Cellular Biochemistry
Pleun Maarssen
Inhoudsopgave
Interaction in aqueous systems ............................................................................................................................................................... 2
Water ........................................................................................................................................................................................................... 2
Bonds ........................................................................................................................................................................................................... 2
Acids and bases ............................................................................................................................................................................................ 3
PH ................................................................................................................................................................................................................ 3
Amino acids ............................................................................................................................................................................................ 3
peptides ....................................................................................................................................................................................................... 4
proteins ........................................................................................................................................................................................................ 5
Primary structure ......................................................................................................................................................................................... 5
Secondary structure ..................................................................................................................................................................................... 5
Tertiary structure .......................................................................................................................................................................................... 6
Protein detection and purification ........................................................................................................................................................... 7
Function of detecting and purifying proteins ................................................................................................................................................ 7
Purification ................................................................................................................................................................................................... 7
Column chromatography ............................................................................................................................................................................. 7
protein analysis ............................................................................................................................................................................................ 8
Enzymes ................................................................................................................................................................................................. 9
Working mechanism .................................................................................................................................................................................. 10
Kinetics ....................................................................................................................................................................................................... 10
Equations ................................................................................................................................................................................................... 11
Inhibition .................................................................................................................................................................................................... 11
Cytoskeleton ......................................................................................................................................................................................... 11
actin filaments ........................................................................................................................................................................................... 12
................................................................................................................................................................................................................... 12
Intermediate filaments ............................................................................................................................................................................... 13
Adhesion .................................................................................................................................................................................................... 14
Catabolism of fatty acids and amino acids ............................................................................................................................................. 14
Fats ............................................................................................................................................................................................................ 15
Proteins ...................................................................................................................................................................................................... 17
Bioenergetics ........................................................................................................................................................................................ 18
Organisms perform energy transductions .................................................................................................................................................. 18
Thermodynamics ........................................................................................................................................................................................ 18
Hydrolysis of ATP ........................................................................................................................................................................................ 20
carbohydrates and glycoconjugates ....................................................................................................................................................... 20
carbohydrates ............................................................................................................................................................................................ 20
Receptors and signal transduction ......................................................................................................................................................... 22
Tyrosine kinase receptors ........................................................................................................................................................................... 23
Serine/Threonine kinase receptors ............................................................................................................................................................. 25
EGF receptor signals ................................................................................................................................................................................... 26
G-protein coupled receptor GPCR signals ................................................................................................................................................... 28
TGFB signals ............................................................................................................................................................................................... 28
Cytokines .................................................................................................................................................................................................... 29
Tumor suppressors and oncogenes ........................................................................................................................................................ 29
oncogenes .................................................................................................................................................................................................. 29
DNA tumor viruses ..................................................................................................................................................................................... 30
Cell cycle regulation .............................................................................................................................................................................. 32
Phases of mitosis ........................................................................................................................................................................................ 32
Signaling of cycline ..................................................................................................................................................................................... 33
General characteristics of cancer ............................................................................................................................................................... 34
Normal vs tumor vs stamp cells ............................................................................................................................................................. 35
Tumor cells ................................................................................................................................................................................................. 35
,Interaction in aqueous systems
Water
• 70% of an organisms total weight is water
• Biochemical reactions are studied in aqueous solutions
• Hydrophilic easily dissolved in water, polar compounds
• Hydrophobic difficult to dissolve in water, nonpolar compounds
Bonds
covalent bond
• The bond between two atoms that share a pair of electrons
• More stability for the molecule
• The electron pairs make an electron shell
Hydrogen bond
• Negative attracts positive and form a bond
• the bond between water molecules because they are polar.
• A water molecule can form multiple hydrogen bonds: 3.4 bonds in
water and 4 bonds in ice
• Relatively weak bonds
o Strongest when donor hydrogen acceptor are in a straight line
• Hydrogen bonds responsible for cohesion of water
• Can also bond between macromolecules
o Forms between an electronegative hydrogen acceptor and an hydrogen donor
Amphipathic
• partly hydrophilic and hydrophobic
• if they are exposed to water they form micelles
• can have important biological functions
o drugs can be encapsulated inside
Van der Waals interactions
• weak interatomic attractions
o two uncharged atoms are brought very close together, their surrounding
electron clouds influence each other
• vdWaals force is very weak
▪ 4kJ to break the vdWaals interaction
Ionic interactions
• Interaction between a metal and a non-metal that are opposite charged
• Electrostatic attraction
,Acids and bases
• Weak acids
o Donate H+
• Weak bases
o Accept H+
• Water is a weak acid or a weak base
•
•
• Equilibrium constants
o Kw is always at 25 degrease
o Kw is constant
o So if H+ is very high, then OH- must be low
PH
• pH = -log (H+) and H+ = 10-ph
• -7
pHwater = -log(1.0 x 10 ) = 7
• PH measurements are very important
o pH can effect structure and functions of proteins
o A different pH can be a diagnostic mark
▪ Blood
▪ Urine
• pKa = -log[Ka]
• Henderson-Hasselbalch equation →
• Titration curve (see picture)
o
o Plot of pH and the amount of base added until the acid in neutralized
• Buffers are near a pH of 7
Amino acids
• 20 different Animo acids
• Differences in the R group
• Nomenclature
o Naming of the amino acids:
o Proline pro p
o Glutamine gln q
• Stereoisomerism
o 4 different groups to C in the centre
o Enantiomers (mirror images)
, • Classification
o Non-polar
▪ Hydrophobic
▪ Easy dissolved in water
o Aromatic
▪ Relatively non-polar
▪ Hydrophobic
▪ Can absorb ultraviolet light
at 280 nm
o Polar uncharged
▪ Relatively hydrophilic or
relatively hydrophobic (half
of both)
▪ Can form hydrogen bonds
▪ Capable of forming covalent
bonds
o Polar charged positive
▪ Histidine can serve as a H+ donor and acceptor
▪ hydrophilic
o Polar charged negative
▪ Hydrophilic
• Zwitterions
o Dipolar
o function as base and acids
o have negatively and positively charged groups
• Amino acids are able to give or take an H+ so the titration curve
can looks different
o Multiple buffer regions
o Ionizable R groups have more complex titration curves
o Isoelectric point (PI)
▪ Pl is the Ph where the electric charge is 0
▪ Example: PIgly = 0.5 (pK1 + pK2)
▪ Henderson-Hasselbalch equation
peptides
• Peptides are a chains of amino acids
• Peptides has an amino-terminal and a carboxyl-terminal at the end, these groups are
charged
• The R groups contribute to acid-base properties of the peptide
• Peptides have characteristic titration curves and characteristic PI’s
• pKa of free amino acids can differ from the pKa when it is a polypeptide
• functions of peptides
o hormones and pheromones
▪ insuline (sugar)
▪ sex peptide (fruit fly mating)
Pleun Maarssen
Inhoudsopgave
Interaction in aqueous systems ............................................................................................................................................................... 2
Water ........................................................................................................................................................................................................... 2
Bonds ........................................................................................................................................................................................................... 2
Acids and bases ............................................................................................................................................................................................ 3
PH ................................................................................................................................................................................................................ 3
Amino acids ............................................................................................................................................................................................ 3
peptides ....................................................................................................................................................................................................... 4
proteins ........................................................................................................................................................................................................ 5
Primary structure ......................................................................................................................................................................................... 5
Secondary structure ..................................................................................................................................................................................... 5
Tertiary structure .......................................................................................................................................................................................... 6
Protein detection and purification ........................................................................................................................................................... 7
Function of detecting and purifying proteins ................................................................................................................................................ 7
Purification ................................................................................................................................................................................................... 7
Column chromatography ............................................................................................................................................................................. 7
protein analysis ............................................................................................................................................................................................ 8
Enzymes ................................................................................................................................................................................................. 9
Working mechanism .................................................................................................................................................................................. 10
Kinetics ....................................................................................................................................................................................................... 10
Equations ................................................................................................................................................................................................... 11
Inhibition .................................................................................................................................................................................................... 11
Cytoskeleton ......................................................................................................................................................................................... 11
actin filaments ........................................................................................................................................................................................... 12
................................................................................................................................................................................................................... 12
Intermediate filaments ............................................................................................................................................................................... 13
Adhesion .................................................................................................................................................................................................... 14
Catabolism of fatty acids and amino acids ............................................................................................................................................. 14
Fats ............................................................................................................................................................................................................ 15
Proteins ...................................................................................................................................................................................................... 17
Bioenergetics ........................................................................................................................................................................................ 18
Organisms perform energy transductions .................................................................................................................................................. 18
Thermodynamics ........................................................................................................................................................................................ 18
Hydrolysis of ATP ........................................................................................................................................................................................ 20
carbohydrates and glycoconjugates ....................................................................................................................................................... 20
carbohydrates ............................................................................................................................................................................................ 20
Receptors and signal transduction ......................................................................................................................................................... 22
Tyrosine kinase receptors ........................................................................................................................................................................... 23
Serine/Threonine kinase receptors ............................................................................................................................................................. 25
EGF receptor signals ................................................................................................................................................................................... 26
G-protein coupled receptor GPCR signals ................................................................................................................................................... 28
TGFB signals ............................................................................................................................................................................................... 28
Cytokines .................................................................................................................................................................................................... 29
Tumor suppressors and oncogenes ........................................................................................................................................................ 29
oncogenes .................................................................................................................................................................................................. 29
DNA tumor viruses ..................................................................................................................................................................................... 30
Cell cycle regulation .............................................................................................................................................................................. 32
Phases of mitosis ........................................................................................................................................................................................ 32
Signaling of cycline ..................................................................................................................................................................................... 33
General characteristics of cancer ............................................................................................................................................................... 34
Normal vs tumor vs stamp cells ............................................................................................................................................................. 35
Tumor cells ................................................................................................................................................................................................. 35
,Interaction in aqueous systems
Water
• 70% of an organisms total weight is water
• Biochemical reactions are studied in aqueous solutions
• Hydrophilic easily dissolved in water, polar compounds
• Hydrophobic difficult to dissolve in water, nonpolar compounds
Bonds
covalent bond
• The bond between two atoms that share a pair of electrons
• More stability for the molecule
• The electron pairs make an electron shell
Hydrogen bond
• Negative attracts positive and form a bond
• the bond between water molecules because they are polar.
• A water molecule can form multiple hydrogen bonds: 3.4 bonds in
water and 4 bonds in ice
• Relatively weak bonds
o Strongest when donor hydrogen acceptor are in a straight line
• Hydrogen bonds responsible for cohesion of water
• Can also bond between macromolecules
o Forms between an electronegative hydrogen acceptor and an hydrogen donor
Amphipathic
• partly hydrophilic and hydrophobic
• if they are exposed to water they form micelles
• can have important biological functions
o drugs can be encapsulated inside
Van der Waals interactions
• weak interatomic attractions
o two uncharged atoms are brought very close together, their surrounding
electron clouds influence each other
• vdWaals force is very weak
▪ 4kJ to break the vdWaals interaction
Ionic interactions
• Interaction between a metal and a non-metal that are opposite charged
• Electrostatic attraction
,Acids and bases
• Weak acids
o Donate H+
• Weak bases
o Accept H+
• Water is a weak acid or a weak base
•
•
• Equilibrium constants
o Kw is always at 25 degrease
o Kw is constant
o So if H+ is very high, then OH- must be low
PH
• pH = -log (H+) and H+ = 10-ph
• -7
pHwater = -log(1.0 x 10 ) = 7
• PH measurements are very important
o pH can effect structure and functions of proteins
o A different pH can be a diagnostic mark
▪ Blood
▪ Urine
• pKa = -log[Ka]
• Henderson-Hasselbalch equation →
• Titration curve (see picture)
o
o Plot of pH and the amount of base added until the acid in neutralized
• Buffers are near a pH of 7
Amino acids
• 20 different Animo acids
• Differences in the R group
• Nomenclature
o Naming of the amino acids:
o Proline pro p
o Glutamine gln q
• Stereoisomerism
o 4 different groups to C in the centre
o Enantiomers (mirror images)
, • Classification
o Non-polar
▪ Hydrophobic
▪ Easy dissolved in water
o Aromatic
▪ Relatively non-polar
▪ Hydrophobic
▪ Can absorb ultraviolet light
at 280 nm
o Polar uncharged
▪ Relatively hydrophilic or
relatively hydrophobic (half
of both)
▪ Can form hydrogen bonds
▪ Capable of forming covalent
bonds
o Polar charged positive
▪ Histidine can serve as a H+ donor and acceptor
▪ hydrophilic
o Polar charged negative
▪ Hydrophilic
• Zwitterions
o Dipolar
o function as base and acids
o have negatively and positively charged groups
• Amino acids are able to give or take an H+ so the titration curve
can looks different
o Multiple buffer regions
o Ionizable R groups have more complex titration curves
o Isoelectric point (PI)
▪ Pl is the Ph where the electric charge is 0
▪ Example: PIgly = 0.5 (pK1 + pK2)
▪ Henderson-Hasselbalch equation
peptides
• Peptides are a chains of amino acids
• Peptides has an amino-terminal and a carboxyl-terminal at the end, these groups are
charged
• The R groups contribute to acid-base properties of the peptide
• Peptides have characteristic titration curves and characteristic PI’s
• pKa of free amino acids can differ from the pKa when it is a polypeptide
• functions of peptides
o hormones and pheromones
▪ insuline (sugar)
▪ sex peptide (fruit fly mating)
