Chapter 5: Systems biology
Researchers study living
organisms in terms of their
underlying network structure
rather than their individual
The goal is to understand how the
organization of the cell arises by
complex interactions between its
various components and parts.
Four system works together
1. Interior of the nucleus
3. Endomembrane system
4. Semiautonomous organelles ex. Mitochondria, chloroplasts
• protein-protein interactions critical
• Continual synthesis new molecules and breakdown unwanted components
From genome to transcriptome to proteome...
Genomes, proteomes and cell structure/function and organization
Proteome is responsible for the structure and function of cells
Gene and protein regulation causes the proteome to be dynamic
Proteins have sorting signals (must be in the right place).
Cells require pre-existing organization
Structure determines function. Jobs are derived from complements of proteins; might be some overlap.
Own proteome: different jobs, different machines (While genome is static
even when genes are being turned on and off, but proteome is changing
from minute to minute).
b) Isolate proteomes, they would be different, but genomes would be the same.
- Proteome, controlled by genome.
- Protein-protein interactions critical
- Continual synthesis new molecules and breakdown unwanted components.
They will be tightly bound together (but not covalent bonding) other bonding that hold
Molecular machines (multi-unit machine).
A machine is an object that has moving parts and does useful work :
• provide structure and organization to cells
• ATP synthase is a molecular machine
– Molecular recognition allows for complex assembly
• Subunits recognize each other and bind in a specific way
Illustrates molecular machines: ATS synthase found in bacteria,
mitochondria and chloroplasts. ATP synthase subunits self-assemble
based on shape but the site structure most also be correctly oriented
relative to the cell membrane to function. (protons are moved =
gradient): turns kinetic energy into potential energy – when we get
protons through ATP synthesis, kinetic energy can be used to make
chemical energy to make covalent bonds.
Other molecular machines
a) Ribosomes in the act of making polypeptides
- Compartmentation, allow you to separate different environments. -
- Proteins are what controls gene activity.
Flagellum, microtubulars attached to motor proteins held in place so
when it undergoes cycle of change; pulls on microtubular. Protein
protein interaction + protein-RNA and RNA-RNA interaction where
ribosomes will recognize and recreate rRNA and tRNA … Introduct
concept: elegant molecular machine : subunit to mRNA.
b) The flagella of sperm contain a molecular machine for locomotion
Cytoskeleton: cytoskeleton contributes to structure
and cell movement. Serve as meshwork within a cell.
Important role in getting things where they have to be
in the cell.
Intermediate filaments less dynamic… than…
a) Bioconcave disk shape of red blood cells
b) Cytoskeletal connections to the red blood cell
membrane Role of cytoskeleton in moving things around
(neyron: microtubule drawing). Alpha and Beta – non
covalent, polymerizing, and depolimerizing…
provide a road way to move cargo. Ability to bind
will change when they come in contact with tubuline,
they ones motor proteins will face.
High enough affinity – tightness in bonding, but not
high enough to not be able to pull them apart.
Modulated by different events in the cell.
Must have their own genome and increase in number via
binary fission = binary fission = division of cells. (ex.
peroxixomes have the ability to do binary fission – but not
part of semiautonomous organelles, because they don’t their
own genome). Circular DNA, own proteins created, own
genome, double membrane (derived from an engulfing
event), go through binary fission.
Dual Origin Proteomes: some included by nuclear genome,
and some by their own. Vast majority are encoded by nuclear
genome and some from their own.
-> include: outer membrane of nuclear envelope,
endoplasmic reticulum, Golgi apparatus, lysosomes,
peroxisomes, vacuoles, secretary vesicles, and plasma membrane (Nuclear envelope
attached, but Golgi is not – rather receives vesicles)
Role: Transport of membrane
vesicles among its various
components: gets proteins to
destination. Major site of
metabolic reactions : most of
cell’s lipids and proteins are
made in ER membrane. ->
synthesis of proteins and lipids
- Storage and recycling or
organic molecules ex. Vacuoles
(proteins, carbs, fats)
- Breaking down of molecules
ex. Lysosomes Notes on previous image: Nuclear envelope creates space for nucleus (nucleus not part of endomembrane system).
Synthesis of membrane phospholipids in ER
Cytosol and endomembrane system: work together to synthesize most lipids. (occurs in
1) fatty acids activated by attachment of CoA molecules
2) fatty acids bond glycerol-phosphate + inserted into cytosolic leaflet of ER membrane
3) phosphate removed by a phosphatase enzyme
4) Appreciate role of ER : lipid biosynthesis
5) flippases transfers some of the phospholipids to other leaflet.
*definition of enzymes
Lipid transfer throughout a eukaryotic cell
* Compartmentation needed for lipid synthesis.
Function associated to position in membrane. Put energy into flipping, must go through interior of
membrane to go through hydrophilic to hydrophobic environment – needs energy. Feature investigation
Palade demonstrated that secreted proteins move sequentially through organelles of the