Molecular and Cellular Biology

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Molecular and Cellular Biology
BCB 444/544 Introduction to BioinformaticsLect
ure 5

• 5_Aug30

Some slides adapted from a presentation by Erin
Garland
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Announcements
Knowledge-based Approaches to Predicting Protein
Interface Hot Spots Julie Mitchell Department
of Mathematics and Biochemistry BACTER Institute
for Computational Biology University of
Wisconsin, Madison Today at 310 in 1420 MBB
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Eukaryotic Cell
Lots of compartments Compartments are called
organelles
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Prokaryotic Cell
No separate compartments
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Cytoskeleton
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Extracellular Matrix
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Cell cycle
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The Central Dogma
Gene expression the whole process of going from
DNA to RNA to Protein
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Information flow in the cell

• DNA -gt RNA -gt protein
• Transcription DNA to RNA
• Translation RNA to protein
• Exceptions reverse transcription, RNA splicing
  and editing, protein post-translational
  modification

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DNA replication

• Replication is semiconservative
• Each child strand has one of the parent strands

Replication fork

• Replication only occurs in the 5 to 3 direction

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Transcription
DNA encoding gene messenger RNA
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Translation
Codon 3 bases that code for an amino acid
messenger RNA protein
Amino acids
tRNA
mRNA
ribosome
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Genetic code
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Mutations

• Nonsense stop codon in the wrong place
• Missense mutation that results in an amino acid
  change in the protein
• Synonymous mutation in the DNA that does not
  result in an amino acid change in the protein
• Non-synonymous does change the amino acid

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Protein function

• Proteins are the primary molecules responsible
  for cellular function
• They have complex structure and some can perform
  chemical reactions (enzymes)

DNA structure
Protein structure (dystrophin)
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Protein localization
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RNA function

• Some specialized RNA molecules have function

Ribosomes contain both RNA and protein
Ribozymes are RNA-based enzymes capable of RNA
cleavage

• RNA molecules may be the precursors to life as
  they can both
• Form complementary base pairs and replicate (like
  DNA)
• Perform enzymatic functions (like proteins)

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3 classical types of RNA

• mRNA messenger RNA
• tRNA transfer RNA
• rRNA ribosomal RNA
• Lots of others siRNA, miRNA, piRNA, snRNA,
  snoRNA,

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Genes
Genes are not just beads on a string they
have complex structure
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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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Gene regulation

• 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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Promoters

• RNA polymerase binds and transcription begins at
  the promoter
• Transcription regulation focuses on the promoter

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Enhancers and repressors
Regions further upstream from the promoter have
binding sites for enhancer and repressor proteins
promoter
enhancer
gene
10-50,000 bp
repressor
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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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Web resources

• BioTechs Life Science Dictionary
• Online textbooks NCBI bookshelf