Introduction to Biology

Diversity of Life

 Classification of living organisms on the basis of cell structure

 Prokaryotes

 Eukaryotes

 The name is from the Greek, meaning ―truly nucleated,‖ from the words eu,
―well‖ or ―truly,‖ and karyon, ―kernel‖ or ―nucleus‖.

Ref: Book-Molecular Biology of the Cell (Alberts)

Diversity of Life

Ref: Book-Molecular Biology of the Cell (Alberts)

Cell Structure

 Prokaryotic cells

https://www.youtube.com/watch?v=HJPvCnH6KkI

 Eukaryotic cells

https://www.youtube.com/watch?v=URUJD5NEXC8
 Eukaryotes vs Prokaryotes

https://www.youtube.com/watch?v=zZtcMBTQaS4
Prokaryotic vs Eukaryotic Cell

Book- Molecular Cell Biology by Lodish

 Universal Features of Cells

 Vehicle for the hereditary information that defines the species

 Cell includes the machinery to gather raw materials from the environment,
and to construct out of them a new cell in its own image, complete with a
new copy of the hereditary information.

 Nothing less than a cell has this capability.

 All Cells Store Their Hereditary Information in the Same Linear Chemical
Code

 A, T, C, G

Ref: Book-Molecular Biology of the Cell (Alberts)

 Polymerization of DNA
 Replication- Templated Polymerization

 Each monomer in a single DNA strand—that is, each nucleotide—consists of two

parts:

 a sugar (deoxyribose) with a phosphate group attached to it

 a base, which may be either adenine (A), guanine (G), cytosine (C) or thymine (T)

 sugar is linked to the next via the phosphate group, creating a polymer chain
composed of a repetitive sugar-phosphate backbone with a series of bases
protruding from it

Ref: Book-Molecular Biology of the Cell (Alberts)

DNA Polymerization

Ref: Book-Molecular Biology of the Cell (Alberts)

Central Dogma

Ref: Book-Molecular Biology of the Cell (Alberts)

 Biological Diversity

 Article 2 of the Convention on Biological Diversity/Rio Convention, 1992) defines

biodiversity as

 ‗the variability among living organisms from all sources including, inter alia, terrestrial,
marine and other aquatic ecosystems and the ecological complexes of which they are
part; this includes diversity within species, between species and of ecosystems‘.

Minelli A. Diversity of Life. e LS. 2001 May 30.

 Levels of Biological Diversity

 Genetic diversity

 Heritable variation within a single species, including the differences among individuals
in a local population

 Species diversity

 Taxonomic Diversity

 Ecosystem diversity

 Differences among aquatic and terrestrial landscapes or vegetation types, such as a pond
and a seashore, a conifer forest and an alpine meadow

Minelli A. Diversity of Life. e LS. 2001 May 30.

 Diversity of Life

 Two major aspects of geographical diversity of the physical environment that

allow living beings to become numerous:

 Habitat heterogeneity at local, regional, continental and even global scale

 Multiple adaptations developed by most living beings in relation to the other organisms

with which they interact, be these competitors, prey, predators, hosts or symbionts.

Minelli A. Diversity of Life. e LS. 2001 May 30.

 History of Life

 Life was represented only by prokaryotic, mostly unicellular forms, later

accompanied by the first, still unicellular, eukaryotes

 Two evolutionary transitions proved to be of fundamental importance for the

subsequent history of biological diversity:

 the origin of sex

 origin of multicellularity
Estimate of Diversity

 Most commonly used descriptor of species diversity is species number.

 Improve the information content of biodiversity estimates
 Suggested - incorporate measures of phylogenetic relatedness among the species
present in a given area

 Current level of knowledge varies greatly between different groups

Minelli A. Diversity of Life. e LS. 2001 May 30.

 Evolution and Phylogeny

 Earth formed about 4.5 billion years ago, 1 billion years later, Earth saw the
emergence of life, the evidence of which can be found in fossils

 3 major phases of evolution

 Appearance of prokaryotic organisms

 Eukaryotes

 Multicellular organisms

Sarma H, Pradhan S, Mattaparthi VS, Kaushik S. Phylogenetic Analysis: Early Evolution of Life.
Origin of Life and evolution
 Evolution and Phylogeny
 Evolution - Transition or adaptation of an organism, in response to the environmental
conditions over the course of time.

 Evolution can be classified into three types

 Chemical evolution-Majorly denotes the prebiotic (before biology) formation of organic

molecules in the period between the formation of the earth and the first appearance of a
living cell

 Molecular evolution- Refers to the changes in living systems that have occurred
thereafter, eventually leading to the formation of unicellular and multicellular
organisms

 Darwinian evolution- Refers to the events after molecular evolution, which led to the
speciation as seen today on Earth.
Chemical Evolution
 Spontaneous generation:
 Oparin and Haldane experiment-
 Haldane, in particular, was fascinated with the experiments where organic molecules
were formed from the mixture of H2O, CO2, and NH2 in the presence of ultraviolet
light.
 Haldane further suggested that the strong reducing conditions may have been present
at that time, which paved the way for the atmosphere of the early earth.
 Haldane‘s article in 1929 recommended that the earth’s prebiotic soup would have
formed first, after which organic mixes of simple sugars and amino acids came into
being (Haldane, 1929).
 Oparin, on the other hand, stated that the primordial soup consisting of organic
molecules could be created in an anaerobic atmosphere in the presence of sunlight,
wherein the coacervate droplets would be formed as a result of the complex reaction
undergone by the organic molecules(Oparin, 1924).
 Miller and Urey experiment
 Established the capability of the earth‘s primitive atmosphere in building life from
inorganic materials. It proved that the conditions existing in the earth’s primitive
atmosphere were sufficient enough to form organic molecules like amino acids.
Molecular Evolution

 Actual chemical evolution would depend upon the polymerization or

condensation of these monomers into polymers (macromolecules like

polypeptides, polysaccharides)

 Sydney Fox and his team in the 1950s synthesized some peptide like products by

heating a dry mixture of amino acids at the temperature between 150 and 180 C,

which they termed as proteinoids, meaning a thermal protein.

Origin of cells and organized structure

 Macromolecules, due to their intermolecular forces, may have aggregated to form

the membrane-enclosed droplets known as coacervates and microsphere, which
exhibits features similar to that of a living system (selective permeability, and
energy use).

 Coacervates (meaning ―to assemble together or cluster‖) are an agglomeration of

colloidal particles in a liquid phase that stays in the form of minuscule droplets.

 Coacervates display a number of compelling features:

 • exchange substance with the environment,

 • increases in size,

 • selective concentration of the compounds within them

Membrane defined the first cell

 This idea was first proposed by Haldane (1929), saying that ―the cell consists of
numerous half‐living chemical molecules suspended in water and enclosed in
an oily film. When the whole sea was a vast chemical laboratory the conditions for
the formation of such films must have been relatively favourable.…‖.

 Goldacre (1958) went on to suggest that the first cell membranes may have been
formed as a result of the wave-action behavior of the lipid‐like surfactants.

 Bangham et al. (1965) were the first group to prove that phospholipids readily
formed lipid-bilayer vesicles, called liposomes.
Membranes formed the first cell
Current model for origin of life hypothesis-
Was it RNA, proteins, or lipids?
Darwinian Evolution

 “descent with modification,” which states that all species have evolved over the
time from a “common ancestor” through the process of natural selection
 Homology and Development

 Richard Owen introduced the term homolog in 1843, defining it as “the same
organ in different animals under every variety of form and function.”

 He next defined analogs as a “part or organ in one animal which has the same
function as another part or organ in a different animal” (Owen, 1848).

 Homologs

 Paralogs – homologous sequences separated by a gene duplication event

 Orthologs – homologous sequences separated by a speciation event (when one

species diverges into two) (Fitch, 1970; Panchen, 1994)
Orthologs and Paralogs
Speciation

 An evolutionary process that gives rise to two or more new and distinct biological

species as a result of lineage- splitting from ancestral population.

 Primal causes of speciation:

 Natural Selection

 Genetic Drift

 Mutation
 Speciation
 Natural selection- It is a process of diversification in survival and reproduction
rate of individuals due to variation in their phenotypes.
 Speciation

 Genetic drift- is the adjustment in the recurrence of a previous gene variant

(allele) in a populace because of impact of random sampling
 Drift can cause allele fixation in a population
 Genetic Bottleneck- This is an evolutionary event where a population reduces
drastically to a smaller size as a result of environmental factors, like
earthquakes, floods, fires, disease, or droughts, or human activities, like
genocide. This causes reduction in the genetic diversity
Bottleneck Effect
Speciation
 Mutation
 Randomness of mutation is the prerequisite for Darwinian evolution where changes in
the heritable feature in an organism occur randomly, without the interference from the
organism‘s environment
 Maybe beneficial/not beneficial
 Survival in the environment
 Alcohol dehydrogenases in yeasts that help them to consume accumulated alcohol
Concept of Common Ancestor

 ―Therefore, I should infer from analogy that probably all the organic beings which
have ever lived on this earth have descended from some one primordial form, into
which life was first breathed‖ (Darwin, 1859)
Concept of Common Ancestor

 LUCA- ―last universal common ancestor‖

 Denote the most current common ancestor of all life forms on earth that share a common
descent.
 Last known LUCA - morphologically and metabolically diverse
 Temperature adaptive
 Contained an RNA genome
 Paleoarchean era
 Probably similar to extremophiles
 Phylogenetics
 The science of studying the evolutionary relatedness among biological groups and
a phylogenetic tree is used to graphically represent this evolutionary relation
related to the species of interest.
 Phylogenies are useful for organizing knowledge of biological diversity, for
structuring classifications, and for providing insight into events that occurred
during evolution.

Figure -Elements of a phylogram

Phylogenetic Tree of Contemporary
organisms
References
 Anderson, Michael; Anderson, Susan Leigh (2007-12-15). "Machine Ethics: Creating an Ethical
Intelligent Agent". AI Magazine. 28 (4): 15–15. doi:10.1609/aimag.v28i4.2065. ISSN 2371-9621.

 Minelli A. Diversity of Life. e LS. 2001 May 30.

 Book- Molecular Biology of the cell (Alberts)

 Sarma H, Pradhan S, Mattaparthi VS, Kaushik S. Phylogenetic Analysis: Early Evolution of Life.

 https://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-
41956/#

 Book- Molecular Cell Biology by Lodish

 Further reading- Phylogeny (https://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_05)

Artificial Intelligence in
Biological Sciences
 Artificial Intelligence

Rich, E. and K. Knight (1991). Artificial Intelligence. New

York: McGraw Hill. “Artificial Intelligence (AI) is the study of
how to make computers do things which at the moment,
humans do better.”
Need for the amalgamation- Big Data

 Data Collection

 Data Analysis

 Data Interpretation
 AI in BI

 Evolution

 Omics

 Systems Biology

 Experimental Data Analysis and Interpretation

Platforms

 Open Targets Platforms

 DeepChem

 CheXNet
 Case Studies

 Origin of Novel Coronavirus (COVID-19): A Computational Biology Study

using Artificial Intelligence
 Nguyen TT, Abdelrazek M, Nguyen DT, Aryal S, Nguyen DT, Khatami A. Origin of
novel coronavirus (COVID-19): a computational biology study using artificial
intelligence. BioRxiv. 2020 Jan 1.

 Artificial Intelligence (AI) applications for COVID-19 pandemic

 Lin L, Hou Z. Combat COVID-19 with artificial intelligence and big data. Journal of
travel medicine. 2020 Jul;27(5):taaa080.
 Artificial Intelligence (AI)-Based Systems Biology Approaches in Multi-Omics
Data Analysis of Cancer
 Biswas N, Chakrabarti S. Artificial Intelligence (AI)-Based Systems Biology Approaches
in Multi-Omics Data Analysis of Cancer. Frontiers in Oncology. 2020;10.
 Benefits of AI in Covid-19

 Early detection and diagnosis of the infection- Red Flags

 Monitoring the treatment

 Contact tracing of the individuals

 Projection of cases and mortality

 Development of drugs and vaccines

 Reducing the workload of healthcare workers

 Prevention of the disease