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COT 6930
HPC and Bioinformatics
Introduction to Molecular Biology
Xingquan Zhu
Dept. of Computer Science and Engineering
Outline
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Cell
DNA
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DNA Structure
DNA Sequencing
RNA (DNA-> RNA)
Protein
Life begins with Cell
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Cells are fundamental working units of every living
system.
A cell is the smallest structural unit of an organism that is
capable of independent function
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Unicellular organism (Any living being consisting of a single cell):
mainly bacteria
Multicellular organism (Organisms consisting of more than one
cell): Plant and animal
All cells have some common features
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Membrane, cytoplasm
Cell is able to survive and multiply independently in
appropriate environment
There are estimated about 6x1013 (60 trillions) cells in a
human body, of about 210 distinct cell types
Cells may have different sizes: a human red blood cell
may be 5 microns in diameter while some neurons are
about 1 m long (from spinal cord to leg)
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Name a cell visible with naked eyes..
Cell
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The basic unit of life
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Every living thing is made of cells.
Every cell comes from a pre-existing cell
All of life’s functions are cellular
Living organisms (on Earth) require ability to
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Separate inside from outside (lipids)
Build 3D machinery to perform biological functions (proteins)
Store information on how to build machinery (DNA)
Organisms – Eukaryotes and Prokaryotes
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Every organism is composed of one
of two radically different types of
cells: prokaryotic cells or
eukaryotic cells.
Prokaryotic cells are simpler than
eukaryotic cells
Prokaryotes are (mostly) single
cellular organisms
Eukaryotic cell has a nucleus,
separated from the rest of the cell by
a membrane
Eukaryotes can be single cellular
(Yeast) or multicellular (animals,
plants)
Organisms – Eukaryotes and Prokaryotes
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
Structure of a Eukaryotic Cell
• Nucleus contains chromosomes,
which are the carrier of the
genetic material
• Organelles like centrioles,
lysosomes, golgi complexes are
enclosed compartments within
the cell and are responsible for
particular biological processes
• Area of the cell outside the
nucleus and the organelles is
called the cytoplasm
Composition of Cells
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Cell membrane
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Boundary between cell and outside world
Cell membranes consist of two layers of lipid
molecules with hydrophobic ends facing in (keeps
water out)
Nucleus
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Contain genetic material
Separated from the rest of the cell by a nuclear
membrane
The nucleus
1. nuclear envelope
2. nucleolus
3. chromosomes
chromosomes
All Cells have common Cycles
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Growth of a single cell and
its subsequent division is
called the cell cycle
M: Mitosis
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Prokaryotes, particularly
bacteria, are extremely
successful at multiplying.
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Multicellular organisms
typically begin life as a single
cell. The single cell has to
grow, divide and differentiate
into different cell types to
produce tissues and in
higher eukaryotes, organs
All cells come from pre-existing cells
Molecular Biology: Studying life
at the molecular level
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DNA
Protein
RNA
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mRNA
rRNA
tRNA
Protein synthesis
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Protein transcription
Protein translation
Molecules of Life
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All Life depends on 3 critical molecules –
DNA, RNA, and Protein
All 3 are specified linearly
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DNA and RNA are constructed from nucleic acids
(nucleotides)
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Can be considered to be a string written in a four-letter
alphabet (A C G T/U)
Proteins are constructed from amino acids
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Strings in a twenty-letter alphabet of amino acids
Central dogma of molecular biology
DNA
RNA
protein
phenotype
DNA, RNA, Protein
Self replication and genetic code
DNA DNA → DNA (Replication)
RNA DNA → RNA (Transcription / Gene Expression)
Protein RNA → Protein (Translation)
Outline
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Cell
DNA
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DNA Structure
DNA Sequencing
RNA (DNA-> RNA)
Protein
DNA (Deoxyribonucleic Acid )
Structure
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Physical structure
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Double (stranded) helix
Sugar & phosphate groups form backbone
Complementary bases (A-T, C-G) connected by hydrogen bond
5’ = end w/ free phosphate group
3’ = end w/ free oxygen group
DNA
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Composition
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Sequence of nucleotides
Deoxyribonucleotide = deoxyribose sugar + phosphate group +
base
Nucleotide Bases
Nucleotides
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The five-carbon sugar (a pentose) in nucleotides has two types
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Deoxyribose, which has a hydrogen atom attached to its #2 carbon atom
(designated 2') : DNA
Ribose, which has a hydroxyl group atom there: RNA
DNA structure
Why 5’ and 3’
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Deoxyribonucleotide = deoxyribose sugar +
phosphate group + base
The deoxyribose sugar in DNA is a pentose, a five-carbon sugar. Four carbons
and an oxygen make up the five-membered ring; the other carbon branches off
the ring. The carbon constituents of the sugar ring are numbered 1'-4'
(pronounced "one-prime carbon"), starting with the carbon to the right of the
oxygen going clockwise. The fifth carbon (5') branches from the 4' carbon.
DNA - Denaturation,
Hybridization
DNA
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For bioinformatics
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DNA can be represented as a sequence of letters
(A,C,G,T)
5’ A T A C G T A 3’
3’ T A T G C A T 5’ (matching strand, redundant)
Terms
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Base pair (bp) – one pair of DNA bases (1 letter)
Gene – section of DNA that produces a functional product
Chromosome – physical linear sequence of DNA
Genome – entire collection of DNA for an organism
 E Coli 1 chromosome 5 x 106 bases (5 Mbps)
 Drosophila 8 chromosomes 2 x 108 bases (200 Mbps)
 Human 48 chromosomes 3 x 109 bases (3 Bbps)
DNA Replication
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DNA can be replicated
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DNA strands are split
DNA polymerase (enzyme) reads one strand (template)
Builds new (complementary) strand to form duplicate DNA
DNA fascinating fact
Each cell has 2m of DNA
Average person has 75 trillion cells = 75 * 1012
Length of DNA in a person = 150 * 1012 m
Each person has enough DNA to go to the sun and
back 500 times
Organization of DNA in chromosomes
Histone proteins
3 bases/ amino acid
27,000 bases/ protein (1 gene)
3,000,000,000 base pairs/ genome
20,000 genes/ genome
Human Genome Project
homologous
Genome
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Gene: Contiguous subparts
of single strand DNA that are
templates for producing
proteins.
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Chromosomes: compact
chains of coiled DNA
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Genome: The set of all
genes in a given organism.
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Noncoding part: The function
of DNA material between
genes is largely unknown.
Source: www.mtsinai.on.ca/pdmg/Genetics/basic.htm
More Terminology
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The genome is an organism’s complete set of DNA.
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Human genome has 23 pairs of chromosomes.
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A bacteria contains about 600,000 DNA base pairs
Human and mouse genomes have some 3 billion.
Each chromosome contains many genes.
Gene
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Basic physical and functional units of heredity.
Specific sequences of DNA bases that encode
instructions on how to make proteins.
DNA sequences
in the human genome
DNA homologies
98.7%
Outline
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Cell
DNA
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DNA Structure
DNA Sequencing
RNA (DNA-> RNA)
Protein
DNA Sequencing (Sanger’s
Dideoxy Method)
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Method for identifying short DNA sequences
Algorithm
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Replicate DNA with (color-labeled) dideoxy-nucleotides
 Creates fragments of DNA
Apply gel electrophoresis
 Separates fragments based on size
Machine scans gel
 Records level of color found at each position
Software calls bases
 Predicts base at each position
Limitations
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Upper bound of 700-800 bases on sequence length
Larger DNA sequences will need to be assembled
DNA Sequencing
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Dideoxynucleotides
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Similar to normal nucleotide base
Missing 3’ hydroxyl group terminates DNA sequence
May be chemically modified to fluoresce under UV light
DNA Sequencing
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Example for GCGAATGTCCACAACGCTACAGGTG
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Replicate DNA in the presence of dideoxy-Cytidine (ddC)
Replication terminates when ddC is used instead of C
Produces the following DNA fragments
 GC
 GCGAATGTC
 GCGAATGTCC
 GCGAATGTCCAC
 GCGAATGTCCACAAC
 GCGAATGTCCACAACGC
 GCGAATGTCCACAACGCTAC
DNA Sequencing
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Gel electrophoresis
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Place DNA fragments in gel
Apply electric field
Speed of fragment is determined
by size
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Smaller = faster
Larger = slower
After given time
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Fragments are separated in gel
Fragments are sorted by size
(number of bases)
Gel electrophoresis
DNA Sequencing
DNA Sequencing
Outline
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Cell
DNA
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DNA Structure
DNA Sequencing
RNA (DNA-> RNA)
Protein
Central Dogma of Biology:
DNA, RNA, and the Flow of Information
Replication
Transcription
Translation
Ribonucleic acid (RNA)
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Composition
 Sequence of nucleotides
 Ribonucleotide = ribose sugar + phosphate group + base
Major difference between DNA and RNA
 RNA: usually single stranded
 RNA: ribose sugar, DNA: Deoxyribose sugar
 RNA: Uracil (U) instead of Thymine (T)
DNA → RNA (Transcription / Gene Expression)
 RNA polymerase (enzyme)
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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
Resulting RNA sequence = transcript
Ribonucleotides
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The five-carbon sugar (a pentose) in nucleotides has two types
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Deoxyribose, which has a hydrogen atom attached to its #2 carbon atom
(designated 2') : DNA
Ribose, which has a hydroxyl group atom there: RNA
Transcription Example (1)
Transcription Example (2)
Transcription Example (3)
Transcription Example (4)
Transcription Example
What is Enzyme?
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Proteins that catalyze (i.e. accelerate) chemical reactions
 They are not living things
 Two types of Enzyme
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Join specific molecules together to form new molecules
Break specific molecules apart into separate molecules
Things about Enzyme
 Enzymes are specific: Performing only one specific job, about
3000 types enzymes identified so far
 Enzymes are catalysts: Can perform that same job over and over
again, millions of times, without being consumed in the process.
 Enzymes are efficient:
 Enzymes are natural: Once they have done their job, enzymes
break down swiftly and can be absorbed back into nature
Outline
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Cell
DNA
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DNA Structure
DNA Sequencing
RNA (DNA-> RNA)
Protein