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MCAT
Course: MCAT > Unit 9
Lesson 10: Proteins- Proteins questions
- Amino acid structure
- Alpha amino acid synthesis
- Classification of amino acids
- Peptide bonds: Formation and cleavage
- Four levels of protein structure
- Conformational stability: Protein folding and denaturation
- Non-enzymatic protein function
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Amino acid structure
Amino acids are the building blocks of proteins. They contain an amino group, carboxylic acid group, alpha carbon, and side chain. Most amino acids have a chiral carbon, which allows them to rotate polarized light. Amino acids can have either an L- or D- configuration, but only the L- form is found in the human body. Created by Tracy Kim Kovach.
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2 configurations were mentioned, she said the "L" refers to the human body, but what does the "D" refer to?(20 votes)
it's important to take note of her word choice here. She said that 'L' is the only one found in the human body; not that 'L' refers to the human body. 'L' enantiomers can be found in many places in the world and so can 'D', but the human body has a restriction. The human body can only make 'L'. If you were to synthesize enantiomers (like amino acids) in a laboratory, you'd find that it's possible to get a 50/50 production of 'L' and 'D' enantiomers depending on your reaction mechanism.
P.S. If you want to know more about this, you can view the lecture series on Organic Chemistry as it is elaborated further there.(63 votes)
I dont get the part where she says that u cant super impose the L and D amino acids. Cud someone explain it to me? Thank you(12 votes)
So Ill start with the word "Superimpose": which means to place directly in the position of the other object without altering any of the bonds. When you look at your right hand and your left hand, when you slide them over one another or superimpose them, your thumb matches up to your pinky, not to your other thumb. The same is true for the molecules, no matter how you rotate them in space, their groups will never match up when placed atop one another. BUT, when you reflect them over a line of symmetry, they will be a perfect reflection.
I hope that helps!(34 votes)
What is the 21st amino acid? I was always taught 20.(11 votes)
Selenocysteine(18 votes)
6:00. Why exactly does the fact that glycine's R group is simply an H atom make its alpha carbon non-chiral, whereas the alpha carbon is chiral in all other amino acids with their different R groups? I don't quite follow this. Does having one H atom for a side chain uniquely alter glycine's optical properties? Thanks very much.(5 votes)- A chiral C-atom means that the atom is bound to four different groups. In glycine there are two H-atoms which means there are not four different groups bound to the C-atom. In all the other aminoacids the alpha C-atom is bound to four different groups.
I'm sorry that my english is bad, but I hope i could answer your question.(35 votes)
What is the difference between ATP and ADP? I hear these terms thrown around a lot...(3 votes)
ATP(adenosine triphosphate) is the universal energy currency of cells
ADP(adenosine diphosphate)
basically ATP has one more phosphate group than ADP, and because ATP has one more phosphate group than ADP, it contains more potential energy because more bonds could be broken
ATP forms ADP when it breaks a phosphate group to utilize its bond energy to do work, and ADP forms AMP (adenosine mono-phosphate)(15 votes)
- I am a little confused on the geometry. On the pink drawing, saw H is going out, R is going in, and NH2 and COOH are on the same plane. That adds to be 3 planes for the groups connected to the carbon.
However, on the Fischer drawing, she explained that NH2 and H are coming towards you, and COOH and R are going away from you, that adds to only 2 plains, so aren't these different?(5 votes)
The way I like to think about the Fischer Projection is like a stick man wearing a bow-tie facing you. The bow-tie is the horizontal line, and the guy is the vertical line. Like the lobes of a bow-tie come out towards you, so do the groups attached in the horizontal line. The vertical line leans away from you, not 180 degrees opposite, but just leans away slightly. This is why the model is still 3-dimensional.(7 votes)
- @5:43, approx., where would the light source come from if these processes are happening internally?(2 votes)
There would be no light under normal conditions. It's just that if you extract and purify an amino acid and then shine polarised light through it, the light will be rotated. It's an experimental technique for analysing amino acids, not a natural process.(15 votes)
At9:23, she indicates that L stands for Left. Just after than, she indicates that D stands for Right in Latin. Why didn't they use the Latin word for Left?(1 vote)
The D stands for dextrorotatory or dextrorotary (from the Latin "dexter" meaning "on the right side"), meaning that plane polarized light is rotated clockwise or to the right.
The L stands for levorotatory or levorotary (from the Latin "laevus" meaning "on the left side"), meaning that plane polarized light is rotated counterclockwise or to the left. So the Latin words for both directions are used.
Hope this helps. ^ ^(13 votes)
- What does 'fischer' means exactly?(2 votes)
type of diagram/ way of drawing. My SWAG as to the origin of the name would be the creator's last name is/was Fischer.
That said, I'm now wondering if you're just making a pun of Fischer Model vs. Fisher's Exact Test (statistical significance). Because L-amino acids would totally be present in statistically significant numbers in the human body, and you can use both Fischer and Fisher to illustrate this pun.(6 votes)
at3:16Tracy talks about the no. of amino acid .Are there only 20 of them or are there more?(2 votes)- There are only 20 "natural" amino acids - amino acids that are naturally incorporated into proteins by living organisms. When people refer to amino acids, they are typically referring these 20 natural ones used and created by living things.
That being said, the name, "amino acid" only requires a molecule to have both a carboxylic acid functional group and an amine functional group. So you can design an "amino acid" with almost any shape and chemistry you can imagine.(4 votes)
6:00Video transcript
Hey, so we're going to be
talking about amino acids, and specifically with regards
to amino acid structure. And before we dive
on into this topic, I think it's nice to kind
of take a step back and take a big-picture view
of amino acids and kind of figure out--
where do they exactly fit in the grand scheme of
biochemistry and specifically human metabolism? And I think the
best way to do this is to take a real-world example
of a human protein called hemoglobin. Now, what is hemoglobin? Well, hemoglobin is found
within the red blood cells that flow all
through our bloodstream. So here's my little
red blood cell. And each red blood cell is
chock-full of this hemoglobin protein. I'm just going to write
it out as each Hgb here. And this hemoglobin
protein is what is actually responsible for
picking up oxygen. When this little
red blood cell flows through the vessels
and the lungs, picks up oxygen, and then
transports this oxygen to all the various
tissues within our bodies. And so you can kind of think of
hemoglobin as a car of sorts. My favorite car
is a Porsche 911. If you want to be more
environmentally friendly, you could think of a Prius,
or something like that. So whatever your
car is, oxygen is like the passenger for that car. And so hemoglobin
goes by the lungs, picks up oxygen, delivers
it to the tissues. And then tissues are
just groups of cells that are of a similar
type, and so each of the cells in these
tissues then takes the oxygen and uses it to generate
adenosine triphosphate, or ATP, which is the
energy source for all the various metabolic processes
that go on within our cells to help keep us alive. So now where do amino
acids fit into all of this? Well, amino acids are
the building blocks of this hemoglobin protein. And so without amino acids,
this entire vitally important process wouldn't
be able to occur. Now, sticking with
the car analogy just a little bit
longer, just like we have different types of
components that come together to form different types
of cars, whether it be a Porsche or a
Prius, what have you, you can have different
types of amino acids. And there are 20 of them-- to be
exact-- that can come together to form countless, countless
different types of proteins. And so now that you have an
idea of where amino acids fit in this bigger picture
of a metabolic process, let's go ahead and
take a closer look at what the actual structure
of an amino acid is. First, we have the amino group. And then we have the
carboxylic acid group. And already you can start to see
where the name amino acid comes from. You have amino, from
the amino group, and then you have acid from
this carboxylic acid group here. And then linking the two
groups is this carbon atom, which we call the alpha carbon. And then bound to
the alpha carbon is a hydrogen atom as well as a
unique side chain, or R group. We just use R to denote
any generic side chain. So each of the amino acids has
this same generic structure, and what makes each
of the 20 amino acids different from each
other is this R group, or the side chain. So each of the side
chains for the amino acids is going to look different. One thing that's
important to note is that this carbon
atom, the alpha carbon, is also known as
a chiral carbon. And what does a chiral
carbon mean again? Well, a chiral carbon
is a carbon atom that has four unique
groups bound to it. So if we take a
look at this carbon, we can see that one group
that's bound is the amino group. Another group is the
carboxylic acid group. The hydrogen atom
makes the third group, and then the fourth
group bound to it is the R group or
the side chain. And so the alpha
carbon in amino acids is considered a chiral carbon. And remember that
chirality really refers to optical activity. In other words, if you were to
shoot plain, polarized light at an amino acid, then
because this carbon is chiral, it would rotate to that light. And so that's what chirality
is really referring to. It's referring to
optical activity. Now, it's important
to note that there is one exception among the
amino acids for chirality, and that is the
amino acid glycine. And that's because the side
chain, or R group, for glycine is just a hydrogen atom. It is the simplest of all side
chains, just one hydrogen atom. And so if you were to substitute
a hydrogen atom in place of this R group, you
would see that you have a duplication
of atoms coming off of this alpha carbon in
the case for glycine. And so glycine is
the only amino acid that does not have
a chiral carbon. So that's just important
to make note of. So let's give ourselves a
little bit more room here. Now, another way
that you can portray the structure of
an amino acid is with something called
a Fischer projection. And Fisher projections help
to highlight the relationship of the four groups
around a chiral carbon. So let me draw
that for you here. First, you have
your amino group, and up top you have
your carboxylic acid. Here is your hydrogen
atom, and at the bottom is the side chain, or R group. And just to orient you a
bit, here in the center is the chiral carbon,
the alpha carbon here. And then you have
the four groups coming off of the chiral carbon. And the horizontal
bonds here-- you can kind of picture
those as coming out of the plane of the
computer towards you. And then these
vertical bonds here are coming out of the plane
of the computer away from you. And this particular
configuration is called an L-amino acid. And conversely, you can
have the mirror image of this, which I'll
draw for you here. And this particular
configuration is called a D-amino acid. And these two configurations
are called enantiomers. And enantiomers are
mirror-image molecules that are not superimposable. So you can picture-- these are
mirror images of each other, but if you were to take
this D-amino acid and try to superimpose it on the L-,
you wouldn't be able to do that. You can kind of think of
these two configurations like your left and right
hand, and although your left and right hand are mirror
images of each other, you can't superimpose
them on one another. And that's the
relationship between an L- and a D-configuration
for Fischer projections. And these two configurations
look awfully similar and are really easy to
mix up, and so the way that I like to
keep them straight is if I look at where the
amino group is-- let's take the L amino acid. If I look at where
the amino group is, I can see that it is to
the left of the projection, so L is for left amino group. Now, if I look at
the D amino acid, I again look for
the amino group, and I see that it's to the
right of this configuration. And so D, which actually means
dextro, or right, in Latin, is for right amino group. That's kind of how I like
to keep them straight. So why is it important
to distinguish between L- and D-amino acids? Well, the L- form
of an amino acid is the only form that you will
find within the human body, and so that's really
important to remember-- that the L-configuration
is the kind that you find within humans. All right. Now how about we review a
little bit about everything that we learned? First, we sort of
got a big picture of where amino acids fit in
a larger metabolic process, such as in the
example of hemoglobin. And then we learned
about the structure of an amino acid and the fact
that the central alpha carbon is a chiral carbon
with optical activity, and the one exception
to this rule is the amino acid glycine,
which just has the simplest side chain of a hydrogen
atom, and therefore it is not a chiral molecule. And then we also learned
about the Fischer projections for amino acids and the fact
that the L-configuration of an amino acid is
the only one that you find within the human body. And there you have it.