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Instructor
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•
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Prof. Chandrama P. Upadhyaya
220, Life Sciences Building
100-3470-8050, 02-450-3739
[email protected]
Teaching Assistant
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Mr. Eom Hee-Seok
209 Life Sciences Building
02-450-3739, 02-3436-5439
[email protected]
Molecular Biology
Fourth Edition
Robert F. Weaver
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Evaluation
• Three examinations counting 35% each.
•
- Mid term Exam (date to be announce)
•
- Final Exam (date to be announce)
• Attendance 20%
• Home work 10%
A: RNA & Transcription: DETAILS
2
Chapter 1: Basic mechanism of Transcription
Chapter 2 : Post Transcriptional event: Messenger RNA processing I_Splicing
Chapter 3: Messenger RNA processing II _ Capping and Polyadenylation
Chapter 4: Other RNA Processing Events
B: Protein Synthesis or Translation: Details
3
Chapter 5: Mechanism of Translation I_ Initiation
Chapter 6: Mechanism of Translation II_ Elongation and Termination
Chapter 7: Ribosomal and Transfer RNA
C: DNA and Replication mechanism
1
Chapter 8: DNA Replication I: Basic Mechanism and Enzymology
Chapter 9: DNA Replication II: Detailed Mechanism
Chapter 10: Homologous Recombination
DNA
Chapter 11: Genomics. Proteomics and Bioinformatics
RNA
Protein
Chapter 1
INTRODUCTION TO
GENOMICS, BIOINFORMATICS
& PROTEOMICS
• We are in the midst of a "Golden Era" of
biology.
• The revolution is mostly about treating
biology as an information science, not only
specific biochemical technologies.
GENOMICS
 Study of sequences, gene organization &
mutations at the DNA level
 This also deals with the study of
information flow within a cell
Central Dogma
DNA
Genotype
RNA function &
structure
Protein sequence
RNA
Protein structure
Protein
Protein Function
Phenotype
THE HUMAN GENOME PROJECT
3 billion bases
30,000 genes
http://www.genome.gov/
•
Would it be important to know your
personal DNA sequence?
•
Would you want to know if you were
susceptible to a disease? Why or why
not?
IMPACT OF GENOMICS ON MEDICINE
•
•
•
How to characterize new diseases?
What new treatments can be
discovered?
How do we treat individual
patients? Tailoring treatments?
IMPLICATIONS FOR BIOMEDICINE
• Physicians will use genetic information to
diagnose and treat disease.
• Virtually all medical conditions have a
genetic component
• Faster drug development research:
(pharmacogenomics)
• Individualized drugs
• All Biologists/Doctors will use gene
sequence information in their daily work
normal
BIOMARKERS AND GENE EXPRESSION
malignant
WHAT IS BIOINFORMATICS?
What is bioinformatics?
• Interface of biology and computers
• Conceptualizing biology in terms of
molecules and then applying
“informatics” techniques from math,
computer science, and statistics to
understand and organize the information
associated with these molecules on a
large scale
HOW DO WE USE BIOINFORMATICS?
• Store/retrieve biological information (databases)
• Retrieve/compare gene sequences
• Predict function of unknown genes/proteins
• Search for previously known functions of a gene
• Compare data with other researchers
• Compile/distribute data for other researchers
There are three major public DNA databases
EMBL
GenBank
Housed
Housed
at EBI
at NCBI
European
National
Bioinformatics
Center for
Institute
Biotechnology
Information
Go to NCBI website
http://www.ncbi.nlm.nih.gov/
DDBJ
Housed
in Japan
SIMILARITY SEARCH: BLAST
A tool for searching gene or protein sequence
databases for related genes of interest
Alignments between the query sequence
and any given database sequence, allowing
for mismatches and gaps, indicate their
degree of similarity
The structure, function, and evolution of a
gene may be determined by such comparisons
http://www.ncbi.nlm.nih.gov/BLAST/
PubMed is…
• National Library of Medicine's search service
• 12 million citations in MEDLINE
• links to participating online journals
• PubMed tutorial (via “Education” on side bar)
Entrez integrates…
• the scientific literature;
• DNA and protein sequence databases;
• 3D protein structure data;
• population study data sets;
• assemblies of complete genomes
Entrez is a search and retrieval system
that integrates NCBI databases
OMIM is…
•Online Mendelian Inheritance in Man
•catalog of human genes and genetic disorders
•edited by Dr. Victor McKusick, others at JHU
Books is…
• searchable resource of on-line books
TaxBrowser is…
• browser for the major divisions of living organisms
(archaea, bacteria, eukaryota, viruses)
• taxonomy information such as genetic codes
• molecular data on extinct organisms
Structure site includes…
• Molecular Modelling Database (MMDB)
• biopolymer structures obtained from
the Protein Data Bank (PDB)
• Cn3D (a 3D-structure viewer)
• vector alignment search tool (VAST)
DATA MINING
Handling enormous amounts of data
Sort through what is important and what is not
Manipulate and analyze data to find patterns
and variations that correlate with biological
function
NEED FOR IMPROVED BIOINFORMATICS
Genomics:
Proteomics:
Human Genome Project
Gene array technology
Comparative genomics
Functional genomics
Global view of protein
function/interactions
Protein motifs
Structural databases
Human Genome Project
HUMAN GENOME PROJECT STATUS
Working draft of human genome reported by 2 groups allowed
estimates that genome contains fewer genes than anticipated – 25,000
to 40,000
About half the genome has derived from the action of transposons
Transposons themselves have contributed dozens of genes to the
genome
Bacteria also have donated dozens of genes
Finished draft is much more accurate than working draft, but there are
still gaps
Information also about gene birth and death during human evolution
Applications of Genomics: Functional Genomics
• Functional genomics refers to those areas that deal
with the function or expression of genomes.
• All transcripts an organism makes at any given time
is an organism’s transcriptome.
• Use of genomic information to block expression
systematically is called genomic functional profiling.
• Study of structures and functions of the protein
products of genomes is proteomics
Transcriptomics
• This area is the study of all transcripts an organism
makes at any given time.
• Create DNA microarrays and microchips that hold 1000s
of cDNAs or oligos.
• Hybridize labeled RNAs from cells to these arrays or chips
• Intensity of hybridization at each spot reveals the extent of
expression of the corresponding gene
• Microarray permits canvassing expression patterns of
many genes at once.
• Clustering of expression of genes in time and space
suggest products of these genes collaborate in some
process
PROTEOMICS
• Uses information determined by
biochemical/crystal structure methods
• Visualization of protein structure
• Make protein-protein comparisons
• Used to determine:
conformation/folding
antibody binding sites
protein-protein interactions
computer aided drug design
PROTEIN SEPARATIONS AND ANALYSIS
Current research in proteomics requires first that
proteins be resolved, sometimes on a massive
scale.
Best tool for separation of many proteins at once is 2-D
gel electrophoresis
After separation, proteins must be identified
Best method of identification involves digestion of
proteins one by one with proteases
Then identify the peptides by mass spectrometry
In the future, microchips with antibodies attached
may allow analysis of proteins in complex mixtures
without separation
MALDI-TOF MASS SPECTROMETRY
Detecting Protein-Protein Interactions
24-38
Protein Interactions
• Most proteins work with other proteins to
perform their functions.
• Several techniques are available to probe these
interactions.
• Yeast two-hybrid analysis has been used for
some time, now other methods are available
• Protein microarrays
• Immunoaffinity chromatography with mass
spectrometry
• Other combinations
DNA
genomic
DNA
databases
RNA
cDNA
ESTs
UniGene
protein
protein
sequence
databases
phenotype
educators
students
bioinformatics
researchers
institutions