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GEK1530. Nature’s Monte Carlo Bakery: The Story of Life as a Complex System. Frederick H. Willeboordse [email protected]. Fibers, Proteins & Membranes. Lecture 2. In this lecture we continue our quest for building blocks and see how Fibers, proteins and membranes are constructed. - PowerPoint PPT Presentation
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GEK1530Frederick H. [email protected]
Nature’s Monte Carlo Bakery:The Story of Life as a Complex System
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Fibers, Proteins & Membranes
Lecture 2 In this lecture we continue our quest for building blocks and see how Fibers, proteins and membranes are constructed.
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The Bakery
AddIngredients
Process
Flour Water Yeast
Knead Wait Bake
Get some units - ergo building blocks
Eat & Live
Get something wonderful!
mix n bake
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Flour
Thus far, we’ve discussed: Carbohydrates 66Water 11Fiber 10Protein 9Fat 2Ash 2
Let us now look at fibers
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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? !
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OH HCC
OH
HHO C
OHH C
CH2OH
OHH CC
OH
HO COHH COHH C
H
1
2
3
4
5
1
2
3
5
6
Aldehyde group
Hydroxyl group
C
C
C
O
OH3
1
5
CH2OH6
OH
HH
H
Glucose
In aqueous solution
Six Carbon Sugar
Glucose Building Blocks
OHH C6
OHH C4
H C
OH4
H
COH
2
H
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Isomers are molecules with the same chemical formula but a different structure.
Isomers
– D,L
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)
Note: Some isomers have unique names and others don’t.
and indicate whether the C1 hydroxyl extends above or below the ring.
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Glucose Chains
Cellulose - linkedStarch - linked
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Proteins
The last major ingredient of flour is proteins
Carbohydrates 66Water 11Fiber 10Protein 9Fat 2Ash 2
Usually we think of proteins as meat. But proteins are essential for all cells.
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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.
Proteins
Abbrev.Full Name Side chain type
A Ala Alanine hydrophobic
C Cys Cysteine hydrophilic
D Asp Aspartic acid acidic
E Glu Glutamic acid acidic
F Phe Phenylalanine hydrophobic
G Gly Glycine hydrophilic
H His Histidine basic
I Ile Isoleucine hydrophobic
K Lys Lysine basic
L Leu Leucine hydrophobic
Abbrev.Full Name Side chain type
M Met Methionine hydrophobic
N Asn Asparagine hydrophilic
P Pro Proline hydrophobic
Q Gln Glutamine hydrophilic
R Arg Arginine basic
S Ser Serine hydrophilic
T Thr Threonine hydrophilic
V Val Valine hydrophobic
W Trp Tryptophan hydrophobic
Y Tyr Tyrosine hydrophilic
These building blocks are 20 types of amino acids (recently the existence of 2 more amino acids in proteins has been reported)
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Amino Acids
Amino Acids only contain five! Elements:
H – Hydrogen
C – Carbon
N – Nitrogen
H
C
N
OO - Oxygen
S – Sulfur S
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Amino Acids have a well defined structure and are built up of 3 parts.
A carboxyl group
A amino group
A side chain
CO
HO
NH
H
Polar solubleOften looses the H+ becomes negatively
charged acid
Polar solubleOften gains an H+ becomes positively
charged base
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
Structure
R
Amino Acids
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CO
HON
H
H
R
C
H
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:
CH2 CH2 CH2 NH C
NH
NH2
Structure
Amino Acids
=
R
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The side chains can be polar, non-polar and ionic (i.e. charged).
RNon-polar
CH3
Exa
mpl
e S
ide
Cha
in E
nds
OH CO O-
NH3+
Carboxyl-> Acidic
Amino-> Basic
Pol
ar
Charged
Methyl Hydroxyl
Electrostatics
Amino Acids
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Chime
Amino Acids
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Amino Acids
Amino Acids can be joined together by a so-called peptide bond.
CO
HON
H
HR
C
H
CO
HON
H
H
R
C
H
Con
dens
atio
n o
f H
2OC
O
NH
HR
C
H
CO
HON
H
R
C
H
Peptide Bond
Peptide Bond
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Polypeptide 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.
C
O
NH
HR
C
H
C
O
N
H
R
C
H
Peptide Bond
N
H
CO
HOR
C
H
Peptide Bond
The number of amino acids in a polypeptide chain is usually between 40 and 500 (but fixed for each type of protein).
Chains
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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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So we see that in order to arrive at proteins we need to go through several layers:
Atoms
Sub-units
Amino Acids
Polypeptide Chains
Hierarchy
Proteins
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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.
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Protein Folding
There are four different levels of folding (organization):
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
The sequence of amino acids
Consists of a sequence of -helices and -sheets
The further folding of the secondary structure in three dimensions.
Formed when a protein consists of several polypeptide chains (each having its own tertiary structure)
Fold & Modify
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Protein Folding
Secondary structures:
-helix
-sheet
Fold & Modify
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Tertiary structure:
Fold & Modify
Protein Folding
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Quaternary structure:
Hemoglobin
Fold & Modify
Protein Folding
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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
Ethanol (the alcohol in alcoholic drinks)
Carbon dioxide
But what is life?
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What is Life?
One way to answer this question would be to require certain properties that we associate with living things.
For example: It must have legsIt must have metabolism
Obviously a bad choice. Many living thing do not have legs.
This sounds much more reasonable.
Unfortunately, there are things that behave just as if they had a ‘living’ metabolism, but these things are not alive.
BUT!
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What can be considered to have metabolism but not life?
Fire!
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.
I’m aliiiiive!
What is Life?
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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
Mutation
Heredity
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).
What is Life?
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Membranes
Nevertheless, it does seem to be reasonable to state that there should be some separation between ‘inside’ and ‘outside’.
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?
A nice cozy house to live in. (note: this is in an out-of-equilibrium state compared to its
environment)
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H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
OC
OH
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
OC
OH
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
C
C
C
H
H
H
HGlycerolFatty acidHydrocarbon chain
+
O
H..
-N C
OH
POC
OH
H H
H
HFatty acid replaced by phosphate group and nitrogen containing molecule
Phospholipids - Cephalin
Cephalin = Phosphatidylethanolamine
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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.
Hydrophilic
HeadFatty Acid
Fatty Acid
Gly
cero
l
PhosphoricAcid
Amino AlcoholLong Hydrophobic Tails
Graphical representation of phospholipid
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Phospholipids
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The interesting thing is that phospholipids can form bi-layers
The properties of the bi-layer are rather different from those of its elements
Schematically, phospholipids can be drawn as
where the hydrocarbon chains are represented as wiggly tails.
~5nm
Phospholipids - schematically
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Chime
Bilayer Single Phospholipid
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Micelles Vesicles
The bi-layer is semi-permeable,H2O, e.g., can diffuse through.
Hence again, we see that the sum is different from the elements so lets jump the gun and draw some conclusions …
Giant vesicles can be larger than 1 m!
Phospholipids - Spatial Organization
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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.
Towards biological bilayers
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Biological Membranes
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Biological Membranes
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In short
Fatty Acids
TriglyceridesPhospholipids
Cholesterol
Proteins
Lipid VesiclesBiologicalMembranes
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Wrapping up
Building BlocksProteinsMembranes
Key Points of the Day
Give it some thought
References
What is life?
Consequently, a cellular environment is easily formed. What else would one need for some kind of life?
Under the right circumstances, vesicles can form spontaneously.
http://www.cem.msu.edu/~reusch/VirtualText/carbhyd.htmhttp://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/sugar.htm
http://info.bio.cmu.edu/Courses/03231/BBlocks/BBlocks.htm