Download H - Frederick H. Willeboordse

Nature’s Monte Carlo Bakery:
The Story of Life as a Complex System
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Frederick H. Willeboordse
[email protected]
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Atoms, Bonds, Carbohydrates & Fats
Lecture 1
This lecture starts with the most
basic building blocks, atoms, and
shows how they combine in
organic and inorganic matter.
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The Bakery
Flour
Water
Get some units
- ergo building blocks
Add
Ingredients
mix n bake
Get something
wonderful!
Process
Knead
Yeast
Wait
Bake
Eat & Live
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The Simplest Unit - Water
Hydrogen
Oxygen
How do these combine?
To answer that we first
need to ask
Where do they come from?
What do they consist of?
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How it all started
Let’s start at the beginning…
About 13 billion years ago there
was a ‘big bang’ that created our
universe.
At first our universe was very
hot consisting of what one could
call ‘melted’ matter.
After a few hundred thousand
years it had cooled to the point
where matter ‘condensed’ to the
form that still exists today.
Hubble picture of NGC6822 (NASA)
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Matter
Most of the matter was Hydrogen
and Helium and a few other light
elements.
This compacted into stars where
the lighter elements were burnt
yielding heavier elements (up to
iron).
Even heavier elements (like lead
and gold) were created in
supernovae.
All in all a bit more than 100
elements are known but only a few
of them are important for life.
Hubble picture of IC4406 (NASA)
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Star Systems
Some of the ‘leftovers’ from
supernovae (combined with
varying amounts of the original
matter) lead to solar systems
with planets.
Supernova 1987A
Earth is one such planet
and life originated around
4 billion years ago probably as a
simple bio-chemical process.
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Atoms
The smallest unit of an
element is the atom.
Atoms are built up from only
3 types of so-called
elementary particles. Protons,
neutrons and electrons.
The simplest atom is the
Hydrogen atom. It consists of
one proton and one electron.
Protons have an electric charge
of +1, neutrons have no electric
charge and electrons have an
electric charge of -1.
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Atoms
In their basic state, atoms are
neutral and that means that they
have as many electrons as
protons.
The electrons are arranged in socalled shells around the nucleus
(the central part of the atom
where the protons and neutrons
reside).
The chemical properties of the
atoms are mainly determined by
the number of electrons in the
outermost shell.
Core of Galaxy NGC4261 (NASA)
A massive black hole!
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Atoms
This figure shows, schematically, how the electrons are arranged in shells
He
H
Li
H - Hydrogen
Li - Lithium
Be - Beryllium
Be
B
B - Boron
C - Carbon
N - Nitrogen
C
O - Oxygen
F - Carbon
N
O
F
Ne
He - Helium
Ne - Neon
Now there’s a key property: Atoms like it when shells are full.
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Atomic Bonds
That means:
He
H
Li
•
•
•
Be
B
C
N
O
F
Ne
He and Ne are very happy (hence they hardly react
and are therefore called noble gasses).
Li has an electron too ‘many’ and F an electron too
‘little’. In the same way, O has 2 electrons too ‘little’
H is a bit special ….
The physical/chemical basis of all life is the fact that atoms can interact and form “bonds”.
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Covalent Bond
Take 2 hydrogen atoms
Each hydrogen atom has only 1
electron. This is one too little for
a complete first shell.
H
One possibility would be that one atom gives up
an electron and the other receive one electron.
Then the two hydrogen ions could form a socalled ionic bond.
(In fact this is not a stable configuration and
hence does not occur).
H
H
H+
H
H-
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Covalent Bond
Ionic bonds are not so strong, however, and it turns out that
there is an energetically more favorable solution: Sharing!
H
H
Atoms can share a single electron
but (depending on the element) also
two or three electrons. E.g. in carbon
double bonds are quite common.
H
H
C
C
H
H
Ethylene
Like this each atom has in a sense two electrons. This is called
a covalent bond and it is quite strong.
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Water
Now let’s get back to water
Here we have to combine one oxygen with two hydrogen atoms.
O
H
H
One electron too little
for a full shell.
Two electrons too little
for a full shell
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Covalent Bond
Water (H2O) is formed by covalent bonding of
two Hydrogen atoms and one Oxygen atom.
At first one might
think it looks
somewhat like this.
H
O
H
However, this is not really the case. The six electrons of
the Oxygen (repelling each other due to their equal
charges) want to be as far from each other as possible.
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Covalent Bond
This can be achieved by basically in this way:
The electrons spread out along the x,y,z axis
In a covalent bond, the pairing
electrons of two atoms want to
overlap as much as possible
while staying away from other
electrons as far as possible.
Hence in first instance we’ll get
a 90o arrangement.
x,y,z-axes
H
O
H
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Covalent Bond
The Oxygen atom turns out to pull at the
electrons a bit harder than the Hydrogen atom.
bit
Consequently, there is a slight charge shift
+
towards the Oxygen atom.
bit
bit
-H
O
H
bit
bit
Since equal charges repel,
the two hydrogen atoms
will be pushed out a bit.
This then leads to water’s
‘V’ shape.
--
bit
+
bit
H
+
O
H
bit
+
Of course, one would really need quantum mechanics to explain what’s going in detail.
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Chime - Water
bit
--
bit
+
bit
H
O
H
bit
+
Ball and Stick
Van der Waals Radii
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Atomic Bonds
So we’ve seen that atoms stick together due to bonds.
Are there other bonds?
Yes:
Polar Bond
Ionic Bond
Vd. Waals Bond
Metallic Bond
Let’s have a look a
some of these
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Polar Bond
A covalent bond that leads to one side
of a molecule having a bit a different
net charge than the other is called a
polar covalent bond and this in turn
gives rise to another type of
electrostatic bond.
The hydrogen bond
bit
When one of the atoms
involved is hydrogen, this bond
is called a hydrogen bond and
of particular importance in
biology.
--
bit
+
bit
H
O
Attractive
force.
H
bit
+
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Ionic Bonds
When Na and Cl come close, Na
can give up an electron to Cl.
We then have two ions with opposite
charges that attract each other.
This attractive force can hold the ions
together to form a compound we all
know. SALT.
This bond is called ionic bond.
Na
Cl
Sodium has one
electron too many.
Chlorine has one
electron too little.
Na+
Sodium thus becomes
a positively charged
ion.
Cl-
Chlorine thus becomes
a negatively charged
ion.
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vd Waals Interaction
Lastly, when molecules or parts of larger molecules are nearby,
the electrons can behave in a synchronized way such that they
avoid each other as much as possible.
This is called:
Van der Waals Interaction
The net result of this
interaction is a very weak
attractive force.
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J. D. van der Waals
Johannes Diderik van der Waals
First was a school teacher because he didn’t know the
classical languages which were required for obtaining
university degrees when he was young.
After the laws changed, he obtained his doctorate degree at
age 36 with a ground-breaking study on the transition from
gaseous to liquid form. He was the first one to realize that
the volumes and intra-molecular forces of atoms and
molecules were necessary to establish the relationship
between pressure, volume and temperature of liquids and
gasses.
Nobel Prize in Physics 1910
Born: 23 Nov 1837 in Leyden, Holland
Died: 8 Mar 1923 in Amsterdam, Holland
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Relative Strengths
Covalent Bond:
Ionic Bond:
Polar Bond:
Vd Waals:
~ 35-110kilocalories/mole
~ 10 kilocalories/mole
~ 4-5 kilocalories/mole
~ 1-2 kilocalories/mole
In aqueous
solutions
calorie (with a small c): The energy required to raise the
temperature of 1g of water from 14.5 to 15.5 degrees
centigrade.
Mole: That amount of any particular substance having a
mass in grams numerically the same as its molecular or
atomic weight.
Note: 1c ~ 4.186J; The energy content of fat ~ 9kcal/g, proteins &
carbohydrates ~ 4kcal/g
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Water
Back to water again
Although not really a complex system we already see that the
properties of water are very different from its building blocks
Hydrogen and Oxygen.
E.g. Liquid more
dense than solid
Solubility:
Polar like water will dissolve ionic compounds and covalent
compounds which ionize.
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Flour
Typical White Wheat Flour Composition:
Carbohydrates
Water
Fiber
Protein
Fat
Ash
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10
9
2
2
The most common is carbohydrate which is, as the name
indicates, based on carbon.
So let’s have a closer look at carbon.
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Carbon
Why is carbon so important?
Four unpaired electrons available
for covalent bonding
Many possibilities to molecules
Carbon is quite abundant
Graphite
Coal
Diamond
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Hydrocarbons
Carbon easily bonds with other carbons and with hydrogen
HHH
Branched C
HCCC H
HHH
Propane
H
Cyclic C
HCH
Chained C
H
C
H
H H HH
HCCC H
H C CCC H
HHH
Isobutane
H
H
H
C
H
C
H
H
Cyclopropane
H H HH
Butane
Substitution of other atoms leads to derivative hydrocarbons.
There are more than half a million of these in nature.
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Chime - Hydrocarbons
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Functional Groups
Many hydrocarbons and other organic compounds have
so-called functional groups attached to them.
These are often used in the names of these compounds.
Some of the major functional groups are:
C
O
H
Aldehyde
O
C
OH
Carboxyl
H
N
H
Amino
O
P OH
OH
Phosphate
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Carbohydrates
With the aldehyde group, simple
carbohydrates like glucose can be made.
Glucose
A Haworth projection has the following characteristics:
C
O
H
Aldehyde
Carbon is the implicit type of atom. In the example on the right, the
atoms numbered from 1 to 6 are all carbon atoms.
Hydrogen atoms on carbon are implicit. In the example, atoms 1 to 6
have extra hydrogen atoms not depicted.
Haworth projection
A thicker line indicates atoms that are closer to the observer. In the
example on the right, atoms 2 and 3 (and their corresponding OH
groups) are the closest to the observer, atoms 1 and 4 are further from
the observer and finally the remaining atoms (5, etc.) are the furthest.
Pure carbohydrates contain carbon, hydrogen and oxygen
in a 1:2:1 ratio but there are also deviations like in e.g. the
famous deoxyribose.
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Carbohydrates
Glucose, also a product of photosynthesis, is used as a
source of energy in plants and animals.
Glucose can be a building block. It can combine with other
glucose molecules to from long structures.
In chemistry, a simple molecular structure that can
somehow chain together to from big structures is called a
monomer while the resulting big structure is called a
polymer.
The carbohydrate we find in flour consists of such
glucose polymers (this gives starch)
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Chains with C
We have seen how combining carbon leads to
sugars and starch.
Do we have something else?
C
O
OH
Carboxyl
Lipids
Fat or fat-like compounds.
In their simplest form they are hydrocarbons with
a carboxyl group at one end.
Fats consist of glycerol and fatty acids
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Larger molecules
H
C
H
Larger Molecules are obtained by stringing
together many of these elements.
This kind of element is non-polar and thus
not soluble in water.
The simplest lipid is a fatty acid. It consists of a hydrocarbon
chain with a carboxylic acid at one end.
HHHH HHHHHHHHHHH
HCCCC CCCCCCCCCCC C
HHHH HHHHHHHHHHH
O
OH
Palmitic Acid – one type of fatty acid (e.g. lard is about 25%
made of palmitic acid).
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Acids
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
Hydrochloric Acid
Ammonia
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Tristearin
Fatty acid
HHHHHHHHHHHHHHHHH O
Hydrocarbon chain
Glycerol
H
HCCCCCCCCCCCCCCCCC COC H
HHHHHHHHHHHHHHHHH
HHHHHHHHHHHHHHHHH O
HCCCCCCCCCCCCCCCCC CO C H
HHHHHHHHHHHHHHHHH
HHHHHHHHHHHHHHHHH O
HCCCCCCCCCCCCCCCCC COC H
HHHHHHHHHHHHHHHHH
Tristearin is a common animal fat
H
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Fats
Fats and building blocks
Again, although just as water not really a complex
system we see that the properties of fat are very
different from its building blocks Carbon, Hydrogen
and Oxygen.
Would a ‘small’ change to the structure matter?
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Soap
If one takes a fat like tristearin on the previous slide and
heats it with an alkaline substance like potassium hydroxide
(KOH), one obtains soap.
HHHH HHHHHHHHHHH
O
HCCCC CCCCCCCCCCC C
O-K+
HHHH HHHHHHHHHHH
Polar
A potassium soap. Mixing this with table salt solution (NaCl)
one can replace the Potassium ion with an Sodium ion to obtain
the softer Sodium soap.
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Soap
The head is hydrophilic
and hence soluble in
water.
HHHH HHHHHHHHHHH
O
HCCCC CCCCCCCCCCC C
O-K+
HHHH HHHHHHHHHHH
The tail, however, is hydrophobic
and hence soluble in oil.
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Soap
As a result of the head-tail properties, soap molecules in
water can from micelles with grease on the inside.
Schematic representation
of a soap molecule
Water
In this way the grease can be rinsed away.
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Key Points of the Day
Building Blocks
Bonds
Sugars
Fat/Soap
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Give it some thought!
What is a bakery?
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References
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