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					Nature’s Monte Carlo Bakery:
The Story of Life as a Complex System


                        GEK1530
                 Frederick H. Willeboordse
                 frederik@chaos.nus.edu.sg



                                             1
       Fibers, Proteins & Membranes


Lecture 2          In this lecture we continue our
                   quest for building blocks and see
                   how Fibers, proteins and
                   membranes are constructed.




                                                       2
                                                          GEK1530


  The Bakery
                            Water
                    Flour           Yeast

                                          Get some units
               Add                    - ergo building blocks
            Ingredients                       mix n bake

Process                                     Get something
                                             wonderful!




    Knead    Wait           Bake             Eat & Live
                                                              3
                                                  GEK1530


   Flour
Thus far, we’ve discussed:   Carbohydrates   66
                             Water           11
                             Fiber           10
                             Protein         9
                             Fat             2
                             Ash             2




Let us now look at fibers

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                                                                GEK1530


   Fibers
The fibers found in flour consist of cellulose which is the
material that makes up the cell walls in plants (note cell walls –
i.e. cell membranes - in animals are made up of a different
material).

It is a long chain of glucose, or in other words, a polysaccharide.


But wait a moment! Didn’t we say that
starch is a polysaccharide made with
glucose monomers too?                         !
                                                                      5
                                                                 GEK1530


  Glucose Building Blocks

Six Carbon Sugar
                                                   CH2OH
                                                   6
  H       O
     C1                                            C5        O
  H 2C    OH                                    H               H
                                                   H
 HO 3C    H                    Aldehyde group
                                                 C4             C1
                   H       O
  H 4C    OH                                    OH OH        H OH
                    C  1                            C3       C2
  H 5C    OH    H 2C OH                             H        OH
  H 6C    OH   HO 3C H
     H                                                 Glucose
                H 4C OH
                               Hydroxyl group
                H 5C OH
                   CH2OH
                   6


                                                                     6
                                                                GEK1530


   a,b – D,L

Isomers           Isomers are molecules with the same
                  chemical formula but a different structure.

D- and L- sugars are mirror images of one another
and the designation is with respect to the asymmetric
carbon the furthest from the aldehyde or keto group.
(a ketone is a functional group where we have R1-
C(=O)-R2 instead of R1-C(=O)-H as in aldehyde)


   a and b indicate whether the C1 hydroxyl
   extends above or below the ring.




Note: Some isomers have unique names and others don’t.
                                                                    7
                                                 GEK1530


Glucose Chains




  Starch  a - linked   Cellulose  b - linked
                                                     8
                                                              GEK1530


   Proteins
The last major ingredient of       Carbohydrates      66
      flour is proteins            Water              11
                                   Fiber              10
                                   Protein            9
                                   Fat                2
                                   Ash                2
Usually we think of proteins as meat. But proteins are essential
for all cells.




                                                                   9
                                                                                     GEK1530


    Proteins
Most of the dry mass of a cell consists of proteins. Proteins
fulfill a myriad of functions in a cell. Yet, they are built up of
relatively simple building blocks.

These building blocks are 20 types of amino acids (recently the
existence of 2 more amino acids in proteins has been reported)
            Full Name       Side chain type               Full Name    Side chain type
Abbrev.                                       Abbrev.
A     Ala   Alanine         hydrophobic       M     Met   Methionine   hydrophobic
C     Cys   Cysteine        hydrophilic       N     Asn   Asparagine   hydrophilic
D     Asp   Aspartic acid   acidic            P     Pro   Proline      hydrophobic
E     Glu   Glutamic acid   acidic            Q     Gln   Glutamine    hydrophilic
F     Phe   Phenylalanine   hydrophobic       R     Arg   Arginine     basic
G     Gly   Glycine         hydrophilic       S     Ser   Serine       hydrophilic
H     His   Histidine       basic             T     Thr   Threonine    hydrophilic
I     Ile   Isoleucine      hydrophobic       V     Val   Valine       hydrophobic
K     Lys   Lysine          basic             W     Trp   Tryptophan   hydrophobic
L     Leu   Leucine         hydrophobic       Y     Tyr   Tyrosine     hydrophilic


                                                                                         10
                                                GEK1530


  Amino Acids

Amino Acids only contain five! Elements:



 H – Hydrogen        H         O - Oxygen   O




 C – Carbon          C


                               S – Sulfur   S




 N – Nitrogen        N




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                                                                                          GEK1530


   Amino Acids
Structure       Amino Acids have a well defined structure and are built up of 3 parts.

                                                   Polar  soluble
                                        O          Often looses the H+  becomes negatively
 A carboxyl group                 C                                      charged acid
                                        OH

                                        H           Polar  soluble
                                                    Often gains an H+  becomes positively
  A amino group                     N                                   charged base
                                        H

  A side chain                  R

 An acid is a substance that increases the concentration of Hydrogen (H+) ions in water
 A base is a substance that decreases the concentration of Hydrogen (H+) ions in water

                                                                                              12
                                                                         GEK1530


  Amino Acids
Structure                          H
                          H                  O
                              N    C     C
                          H                  OH
                                  R
            Amino group                           Carboxyl group




 The side chain R can be as simple as a Hydrogen atom or
 more complicated as in arginine where it is:

                                                           NH
                              R=       CH2 CH2 CH2 NH      C       NH2



                                                                            13
                                                                                                          GEK1530


  Amino Acids
Electrostatics
                                      The side chains can be polar, non-polar and ionic (i.e. charged).




                                                      R
   Example Side Chain Ends




                                                  Polar
                              CH3                  OH                     C              NH3+
                                                                       O O-
                             Methyl             Hydroxyl                Carboxyl       Amino
                                                                        -> Acidic      -> Basic




                                                                                                             14
                GEK1530


  Amino Acids
Chime




                   15
                                                                                  GEK1530


  Amino Acids
Peptide Bond    Amino Acids can be joined together by a so-called peptide bond.




                                      Condensation
                                                                 R




                                      of H2O
                H
        H                    O                           H                   O
            N   C       C                                    N   C       C
        H                    OH                          H                   OH
                                                                 H
                 R

                                                             R
                              H       O
                  H                                                  O
                       N      C       C N                    C   C
                  H                                                  OH
                                                     H       H
                              R
                                    Peptide Bond

                                                                                     16
                                                                 GEK1530


  Polypeptide Chains
Chains
  In this way amino acids can be made into long chains that
  are called peptide chains when they have less than about
  30-50 amino acids long and polypeptide chains otherwise.

                                 R
             H     O                        H H
     H                                                      O
         N   C     C N           C    C     N C         C
     H                                                      OH
                         H       H    O             R
              R
                  Peptide Bond       Peptide Bond


  The number of amino acids in a polypeptide chain is usually
  between 40 and 500 (but fixed for each type of protein).
                                                                    17
                                                                  GEK1530


  Proteins
Proteins are made up of one or more polypeptide chains

  Proteins fold due to the interactions in the protein. The
  hydrophobic side chain e.g. tend to cluster on the inside while
  the hydrophilic chains are on the outside.

  The way a protein folds is a direct consequence of the
  sequence of its amino acids and occurs spontaneously (i.e. in
  a self-organized manner).

  The way it is folded has a strong influence on its biological
  function.

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                                                              GEK1530


   Proteins
So we see that in order to arrive at proteins we need to go
through several layers:

                                 Hierarchy

    Atoms

    Sub-units

   Amino Acids

    Polypeptide Chains



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                                                                GEK1530


  Fold & Modify
Protein Folding


 Proteins are only effective when
 folded correctly.

 Eventually, how a protein can fold is
 based on its amino acid sequence.

 However, after the initial stage, it may have the help of
 chaperone molecules.

 What is essential here, is that this process is very robust.


                                                                   20
                                                                   GEK1530


   Fold & Modify
Protein Folding

There are four different levels of
folding (organization):


   Primary structure        The sequence of amino acids

                            Consists of a sequence of a-helices
   Secondary structure      and b-sheets

                            The further folding of the secondary
   Tertiary structure       structure in three dimensions.
                            Formed when a protein consists of
   Quaternary structure     several polypeptide chains (each
                            having its own tertiary structure)
                                                                      21
                        GEK1530


  Fold & Modify
Protein Folding



Secondary structures:


          a-helix



          b-sheet


                           22
                      GEK1530


   Fold & Modify
Protein Folding

Tertiary structure:




                         23
                        GEK1530


  Fold & Modify
Protein Folding

Quaternary structure:




           Hemoglobin

                           24
                                                            GEK1530


   Yeast
Yeast is a unicellular fungus and thus a life-form.

In the absence of oxygen, yeast can extract energy from glucose
by the following reaction:

C6H12O6 (glucose) →2C2H5OH + 2CO2

                                      Carbon dioxide

Ethanol (the alcohol in alcoholic drinks)

But what is life?

                                                                  25
                                                                        GEK1530


   What is Life?

One way to answer this question would be to require
certain properties that we associate with living things.

                                             Obviously a bad choice.
                                             Many living thing do not
For example: It must have legs               have legs.
             It must have metabolism
                                             This sounds much more
                                             reasonable.

                                                    BUT!

 Unfortunately, there are things that behave just as if they
 had a ‘living’ metabolism, but these things are not alive.


                                                                           26
                                                                                 GEK1530


What is Life?


What can be considered to have metabolism but not
life?

                         Fire!                   I’m aliiiiive!

Atoms go in, change and go out. This process is essential for the survival to
the phenomenon. The overall phenomenon is constant (i.e. there is a flame)
for as long there is food (oxygen, fuel …). There even can be replication (one
fire can light another fire).


But obviously, we do not consider fire to be alive.


                                                                                    27
                                                                                         GEK1530


What is Life?


Is there a better way to describe what is life?

One could look at the properties that are required for a
population to evolve by natural selection.

         Multiplication
                                                    Heredity
                                  Mutation
For individuals of the population, the requirement should be made a bit less strict in
that at least the parents fulfill the above requirement (a mule e.g. cannot multiply).



                                                                                            28
                                                                           GEK1530


   Membranes
Nevertheless, it does seem to be reasonable to state that there
should be some separation between ‘inside’ and ‘outside’.

                      A nice cozy house to live in. (note: this is in an
                         out-of-equilibrium state compared to its
                                      environment)


Let us go back to the fatty acid we discussed before. We saw
that a small change can give us soap. Are there other interesting
changes one can make?




                                                                              29
                                           GEK1530


Phospholipids - Cephalin
          Fatty acid
Hydrocarbon chain    Glycerol
  HHHHHHHHHHHHHHHHH O H
 HCCCCCCCCCCCCCCCCC COC H
    HHHHHHHHHHHHHHHHH
    HHHHHHHHHHHHHHHHH O
 HCCCCCCCCCCCCCCCCC CO C H
    HHHHHHHHHHHHHHHHH
Fatty acid replaced by          +
                              HHH O
phosphate group and nitrogen  ..
                             HNCC OPOC H
containing molecule
                              H H H O- H
Cephalin = Phosphatidylethanolamine
                                              30
                                                                    GEK1530


Phospholipids

For phospholipids we can start with a fat too but in this
case one fatty acid is replaced by a phosphoric acid to
which an amino alcohol is attached.



                         Fatty Acid



                                      Glycerol
                                                 Phosphoric
                         Fatty Acid              Acid
    Long Hydrophobic Tails                          Amino Alcohol


     Graphical representation
     of phospholipid


                                                                       31
                GEK1530


Phospholipids




                   32
                                                                GEK1530


  Phospholipids - schematically

Schematically, phospholipids The interesting thing is that
can be drawn as              phospholipids can form bi-
                             layers


where the hydrocarbon
chains are represented as     ~5nm
wiggly tails.


                              The properties of the bi-layer
                              are rather different from those
                              of its elements

                                                                   33
                                        GEK1530


Chime




        Bilayer   Single Phospholipid


                                           34
                                                                  GEK1530


Phospholipids - Spatial Organization

Micelles                                          Vesicles




                                The bi-layer is semi-permeable,
                                H2O, e.g., can diffuse through.

                                   Giant vesicles
                                   can be larger
                                   than 1 mm!
Hence again, we see that the
sum is different from the
elements so lets jump the gun
and draw some conclusions …
                                                                     35
                                                                                          GEK1530


  Towards biological bilayers
One important aspect of bilayers is their fluidity. In biological membranes the
bilayers are in a so-called liquid crystal state. That is to say, the overall structure
of the layer remains but individual phospholipids can move around inside the
layer.

 As you may know, at room temperature, many fats are about to become solid but
clearly, a membrane of a living organism cannot be solid…
Similarly, at low enough temperatures, lipid bilayers can become crystalline.
Clearly, packing the hydrocarbon tails is easier when they are straight and
therefore one way to lower the temperature is to have tails with kinks. Kinks are
due to double bonds.

Another way is the insertion of other suitable molecules that disrupt the packing
of the tails. The main such molecule is cholesterol. Besides lowering the
temperature at which the bilayer becomes crystalline, cholesterol also reduces the
mobility of the phospholipids in the liquid crystal phase. Hence it makes a
membrane less fluid.


                                                                                             36
                       GEK1530


Biological Membranes




                          37
                       GEK1530


Biological Membranes




                          38
                                                      GEK1530


In short


Fatty Acids
                             Cholesterol
                                           Proteins
                Phospholipids
Triglycerides

                                    Biological
                Lipid Vesicles      Membranes




                                                         39
                                                                        GEK1530


  Wrapping up
Key Points of the Day         Building Blocks
                              Proteins
                              Membranes

Give it some thought
                                                What is life?
 Under the right circumstances, vesicles can form
 spontaneously.     Consequently, a cellular environment is easily formed.
                   What else would one need for some kind of life?

References
          http://www.cem.msu.edu/~reusch/VirtualText/carbhyd.htm
          http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/sugar.htm

         http://info.bio.cmu.edu/Courses/03231/BBlocks/BBlocks.htm
                                                                              40

				
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posted:11/12/2011
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