GEK1532 Proteins
-
Upload
givena2ndchance -
Category
Documents
-
view
220 -
download
0
Transcript of GEK1532 Proteins
-
8/6/2019 GEK1532 Proteins
1/31
GEK1532
Proteins
Thorsten WohlandDep. Of Chemistry
S8-03-06Tel.: 6516 1248
E-mail: [email protected]
http://www.cellsalive.com/
Book: Biochemistry, Voet, chapter 4 and chapter 7
-
8/6/2019 GEK1532 Proteins
2/31
Critique of the WCS Are there non-trivial constraints on colour categorization?
B.A.C. Saunders, J. van Brakel
Behavourial and Brain Sciences (1997), 20, 167-179
4. The unique hues are defined by so- called opponent channels. That is, thebrain always compares
a) red (L come) to green (M cone) and
b) blue (S cone) to yellow (M cone + L cone).
2. Hue, Saturation and Brightness completely describe color.
3. There are 4 hues: green, red, blue, yellow
1. Color is an objective property equally defined by all human beings.
-
8/6/2019 GEK1532 Proteins
3/31
P roblemWe have reviewed different theories that can explain different aspects of our color vision:
1. Tristimulus theory: Since we can mix all colors with 3 (abstract colors) our vision should be based on three different sensors (cones). The theory can
explain complementary colors, metamers and is a good tool for theclassification of colors.
2. Opponent color theory: This theory is based on 4 colors (plus an achromaticbrightness channel). It explains many effects of perception not easily explainedby the tristimulus theory: hue cancellation experiments, existence of only two
different kinds of dichtomacy (red-green, blue-yellow deficiencies).
Then we took a look at the WCS and its criticism by Saunders and Brakel. Thisshowed that few of the things we took for granted up to now are really evidentor have a unshakable basis.
So is there any basis on which we can found our investigation of color vision?
-
8/6/2019 GEK1532 Proteins
4/31
Hydrophobic effect
-
H HO+
-
H HO+
In the liquid phase most water molecules are hydrogen bonded
-H H
O+
-
H HO+
-
H HO+-
H HO+
-
H HO+
-
H HO+
-
H HO+
-
H HO+
-
8/6/2019 GEK1532 Proteins
5/31
Hydrophobic effect
-
H HO+
-
H HO+
We get a separation of the non-polar molecule from water; We say themolecule is hydrophobic (it hates water).
Introducing non-polar, hydrophobic elements like the tail of alipid into water disrupts the structure of water
-H H
O+
-
H HO+
-
H HO+
-
H HO+
-
8/6/2019 GEK1532 Proteins
6/31
-
8/6/2019 GEK1532 Proteins
7/31
R evision: Hydrophilicity,
Hydrophobicity, and AmphipathicityHydrophilic: water loving, dissolves well in water
+
H2O
Alcohol (ethanol)
Hydrophobic: water hating, dissolves badly in water +
H2O
oil
Amphipathic: consist of a hydrophilic and ahydrophobic part +
H2O
lipid
-
8/6/2019 GEK1532 Proteins
8/31
R evision: What are lipids?Glycerophospholipids
P olar head group
backbone
Non-polar,hydrophobic tail
-
8/6/2019 GEK1532 Proteins
9/31
R evision: Amphipathic molecules
Hydrophobic
Hydrophilic
-
8/6/2019 GEK1532 Proteins
10/31
R evision: Why membranes?Compartmentalization:
The bilayer separates theinside of a cell (the cytoplasmor intracellular space) from theoutside of the cell (extracellular
space)
Average residence time of water molecules: 0.02 s
Average residence time of ions(Cl- or Na +): 8 h
2-5 nm
Na +, Cl -
-
8/6/2019 GEK1532 Proteins
11/31
P roteinsP roteins are the molecules that are at the center of activity in biologicalprocesses.
Enzyme: they catalyze reactions.
Regulators: they regulate all kinds of action in the cell or body.
Storage and transport: E.g. O 2 transport in blood.
Signal transduction: they hand on signals and are responsible form communication.
Sensors: eyes, taste, smells
All proteins are built out of 20 basic building blocks, so called amino acids.These amino acids have different properties and the sequence in which theyare put together to build a protein determines how the protein functions andwhat it does.
The sequence of the amino acids in the proteins is given in the DNA.
-
8/6/2019 GEK1532 Proteins
12/31
Amino Acids
NH2
H
COOH
C
R
L-amino acid D-amino acid
-
8/6/2019 GEK1532 Proteins
13/31
P eptide bond
In aqueous solution (pH=7.4)
-
8/6/2019 GEK1532 Proteins
14/31
-
8/6/2019 GEK1532 Proteins
15/31
A possible sequence
You have the choice of 20 amino acids at every position in a protein/peptide.Thus for a di-peptide you have 20*20 = 400 possibilities.
For a tri-peptide you have 20*20*20 = 8000 possibilities.
For a peptide with 10 aa you have 20 10 = 10240*10 9 possibilities.
P roteins have anything between 30 to 1000 aa!
-
8/6/2019 GEK1532 Proteins
16/31
-
8/6/2019 GEK1532 Proteins
17/31
Interactions3. Hydrogen bonds (polar amino acids with polar amino acids)
See e.g.: http://www-structure.llnl.gov/Xray/tutorial/protein_structure.htm
Hydrogen bonding
-
8/6/2019 GEK1532 Proteins
18/31
Structure elements
-
8/6/2019 GEK1532 Proteins
19/31
Secondary Structure
E-helix F-sheet
-
8/6/2019 GEK1532 Proteins
20/31
Tertiary StructureSecondary structure elements
3D structure,
side view
3D structure,top view
-
8/6/2019 GEK1532 Proteins
21/31
Tertiary Structure
-
8/6/2019 GEK1532 Proteins
22/31
-
8/6/2019 GEK1532 Proteins
23/31
-
8/6/2019 GEK1532 Proteins
24/31
Signal transduction, transport of molecules
-
8/6/2019 GEK1532 Proteins
25/31
-
8/6/2019 GEK1532 Proteins
26/31
3. Conformational change and bindingof other proteins on the inside2. Binding of ligand to receptor
Ligand
R eceptor
1.
P rotein inside the cell
Outside of cell
(extraxellular space)
Inside of cell(cytoplasm)
-
8/6/2019 GEK1532 Proteins
27/31
R eceptors: ligand-gated channels
Ions can flow (Ca 2+,Na +, K+ etc.)
-
8/6/2019 GEK1532 Proteins
28/31
R eceptors: Inhibition
Ions cannot flow (Ca 2+,Na +, K+ etc.)
-
8/6/2019 GEK1532 Proteins
29/31
R eceptor proteins
Transmission of signals from outside toinside of a cell
Binding of ligands outside Conformational changes
A) Binding of proteins on the cytoplasmic sideB) Opening of a pore for ion transport
Inhibition
-
8/6/2019 GEK1532 Proteins
30/31
Energy sourceMany of the reactions catalyzed need some energy to proceed. This energy isoften provided by so-called triphosphates
ATP -> AD P -> AMP
ATP : Adenosine triphosphate
AD P : Adenosine diphosphate
AMP : Adenosine monophosphate
The triphosphates can be convertedinto di- or monophosphates torelease energy that is stored in their molecular bonds.
There exist not only AT P but as wellthe other triphosphates GT P , UT P ,CT P .
-
8/6/2019 GEK1532 Proteins
31/31
Summary There are 20 amino acids with varying characteristics
(polar, non-polar, charged) The secondary and higher structure of proteins is
determined by the sequence of amino acids (primarystructure) and their interactions with each other The correctly folded protein can have several functions:structural, enzymatic, communication and transport
The most important proteins for us are the so-calledreceptor proteins that establish the communicationbetween cells or of cells with the outside.
Vision, olfaction and taste are all based on receptor proteins that recognize specific signals