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					Biological Pathways



           Janick Mathys
    Biological Pathways
• Definition
• Biochemical compounds
• Biological interactions
• Energy
• Control interactions
• Levels of abstraction
• Types of biological pathways
• Integration of pathways
• Inference Issues
          Biological Pathways

Definition:
A biological pathway is a sequence of interactions
between biochemical compounds aimed at the
maintenance and control of the flow of information,
energy and biochemical compounds in the cell and
the ability of the cell to change its behaviour in
response to stimuli.
          Biological Pathways

Definition:
A biological pathway is a sequence of interactions
between biochemical compounds aimed at the
maintenance and control of the flow of information,
energy and biochemical compounds in the cell.

Main types of compounds in the context of pathways:
- proteins and protein complexes
- (part of) genes
- metabolites
 Biochemical compounds
• (part of) genes
• proteins and protein complexes
• metabolites
   – Amino acids and peptides : A, C, F, G, H, S…
   – Carbohydrates (sugars)
   – Cell-structure components
   – Cofactors, prosthetic groups and electron carriers: vitamins
   – Fatty acids and lipids
   – Nucleotides and nucleic acids: A, C, T, G
   – Monocarbon compounds: CO, CH4, CH3OH
   – Essential elements: S, P, O2, Fe, radicals
   – Aromatic compounds:
     compounds with special stability and properties
     due to a closed loop of electrons (ring structure)
   – …
Biochemical compounds
 genes
 - Fundamental physical and functional units of heredity
 - Ordered sequences of nucleotides located in a particular position on a
 particular chromosome that encodes a specific functional product (i.e. protein
 or RNA molecule)


 regulatory DNA sequences
 - Small conserved sequences that interact with special types of proteins (TF)
 thereby activating or repressing the expression of target genes
 - Located in the promotor region in front of the target gene




             Regulatory                                        RBS      gene
             sequences

                          Promoter
Biochemical compounds
 proteins and protein complexes
 Ras protein                               Protein: 3D-chain of amino acids that
                                            is represented as a linear sequence
                                               of amino acid letter codes and
                                               performs a molecular function


 Transcription initiation complex in eukaryotes
Biochemical compounds
 metabolites
 Any product of metabolism such as an intermediate or an end product that is
 excreted

 Examples:
 - amino acids e.g. cysteine




 - carbohydrates e.g. glucose




 -…
           Biological Pathways

Definition:
A biological pathway is a sequence of interactions
between biochemical compounds aimed at the
maintenance and control of the flow of information,
energy and biochemical compounds in the cell.

Biological Interactions:
         Substrates                 Products
                      Interaction
                           Energy
         Biological Interactions
        Substrates                 Products
                     Interaction
                          Energy

Main types of interactions in the context of pathways:
- Expression
- Assembly/Disassembly
- Transport
- Chemical reactions
            Biological Interactions

I. Expression:
           Gene                                Protein
                           Expression
The process by which a gene's information is converted into a protein
Expressed genes are transcribed into mRNA and translated into protein or
transcribed into RNA but not translated (transfer and ribosomal RNAs).

II. Assembly:
           Protein A                         Complex
                           Assembly
           Protein B
The formation of a complex of proteins, RNA and/or DNA with a molecular
function that cannot be performed by the individual compounds
                Biological Interactions
- Expression:
       fus1        Expression Fus1 protein 1
                              Cell fusion

                                                 mRNA



                                               fus1 DNA

                                   Nucleus
         DNA

                                       fus1
       mRNA


                        Fus1 protein
     AA1 AA2 AA3
                                                          Yeast
                    Biological Interactions
 - Assembly of complexes:
     Ribosomes:
     - complexes of RNA and proteins
     - translate genetic information into protein




Prokaryotes                                         Eukaryotes
                Biological Interactions

Detail: Assembly of the small ribosomal subunit in prokaryotes




                                                                 Prokaryotes
                  16S rRNA
Biological        21 proteins


 Interactions



                     ribosome




    23S rRNA
    5S rRNA
    31 proteins
                                Prokaryotes
             Biological Interactions

III. Transport:
            Compound A                   Compound A
            at location 1                at location 2
                            Transport

Change of location of compounds


IV. Chemical reaction:
         Compound A                     Compound B
                            Reaction
           Biological Interactions

- Transport:
 a. Transport of nascent proteins through plasma membrane of the ER:

   Ribosome - nascent protein complex                     Nascent protein
              in cytoplasm            Transport            in lumen of ER


b. Transport of glucose from the lumen of the intestine into the blood:


    Glucose        Transport        Glucose          Transport    Glucose
  in intestine                  in epithelial cell                in blood
Biological Interactions
                                            Plasma membrane
                                                of the ER
a. Transport of nascent proteins
 into the lumen of the
 endoplasmic reticulum in
 eukaryotes




 ER : organelle of eukaryotic cells
 consisting of a ± continuous system
 of membrane-bound cavities
 throughout the cytoplasm of a cell. Its
 function is the transport of proteins
 that have to be secreted to the membrane
 of the cell.


                              Eukaryotes
Biological Interactions
                                  Plasma membrane
                                      of the ER




b. Glucose transport from the
lumen of the intestine into the
blood stream




                                      Higher Eukaryotes
             Biological Interactions

- Chemical reactions:
1. Redox reactions: Oxidation - Reduction (Photosynthesis):
   transfer of e- from electron donors to electron acceptors
2. Phosphorylation - Dephosphorylation (Signal transduction):
   addition/removal of phosphate groups
3. Hydrolysis:
   breakdown of bonds in compounds through the addition of water
4. Splitting or forming of a C-C bond
5. Isomerisation:
   Change of geometry or structure of a compound
6. Polymerisation
7. …
Chemical Reactions
1. Oxidation – Reduction of NADH – NAD+:




                       H+ + 2e- +
   Chemical Reactions
    2. Phosphorylation:
    Phosphorylation cascade involved
    in the uptake of glucose into the cell




1. Non ionic glucose is pumped through the cell
membrane, which is negatively charged
2. A cascade of phosphorylations and dephos-
phorylations takes place resulting in the phosphorylation
of glucose as it enters the cell
3. The ionic nature of Glucose-6-P prevents it
from escaping back through the membrane                  -OH


                                                               ATP ADP   Prokaryotes
  Chemical Reactions
      3. Hydrolysis:
      hydrolysis of lactose into
      galactose and glucose by
      beta-galactosidase




1. Lactose is pumped through the cell membrane
2. Hydrolysis of lactose into galactose and glucose
immediately as it enters the cell
=> Extra step (energy cost) as compared with the
metabolism of glucose



                                                      Prokaryotes
Chemical Reactions
 4. Splitting C-C bonds:
 Cleavage of fructose-1,6-PP to dihydroxyacetone-P + glyceraldehyde-3-P
 P has the size of fructose core => 2 negative P in close proximity => stress

                      Fructose-1,6-PP aldolase



         Fructose-1,6-PP                         DHAP + GA-3-P

 5. Isomerisation:
 Rearrangment of Glucose-6-P into Fructose-6-P, a more compact and
 lower entropy (more unstable thus more willing to react) molecule

                         Phosphohexose isomerase


           Glucose-6-P                              Fructose-6-P
                   Biological Interactions
       Substrate                                   Product
                           Interaction
                              Energy
• Energy is always required to form chemical bonds
• Energy is sometimes released by the breaking of chemical bonds
• For biological interactions the cell uses 3 energy sources:
  - ATP: Adenosine TriPhosphate
  - GTP: Guanine TriPhosphate
  - Creatine phosphate
• ATP is generated by electron transfer in mitochondria:
  - Electron carriers pick up H+ and e- released by the breakdown of nutrients (e.g. glucose)
  - Electron carriers transfer H+ and e- to electron carriers in the mitochondrial membrane
  - Transfer of e- through the mitochondrial membrane down to O2 releases energy
  - This energy is used to transport the H+ across the mitochondrial membrane
  - Rush of H+ releases energy used for phosphorylation of ADP to generate ATP
    Energy sources

• ATP: Adenosine TriPhosphate
-   Primary energy source of cells
-   Building block for DNA
-   High energy bonds between phosphates
-   Dephosphorylation of outer phosphate to form ADP releases 7.3 kcal/mol
• GTP: Guanine TriPhosphate
-   Secondary energy source of cells
                                                 ! all nucleotides are full of energy
-   Building block for DNA
                                                  e.g. transcription: energy comes
-   Bound by G-proteins for signal transduction         from dNTPs themselves
-   High energy bonds between phosphates
-   Dephosphorylation of outer phosphate to form GDP releases 7.5 kcal/mol
-   (Cleaving the phosphate-ribose bond would release only 5 kcal/mol)
• Creatine phosphate
-   Extra energy source for muscle cells
-   Dephosphorylation releases 10.3 kcal/mol
                          16S rRNA
                          21 proteins

Energy
GTP provides energy
for the assembly of the
large subunit and the
30S complex

                             ribosome




     23S rRNA
     5S rRNA
     31 proteins
                                        Prokaryotes
Energy
                                       Plasma membrane
Transport of nascent proteins              of the ER
into the lumen of the ER in
eukaryotes


GTP provides energy for binding
of ribosome to ribophorin and for
insertion of peptide in the membrane




                         Eukaryotes
Energy
                                     Plasma membrane
                                         of the ER




Glucose transport from the
lumen of the intestine into the                         Na+
blood stream
                                   Na+

ATP provides energy for
                                         Na+
transport of Na+/K+ out/in cell
(against concentration gradient)

! Transport of glucose down                    Higher Eukaryotes
concentration gradient: no ATP
required
    Electron carriers
• NADH: Nicotinamide Adenine Dinucleotide
-   Oxidation to NAD+ releases 52.6 kcal/mol
-   Due to some inefficiency this only allows 3 ATPs to be formed




• FADH2: Flavine Adenine Dinucleotide
-   Oxidation to FAD releases 43.4 kcal/mol
-   Due to some inefficiency this only allows 2 ATPs to be formed
Electron carriers
1. Oxidation – Reduction of NADH – NAD+:




                       H+ + 2e- +
            Biological Interactions
Control Interactions:
Enhance or repress other interactions
   +          -

Main types of control interactions:
- transport facilitation
- enzymatic catalysis
- inhibition
- activation of gene expression
- repression of gene expression
                  Control Interactions


    I. Transport Facilitation:

Compound A at location 1                    Compound A at location 2
                              Transport
                                      +
                             Facilitation

                           Transporter protein
Control Interactions
                                            Plasma membrane
- Transport Facilitation:                       of the ER

a. Facilitation of the transport of
nascent proteins into the lumen
of the endoplasmic reticulum by
ribophorin




                               Eukaryotes
Control Interactions
                                                      Plasma membrane
                                                          of the ER




Transport Facilitation:
b. Glucose transport from the intestine
into the blood stream is facilitated by
- Na+-glucose cotransporter pore
complex
- glucose transporter protein
http://bio.winona.msus.edu/berg/ANIMTNS/FacDiff.htm

Removal of Na+ in epithelial cells is
facilitated by Na+/K+ pump
                                                          Higher Eukaryotes
                    Control Interactions

c. Facilitation of the transport of
glucose and lactose into the cell
by EIICB and lactose permease




                                      Prokaryotes
                    Control Interactions

II. Catalysis of chemical reactions by enzymes:
          Compound A                         Compound B
                               Reaction
                                       +
                               Catalysis

                                Enzyme
  Enzymes:
  Proteins (RNAs) that act as biological catalysts, speeding up reaction
  rate by reducing the amount of required energy
     * by concentrating different substrates
     * by inducing conformational changes in substrates through binding
  Enzymes DO NOT participate in the reaction or alter its direction/nature
              Control Interactions

- Catalytic Enzymes :
1. Redox reactions: oxidase, dehydrogenase
   transfer of e- from electron donors to electron acceptors
2. Phosphorylation - Dephosphorylation: kinase, phosphatase
   addition - removal of phosphate groups
3. Hydrolysis: hydrolase
   breakdown of bonds through the addition (- removal) of water
4. Transfer of a side group: transferases
5. Splitting or forming a C-C bond: desmolase, aldolase
6. Changing geometry or structure of a compound: isomerase, gyrase
7. Joining two compounds through hydrolysis of ATP: ligase
8. Polymerisation: polymerase
                   Control Interactions
  III. Inhibition:
              Compound A                          Compound B
                                   Interaction
                                           -
                                   Inhibition


                                   Compound




Control interactions form a means of using compounds to introduce feedback !
                          Control Interactions
     - Inhibition
        Inhibition of the transport of
        lactose into the cell in prokaryotes
        by a component (EIIAGlc) of the
        glucose transporter complex
        => Catabolite repression


Lactose                     Lactose
                                               1. Glucose is pumped through the cell membrane
extracellular               intracellular      2. A cascade of phosphorylations and dephos-
                Transport                      phorylations takes place resulting in
                                                - the phosphorylation of glucose
                      +                         - the dephosphorylation of EIIAGlc-P into EIIAGlc
                                               3. EIIAGlc shuts down the lactose permease, pre-
                            -                  venting lactose from entering the cell
            Facilitation        Inhibition     Conclusion: Catabolite repression:
                                               This system ensures that bacteria give
                                               preference to the most energetic nutrient
            Lactose permease         EIIAGlc
            Control Interactions
IV. Activation of gene expression:
          Gene                                Protein
                        Expression
                                +
                         Activation

                      Transcription factor
V. Repression of gene expression:
           Gene                                Protein
                          Expression
                                    -
                           repression


                       Transcription factor
            Control Interactions
Activation of gene expression:
                   Control Interactions
Activation of gene expression:
- DNA is packaged into nucleosomes and higher-order
  chromatin structures

-Transcription factor binds specific regulatory element


- Transcription factor recruits chromatin remodeling
  and modifying complexes



- Transcription factor recruits components of the
  transcription initiation complex




- Transcription factor stimulates activity of assembled transcription complex
                      Control Interactions
    Transcription factor (complexes):
•    Proteins that bind to specific regulatory sequences in the DNA
•    Regulate the level of expression of target gene(s) by controlling whether
     and how vigorously the gene is transcribed into RNA
•    The on/off switches and rheostats of a (group of) target gene(s)

    Regulatory DNA sequences
•    Every gene has its own cis-acting regulatory sequences
•    Vary greatly in complexity among genes and organisms

     When active transcription factors associate with the regulatory sequences
     of their target genes, they can function to repress (down-regulate) or
     induce (up-regulate) transcription of the corresponding RNA
              Cysteine




Amino Acids
                           Protein
              (Molecular Function)




                            Pathway
                (Biological process)
              Biological Pathways

•   Metabolic pathways
•   Developmental pathways
•   Signal-transduction pathways
•   Genetic regulatory circuits = genetic networks

• Pathways interact
• Pathways overlap
  => Biochemical compounds are involved in different pathways
                Metabolic Pathways
• Metabolism:
  The sum of all chemical reactions that take place within a cell providing
  energy for vital processes and for synthesizing new organic material

• EcoCyc/HinCyc/MetaCyc:
  Encyclopedia of Escherichia coli Genes and Metabolism
  Encyclopedia of Haemophilus influenzae Genes and Metabolism

• EMP:
  Enzymes and Metabolic Pathways database

• KEGG:
  Kyoto Encyclopedia of Genes and Genomes

• …
                  Metabolic Pathways

• Biosynthesis = Anabolism:
  Sequences of enzyme-catalyzed chemical reactions by which complex
  molecules are formed in living cells from building blocks with simple
  structures
• Degradation = Catabolism:
  Sequences of enzyme-catalyzed chemical reactions by which large
  molecules in living cells are broken down or degraded into building blocks
• Transport:
  Sequences of transport (facilitation) interactions by which compounds are
  transported from one location to another.
• Energy Metabolism:
  Sequences of enzyme-catalyzed chemical reactions by which chemical
  energy obtained from the environment by degradation of nutrients or by
  capturing solar energy (plants) is transformed into energy-rich compounds
  that are required for metabolic processes
               Metabolic Pathways

• Metabolism of:
  –   Amino acids, peptides, proteins and derivatives
  –   Carbohydrates (sugars)
  –   Cell-structure components
  –   Cofactors, prosthetic groups and electron carriers
  –   Fatty acids and lipids
  –   Nucleotides and nucleic acids
  –   Monocarbon compounds
  –   Essential elements
  –   Aromatic compounds
  Metabolic Pathways
• Glycolysis (Embden-Meyerhoff-Parnas pathway) :
  Degradation of glucose
  to pyruvate for generation
  of energy

  Phases:
  1. Preparatory phase:
    - activation of glucose by
      phosphorylations
    - conversion to glyceraldehyde-3-P
      by hexose splitting
  Metabolic Pathways
• Glycolysis (Embden-Meyerhoff-Parnas pathway) :
  Phases:
  2. Pay-off phase:
    - oxidation of glyceraldehyde-3-P
      to pyruvate
    - coupled formation of ATP and
      NADH
Metabolic Pathways
Overlap and integration
of metabolic pathways:
Amino acid metabolism of E.coli
Metabolic Pathways
Overlap and integration
of metabolic pathways:
Entire metabolism of E.coli
Signal Transduction Pathways


                             Signal
                          transduction

                           Phosphorylations!




                                 Genetic
                                 network
           Signal Transduction Pathways
• Mating reaction in yeast:
  Two mating types (a – α)
   - opposite types communicate by
     secreting a pheromone
     (a-factor – α-factor)
   - exposure to pheromones causes
     the cells to stop dividing, alter their
     cell polarity and eventually to fuse
        G protein




    Inactive cell cycle                   P
       arrest factor Far1              MAPKK
                                        Ste5        P         P               Kinase
                                              MAPKK         MAPKK             Ste20 P
STOP cell                              MAPKK Ste7            Ste3
                        P               Ste20
cycle in G1                                                       Kinase complex
                                          P
                    Activated



                                                                                            Nucleus
                                                 Ste12              P
                            Inactive transcription factor                      P
                                                                  Activated
Yeast                                                                               fus1 gene
               Signal Transduction Pathways
• Overlap and integration of signal transduction pathways
  Yeast Pheromone Signaling Pathway




  Humans : MAPK signaling pathway : growth control -> tumor development
  http://www.bio.davidson.edu/courses/Immunology/Flash/MAPK.html
Signal Transduction Pathways
• CSNDB:
  Cell Signaling Networks Database
  http://geo.nihs.go.jp/csndb/

  Contains information on biological
  compounds, their sequences,
  structures, functions and interactions
  which transfer cellular signals in human

  Directed graph representation




         Human MAPK signaling pathway
Genetic networks


                      Signal
                   transduction




                         Genetic
                         network
    Genetic networks
•   Biochemical computers controlling the on/off switches and rheostats of a
    cell at the gene level
•   Dynamically orchestrate the expression level for each gene in the genome
    by controlling whether and how vigorously that gene is transcribed
•   Essential interacting components:
    - Activated transcription factor complex
    - Regulatory DNA sequences
•   Output : RNA and proteins
•   Some of these proteins are the actuators of inhibition and repression
    => main feedback loops
•   Co-regulated target genes often code for proteins that act together to build
    a specific cell structure or to effect a concerted change in cell function
•   Often multiple waves of regulation with first wave products regulating
    expression of another group of genes and so on
Genetic networks
    Genetic networks
•   Genetic network controlled
    by the CtrA response regulator
    in bacteria




                                     Nature Reviews Molecular Cell Biology 3; 167-176 (2002)
Genetic networks
• BRITE :
  Biomolecular Relations in Information
  Transmission and Expression
  http://www.genome.ad.jp/brite/

  Contains information on signal
  transduction pathways and the genetic
  networks they activate (genes, the control
  of their expression and proteins)

  Directed graph representation

  Still under construction
                  Integration of Pathways

                                        Primary                    Terminal
 Input       Signal      Genetic       Outputs:                    Outputs:
                                                      Metabolic
Signals   transduction   networks     Changed RNA                  Changed cell
                                                      pathways
            pathways                   and protein                behaviour and
                                       composition                  structure



                            Feedback circuitry


The integrated network of biological pathways is a cellular input-output device
1. Input signals are captured by appropriate receptors and transduced by signal
   transduction pathways
2. Signal transduction pathways activate genetic networks, causing changes in
   cellular protein and RNA composition
3. The changes in enzyme/inhibitor composition alter the activity of metabolic
   pathways resulting in changed cell behaviour, function and/or structure
                   Biological Pathways

• Inference Issues:
  - Complete network of integrated biological pathways is blueprint of life
   - Genome is only an archiving system of building blocks
   - Regulatory DNA motifs are bar codes to retrieve the building blocks
• Combination of high-throughput experiments, prior knowledge
  and bayesian network inference is necessary
   Experiments:
   - Microarrays
   - Proteome analysis      Expression is result of underlying network
   - Yeast two-hybrid
   - Phosphorylations
Biological Pathways

• First inference results

				
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posted:10/14/2011
language:English
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