Systems Biology Presentation 1

Systems Biology: A layman perspective

EUKARYOTE: ORGANISMS WHOSE CELLS ARE ORGANIZED INTO COMPLEX STRUCTURES ENCLOSED WITHIN MEMBRANES

Biology until now y Reductionism { Identifying individual cellular components and understanding their place in the cell y Description specific y When you studied Mitochondria (the part of the cell

responsible for producing energy), you only cared about Mitochondria and nothing else! y How far will this systematic categorization lead us and what will it accomplish?

Systematic categorization y Great success in many areas of biology y DNA sequencing { Genome sequences are now available { Thanks to those guys who worked hard and did the bookkeeping! y Due to such meticulous categorization, we now have

a lot of data on how the cell and its parts function as a whole and interact.

Biology today y What is the stuff of life? { Still unanswered! y Paradigm shift towards systems approach y Components are now of secondary importance but

the interactions between the components take the primary focus y What type of interactions take place between the ‘components’ of a cell?

Typical interactions y The cell is an extremely complex physical object that y y y y

follows the laws of physics Hence, all the interactions taking place in a cell are chemical reactions But there are so many of them! How do we keep track of what’s going on? Chemical reactions have certain key properties that allow one to quantify such information

Stoichiometric Matrix y All the information in a chemical reaction is

contained within the balancing coefficients y Balancing coefficients are obtained via elemental and charge balancing y Thus, the information is “digital” y Moreover, some reactions are invariant with changes in { {

Temperature Pressure

Links to networks y Single chemical reaction connecting a set of

reactants and products forms a link y If some/all of the reactants and products are involved in other reactions as well, then, it becomes necessary to generalize links to networks. These networks are complex in nature. y Topological properties of such networks give limited information about the actual “functional state” of the network.

Some things to keep in mind y The network view of any biological process inside a y y y y

cell takes place in a crowded interior Cellular (biological) networks are inherently three dimensional Limited usefulness of analogies with man made networks The question of what states to pick as functional states? is very important Furthermore, we cannot expect “exact solutions” since we probably don’t know some of the constraints

Conclusion and lead-up to the next presentation y Consider { 2H + O → 2H O 2 2 2 y Elemental matrix E is defined as follows: H 2 O2 H 2 O ↓

↓

↓

O → ⎛0 2 1 ⎞ ⎜ ⎟ H → ⎝ 2 0 2⎠

y Reaction vector: Reactants are negative and products are

positive S = ( −2 −1 2 ). These are just the coefficients in the equation (-ve for reactants and +ve for products). T

y

ES = 0 {

This is equivalent to “Matter is neither created or destroyed”.

End of presentation 1

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