This document is a summary about the course Cellular biochemistry. It is about the structure, function, detection and purification of proteins. The summary also describes other macromolecules like fatty acids, lipids, carbohydrates and glycoconjugates. Furthermore, the document describes the functi...
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)
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