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Overview of the

Life Sciences

About Life, The Life Sciences, and theBiologists Way of Life!

BI6101 Introductory Biology

MSc Bioinformatics, AY2012/2013, July Semester

Lecture 1 - Timothy Tan

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Map of the HumanGenome?

You are here

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Map of the HumanGenome?

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Source: Newsweek, August 2001

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What are the Life Sciences?

Life sciences refer to scientific study of the living world as awhole, a new synthesis of several traditional scientificdisciplines including biology, zoology, and botany, andnewer, more specialised areas of study such as biophysics,sociobiology, biotechnology, biopharmaceuticals, tissueengineering, biostatistics, bioinformatics, etc.

This approach has led to many new ideas and discoveriesas well as to an emphasis on ecology, the study of livingorganisms in their natural environments.

Broadly speaking, life sciences include any study orresearch discipline that contributes to the understanding oflife processes.

From Singapore Science Centre Q&Ahttp://www.science.edu.sg/ssc/detailed.jsp?artid=79&type=6&root=4&parent=4&cat=39

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Word Cloud generated by wordle.net from text on http://en.wikipedia.org/wiki/Life_sciences

Life Sciences = Biology ?

WhataretheLifeSciences?

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Taking an IntegrativeApproach to the Teaching of

Life SciencesWhataretheLifeSciences?

L01-7

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www.sciencecartoonsplus.com

WhataretheLifeSciences?

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ScienceSilo Mentality vs.an Integrated Approach?

http://www.flickr.com/photos/tim_best_1972/2925719953/

L01-9

WhataretheLifeSciences?

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BI6101 - Foundations

Only selected key topics will be covered:

Molecular Biology, Biotechnology

Cell Biology, Reproduction, Cellular Energetics

Classical Genetics, Population Genetics

Developmental Biology

Ecology, Biodiversity

Evolution, Molecular Evolution

Some classical biology (botany, zoology)

(Human Physiology)

Hidden curriculum

Ethical, Legal & Social Issues (ELSI)

Self-directed learning, critical evaluation of information

L01-10

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BI6101 Course Structure

Molecular

Building Blocks

Molecular Genetics

Cell

Structure & Function Mitosis & Meiosis (Cell Cycle)

Cellular Energetics (Biochemistry)

Systems

Classical Genetics Developmental Biology

Ecology & EvolutionL01-11

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Biology

Studying the basics - and the basis -of life

L01-12

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Biology as a Science

Biologists tend to:

Classify

Compare

Ask Why? and How?

Formulate theories based on observations to explainnatural phenomena

Adopt a hypothesis-driven methodologyL01-13

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Biologyas

aScience

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http://home.comcast.net/~fsteiger/theory.htm

Biologyas

aScience

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http://www.cs.msstate.edu/~hualin/acss.htmlhttp://ink.primate.wisc.edu/~assay/bioassay.html http://bbu.uwcm.ac.uk/html/research/bioinfo.htm

in vivoin life - studies in living organism

in vitroin glass - studies on living cells orbiological processes in the lab

in silicoin silicon - computational studies,simulations, ie. bioinformatics

Biologyas

aScience

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Bio-XandX-omics

Genomics

DNA: molecular genetics

Whats hidden in junk DNA ?

Transcriptomics

RNA: messenger, ribozyme, riboswitch, antisense

Proteomics

Study of Proteins

Metabolomics

Protein-Protein interactions, cellular function

Epigenetics

Non-inheritable interactions between Proteins, DNAand RNA. Source of complexity and individuality?

Et cetera

L01-18

Biologyas

aScience

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BI6101 aims to provide framework to understandthe Bio in Bioinformatics and other Bio-X fields

L01-19

Word Cloud generated by wordle.net from text on http://en.wikipedia.org/wiki/Bioinformatics

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http://www.lsi.us.es/~isanepo/research.html

Scope of Bioinformatics?

Bioinformatics (BI) is all aboutcollecting, integrating and processingbiologically-derived data,to generate

useful and understandableinformation

Whats in a name?

bioinformatics biological informatics

computational biology

in silico biology

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Molecular BI /Sequence BI

L01-21

atgcatgt

agctgatg

catgcatg

ctagctgtgtatgtct

aatctatta

gcgcggc

gctatcgt

Wikimedia Commons; nexomics.com; semanticlifescience.wordpress.com

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Structural BI

L01-22

http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb2_2.html

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http://abeautifulwww.com/2008/05/29/network-visualization-for-systems-biology/

Systems Biology

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Biomedical Informatics

L01-24

Bioscience

Medicine

Informatics

BioinformaticsBiomedical

Science

Biomedical

Informatics

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So what i s Life?

L01-25

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Defining Life

How do we know this is a living thing?

Feeds

GrowsBreathes

Reproduces

Excretes

Moves

Responds

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Characteristics of Living Things

Growth and development

Reproduction

Respond to Stimuli

Interactions with others and environment Adaptation (Evolution)

Made up of cells

Have nucleic acids as genetic material Acquisition and conversion of energy

Have structure and organisation

But

L01-27

De

finingLife

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http://post.queensu.ca/~forsdyke/prions.htm

Prions

Fred Murphy, CDCSARS Virus

Made up of cells

Have nucleic acids

De

finingLife

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Themodynamics

Entropy generaltendency towardsdisorder / randomness Resulting in lower energy state (energy is released)

things fall apart

ENERGY is needed to create and maintainstructure

Living things are able to use energy to maintainor decrease/reverse entropy

Building biomass (more complex molecules fromsimpler molecules)

L01-29

http://www.sciencecartoonsplus.com/

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... life feeds on negative entropy

the essence of life isthe information in genes

Erwin Schrdinger, What is Life?(1944)

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Information Theory of Life

Encoding of Information

Complexity, not chaos

Confers characteristics

Information Structure Function

Transmission ofInformation

Characteristics can beinherited (Heredity)L0

1-31

Jane Ades, NHGRI

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Life Support

The Prerequisites for Life to Exist

Liquid water (and its peculiar properties!)

Energy (heat)

Organic molecules

contain carbon, hydrogen and oxygen atoms

Other factors that support life

pH (acid, neutral, alkaline)

salinity (concentration of various ions/salts) temperature

redox conditions (reduction-oxidation)

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Some Essential

Biological Concepts

L01-33

www.sciencecartoonsplus.com

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atoms

molecules

macromolecules

cells

tissues

organs

organisms

populations

communitiesecosystems

Hierarchy of Life

organelles

BIOSPHERE

Levels of Biological Organisation

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The Tree of Life

All life is inter-related and descended from acommon ancestor

ie. life begets life, life comes from life

Therefore, there is inherent unity in thediversity of life

The ancestry of all living things can be traced

How?

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Dynamic Tree of Life -http://www.discoverlife.org/mp/20m?tree=Life&flags=all:

L01-36

http://genetics.nbii.gov/systematics.html

http://www.discoverlife.org/mp/20m?tree=Life&flags=all:http://www.discoverlife.org/mp/20m?tree=Life&flags=all:

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Traditional Lineage

Purves et al., Life: The Science of Biology

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A Newer Lineage

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Five Kingdom Classification

KINGDOM STRUCTURAL ORGANISATIONTYPES OF

ORGANISMS

NAMED

SPECIES

ESTIMATED

TOTAL

SPECIES

Monera small, simple single prokaryotic cell(nucleoid is not enclosed by amembrane); some form chains or mats

bacteria, blue-greenalgae, and spirochetes

4,000 1,000,000

Protista large, single eukaryotic cell (nucleus isenclosed by a membrane); some formchains or colonies

protozoans and algaeof various types

80,000 600,000

Fungi Unicellular, multicellular filamentous formwith specialisedeukaryotic cells

fungi, molds,mushrooms, yeasts,mildews, and smuts

72,000 1,500,000

Plantae multicellular form with specialisedeukaryotic cells; do not have their ownmeans of locomotion

mosses, ferns, woodyand non-woodyflowering plants

270,000 320,000

Animalia multicellular form with specialisedeukaryotic cells; have their own meansof locomotion

sponges, worms,insects, fish,amphibians, reptiles,birds, and mammals

1,326,239 9,812,298

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Monera

http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/science/scimeth3.htm

http://www.hhs.gov/asphep/presentation/images/bacteria.jpg

Unicellular bacteria and archaea

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Protists

Unicellular organismsplant-like,

animal-like

fungus-like

L01-41

http://megasun.bch.umontreal.ca/protists/gallery.html

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Fungi

Unicellular, Multicellular

Consumers that digest food externally

L01-42

http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/science/scimeth3.htmhttp://elib.cs.berkeley.edu/photos/fungi/

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Plants

Multicellular

Producers (Photosynthesis)

L01-43

http://elib.cs.berkeley.edu/photos/flora/

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Animals

Multicellular, Move about

Consumers that ingest food

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Prokaryotes and Eukaryotes

Prokaryotes Bacteria and Archaea (Monera)

Latin: Pro before; karyo cell nucleus

Does not have a true nucleus

DNA lies within nucleoid region

Eukaryotes

Everything else!

Latin: Eu true; karyo cell nucleus Has a membrane-bound nucleus

DNA is kept entirely within the nucleusL01-45

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http://www.phschool.com/science/biology_place/biocoach/cells/common.html

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Learning Resources

Dolan DNA Learning Center http://www.dnalc.org/

DNA From the Beginning

http://www.dnaftb.org/

DNA Interactive http://www.dnai.org/

Genetic Science Learning Center

http://gslc.genetics.utah.edu/

National Centre for Biotechnology Education http://www.ncbe.rdg.ac.uk/

Online Biology Book http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html

L01-47

http://www.dnalc.org/http://www.dnaftb.org/http://www.dnai.org/http://gslc.genetics.utah.edu/http://www.ncbe.rdg.ac.uk/http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.htmlhttp://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.htmlhttp://www.ncbe.rdg.ac.uk/http://gslc.genetics.utah.edu/http://www.dnai.org/http://www.dnaftb.org/http://www.dnalc.org/