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VIII
How life works
http://sgoodwin.staff.shef.ac.uk/phy229.html
8.0 Introduction
What are the processes of life?
How does Earth life use free energy to produce complexity and internal
order? How does Earth life store information?
What aspects of Earth life might be found elsewhere?
8.1 The cell
The cell is the fundamental unit of life (and often included as a
requirement for life). Cells have several properties:
Cells are surrounded by a cell wall/membrane (made of lipids and
proteins) that separate the interior of the cell from its surroundings and
moderate the flow of material into/out of the cell (homeostatis).
Cells metabolise, taking-in raw materials and /or energy and
converting them to more complex molecules/energy or decompose
them (anabolism or catabolism).
Cells contain genetic material (DNA or RNA) which is used to build
proteins that are used by the cell.
Cells reproduce by cell division (asexual or sexual).
8.1 Prokaryotic cells
The simplest cells are prokaryotic cells, thought to be the first cells to have
developed.
Prokaryotic cells contain three main
structures:
Nucleoid: the genetic material of
the cell.
Cell wall/membrane: separating
the internal components and liquid
(cytoplasm) from the external
environment.
Ribosomes: molecular structures
that assemble the proteins required
by the cell.
They also often have flagella to
move, and various molecular
machinery.
8.1 Eukaryotic cells
Multi-celled organisms, and many single-celled organisms, are made of
more complex eukaryotic cells. They contain organelles – specialised
sub-units that perform specific functions and allow cells to specialise
(and so allow the development of multi-celled organisms).
Eukaryotic cells have their DNA
stored in a nucleus and have more
and more specialised organelles
than prokaryotic cells.
Some organelles (e.g.
mitochondria) have their own DNA
and are thought to once have been
separate organisms.
8.2 Proteins
Proteins perform many functions:
They catalyse reactions (enzymes), attack foreign bodies (antibodies),
transport information (some hormones), transport material, and form
structures (e.g. hair), regulate ion levels etc. etc. etc.
8.2 Producing proteins: Reading DNA
The process of converting the information stored in DNA into a protein is
very complex and the details are not important to us in this course. The
basic route is:
TRANSCRIPTION:
TRANSCRIPTION A length of DNA that carries the information that will
eventually result in a single protein is a gene. DNA is separated into its
two strands and a particular enzyme (protein) locates the region of DNA
to be transcribed. It then links nucleic acid bases floating around in the
cell onto a messenger RNA strand (mRNA) matching the nucleic acid
sequence on the gene (but replacing T with A and A with U bases).
DNA contains start and stop base sequences to tell the enzyme when to
start and stop a transcription.
8.2 Producing proteins: Reading DNA
TRANSLATION:
TRANSLATION once a mRNA strand has been created it must convert
amino acids into the desired protein. The mRNA connects itself to a
ribosome which attaches amino acids in the correct order to produce
the precise protein (via transfer RNA).
Note that the order of the bases is important and DNA and mRNA/tRNA
have directions, for instance the sequence UUC tells the ribosome to
add a phenylalanine amino acid to the protein, while the CUU sequence
tells the ribosome to add a leucine amino acid.
The number of amino acids in a protein varies from 2 to several
thousand, thus the total number of proteins that can be assembled from
the base set of 20 amino acids is vast.
Aside: Epigenetics
Recently it has become clear that something odd is happening in
genetics...
We inherit our DNA as a mix of our parent's DNA. In each cell (and
globally) various genes are 'switched on' (expressed). Different cells
express different genes depending on their type. Stem cells can
become any type of cell, and their chemical environment acts to tell
them which genes to express and which not. But once they are a
particular cell type they are fixed (except some pluripotent cells).
It was always thought that what genes were expressed was written into
your DNA as well – your DNA set what genes you have and which would
be expressed. The only change could come from random mutations.
But recent developments suggest that environment plays a role, and
environment can change what genes are expressed in a field known as
epigenetics.
8.2 The function of proteins
After a protein has been produced by a ribosome using the information
carried by the mRNA the molecule folds into a complex shape. The
shape is determined by the self-interaction of the amino acids as well as
interactions with the environment and is not encoded in the DNA.
The shape of the protein determines
how it will interact with other
molecules which may be other
proteins (to build structures),
'factors' (e.g. vitamins) that takepart in chemical reactions, foreign
molecules, or DNA during
replication.
8.3 Evolution and illness
If a gene is incorrectly copied it will encode a different sequence that will
do a different thing.
If an organism is 'lucky' the new protein will do a better or new job and
this is one driver of evolution.
If an organism is 'unlucky' the new protein cannot do a vital job and the
organism is ill or dies.
Lactose intolerance is due to a lack of the lactase protein used to
break-down the lactose disaccharide carbohydrate found in milk. Rare
in northern Europeans (<5%), very common in Africa, Asia and the
Americas (>90%). This is encoded on two genes which used to switchoff after infancy but various ethnic groups have developed the ability to
stop the switch-off.
8.3 Important cell processes
There are various key components to cells.
Obviously there needs to be DNA to store information and ribosomes
and other machinery to produce proteins.
The cell also needs mechanisms to produce, store, and release energy,
and do any other jobs that are required.
8.3 Sources of energy
Organisms can be divided into two broad classes:
Autotrophs: able to fix carbon: the conversion of inorganic carbon into
organic molecules. Photosynthesis uses light as an energy source,
chemosynthesis uses chemical energy (an electron donor).
Heterotophs: require organic molecules as their raw materials (and can
then convert this using energy from light or chemical reactions).
An example is humans (heterotrophs) eating carbohydrates in
something like corn (a photosynthesising autotroph).
8.4 Chloroplasts and photosynthesis
Chloroplasts are organelles that conduct photosynthesis. They contain
their own DNA and are thought to have their origin as originally
separate prokaryotic cells (cyanobacteria).
The basic chemical reaction of photosynthesis is:
6CO2 + 12H2O + light ---> C6H12O6 + 6O2 +6H2O
Photosynthesis occurs in two stages: the first uses light
to produce high-energy molecules, the second uses CO2
to convert these molecules into sugars.
The basic structure in photosynthesis is the 'magnesium
ring' in chlorophyll a which means that Mg is a crucial
element in plants (or cyanobacteria).
8.4 Chloroplasts and photosynthesis
Photons excite electrons in the photosynthetic chemical (in most cases
chlorophyll) to a high state. A series of transport reactions moves this
excited electron through a series of intermediary molecules until it forms
ATP and NADPH – two energy storing chemicals.
Photosynthesis is uses either red or blue photons rather than the peak
wavelengths of Solar radiation. It is thought that they evolved in the sea,
and so evolved to use the light available at depths of a few meters.
The energy stored in ATP or NADPH can be used to synthesise sugars
as a long-term energy store in a reaction that does not require light.
8.4 Energy storage in cells
Life stores energy in the form of chemical bonds. The most common
form in eukaryotic cells is as adenosine triphosphate (ATP).
Energy is released through a reaction
with a particular enzyme which
removes a phosphate group:
ATP + H2O -> ADP + HPO4
the reverse reaction occurring when
the organism is at rest and not
requiring immediate energy.
8.4 Respiration
There are two main ways in which energy is turned into ATP in cells.
Anaerobic respiration (no oxygen) where sugars (glucose C6H12O6)
are turned into ATP and lactic acid. Producing 2 ATP per glucose with
a usable energy of ~120kJ per mole of glucose.
glucose
Aerobic respiration (with oxygen) where sugar and oxygen combine
producing H2O and CO2 as waste products from a process that
produces 36 ATP per glucose – which produces ~2160kJ per mole of
glucose.
glucose
Clearly aerobic respiration is a far more efficient energy producer than
anaerobic respiration and provides a huge advantage to those
organisms that can use it (see the oxygen catastrophe later).
Summary
The basic components of living organisms on the Earth is the cell.
The fundamental components of a cell are the cell wall/membrane,
genetic material, and ribosomes. This is all prokaryotic cells contain,
whilst eukaryotic cells are far more advanced and contain internal
structures called organelles.
Ribosomes synthasise proteins from a set of 20 amino acids using
information encoded on DNA or RNA via messenger RNA.
The complex structure of a protein determines how it will interact with
other molecules, many proteins act as catalysts in important
biochemical reactions (these are known as enzymes).
What does this mean for astrobiology?
Terrestrial life depends on the cell and complex biochemical reactions
that take place in a water solution (cytoplasm) within that cell.
Energy for most organisms comes from Solar radiation – directly into
organisms that can photosynthesise light into sugars, and indirectly
into organisms that take-in these sugars and convert them into energy
(e.g. animals).
This is not the only source of energy, some organisms survive without
light, using other sources of energy (we will come to these later, as
they extend the range of possible environments for life).
What does this mean for astrobiology?
Therefore the basic requirements for Terrestrial life are water to act as
a solvent, complex molecules to store energy and information, and
an energy source to drive the reactions (in most cases, ultimately
sunlight).
So the conditions in which biochemical life (as we know it, or can
imagine it) has some ultimate limitations:
The temperature must be low enough for liquids to exist, and low
enough for highly complex molecules to form and remain stable.
Probably <400K.
The temperature must be high enough for liquids to exist and for
molecules to have higher energy states excitable. Probably >100K.
Is it a coincidence that we exist exactly in the middle of this
range?