All life uses 6 major elements If we survey the molecules from which life is constructed we find six that are found in all living things and have often been described as the building block elements of ID: 573458
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Slide1
Life’s Structure: Building the MoleculesSlide2
All life uses 6 major elements
If we survey the molecules from which life is constructed, we find six that are found in all living things and have often been described as the ‘building block’ elements of
life. They are C (carbon), H (hydrogen), N (nitrogen), O (oxygen), P (phosphorus) and S (sulfur). They are sometimes remembered as the odd word, CHNOPS or SPONCH.Slide3
The most common backbone of
the molecules of life is carbon, for example in the simple amino acid,
glycine, in which two carbon atoms form the core of this molecule. The abundance of carbon in biological molecules means that we refer to life on Earth as ‘carbon-based’.
Life is carbon basedSlide4
If we had to identify just one feature of life that stands out when we are discussing the formation of molecules, we would probably say that it has a propensity to form chains. Perhaps this isn’t surprising. Life is complex and if we want to build complex molecules we would intuitively suggest that the best way to do this is to take simple molecules and string them together into more complex chains.
There are four main classes of molecules in life that are made of chains:
ProteinCarbohydrates (Sugars)LipidsNucleic acids
Life has a propensity to form chainsSlide5
The first example is proteins. Proteins are composed of chains of amino acids. These chains are referred to as polypeptides.
Proteins are involved in many functions. They can
act as catalysts, carrying out chemical reactions. These proteins are called enzymes. Proteins are also used in cell membranes to transport molecules, as structural materials and energy transfer molecules. ProteinsSlide6
Proteins
Although there are a vast variety of amino acids in nature, with over 500 known, only twenty of these compounds are commonly used in
life, with two others more rarely used (selenocysteine and pyrrolysine). Slide7
The formation of a peptide bond between two amino acids. This dehydration reaction (involving the release of a water molecule) allows for the assembly of polypeptide protein chains
ProteinsSlide8
An important feature of amino acids is that all of the biological amino acids, apart from glycine, are chiral.
They have mirror image forms like your hands
Chirality
A
lmost
all the amino acids used in life are of the ‘L’ form. The other form ‘D’ (dextrorotatory) form is very rare, although D-amino acids are found in the cell membranes of bacteria and their function is not entirely understood. Slide9
Given four different side chains or more, molecules too can be assembled into left and right handed forms. They are said to be
isomers, which are chemical compounds with the same chemical formula, but different structures. The conventional way to classify chiral molecules is based on the direction that polarised light, when shone at the molecules, is
rotated. The different mirror images tend to rotate it one way or the other. If it is rotated to the left we call it a levorotatory molecule or the ‘L’ form. If it is to the right, or dextrorotatory, we call it the ‘D’ form. When we have an equal mixture of both L and D molecules we say that the mixture is racemic. Specifically, we use the term, enantiomer to refer to two molecules that are chiral or optically active isomers.
ChiralitySlide10
Chains are an important component of many other crucial characteristics of life. For example carbohydrates are used as structural support and as energy molecules (which is why people on diets are interested in how much carbohydrate they eat). Carbohydrates are hydrated carbon atoms with the generic formula, CH
2O and multiples thereof. They are made up of chains of individual sugars such as glucose, C
6H12O6 or fructose, which has the same chemical formula as glucose, but a different structure (it is an isomer)
Carbohydrates (Sugars)Slide11
Sugars join together through a glycosidic bond to form chains, analogous to the peptide bonds in proteins. O-glycosidic bonds are oxygen-bridged links between sugar molecules
. The example is shown of maltose. Glycosidic bonds allow sugar molecules to be linked together. In this case, two glucose molecules have linked together to form the two-sugar molecule, maltose. By adding further units we can produce polysaccharides (carbohydrates
).Carbohydrates (Sugars)Slide12
Another class of compounds are the lipids, which encompass a wide diversity of chained and ring-containing molecules. They include long-chained carboxylic acids (also called fatty acids) which are chains of carbon compounds joined together, mainly through single bonds (e.g. saturated fatty acids) and some containing double bonds (unsaturated fatty acids)
One important group of lipids are the fats or
triglycerides. which are a combination of glycerol and three fatty acids and are found widely in animal fats and plant oils. The energy stored in the many bonds of fatty acids and triglycerides has made them useful as energy storage molecules in life. LipidsSlide13
The molecular structure of some lipids. Free fatty acids are found as energy storage molecules. Triglycerides are found in vegetable oils and animal fats. Phospholipids are involved in cell membrane formation in microbes and other organisms. Cholesterol is a structural component of animal cell
membranes.
LipidsSlide14
Many lipids have the important characteristic of having one end that is charged. This end tends to be attracted to water and the charge helps it to dissolve. We call it the hydrophilic end from the Greek hydro (water) and
philos (love) (it loves water). The other end, which is non-polar, does not dissolve so readily as it is uncharged. It is called the hydrophobic end because it dislikes water (from the Greek,
phobos, or fear). This property of having an uncharged and charged end means that these molecules are also referred to as amphiphilic. The phospholipids are one important class of lipids with a hydrophilic phosphate at one end. They are involved in cell membrane assembly.
LipidsSlide15
Nucleic acids are involved in a number of functions such as information storage. The most
well-known of the nucleic acids is DNA or deoxyribonucleic acid.
Nucleic acids
A The
structure of DNA showing the double helical structure and base pairing between the bases along the centre of the molecule
B
. The base pair components of the DNA (shown for adenine) and the names given to the segments of these
components.Slide16
DNA is not the only type of nucleic acid. Another important type is RNA (ribonucleic acid). RNA is an important part of the architecture of reading the cell’s information and we will return to it when we look at how the genetic code works
RNA
A. The schematic structure and bases of a single strand of RNA. B. The molecular structure of the RNA molecule. The key difference with DNA is the presence of the –OH group (an extra oxygen atom) at the 2’ position of the ribose sugar in the sugar-phosphate backbone, hence the name, ribonucleic acid, in comparison to deoxyribonucleic acid (DNA
).Slide17
The solvent of life
All of the molecules that have been discussed must be assembled in a liquid. Life requires a solvent for chemical reactions to occur. Chemical reactions cannot occur efficiently when a system is completely desiccated as the reactants that we need for chemical reactions cannot easily move and interact
.Slide18
The solvent of life
One solvent that meets these needs, as life on Earth will testify, is H
2O, or water. Of the characteristics that make water a particularly suitable solvent for life, its dipole moment or polarity is a very important one (measured as permittivity or the dielectric constant). The dipole moment of water is such that the molecule readily dissolves both salts and small organic molecules. Salts are important to life as a source of cations and anions, all
of which play a role in a variety of functions such as stabilising membranes or as sources of energy. The dissolution of salts in water as charged ions contributes to the ability of water to act as a medium for chemical reactions that require charged species. The polarity of water also allows for the dissolution of small organic compounds such as amino acids. This property allows water to act as a mediator of the organic polymerisation reactions discussed
before.Slide19
The solvent of life
Other properties of water account for many of its beneficial uses as a biological solvent. Water has a high heat of
vapourisation (in other words it takes quite a lot of energy to get it to vapourise), which promotes a stable liquid phase inside organisms and stabilises temperatures, enhancing the ability of organisms to cope with fluctuating environmental temperature regimens. By contrast, a high heat of vaporisation also implies a high energy loss during evaporation, which is used by multicellular organisms to achieve evaporative cooling against high temperatures in the environment. Slide20
The solvent of life
O
ne of the most discussed properties of water that has been implicated in its biological usefulness is the lower density of ice than water. The property that ice has of floating on water when frozen provides protection for organisms that can remain in liquid water beneath the ice layer. However, the
wood frog (
Lithobates
sylvatica) can tolerate freezing temperatures. The frog transforms glycogen in its blood to the sugar, glucose, in response to internal ice formation at the beginning of winter. These molecules act as protectants against damaging ice crystal
formation. It is
clear that evolutionary strategies do exist to tolerate freezing and that although the physical attribute that ice has to float on water may appear to favour life, it may not, in itself, be a fundamental requirement for life. However, the property has other important implications. Ice formed on the surface of a water body tends to trap energy underneath and thus maintain a liquid state over long time
periods.Slide21
The solvent of life
The wood frog can tolerate freezing temperatures by using glucose as an anti-freeze protectant in its
tissues.Slide22
Alternative chemistries – the core elements
Silicon
What about alternative core elements? One popular suggestion is silicon. As a p-block element of group 14, below carbon in the Periodic Table, it shares many common chemical characteristics to carbon. Silicon can be more reactive than carbon, which is attributed to three characteristics.
Silicon
, like carbon, typically forms four bonds, but unlike carbon it can accept additional electrons and form five or six
bonds. This allows some reactions to occur at lower energies.
Many
silicon bonds with other elements are weaker than in carbon, requiring less energy to break them.
S
ilicon
is more electropositive (a greater tendency to donate electrons) than carbon, leading to strongly polarised bonds with other non-metals which are much more susceptible to chemical reactions.
The more
reactive nature of silicon
may
at first appear to be a
disadvantage, this
high reactivity might make it more conducive to biochemical reactions at low temperatures.Slide23
Alternative chemistries – the core elements
Silicon
Silicon can form stable tetra-, penta- and hexa-coordinated compounds with N, C and O bonds and can form stable covalent bonds with N, P, S and many other elements that are associated with the generation of molecular diversity in carbon biochemistry. Although silicon cannot easily form a six-ring structure like benzene, it can form
a different type of
six-ring structure (
siloxene) in which oxygen atoms hold together the silicon atoms. Cage-like molecular systems such as silsesquioxanes
can be reacted with a wide diversity of side groups to allow for a remarkable diversity of
molecules.Slide24
Alternative chemistries – the core elements
Silicon
A more plausible chemistry involving silicon is a hybrid system with carbon. Silanes are molecules made up of complex arrangements of silicon and hydrogen, analogous to the alkanes in carbon.
Silanes
include hybrid molecules with organic groups.Slide25
Alternative chemistries – the core elements
Silicon
Perhaps one of the most significant limitations of silicon is the tendency it has to form very inert structures with oxygen. Fully oxidised silicon is silica, a highly unreactive compound which makes up quartz and a wide variety of minerals.
A variety of biologically inert silicate structures formed when silicon binds to oxygen. These are the structures that make what we generally refer to as rocks and minerals. They are comprised of the core building block, a silica tetrahedron (SiO
4
)..Slide26
Alternative chemistries – solvents
Ammonia has been one of the most discussed alternatives to water.
Ammonia is less viscous than water (compare 1 centiPoise for water at room temperature to 0.265
cP
for ammonia) and so molecules diffuse through it more quickly, thus chemical reactions could be potentially done faster, or at least substrate diffused faster to sites of reactions
.
However, ammonia has a lower heat of vaporisation (1369 kJ/kg) than water (2257 kJ/kg) and so is less able to accommodate temperature fluctuations.
A
mmonia
is liquid at lower temperatures and has a smaller liquid temperature range at atmospheric pressure (-78 to -34°C). For a cold planetary environment, its low temperature liquid state could be advantageous. Its liquid range can be increased by increasing the pressure, such that about 20
atmospheres,the
boiling point is increased to around 50°C.
Ammonia
presents other challenges for life, most notably the extremely high pH at which ammonia solutions form. Ammonia solutions of 1% or greater have
pHs
greater than
11.0.Slide27
Alternative chemistries – solvents
Solvent
Molecular weight
Liquid range
K at atmospheric pressure
Heat of
vapourisation
kJ/
mol
Viscosity
cP
Dipole moment
(Debye, D)
H
2
O
18
273.1-373.1
2257
1.00
1.85
NH
4
17
195.4-239.8
1369
0.265
1.47
HF
20
190.0-292.7
374.1
0.256
1.91
H
2
SO
4
98
283.5-611.1
56.0
48.4
2.72
CH
4
16
90.7-111.7
480.6
0.184
None
A range of possible solvents for life, their temperature ranges, heat of
vapourisation
, viscosity and dipole moments.Slide28
What have we learned?
Life tends to form chains of molecules. We can recognise three main groups: proteins, carbohydrates and lipids.
Some of their component molecules are chiral. The origin of the entantiomeric preference in life is still not fully understoood.
Carbon is the most versatile molecule for construction of a large array of molecules; the other alternative discussed – silicon – seems much less plausible.
Life requires a solvent to carry out reactions. Water is cosmically abundant and has a range of physical properties conducive to life. Perhaps the most plausible alternative is liquid ammonia.