GEK1532 Proteins

8/6/2019 GEK1532 Proteins

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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


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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.


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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?


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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+


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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+


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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


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R evision: What are lipids?Glycerophospholipids

P olar head group

backbone

Non-polar,hydrophobic tail


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R evision: Amphipathic molecules

Hydrophobic

Hydrophilic


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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 -


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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.


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Amino Acids

NH2

H

COOH

C

R

L-amino acid D-amino acid


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P eptide bond

In aqueous solution (pH=7.4)


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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!


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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


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Structure elements


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Secondary Structure

E-helix F-sheet


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Tertiary StructureSecondary structure elements

3D structure,

side view

3D structure,top view


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Tertiary Structure


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Signal transduction, transport of molecules


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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)


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R eceptors: ligand-gated channels

Ions can flow (Ca 2+,Na +, K+ etc.)


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R eceptors: Inhibition

Ions cannot flow (Ca 2+,Na +, K+ etc.)


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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


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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 .


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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

GEK1532 Proteins

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