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Severe
dietary protein deficiency leads to distinct
symptoms,
and if not resolved, death. Called kwashiorkor
(Ghanan word
meaning “disease from second born”),
the
deficiency leads to changes in osmotic potential in
the bodies
cells as compared to their blood.
Hypoalbuminemia
(low levels of the blood protein
albumin)
lead to fluid leaving the vessels and accumulating
in the
abdomen, called ascites. This often occurs when infants
stop nursing
(like when a second child is born); they take in
enough calories but not enough protein.
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Tofu comes in sixth and soybeans are seventh. This is why
humans have sharp canine teeth – we're meat eaters. You can live
happily (well, somewhat happily) as a vegetarian; you just have to work much
harder at it.
So why is protein so important? How about, because it is one
of the four major biomolecules and without it you die a horrible death? Sounds like a
good reason to me.
Proteins reside in every cell of every living organism, from
prokaryotes to your favorite uncle. There isn’t a job in a cell that proteins
don’t have their hands in; proteins even perform numerous tasks at the
extracellular level. Heck, that spider web hanging from your dusty Stairmaster
is made of protein!
From prokaryotes to spiny echidnas to rosebushes, let’s
look where proteins are involved in life. Proteins provide the structure from
which cells hold their shape and onto which they build a membrane. Proteins do
the talking, providing chemical signals and ways to sense chemical signals.
Proteins do the dirty work; as enzymes they put molecules together, cut them apart, and change
their parts around. And most times, they make these reactions happen faster than
they would otherwise and without being used up in the process.
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Enzymes are
specific for a very few molecules (called
substrates).
Enzymes have a particular shape, and this
allows the
correct substrate to bind and be acted on;
called the lock and key system. Notice that the
enzyme
itself is not altered by the reaction, so it can
work again
on another substrate molecule. However
there are
exceptions – suicide enzymes are inactivated
by their own action, so they only work once.
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A typical cell may contain 10 billion protein molecules. However,
not every cell has the same proteins. Many proteins are necessary for every
cell, but others have specialized functions needed in only some cells. The
exception is unicellular organisms. Their one cell must be able to produce
every kind of protein they might ever need.
Space is at a premium, so cells can’t waste room on proteins
that aren’t needed right now. Therefore, making protein must be efficient, tightly regulated, and fast. Over 2000 new protein molecules are made every second in
most cells, while some proteins exist only to destroy unneeded or old proteins.
Humans can make about 2 million different proteins, but we only
have about 25,000 genes that code for them. We accomplish this by having some genes
produce many different proteins, just by changing the parts of the gene used.
These alternative splice variant
proteins may have different functions even though they come from the same
gene. For example, the cSlo gene is
required for hearing, and each one of the 576
different splice variants is responsible for sensing a different frequency. Biology
is just so dang efficient.
Now that you know how important proteins are, let’s find out
what they are. Proteins are polymers
(poly = many, and mer= subunit) made up of bonded amino acid mers. Proteins come in many
sizes; the TRP-Cage protein of gila monster spit is a polymer of only 20 amino
acids, while the titin protein of your connective tissue is over 38,000 amino
acids long.
Maybe we'll dig into the degeneracy of the genetic code when we
talk about nucleic acids, but for now let’s just accept that DNA triplets code for
different amino acids, and the order of the codons determines the order in which amino acids are linked
to form a specific protein. The order of the different amino acids is the key.
Why? I’m glad you asked.
Amino acids (or aa’s) are all small molecules made up of
carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur – five of last week’s “elements of life.” It’s the arrangement of these elements that makes an amino acid.
Refer to the picture below for a visual aid. The central carbon is bound
to four other things (often called moieities). One is simply a hydrogen.
Another is an amino group (contains
the nitrogen). The third is a carboxylic acid
group. Get it? amino acid.
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While not
the most exciting images, these cartoons should
help you
understand the structure of the amino acid (left)
and the
building of the proteins (right). Each amino acid has
the same
structure, except for whatever the R group might
be. The
amino end of amino acid 2 is joined to the carboxylic
acid of
amino acid 1. The next peptide bond would be between
the carboxy
end of amino acid 2 and the amino end of amino
acid 3.
Notice how water is created each time a peptide bond
is made.
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The fourth group is what makes each aa different. Called an R group, this side chain can be small or big, neutral or charged, and gives the aa its properties. The R stands for something, but that story is just too long.
In glycine, the R group is merely another H, but in tryptophan
it contains complex rings. We have talked about how tryptophan is the least used amino acid; it is bulky and introduces big bends in the peptide. We’ll
show that bends, kinks and other interactions between aa’s are important for
the protein function.
Most organisms can make all the amino acids they need, but
mammals are the exception. We have abandoned (genetically) pathways for making
some aa’s, so we must get them from our diet. These are the essential amino acids, of which there
are nine if you are healthy. Tryptophan must acquired by all animals – good
thing plants still have the recipe.
Ribosomes (made of proteins and nucleic acids) link the
individual aa’s together in the order demanded by DNA via the mRNA. The bond
that connects them is called a peptide
bond, and is a “dehydration” or “condensation” reaction.
Look at the amino acid picture again; the peptide bonding
process kicks out water, ie. dehydration (de = lose, and hydro – water). Water forms from seemingly nowhere, like condensation on your mirror. See how
fitting the names are?
When in a protein chain (also called a peptide), the order
of aa’s is called the protein’s primary (1˚) structure. The primary structure
in turn dictates the secondary (2˚) structure, which is a folding of small
regions of the protein based on the interactions of the side chains of closely
associated amino acids.
In turn, the folding of small regions brings together aa’s
from farther apart, and they fold up based on their interactions. This is the
tertiary (3˚) structure of the protein. If a protein needs more than one
peptide chain to be functional, the shape that those different chains form when
they interact is called the quaternary (4˚) structure.
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These cartoons can help you picture how an individual amino
acid can affect the structure of an entire protein. In the
secondary structure cartoon, there are two basic forms that
the nearby amino acids can form, helices and sheets, other
parts will form no patterned form at all. The tertiary and
quaternary cartoons are for hemoglobin, showing how non-
amino acids may be involved (heme), and how the
individual peptides fit together.
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The hemoglobin that carries oxygen in our red blood cells is
made up of four protein subunits. Why is this important – because what the
protein does in life is completely dependent on its three dimensional shape. Lots
of aa’s means lots of potential shapes. This is in itself one of the greatest
exceptions, since one of the basic tenets of biology is “form follows
function.” But with proteins, function follows form.
For the greatest number of possible combinations and shapes,
it’s lucky that DNA codes for 20 aa’s. Or are there more? Proteinogenic aa’s are those that can be added into a growing
peptide chain, and there are actually 22 of them. The two exceptions are selenocysteine (like cysteine with
selenium substituting for sulfur) and pyrrolysine
(like lysine with a ring structure added to the end).
We talked last week about the functions of selenocysteine
and how it can be incorporated into a peptide even though there isn’t a normal
mRNA codon dedicated to it. Pyrrolysine is similar in that it becomes coded for
after the modification of what is usually a stop codon, in this case UAG (a
signal to add pyrrolysine is located after the UAG codon).
Pyrrolysine is used by methanogenic (methane producing)
archaea and bacteria. It's important in the active site of the enzymes that
actually produce the methane. New research is showing that more organisms than
previously believed use pyrrolysine. A 2011 study identified more than 16
archaea and bacteria with pyrrolysine coding mRNA modifications, but it looks
like there may be more.
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While the
mammalian titin protein is the largest protein
known
(38,136 amino acids), there is a close second in a
bacterium
called Chlorobium chlorochromatii CaD3.
The
gene has
been found for a protein of 36,000 amino acids,
but we don’t
know yet of the protein is actually made. In
archaea, the
halomucin protein from the square prokaryote
Haloquadratum
walsbyi is 9,200 amino acids but is exported
to protect the organism from its extreme environment.
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A 2013 study indicates that the typical modification of the
mRNA that occurs 100 bp downstream of the UAG stop codon isn't even there in some
pyrrolysine-coding genes. One hypothesis is that in genes without the
modification, the UAG sometimes acts as a stop codon and sometimes incorporates
a pyrrolysine. Therefore, there are truncated (prematurely stopped) and full-length
versions of the protein in the cell, and the relative number of each can be
affected by local conditions and stressors.
In this paper, the authors have developed a different
predictor, which doesn’t rely solely on the presence of the modification. Using
it, they have identified many new candidate genes in archaea and bacteria that
could be using pyrrolysines. Here’s my question – all organisms use
selenocysteine, but it seems only arachaea and a few bacteria use pyrrolysine.
Why did it go away in higher organisms? Can it only be used for methane production? Please, no methane production
jokes.
Pyrrolysine and selenocysteine are coded for by mRNA and are
added to proteins, so we definitely have 22 aa’s, but could there be more? You
betcha. There are over 300 non-standard amino acids, but that isn’t such a big
deal. Remember the definition of amino acid; a central carbon with a hydrogen,
a carboxylic acid, an amino group, and something else attached. It isn’t a
wonder there are many of them.
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Bacteria
kill bacteria all the time. They make their own
antibiotics,
called bacteriocins, by modifying
short peptides
so that they
interfere with cell wall synthesis in other strains.
To do this,
they modify amino acids in peptides to non-standard
amino acids,
including lanthionine and 2-aminoisobutyric acid.
Those that
contain lanthionine are called lantibiotics
and are
hot
commodities right now.
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Other non-standard aa’s are produced as intermediates in
other pathways and are not used in proteins. The list of them is great and
their functions are even greater, but some act as neurotransmitters, others are
important in vitamin synthesis, especially in plants. Still think life uses
just 20 amino acids?
Next week we can finish up proteins. Life is very selective
with the form of its amino acids – except when it isn’t.
Theil Have C, Zambach S, & Christiansen H (2013). Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrrolysine containing genes. BMC bioinformatics, 14 PMID: 23557142
Theil Have C, Zambach S, & Christiansen H (2013). Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrrolysine containing genes. BMC bioinformatics, 14 PMID: 23557142
For more
information or classroom activities, see:
Dietary
proteins –
Functions of
proteins –
http://www.unc.edu/depts/our/hhmi/hhmi-ft_learning_modules/proteinsmodule/proteins/proteinfunxn.html
Standard amino
acids –
Peptide bond
–
http://www.chem.wisc.edu/deptfiles/genchem/netorial/modules/biomolecules/modules/protein1/prot15.htm
Protein
structure –
Non-standard
amino acids -
