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Biology_basics.Rmd
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Biology_basics.Rmd
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---
title: 'Bioinformatics for Big Omics Data: Molecular Biology 101'
author: "Raphael Gottardo"
date: "January 14, 2014"
output:
ioslides_presentation:
fig_caption: yes
fig_retina: 1
keep_md: yes
smaller: yes
---
## Outline
- Cells and genomes
- DNA, RNA, proteins
- Central dogma of molecular biology
## Cells and genomes
- A T-cell
<img src="http://upload.wikimedia.org/wikipedia/commons/thumb/6/62/Healthy_Human_T_Cell.jpg/1200px-Healthy_Human_T_Cell.jpg" width=400>
(Source: Wikipedia)
## Cells and genomes
- A Neuron
<img src="http://cdn.thetechjournal.com/wp-content/uploads/HLIC/798ace6285a8ef83e36ebc0667823b99.jpg" width=400>
(Source: thetechjournal.com)
## DNA
<img src="http://news.brown.edu/files/article_images/Senescence1.jpg" width=400>
- DNA (deoxyribose nucleic acid) contains the genetic instructions (A, G, C,T).
- Double stranded (complementary)
G-C, A-T
## RNA
<img src="http://upload.wikimedia.org/wikipedia/commons/d/d4/RNA-codons.png" wid th=400>
(Source: Wikipedia)
- RNA (Ribonucleic acid) ressembles DNA
- Single stranded, much shorter than DNA
- Four bases A, C, G and U.
## Protein
<img src="http://upload.wikimedia.org/wikipedia/commons/9/98/Protein_IL2RA_PDB_1z92.png" width=400>
(Source: Wikipedia)
- Organic compounds (amino acids joined by peptide bonds)
- Essential to the structure and function of all living cells and viruses
- 20 possible amino acids (Lysine, Leucine, etc.)
- Folding → Function
## DNA, RNA and Proteins (and more)
- How do they interact?
- How do we get from DNA to proteins?
## The Central Dogma
<img src="http://2.bp.blogspot.com/_d02IdL2kBZI/RqLBZhAbWfI/AAAAAAAAACU/RVZ8G85Kvyk/s1600/central+dogma+overview.jpg" width=400>
(Source: http://darwinview.blogspot.com/)
- Certain pieces (genes) are transcribed
- Gene ≈ piece of DNA coding for a protein
- Gene → Protein (Gene is expressed)
## Summary
- DNA → RNA → Proteins
- Can measure proteins directly but measuring
- mRNA levels is easier
- mRNA levels (gene expression levels) tell us something about proteins
- How do we measure gene expression levels? Microarrays → Gene expression and more!
- **Understanding gene regulation requires a lot more than just gene expression**: Chromatin, miRNA, alternative splicing, methylation, etc.