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Science · Biology · Macromolecules · Proteins

Introduc!on to proteins and amino acids

Different types of proteins. The structure and proper"es of amino acids. Forma"on of pep"de
bonds.

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Introduc!on
We tend to think of protein as a mass noun: a homogeneous substance,
something that your diet should contain in a certain propor"on. But if you ever
work in a molecular biology lab (say, for a summer internship), protein may
start to look very different to you.

How so? Well, you may see firsthand that protein isn’t just a single substance.
Instead, there are lots and lots of different proteins in an organism, or even in a
single cell. They come in every size, shape, and type you can imagine, and each
one has a unique and specific job. Some are structural parts, giving cells shape
or helping them move. Others act as signals, dri$ing between cells like
messages in a bo#le. S"ll others are metabolic enzymes, pu%ng together or
snapping apart biomolecules needed by the cell. And, odds are, one of these
unique molecular players will become yours for the dura"on of your research!

Proteins are among the most abundant organic molecules in living systems and
are way more diverse in structure and func"on than other classes of
macromolecules. A single cell can contain thousands of proteins, each with a
unique func"on. Although their structures, like their func"ons, vary greatly, all
proteins are made up of one or more chains of amino acids. In this ar"cle, we
will look in more detail at the building blocks, structures, and roles of proteins.

Types and func!ons of proteins

Proteins can play a wide array of roles in a cell or organism. Here, we’ll touch
on a few examples of common protein types that may be familiar to you, and
that are important in the biology of many organisms (including us).

Enzymes
Enzymes act as catalysts in biochemical reac"ons, meaning that they speed
the reac"ons up. Each enzyme recognizes one or more substrates, the
molecules that serve as star"ng material for the reac"on it catalyzes. Different
enzymes par"cipate in different types of reac"ons and may break down, link
up, or rearrange their substrates.

One example of an enzyme found in your body is salivary amylase, which

breaks amylose (a kind of starch) down into smaller sugars. The amylose
doesn’t taste very sweet, but the smaller sugars do. This is why starchy foods
o$en taste sweeter if you chew them for longer: you’re giving salivary amylase
"me to get to work.

Hormones
Hormones are long-distance chemical signals released by endocrine cells (like
the cells of your pituitary gland). They control specific physiological processes,
such as growth, development, metabolism, and reproduc"on. While some
hormones are steroid-based (see the ar"cle on lipids), others are proteins.
These protein-based hormones are commonly called pep"de hormones.

For example, insulin is an important pep"de hormone that helps regulate

blood glucose levels. When blood glucose rises (for instance, a$er you eat a
meal), specialized cells in the pancreas release insulin. The insulin binds to cells
in the liver and other parts of the body, causing them to take up the glucose.
This process helps return blood sugar to its normal, res"ng level.

Some addi"onal types of proteins and their func"ons are listed in the table
below:

Protein types and func!ons

Role Examples Func!ons

Diges"ve Amylase, lipase, Break down nutrients in food into
enzyme pepsin small pieces that can be readily
absorbed

Transport Hemoglobin Carry substances throughout the

body in blood or lymph

Structure Ac"n, tubulin, kera"n Build different structures, like the

cytoskeleton

Hormone Insulin, glucagon Coordinate the ac"vity of different

signaling body systems

Defense An"bodies Protect the body from foreign

pathogens

Contrac"on Myosin Carry out muscle contrac"on

Storage Legume storage Provide food for the early

proteins, egg white development of the embryo or the
(albumin) seedling

Table modified from OpenStax College, Biology.

Proteins come in many different shapes and sizes. Some are globular (roughly
spherical) in shape, whereas others form long, thin fibers. For example, the
hemoglobin protein that carries oxygen in the blood is a globular protein, while
collagen, found in our skin, is a fibrous protein.

A protein’s shape is cri"cal to its func"on, and, as we’ll see in the next ar"cle,
many different types of chemical bonds may be important in maintaining this
shape. Changes in temperature and pH, as well as the presence of certain
chemicals, may disrupt a protein’s shape and cause it to lose func"onality, a
process known as denatura!on.

Amino acids
Amino acids are the monomers that make up proteins. Specifically, a protein is
made up of one or more linear chains of amino acids, each of which is called a
polypep!de. (We'll see where this name comes from a li#le further down the
page.) There are 20 types of amino acids commonly found in proteins.

Image credit: OpenStax Biology.

Amino acids share a basic structure, which consists of a central carbon atom,
also known as the alpha (α) carbon, bonded to an amino group (NH2 ), a
carboxyl group (COOH), and a hydrogen atom.

Although the generalized amino acid shown above is shown with its amino and
carboxyl groups neutral for simplicity, this is not actually the state in which an
amino acid would typically be found. At physiological pH (7.2 - 7.4), the amino
group is typically protonated and bears a posi"ve charge, while the carboxyl
group is typically deprotonated and bears a nega"ve charge.

Every amino acid also has another atom or group of atoms bonded to the
central atom, known as the R group, which determines the iden"ty of the
amino acid. For instance, if the R group is a hydrogen atom, then the amino
acid is glycine, while if it’s a methyl (CH3 ) group, the amino acid is alanine. The
twenty common amino acids are shown in the chart below, with their R groups
highlighted in blue.

Image by "Dancojocari." The image is licensed under a CC BY-SA 3.0 or

GFDL, from Wikimedia Commons.

The proper"es of the side chain determine an amino acid’s chemical behavior
(that is, whether it is considered acidic, basic, polar, or nonpolar). For example,
amino acids such as valine and leucine are nonpolar and hydrophobic, while
amino acids like serine and glutamine have hydrophilic side chains and are
polar. Some amino acids, such as lysine and arginine, have side chains that are
posi"vely charged at physiological pH and are considered basic amino acids.
(His"dine is some"mes put in this group too, although it is mostly
deprotonated at physiological pH.) Aspartate and glutamate, on the other
hand, are nega"vely charged at physiological pH and are considered acidic.

A few other amino acids have R groups with special proper"es, and these will
prove to be important when we look at protein structure:

Proline has an R group that’s linked back to its own amino group, forming a
ring structure. This makes it an excep"on to the typical structure of an
amino acid, since it no longer has the standard NH3 + amino group. If you
think that ring structure looks a li#le awkward, you’re right: proline o$en
causes bends or kinks in amino acid chains.

Cysteine contains a thiol (-SH) group and can form covalent bonds with
other cysteines. We'll see why this is important to protein structure and
func"on in the ar"cle on orders of protein structure

Finally, there are a few other “non-canonical” amino acids that are found in
proteins only under certain condi"ons. [Click here for cool details!]

Pep!de bonds
Each protein in your cells consists of one or more polypep"de chains. Each of
these polypep"de chains is made up of amino acids, linked together in a
specific order. A polypep"de is kind of like a long word that is "spelled out" in
amino acid le#ers4 . The chemical proper"es and order of the amino acids are
key in determining the structure and func"on of the polypep"de, and the
protein it's part of. But how are amino acids actually linked together in chains?

The amino acids of a polypep"de are a#ached to their neighbors by covalent

bonds known as a pep!de bonds. Each bond forms in a dehydra"on synthesis
(condensa"on) reac"on. During protein synthesis, the carboxyl group of the
amino acid at the end of the growing polypep"de chain chain reacts with the
amino group of an incoming amino acid, releasing a molecule of water. The
resul"ng bond between amino acids is a pep"de bond

Image modified from OpenStax Biology.

Because of the structure of the amino acids, a polypep"de chain has

direc!onality, meaning that it has two ends that are chemically dis"nct from
one another. At one end, the polypep"de has a free amino group, and this end
is called the amino terminus (or N-terminus). The other end, which has a free
carboxyl group, is known as the carboxyl terminus (or C-terminus). The N-
terminus is on the le$ and the C-terminus is on the right for the very short
polypep"de shown above.

How do we go from the amino acid sequence of a polypep"de to the three-

dimensional structure of a mature, func"onal protein? To learn how
interac"ons between amino acids cause a protein to fold into its mature shape,
I highly recommend the video on orders of protein structure.

[A!ribu"on and references]

Proteins

Introduc"on to amino acids

Pep"de bond forma"on

Introduc"on to proteins and amino acids

Overview of protein structure

Ter"ary structure of proteins

Orders of protein structure

Prac"ce: Proteins

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Ques!ons Tips & Thanks

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Benjamin Zhu 4 years ago

What is the func"on of amino acid beside forming proteins?

(18 votes) Flag more

Chris!an Krach 4 years ago

Your body needs nitrogen to build its own proteins. The only way to get it
is to eat other proteins, so amino acids/proteins is an important N-
source.
Other slightly modified amino acids are used as hormones. Serotonin is
only a few reac"on steps away from tryptophan (Trp). But humans cannot
synthesize Trp themselves so it has to be eaten first, too.

(20 votes) Flag more

Specman 4 years ago

What is the approximate number of proteins in a human cell? I was reading a blog
recently on the brain and it stated that there were 10 billion proteins in a human
cell? I can't find a clear answer on this searching the internet.

1 comment (12 votes) Flag more

Samuel Rex 4 years ago

This is a hard ques"on to answer, as it can vary a great amount, and

proteins are complex dynamic molecules. It is es"mated that there are
around ~50,000~ proteins. You can find out more here
h#p://www.innovateus.net/health/how-many-proteins-exist-human-
body

3 comments (9 votes) Flag more

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Mark 3 years ago

Why isnt water OH2?

(9 votes) Flag more

briancsherman 3 years ago

Good ques"on! You're not the only one wondering about the order of
elements in a chemical formula!

In 1900 a man named Edwin Hill at the US Patent Office came up with
Hill nota"on for wri"ng chemical formulas, which states that carbon
should be listed first, then hydrogen, with the other elements listed in
alphabe"cal order - with certain excep"ons, like ionic compounds. Ionic
compounds are listed with the posi"ve ion first and the nega"ve ion
a$er. Other excep"ons are oxides, acids, and hydroxides. Oxides have
the oxygen listed last. Acids generally begin with the H for hydrogen,
even when they contain carbon. Most hydroxides end in OH rather than
with the H at the beginning.

Here's some other discussion on how chemical nota"on is wri#en:

h#ps://www.khanacademy.org/ques"ons/how-do-i-know-
what/ka'_9151689

1 comment (15 votes) Flag more

chulman444 4 years ago

N-terminus and C-terminus. What terminates extension of pep"de linkage? Are

they guaranteed not to react with other amino acids? If so how?...is it like how
there aren't any random amino acids beside those 23 men"oned above, because
i.e. for Lynsine, any more hydrocarbon backbone added to the hydrocarbon
backbone of lynsine makes it unstable and is actually impossible or something?

And would they be in zwi#erion at physiological pH? Could this be why the
terminus ARE terminus?

(9 votes) Flag more

Travis Fisher 3 years ago

To answer your first ques"on, you need to look at the process of crea"ng
a pep"de during Transla"on in the Ribosome. Messenger RNA is a
sequence of nucleo"des, three nucleo"des is a codon, and codons code
(go figure) for certain amino acids, codons also code a "start" and "stop".
So in a example the ribosome will read a start codon and start building a
pep"de un"l it reaches a stop codon. There is your termina"on. I'm not
sure how to explain the reasons for the differences in the 23 amino acids.
Ribosomes are almost like computers robo"cally doing what the inpu#ed
code commands it to do.

Also, I wanted to add that this isn't the end of the story. Things happen
to the pep"des a$er transcrip"on within the cell. For example, insulin
isn't transcribed fully func"onal but has to undergo several processes
(cu%ng of pieces, adding) within the cell before it lives up to it's essen"al
func"ons.

(6 votes) Flag more

Dexter Loh 3 years ago

Should I make any dis"nc"on between the quali"es: non-polar and hydrophobic or
polar and hydrophilic? Can I use these terms interchangeably; which is to say, am I
allowed to say non-polar instead of hydrophobic?

(5 votes) Flag more

Four21 3 years ago

Yes, you should make a dis"nc"on. While it is definitely true that most of
the "me they are the same, it is a good idea to keep in mind the
individual defini"ons of polar, non-polar, hydrophobic, and hydrophilic.

(6 votes) Flag more

Nelson9 3 years ago

In the amino acid table, the proline is throwing me off. Isn't proline nonpolar?

(6 votes) Flag more

johra914 3 years ago

According to my textbooks and study material, Proline is nonpolar with

an alipha"c side chain. So, I agree with you. Maybe there was some sort
of "typo" when they made this chart?

(4 votes) Flag more

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hvendidandi 4 years ago

what is a dipep"de?

(1 vote) Flag more

Anu Mohan 4 years ago

Exact Defini"on: a pep"de composed of two amino-acid residues.

(13 votes) Flag more

See 3 more replies

janez31 2 years ago

how are proteins and phenotypes related to one another

(4 votes) Flag more

Prof. Matulik 2 years ago

Provided that a protein has been transcribed and translated or

"expressed" by the genes, that is the direct expression of phenotype.
Large scale that may be seen in an organism as eye color, hair color, etc.,
as each protein has a different func"on.

(4 votes) Flag more

Rmal1103401 3 years ago

If enzymes are proteins, and they can func"on as a part of the diges"ve system,
doesn't that mean that the enzymes will be breaking down other proteins in the
eaten food? So proteins can break down other proteins?

(3 votes) Flag more

David Fabiyi 2 years ago

Yes, you are right the diges"ve enzymes in your stomach do break down
other proteins.

(4 votes) Flag more

Jimena TA 2 years ago

Hi, I remember that in the lipids lesson it said that a specific macromolecule (I don
´t remember its name) was considered to be a lipid just because it was hydrophobic
and in this ar"cle, I found this: "For example, amino acids such as valine and
leucine are nonpolar and hydrophobic." So my ques"on is what is the difference
between the other macromolecule that was called a lipid because of its being
hydrophobic and these proteins?

(3 votes) Flag more

vishalguptakollurugowri 2 years ago

It is the presence of amine group and a carboxylic group with a specific

configura"on that makes a macro molecule to be classified as an amino
acid. If you watch the video again, I am sure you would understand.

1 comment (3 votes) Flag more

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Pep!de bond forma!on Overview of protein structure

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