information storage and processing in biological systems:

Information Storage and Processing in Biological Systems:

A seminar course for the Natural Sciences

Sept. 17 Biological Information, DNA, Gene regulation

Sept 24 Proteins, Enzymes, Biochemistry

Oct 1 Biochemical and Genetic Networks:Chemotaxis/Motility in E. coli and Dictyostelium

Sept 17.

Chapters 1-3 “The Thread of Life” S. Aldridge Cambridge University Press. 1996.

From molecular to modular cell biology. (1999) L. H. Hartwell, J. J. Hopfield, S. Leibler and A. W. Murray. Nature 402 (SUPP): C47-C52.

The challenges of in silico biology. (2000) B. Palsson. Nature Biotechnology 18: 1147-1150.

Genetic Switch: Phage Lambda and Higher Organisms by Mark Ptashne. 2nd edition (1992) Blackwell Science.

It’s a noisy business! Genetic regulation at the nanomolar scale. H. Harley and A Aarkin. Trends In Genetics February 1999, volume 15, No. 2

Simulation Of Prokaryotic Genetic Circuits. H. H. Mcadams and A. Arkin. Annu. Rev. Biophys. Biomol. Struct. 1998. 27:199–224

Reading List for Sept 17.2001

Student Presentation Topic:

Bioinformatics: Overview and future challenges

Melissa Dobson

What is “biological information” and how is it “Stored” and Processed”?

M.C. Escher Spirals

What is “biological information”?

Genetic (DNA and RNA)

Epigenetic (DNA modification)

Non-Genetic Inheritance (template dependent replication)

Physiological-Cellular Level (Structural/Metabolism/Signal Transduction)

Simplified Connectivity of Map of Metabolism

Each node represents a chemical in the cell (E. coli)Each connection represents an enzymatic step or steps

Physiological- Organism Level(Structural/Metabolism/Signal Transduction,

Development, Immune System)

Populations (Population dynamics, Evolution

Ecosystem (Interacting Populations, environment populations )

The“Central Dogma”

The central dogma relates to the flow of ‘genetic’ information in biological systems.

transcription

translation

Protein

DNARNAProtein

Overview of Biological Systems

Organization of the Tree of Life

Three evolutionary branches of life:Eubacteria, Archaebacteria, Eukaryotes

The macroscopic world represents a small portion of the tree.

The Eubacteria (bacteria), Archaebacteria (archae), and Eukaryotes represent three fundamental differences in organization of the cell.

Major Similarities:Genetic codeBasic machinery for interpreting the code

Major Differences:Organization of genesOrganization of the cell

sub-cellular organelles in Eukaryotes * cytoskeletal structure in Eukaryotes **

No true multicellular organization in bacteria and archae (there are many single celled eukaryotes).

* compartmentalization of function

** morphologically distinct cell structure

Bacteria

Morphologically “simple” - shape defined by cell surface structure.

Transcription (reading the genetic message) and Translation (converting the genetic message into protein) are coupled- they take place within the same compartment (cytoplasm).

Compartmentalization of Function in eukaryotic cells

Transcription (reading the genetic message) and Translation (converting the genetic message into protein) occur in different compartments in the eukaryotic cell.

Example of single celled eukaryotic organisms

Morphological diversity (cytoskeleton as well as cell surface structures)

There are many distinct morphological cell types within a multicellular organism.

Morphological diversity arises from cytoskeletal networks - architectural proteins

Some ‘Model’ Experimental Eukaryotic Organisms

Caenorhabditis elegans (round worm)

Saccharomyces cerevisiae

Drosophila melanogaster (fruit fly)

Antirrhinum majus (snapdragons )Arabidopsis thalianaZebrafish

Bacteriophage (Phage) and Viruses

1) genetic material / nucleic acid 2) protective coat protein

The information for their own replication and the means to “target” the correct cell/host but no interpretive machinery

Constraints in Biological Systems

Chemical/Physical constraints• stability of biological material• reaction rates and diffusion rates

- properties of biochemical reactions (enzymes) differ from chemical reactions

• time dependency of many steps - time scales over many orders of magnitude for different steps

-receptor ligand binding msec-biochemical response sec-genetic response minutes- hours-days

• statistical properties of ‘small-scale” chemistry, i.e. where concentration of reacting molecules is low.

Evolutionary constraints• a biological system is constrained by it’s own evolutionary history (and also ‘biological’ history)

“Alarm clock” from the movie Brazil

Evolution of new functions is rarely de novo invention but is typically due to the modification of pre-existing functions/structures.

Modularity• Is the cell/organism designed in a modular fashion?

• Can we approximate cell behavior into modules?

•- Can interactions of cells, individuals, organisms be treated in a similar way?

Coarse graining• At what level of detail do we need to study/model a system to extract information about the underlying mechanisms?

• What level of detail is required to define the “state” of the cell, the individual, the population and ecosystem…?

• Can we define the “state” of the cell or only “states” of modules?

Stochastic variations and Individuality

• What is the source of stochastic variation (independent of genetic variation)?

• In genetically identical populations, does this play a role in adaptation?

• What role do stochastic processes play in development?

Robustness

• Despite stochastic variations, many cellular processes are extremely robust (genetic networks, biochemical networks, cell divisions, development,…)

• How does the cell overcome the limitations imposed by stochastic variations?

• Where does robustness arise? Is it a network property?

DNA Basics

Four bases A - adenineT - thymineC - cytosineG - guanine

anti- parallel double stranded structure with specific bonding between the two strands:

A T base pairingC G base pairing

DNA Structure

A - TC - GG - CA - TT - AG - CG - CG - CT - A

• DNA is composed of two strands

• Each strand is composed of a sugar phosphate backbone with one of four bases attached to each sugar

•The arrangement of bases along a strand is aperiodic

• The two strands are arranged anti-parallel

• There is base specific pairing between the strands such that A pairs with T and C with G, consequently knowing the sequence of one strand gives us the sequence of the opposite strand.

Chemical Structure of DNA The Double Helix

DNA Replication• Template copying• Semi-conservative

ACGATGGGT - A

A - T G C T A C C C A

The Genetic Code – Triplet Code

- directional (always read 5’ 3’)- each triplet of bases codes one amino acid (Codon)- degenerate (many AA have more than one codon)

For a given sequence there are three possible reading frames

DNA contains information about the start and end of the gene as well as when to make or if to make transcribe the information.

DNA as an information molecule

• DNA sequence itself

• DNA sequence as a code of protein (sequence/properties of the protein)

• DNA sequence as controlling elements and recognition sites for cellular machinery

• DNA secondary structure and chemical modifications (e.g. methylation)

• genetic networks from multiple controlling elements and recognition sites with multiple genes and feedback and or feedforward systems

5001 CATAAACCGG GGTTAATTTA AATACTGGAA CCGCTTACCA ATAAGACTAA GTATTTGGCC CCAATTAAAT TTATGACCTT GGCGAATGGT TATTCTGATT -2 end of luxS ***I ? gene start +1 MetGlnPhe LeuGlnPhe PhePheArgGln ArgGlnLeu PheIleAla 5051 ATATGCAATT CCTGCAGTTT TTCTTTCGGC AGCGCCAGCT CTTTATTGCT TATACGTTAA GGACGTCAAA AAGAAAGCCG TCGCGGTCGA GAAATAACGA -2 leHisLeuGlu GlnLeuLys GluLysProLeu AlaLeuGlu LysAsnSer

+1 hrProAspArg ArgArgLeu HisProGlyMet IleAspCys GluAlaIle 5501 CCCCGGACCG CCGGCGCTTG CATCCGGGTA TGATCGACTG CGAAGCTATC GGGGCCTGGC GGCCGCGAAC GTAGGCCCAT ACTAGCTGAC GCTTCGATAG -2 lyArgValAla ProAlaGln MetArgThrHis AspValAla PheSerAsp

+1 *** end of ? gene 5551 TAATAATGGC ATTTAGTCAC CTCCGATAAT TTTTTAAAAA TAAACTGAAC ATTATTACCG TAAATCAGTG GAGGCTATTA AAAAATTTTT ATTTGACTTG -2 LeuLeuProMet luxS start

5’---CTCAGCGTTACCAT---3’3’---GAGTCGCAATGGTA---5’

5’---CUCAGCGUUACCAU---3’

N---Leu-Ser-Val-Thr---C

PROTEIN

Transcription

Translation

1) DNA has sequence information which is TRANSCRIBED into RNA (i.e. it is a template) and TRANSLATED from RNA into protein (Genetic Code).

Two ways of thinking about “information” in DNA

• In RNA T’s are replaced by U’s• Some gene products are RNA, i.e. they are not translated (e.g. tRNA, rRNA)

2) DNA has sequence information at a structural level. This form of information directs the ‘interpretative machinery’ in the cell (protein complexes), in most instances binding sites for proteins. This type of ‘information’ is important for example in determining where (along a sequence of DNA) and when a gene may be turned on, initiation of DNA replication, packaging of DNA etc…

i.e - Regulation

Two ways of thinking about “information” in DNA

2’holoenzymefactor

-35 -10

The Basic Transcription Components (Bacterial)

Promoter - binding site for RNA polymerase, defines where the process will begin.

RNA Polymerase

TranscriptionMachinery

Promoter Binding

Open Complex Formation

Promoter Clearance

-35 -10

Messenger RNA (mRNA)

Transcriptional Regulators are proteins that act to modulate gene expression.

Proteins that negatively regulate expression (i.e decrease transcription) are called Repressors and those that act positively (i.e. increase transcription of a gene) are called Activators.

These proteins act by binding at specific DNA sites are modulate RNA polymerase function. These binding sites are called operators.

Regulation of Gene Expression: The Basics

-35 -10

promoteroperator

-35 -10

startX

Repression can be viewed as a competition for binding between the polymerase and the repressor (an oversimplification).

Repressor

-35 -10

promoteroperator

An Activator promotes RNA polymerase biding activity through direct protein-protein interactions (an oversimplification).

Activator

• Any DNA binding protein, with an appropriately placed binding site can act as a repressor. Activation requires specific protein-protein interaction between the activator and RNA polymerase.

• Typically bacterial promoters are regulated by a few proteins at most and the control regions tend to be quite small.

• Eukaryotic gene regulatory regions can be very large and involve many transcriptional regulators.

• Activation and repression depend on positioning of operator sites.

• Multiple inputs can be integrated at the level of gene expression.

The interaction of a DNA-Binding Protein (such as RNA Polymerase or transcriptional regulators) is dependent on the ‘affinity’ of the protein for the binding site. This affinity will vary under different physiological conditions, as the concentration of the protein changes and also will depend on the binding site itself.

The optimal binding site is usually close to the consensus sequence for that site obtain by aligning all the know binding sites. On can thus have a range of ‘activity’ at different promoters/operators by having differences in DNA binding sites.

Consensus Binding Sites

E. coli Promoters -35 box -10 box

Consensus TTGACA- N17- TATAAT

Examples: TTGATA- N16- TATAATTTCCAA- N17- TATACTTGTACA- N19- CATAATTTGATC- N17- TACTATTTGACA- N17- TAGCTT

“Activity” of Transcriptional Regulators in Response to ‘Signals’

Case 1. Affinity of the protein for DNA may be modified by binding a ‘ligand’ (Allosteric mechanism). Case 2. Affinity of the protein may be affected by covalent modification such as phosphorylation.

Both of these mechanisms (ligand binding and post-translational modification) are common themes in the regulation of proteins, not just in transcription control.

R R-DNA x DNA

Rx Rx-DNA

Regulation of Gene Expression

RNA polymerase bindingOpen Complex Formation Transcription

mRNAmRNA stabilityTranslation

Protein Polypeptide foldingProtein stability

Both positive and negative regulation can occur at any step in this process.

The lac operon:A simple example of regulation of gene expression

LacI(Repressor)

Constitutively expressedi.e. not regulated

lacZ lacY lacA

LacZ - -galactosidase (enzyme degrading lactose)LacY - permease (lets lactose into cells)LacA - transacetylase

lacI lacZ lacY lacA

LacI(Repressor)

lacI lacZ lacY lacA

LacI(Repressor)

+ lactose(allolactose)

Inducer

LacI-Inducer complex cannot bind DNA

lacI lacZ lacY lacA

LacI(Repressor) LacZ - -galactosidase (enzyme degrading lactose)

LacY - permease (lets lactose into cells)LacA - transacetylase

lacI lacZ lacY lacA

In the absence of lactose in the environment, the lacZYA operon is essentially OFF with a low probability of expression.

lacI lacZ lacY lacA

In the presence of lactose in the environment, the lacZYA operon is ON with a high probability of expression.

COMPLICATIONS!

lacI lacZ lacY lacA

O1O3 O2

1) There are actually three operator sites that LacI can bind. Each has a different affinity.

O2 is within the gene

COMPLICATIONS!

lacI lacZ lacY lacA

O1O3 O2CAP

2) There is a transcriptional activator (CAP) that is required for expression of the lacZYA operon.

O1O3 O2CAP

ON State

CAP binding facilitates RNA polymerase binding and activates transcription.

O1O3 O2CAP

LacI binding to two sites (O1 and O2) results in blocking of transcription (promoter clearance) by RNA polymerase and repression.

O1O3 O2CAP

LacI binding to two sites (O1 and O3) results in exclusion of RNA polymerase and repression.

Two regulators- CAP and LacI = Signal Integration

Two LacI operators required = Cooperativity(repression does not show a linear dependence of ‘active’ lacI)

LacI acts as dimer – tetramer = more potential Cooperativity!

O2 and O3 are redundant- not obvious effects of deleting one.

Hysteresis in the lac operon expression

Lactose concentration

The expression of the lacZYA operon increases in a culture of bacteria as the concentration of lactose in the environment goes up.

The expression of the lacZYA operon decreases in a culture of bacteria as the concentration of lactose in the environment goes down but it does not follow the same dependence on lactose.

Why? Consider the two situations at some concentration of lactose

The response of the cell to lactose is dependent on the state of the cell (i.e. the cell’s history)

No induction. Continued Induction.

Uninduced cell Pre-induced cell

LacY permease pumps lactose into the cell, accumulating it above the threshold concentration

information storage and processing in biological systems:

biological information

biological systems

information storage

genetic networks

genetic switch

genetic regulation

immune systemwhat

modular cell biology

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