An Introduction to Bioinformatics Algorithms
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Molecular Biology Primer
Angela Brooks, Raymond Brown, Calvin Chen, Mike Daly,
Hoa Dinh, Erinn Hama, Robert Hinman, Julio Ng, Michael
Sneddon, Hoa Troung, Jerry Wang, Che Fung Yung
An Introduction to Bioinformatics Algorithms
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Three main branches to the tree of life
•According to the most recent evidence, there are three main branches to the tree of life.
•Prokaryotes include Archaea (“ancient ones”) and bacteria.
•Eukaryotes are kingdom Eukarya and includes plants, animals, fungi and certain algae.
An Introduction to Bioinformatics Algorithms
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Life begins with Cell
• A cell is a smallest structural unit of an organism
that is capable of independent functioning
• Fundamental working units of every living system.
• All cells have some common features
An Introduction to Bioinformatics Algorithms
Cells
• Chemical composition-by weight
• 70% water
• 7% small molecules
• salts
• Lipids
• amino acids
• nucleotides
• 23% macromolecules
• Proteins
• Polysaccharides
• lipids
• biochemical (metabolic) pathways
• translation of mRNA into proteins
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An Introduction to Bioinformatics Algorithms
2 types of cells: Prokaryotes
v.s.Eukaryotes
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An Introduction to Bioinformatics Algorithms
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Prokaryotes and Eukaryotes,
continued
Prokaryotes
Eukaryotes
Single cell
Single or multi cell
No nucleus
Nucleus
No organelles
Organelles
One piece of circular DNA Chromosomes
No mRNA post
Exons/Introns splicing
transcriptional modification
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Prokaryotes v.s. Eukaryotes
Structural differences
Prokaryotes
Eukaryotes
 Eubacterial (blue green algae)
and archaebacteria
 only one type of membrane-plasma membrane forms
 plants, animals, Protista, and fungi
 the boundary of the cell proper
 The smallest cells known are
bacteria
 Ecoli cell
 3x106 protein molecules
 1000-2000 polypeptide species.
 complex systems of internal
membranes forms
 organelle and compartments
 The volume of the cell is several
hundred times larger
 Hela cell
 5x109 protein molecules
 5000-10,000 polypeptide species
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Prokaryotic and Eukaryotic Cells
Chromosomal differences
Prokaryotes
 The genome of E.coli contains
amount of t 4X106 base pairs
 > 90% of DNA encode protein
 Lacks a membrane-bound nucleus.
 Circular DNA and supercoiled
domain
 Histones are unknown
Eukaryotes
 The genome of yeast cells contains
1.35x107 base pairs
 A small fraction of the total DNA
encodes protein.
 Many repeats of non-coding
sequences
 All chromosomes are contained in
a membrane bound nucleus
 DNA is divided between two or
more chromosomes
 A set of five histones

DNA packaging and gene
expression regulation
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Surrounding the Cell
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Cell Membrane
• Outer membrane of cell
that controls movement
in and out of the cell
• Double layer
http://library.thinkquest.org/12413/structures.html
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Cell Wall
• Most commonly found
in plant cells &
bacteria
• Supports & protects
cells
http://library.thinkquest.org/12413/structures.html
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Inside the Cell: Organelles
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Nucleus
• Directs cell activities
• Separated from cytoplasm by nuclear
membrane
• Contains genetic material - DNA
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Nuclear Membrane
• Surrounds nucleus
• Made of two layers
• Openings allow
material to enter and
leave nucleus
http://library.thinkquest.org/12413/structures.html
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Chromosomes
• In nucleus
• Made of DNA
• Contain instructions
for traits &
characteristics
http://library.thinkquest.org/12413/structures.html
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Chromosomes
Organism
Number of base pair
number of Chromosomes
--------------------------------------------------------------------------------------------------------Prokayotic
Escherichia coli (bacterium)
4x106
1
Eukaryotic
Saccharomyces cerevisiae (yeast)
Drosophila melanogaster(insect)
Homo sapiens(human)
Zea mays(corn)
1.35x107
1.65x108
2.9x109
5.0x109
17
4
23
10
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Nucleolus
• Inside nucleus
• Contains RNA to build
proteins
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Cytoplasm
• Gel-like mixture
• Surrounded by cell membrane
• Contains hereditary material
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An Introduction to Bioinformatics Algorithms
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Endoplasmic Reticulum
• Moves materials around
in cell
• Smooth type: lacks
ribosomes
• Rough type (pictured):
ribosomes embedded in
surface
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Ribosomes
• Each cell contains
thousands
• Make proteins
• Found on ribosomes
& floating throughout
the cell
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Mitochondria
• Produces energy through
chemical reactions –
breaking down fats &
carbohydrates
• Controls level of water and
other materials in cell
• Recycles and decomposes
proteins, fats, and
carbohydrates
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Golgi Bodies
• Protein 'packaging
plant'
• Move materials within
the cell
• Move materials out of
the cell
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Lysosome
• Digestive 'plant' for
proteins, fats, and
carbohydrates
• Transports undigested
material to cell
membrane for removal
• Cell breaks down if
lysosome explodes
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An Introduction to Bioinformatics Algorithms
Vacuoles
• Membrane-bound
sacs for storage,
digestion, and waste
removal
• Contains water
solution
• Help plants maintain
shape
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An Introduction to Bioinformatics Algorithms
Chloroplast
• Usually found in plant
cells
• Contains green
chlorophyll
• Where photosynthesis
takes place
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All Cells have common Cycles
• Born, eat, replicate, and die
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Signaling Pathways: Control Gene
Activity
• Instead of having brains, cells make decision
through complex networks of chemical
reactions, called pathways
• Synthesize new materials
• Break other materials down for spare parts
• Signal to eat or die
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Example of cell signaling
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An Introduction to Bioinformatics Algorithms
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Cells Information and Machinery
• Cells store all information to replicate itself
• Human genome is around 3 billions base pair long
• Almost every cell in human body contains same
set of genes
• But not all genes are used or expressed by those
cells
• Machinery:
• Collect and manufacture components
• Carry out replication
• Kick-start its new offspring
(A cell is like a car factory)
An Introduction to Bioinformatics Algorithms
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Overview of organizations of life
•
•
•
•
Nucleus = library
Chromosomes = bookshelves
Genes = books
Almost every cell in an organism contains the
same libraries and the same sets of books.
• Books represent all the information (DNA)
that every cell in the body needs so it can
grow and carry out its vaious functions.