BCB 444544

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BCB 444/544
Lecture 4 Biology Background Biological
Databases 4 Sep 3

• Thanks to Drena Dobbs (ISU for many borrowed
  modified PPTs

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Required Reading (before lecture)

• Thurs Sep 4 - Lab 2
• Databases, ISU Resources, Pairwise Sequence
  Alignment
• Fri Sep 5 - for Lecture 5
• Pairwise Sequence Alignment
• Chp 3 - pp 31-41 Xiong Textbook

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Last Friday in a nutshell

• Main molecules we will deal with are DNA, RNA,
  and proteins
• DNA carries information, made up of 4
  nucleotides
• RNA involved in all aspects of gene expression,
  also made up of 4 nucleotides
• Proteins perform most functions and form most
  structures, made up of 20 amino acids
• Genes have a complex structure

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RNA and DNA Structures
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Protein Structure
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Sequence-Structure-Function

• Amino acid sequence determines protein structure
• Protein structure determines function

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The Central Dogma
Gene expression the whole process of going from
DNA to RNA to Protein
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Gene structure

• Genes are fragmented, containing
  non-protein-coding introns between the functional
  exons

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Gene splicing
Introns are removed before mRNA leaves the nucleus
DNA
Transcribed RNA
Introns removed by splicing
mRNA
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Regulation of gene expression

• Genes are regulated transcriptionally by proteins
  that interact with DNA elements around the gene
• DNA level
• Promoters
• Enhancers and repressors
• Chromatin level (X-inactivation)

• Genes are also regulated
• Post-transcriptionally
• Post-translationally

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Transcription factor binding sites

• Promotors, enhancers, and repressors are all
  binding sites for transcription factors (proteins
  that bind DNA and affect transcription)

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Mutation

• DNA mutation is any change in DNA sequence

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Role of mutation in evolution
Mutation is not all bad!

• Occurs at a high rate in all our cells and does
  NOT always have negative effects

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Beneficial mutations
Changes in DNA sequence can be beneficial
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Eukaryotic Cell
Lots of compartments called organelles
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Prokaryotic Cell
No separate compartments
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Prokaryotes vs. Eukaryotes

• All of our gene examples so far have been showing
  eukaryotic genes
• Prokaryotic genes are not as complex

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Prokaryotes vs. Eukaryotes
Eukaryotic Gene
Prokaryotic Gene
Important difference no introns!
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Protein localization
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Types of RNA

• http//en.wikipedia.org/wiki/List_of_RNAs
• I counted 25 different types of RNAs on listed on
  this page

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Web resource

• Online textbooks NCBI bookshelf

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2- Biological Databases

• Xiong Chp 2
• 2 Introduction to Biological Databases
• What Is a Database?
• Types of Databases
• Biological Databases
• Pitfalls of Biological Databases
• Information Retrieval from Biological
  Databases
• Summary
• Further Reading

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Types of Databases

• 3 Major types of electronic databases
• 1- Flat files - simple text files
• no organization to facilitate retrieval
• 2- Relational - data organized as tables
  ("relations")
• shared features among tables allows rapid search
• 3- Object-oriented - data organized as "objects"
• objects associated hierarchically

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Biological Databases

Currently - all 3 types, but MANY flat
files What are goals of biological
databases? 1- Information retrieval 2-
Knowledge discovery
Important issue Interconnectivity
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Types of Biological Databases

• 1- Primary
• "simple" archives of sequences, structures,
  images, etc.
• raw data, minimal annotations, not always well
  curated!
• 2- Secondary
• enhanced with more complete annotation of
  sequences, structures, images, etc.
• usually curated!
• 3- Specialized
• focused on a particular research interest or
  organism
• usually - not always - highly curated

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Examples of Biological Databases

• 1- Primary
• DNA sequences
• GenBank - US
• European Molecular Biology Lab - EMBL
• DNA Data Bank of Japan - DDBI
• Structures (Protein, DNA, RNA)
• PDB - Protein Data Bank
• NDB - Nucleic Acid Databank

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Examples of Biological Databases

• 2- Secondary
• Protein sequences
• Swiss-Prot, TreEMBL, PIR
• these recently combined into UniProt
• 3- Specialized
• Species-specific (or "taxonomic" specific)
• Flybase, WormBase, AceDB, PlantDB
• Molecule-specific,disease-specific

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Pitfalls of Biological Databases

• Errors!
• Lack of documentation about quality or
  reliability of data
• Limited mechanisms for "data checking" or
  preventing propagation of errors (esp.
  annotation errors!!)
• Redundancy
• Inconsistency
• Incompatibility (format, terminology, data
  types, etc.)

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Information Retrieval from Biological Databases

• 2 most popular retrieval systems
• ENTREZ - NCBI
• will use a LOT - Introduced in Lab 2
• SRS - Sequence Retrieval Systems - EBI
• will use less, similar to ENTREZ
• Both
• Provide access to multiple databases
• Allow complex queries

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WebCT Question

• Do you know any program or database to find or
  predict the small non-coding RNAs in the
  completely sequenced genome? Specifically, in the
  bacterial genomes?
• Noncoding RNA database
• http//biobases.ibch.poznan.pl/ncRNA/

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SUMMARY 2- Biological Databases
BEWARE!