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
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
gene RBS
Regulatory sequences
Promoter
Biochemical compounds
proteins and protein complexes
Ras protein
Transcription initiation complex in eukaryotes
Protein: 3D-chain of amino acids that is represented as a linear sequence
of amino acid letter codes and performs a molecular function
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
Interaction Products
Biological Interactions
Main types of interactions in the context of pathways:
- Expression
- Assembly/Disassembly - Transport
- Chemical reactions
Substrates
Interaction Products
Energy
Biological Interactions
I. 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:
The formation of a complex of proteins, RNA and/or DNA with a molecular
Gene Expression Protein
Protein A
Assembly Complex
Protein B
Biological Interactions
- Expression:
fus1 Expression Fus1
Cell fusion protein 1
DNA Nucleus
mRNA
fus1 DNA
fus1 mRNA
AA1 AA2 AA3 Fus1 protein
Yeast
- Assembly of complexes:
Ribosomes:
- complexes of RNA and proteins
- translate genetic information into protein
Biological Interactions
Detail: Assembly of the small ribosomal subunit in prokaryotes
Prokaryotes
Biological Interactions
Biological
Interactions
ribosome
23S rRNA
16S rRNA 21 proteins
Biological Interactions
III. Transport:
Change of location of compounds
IV. Chemical reaction:
Compound A at location 1
Transport
Compound A at location 2
Compound A
Reaction Compound B
- Transport:
a. Transport of nascent proteins through plasma membrane of the ER:
b. Transport of glucose from the lumen of the intestine into the blood:
Biological Interactions
Ribosome - nascent protein complex
in cytoplasm Transport Nascent protein in lumen of ER
Glucose
in intestine Transport Glucose
in epithelial cell Transport Glucose
in blood
Biological Interactions
a. Transport of nascent proteins into the lumen of the
endoplasmic reticulum in eukaryotes
Plasma membrane of the ER
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.
Biological Interactions
b. Glucose transport from the lumen of the intestine into the blood stream
Plasma membrane of the ER
Higher Eukaryotes
- 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. …
Biological Interactions
1. Oxidation – Reduction of NADH – NAD+:
Chemical Reactions
H+ + 2e- +
2. Phosphorylation:
Phosphorylation cascade involved in the uptake of glucose into the cell
Chemical Reactions
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
ATP ADP Prokaryotes
-OH
3. Hydrolysis:
hydrolysis of lactose into galactose and glucose by beta-galactosidase
Chemical Reactions
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
Fructose-6-P
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
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
Chemical Reactions
Glucose-6-P
Phosphohexose isomerase
Fructose-1,6-PP DHAP + GA-3-P
Fructose-1,6-PP aldolase
Biological Interactions
• 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
Substrate
Interaction Product
Energy
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 - Building block for DNA
- Bound by G-proteins for signal transduction - 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
! all nucleotides are full of energy e.g. transcription: energy comes
from dNTPs themselves
Energy
ribosome
23S rRNA
16S rRNA 21 proteins
GTP provides energy for the assembly of the large subunit and the 30S complex
Energy
Transport of nascent proteins into the lumen of the ER in eukaryotes
Plasma membrane of the ER
Eukaryotes
GTP provides energy for binding of ribosome to ribophorin and for insertion of peptide in the membrane
Energy
Glucose transport from the lumen of the intestine into the blood stream
ATP provides energy for
transport of Na+/K+ out/in cell (against concentration gradient)
! Transport of glucose down
Plasma membrane of the ER
Higher Eukaryotes
Na+ Na+
Na+
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
1. Oxidation – Reduction of NADH – NAD+:
Electron carriers
H+ + 2e- +
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
Biological Interactions
+ -
Compound A at location 1
Transport Compound A at location 2
Facilitation
Transporter protein +
I. Transport Facilitation:
Control Interactions
Control Interactions
- Transport Facilitation:
a. Facilitation of the transport of nascent proteins into the lumen of the endoplasmic reticulum by ribophorin
Plasma membrane of the ER
Eukaryotes
Control Interactions
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
Plasma membrane of the ER
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:
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 Compound A
Reaction Compound B
Catalysis
Enzyme
+
- 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
Control Interactions
III. Inhibition:
Compound A
Interaction Compound B
Inhibition
Compound
-
Control interactions form a means of using compounds to introduce feedback !
Control Interactions
- Inhibition
Lactose
extracellular
Transport
Lactose intracellular
Facilitation
Lactose permease
+
- Inhibition
EIIAGlc Inhibition of the transport of
lactose into the cell in prokaryotes by a component (EIIAGlc) of the glucose transporter complex
=> Catabolite repression
1. Glucose is pumped through the cell membrane 2. A cascade of phosphorylations and dephos- 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
Conclusion: Catabolite repression:
This system ensures that bacteria give preference to the most energetic nutrient
Control Interactions
IV. Activation of gene expression:
V. Repression of gene expression:
Gene Expression Protein
Activation
Transcription factor
+
Gene Expression Protein
repression
-
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
Control Interactions
Activation of gene expression:
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)
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
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
Genetic network
Phosphorylations!
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
Kinase Ste20 P
MAPKK Ste3 MAPKK
MAPKK Ste7 Ste20 MAPKK
Ste5 P P
P
P
Nucleus
STOP cell P
cycle in G1
G protein
Inactive cell cycle arrest factor
Activated
Kinase complex Far1
Signal Transduction Pathways
• Overlap and integration of signal transduction pathways
Yeast Pheromone Signaling Pathway
Humans : MAPK signaling pathway : growth control -> tumor development
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
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
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
Input Signals
Signal transduction
pathways
Genetic networks
Primary Outputs:
Changed RNA and protein composition
Metabolic pathways
Terminal Outputs:
Changed cell behaviour and
structure
Feedback circuitry
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 - Yeast two-hybrid - Phosphorylations
Expression is result of underlying network
Biological Pathways
• First inference results
