The Big Picture

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The Big Picture
How many processes can you name? http//www.youtub
e.com/watch?vJY7nQ_5o_zofeaturerelated
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Lecture 0Basics of Molecular Biology
SynBUM MIT iGEM Team 2010 Create Your Own
Bacterial Air Freshener 1/6/2011
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What you will learn in this lecture

• The cell as the basic unit of life
• Structure of Important Macromolecules
• DNA
• RNA
• Proteins
• The Central Dogma
• Transcription
• Translation
• Regulation
• Correlation to Synthetic Biology

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Cells - Fundamental working units of every living
system.
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Comparison of Prokaryotic and Eukaryotic Cells
Prokaryotes Eukaryotes
Single cell Single or multi cell
E. coli chromosome 4X106 bp Yeast chromosome 1.35x107 bp
90 of DNA encode protein Small fraction of DNA encodes protein Many repeats of non-coding sequences
No nucleus Nucleus
No organelles Organelles
One piece of circular DNA Chromosomes
No mRNA post transcriptional modification Exons/Introns splicing
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All Cells Divide
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Cell Cycle The Chromosomal View
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The Central Dogma
Control/ Info Center -Genes -Regulatory elements
The messenger -mRNA, tRNA, rRNA Also can
be -Ribozymes -siRNA
The machinery -Enzymes -Signaling -Replication -M
any more
DNA Replication
DNA
RNA
Proteins
Transcription
Translation
Information carried by mRNA is used to make
proteins
Information encoded in DNA is passed to mRNA
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• But first, what are DNA, RNA, and Proteins?

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Where are we?

• The cell as the basic unit of life
• Structure of Important Macromolecules
• DNA
• RNA
• Proteins
• The Central Dogma
• Transcription
• Translation
• Regulation
• Correlation to Synthetic Biology

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DNA The Code of Life
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DNA Replication
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DNA Replication (E. Coli)
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DNA Replication (Eukaryote)
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RNA
RNA DNA
Single Stranded Double Stranded
Temporary (mRNA) Stable
Uracil Thymine
Ribose Deoxyribose

• mRNA
• tRNA
• rRNA
• miRNA/siRNA
• Ribozymes

http//www.cgl.ucsf.edu/home/glasfeld/tutorial/trn
a/trna.gif
tRNA linear and 3D view
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Main types of RNA

• mRNA this is what is usually being referred to
  when we say RNA. This is used to carry a
  genes message after transcription
• tRNA transfers genetic information from mRNA to
  an amino acid sequence during translation
• rRNA ribosomal RNA. Part of the ribosome which
  is involved in translation

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Proteins are made of Amino Acids
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Proteins are the Workhorses of the Cell
Tertiary Structure
Primary Structure
Secondary Structure
Quaternary Structure
? pleated sheet
H3N Amino end
Examples of amino acid subunits
? helix
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Where are we?

• The cell as the basic unit of life
• Structure of Important Macromolecules
• DNA
• RNA
• Proteins
• The Central Dogma
• Transcription
• Translation
• Regulation
• Correlation to Synthetic Biology

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The Central Dogma Revisited
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Slight Variations of the Central Dogma
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Transcription Terminology

• Phosphodiester Bond
• Promoter
• RNA (ribonucleotide)
• RNA Polymerase II
• Terminator

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Transcription

• 3 Main stages Initiation, elongation, and
  termination
• Catalyzed by RNA Polymerase
• Eukaryotes process mRNA this does not occur in
  prokaryotes.

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Translation Terminology

• Codon
• mRNA
• Ribosome
• rRNA
• tRNA
• Anti-codon
• C-Terminal
• N-terminal

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Translation Accuracy

• Requires 2 correct matches
• Between tRNA and correct amino acid
• Between tRNA codon and mRNA anticodon

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Building a Polypeptide

• The three stages of translation
• Initiation
• Elongation
• Termination
• All three stages require protein factors that
  aid in the translation process

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RNA to Protein Instruction Book of Life

• Start with Methionine
• End with a stop codon
• Note the degeneracies for each amino acid

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Translational Initiation
Large ribosomal subunit
3?
5?
U
C
A
P site
Met
Met
3?
5?
A
G
U
Initiator tRNA
GDP
GTP
E
A
mRNA
5?
5?
3?
3?
Start codon
Small ribosomal subunit
Translation initiation complex
mRNA binding site
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Translational Elongation
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Translational Termination
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Almost-Unsimplified Overview
http//www.youtube.com/watch?vGkdRdik73kU
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Where are we?

• The cell as the basic unit of life
• Structure of Important Macromolecules
• DNA
• RNA
• Proteins
• The Central Dogma
• Transcription
• Translation
• Regulation
• Correlation to Synthetic Biology

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The cell is not a sac of chemicals

• Homeostasis
• Levels of Gene Regulation
• Pre-transcriptional
• Pre-translational
• Post-translational
• Gene/protein interactions
• Negative Feedback
• Positive Feedback

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Negative Feedback
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Positive Feedback
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Protein Interactions within the cell
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Synthetic Biology How to get the cell to do what
we want?

• Mix and match promoters, regulatory sites, and
  coding sequences to build logic circuits

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The possibilities are endless!

• Control signaling pathways
• Search and destroy cancer cells, pathogens
• Control metabolic pathways
• Clean up oil spills
• Make novel biomaterials
• Hijack the cells differentiation pathways to
  direct differentiation
• T-cell differentiation? cure AIDS
• Make artificial organs
• Make new pathways
• Electricity generating bacteria