided into $G_1$ (gap 1), S (active DNA synthesis), and $G_2$ (gap 2) phases.

Mitosis

Division phase in somatic cells consisting of prophase, metaphase, anaphase, and telophase, resulting in two identical diploid daughter cells.

Meiosis

A reductional division in germ cells resulting in four genetically different haploid gametes, involving processes like crossing over in Prophase I.

Cyclin-Dependent Kinases (CDKs)

Enzymes that, when activated by regulatory proteins called cyclins, control the progression through various stages of the cell cycle.

p53 and Rb (Retinoblastoma protein)

Tumor suppressor proteins that regulate the cell cycle by detecting DNA damage and controlling the G1 to S phase transition.

Genetic Algorithm (GA)

A search and optimization technique inspired by biological evolution that uses selection, crossover, and mutation to improve solution quality over generations.

Fitness Function

A problem-specific mathematical formulation in a Genetic Algorithm that evaluates how well a potential solution (chromosome) solves the given problem.

Crossover (Genetic Algorithm)

An operator used to create superior offspring by combining parts from two selected parent chromosomes.

Mutation (Genetic Algorithm)

An operator that makes random changes to genes in offspring to maintain population diversity and avoid local optima.

Evolutionary Computing

A collection of algorithms inspired by Darwinian evolution (selection, variation, inheritance) used to model complex biological behaviors like tumor growth and tissue regeneration.