A protein is a biomolecule that is used to create structure in living organisms. It can also be used as a catalyst and an enzyme to aid in carrying out essential functions within a cell, such as transporting nutrients and oxygen around the body. Proteins are made up of a chain of amino acids with multiple bonds that form a protein’s shape.
What is the Shape of a Protein Molecule?
A protein molecule can be viewed as a long chain of amino acids. These amino acids are joined by peptide bonds which form the backbone of the protein. Amino acids have a characteristic structure composed of a carbon-nitrogen group. An amine group is attached to the first carbon atom and a carboxyl group attached to the second carbon.
The amino acids are connected via a sulfhydryl group, an oxygen-containing functional group. This sulfhydryl group is the site of attachment for many enzymes.
Amino Acid Structure
Amino acids are the monomers that link to form a polypeptide. There are over 20 different types of amino acids found in nature. All amino acids have a similar structure with the grouping of carbon, hydrogen, and oxygen atoms in their skeleton.
Types of Amino Acids
Amino acids are classified according to their properties. Because the makeup of amino acids is so important, each amino acid has a three-letter abbreviation that identifies it. They are as follows:
Ala – Alanine, Arg – Arginine, Asn – Asparagine, Asp – Aspartic acid, Cys – Cysteine, Gln – Glutamine, Glu – Glutamic acid, His – Histidine, Ile – Isoleucine
Protein molecules take different structures depending on the sequence of amino acids. There are three main levels of the protein structure, namely primary, secondary, tertiary, and quaternary.
The primary structure is the order of amino acids in a protein; usually, this is written as a chain of letters determining the sequence. The first amino acid in the chain is known as the N-terminal or amino-terminal end. This end binds to other peptide chains and also helps protect the protein from being broken down.
The DNA gene that encodes a particular protein determines the amino acid sequence for that protein. Many genes may contribute to the primary structure of a protein through the use of alternative splicing.
Any change in the sequence of amino acids changes the shape of the protein. This fact explains why proteins from different organisms can have vastly different shapes.
For example, a protein from a human differs greatly in the peptide sequence, conformation, and overall structure compared to a bacterial protein. This is why vaccines are developed to resemble a protein from the organism of concern while having no biological function.
Sickle cell anemia is an example of a genetic disorder caused by the change in amino acid sequence at a specific place. The change causes a protein to be folded to destroy its function and change the shape of the red blood cell.
When two proteins interact, they bind to each other. If the shape of amino acid changes, it can also change how a protein binds to another protein. This change can make the protein more or less likely to bind with a certain molecule, an example of a conformational change.
The hemoglobin molecule is an example of a protein that carries oxygen in the blood and is responsible for transporting it through the different parts of the body. Hemoglobin contains iron, which gives the molecule a red color.
In the body, many amino acids are bound to iron molecules through their sulfhydryl group, making them a form of Iron-Sulfur Cluster. The binding site on the hemoglobin molecule has two atoms of iron attached to it.
Each of the atoms interacts separately with the binding sites on two different hemoglobin molecules. This arrangement allows for four hemoglobin molecules to bind together, forming a tetramer.
The secondary structure is determined by the hydrogen bonds and hydrophobic interactions that form between the amino acids. This structure determines how a protein will fold and how it interacts with other molecules.
Amino acids have a single point of attachment to the backbone, which allows them to contact the other amino acids around them.
The hydrogen bonds form between two amino acids approximately three angstroms apart from each other. Hydrophobic interactions form between the hydrophobic portions of the amino acids. The parts that are not involved with these interactions are called polar because they have an uneven distribution of protons and electropositive and electronegative atoms.
The amino acids in a protein can be grouped into two basic categories: hydrophobic and polar. The hydrophobic amino acids group together to form chunks of a protein called alpha-helices. These chunks create a spiral shape that can be seen in the secondary structures of many proteins.
The peptide bonds between different amino acids form hydrogen bonds, and the backbone of the protein also forms hydrogen bonds. The electrostatic interactions between different amino acids hold together other parts of the secondary structure. There are two types of interactions: polar and nonpolar.
The protein globin is an example of a protein that contains structural elements that are highly conserved in most proteins. Hydrophobic interactions play a large role in determining the secondary structure of globin and help determine how the protein interacts with membranes.
The Alpha helix(α) and the β pleated Sheet are the common types of protein secondary structures.
The alpha helix is a structure that consists of coils made up of amino acid residues (AAs), with the polar hydrophilic heads pointing inside and the nonpolar hydrophobic tails pointing outside.
The residues in this motif form hydrogen bonds between each other with their side chain groups and the main chain. The amino acids that form this structure are kept together by hydrophobic interactions between residues with similar characteristics.
Amino acids in α-helices are arranged so that the polar groups point towards the inside while the nonpolar groups stick out at the surface. This structure is formed because of the amino acid side chains: for example, when an aliphatic or a polar and charged group are placed next to each other, they will form a hydrophobic region.
The residues near the helical backbone and in direct contact with it, making up the main chain, are usually hydrophilic. When most side chains form hydrogen bonds, they face each other and are exposed to the outside of the helix. In contrast, when two residues form a hydrogen bond, and one faces the helix inside the helix, the other will face the outside of the helix.
When a residue facing outwards forms a hydrogen bond with another group, the residue or group will face outwards because the main chain isn’t affected by this external force. Hydrogen bonds can only occur between pairs of residues, and in α-helices, they are usually between the amide carbonyl O and an amine nitrogen H on another residue.
The third most common junction is when the side chain of the first residue forms a hydrogen bond with the main-chain carbonyl carbon O, and the amine group N forms a hydrogen bond with the carbonyl O of another residue.
When residues form hydrogen bonds that face the inside of the helix, they are considered internal. Hydrogen bonds between residues that face toward the outside will be called surface interactions.
β pleated Sheet
The β pleated Sheet is a common secondary structure that consists of parallel beta-sheets. Although the individual strands are not as stable as an alpha-helix, they can fold together into a stable structure in certain cases.
The main chain of each strand is formed by the carbonyl groups and the amine groups of the residues, while pairs of nonpolar amino acid residues are from the side chains. The interactions between the strands are van der Waals interactions that form because the nonpolar groups on these residues attract each other.
For example, when large and small residues are next to each other, they will have no problem forming a nonpolar interaction. The main chain of beta-pleated sheets also forms hydrogen bonds between the C=O and N-H groups of residues.
The hydrogen bonds form when two residues diagonally opposite each other form angles of approximately 137 degrees.
The residues in a single strand are held together by these hydrogen bonds. Because of the nonpolar interaction, the residues on one side of a strand are nonpolar and have their polar groups facing away from each other. The opposite is true for the second strand.
Polar residues are usually found on the edges of this structure, and they interact with water and other polar groups to form hydrogen bonds. Small nonpolar residues form van der Waals interactions with other neighboring strands.
The most common source of β pleated sheets is when a polypeptide chain folds into a hairpin.
The tertiary structure of a protein is determined by the interactions between the side chains or R-groups of the amino acids in the polypeptide chain.
Because of these interactions, there are many different possible arrangements for a polypeptide chain. The interactions between the side chains must be strong enough to form a stable structure and keep the polypeptide folded.
The interactions form when the dipole moment of a side chain attracts or repels the charge of another group’s dipole moment.
Disulfide bonds are non-covalent bonds that are formed between two cysteine side chain residues. A disulfide bond forms when the sulfur atoms of two cysteine residues are close enough to form a covalent bond. The sulfur atoms in the cysteines are oxidized; therefore, this is a redox reaction.
The quaternary structure is the final step of protein folding. It results in a functional protein having active sites for catalysis or binding. This structure forms when two or more polypeptide chains come together [polymerization].
Usually, this happens when two or more polypeptide chains come together through disulfide bonds. This is known as intermolecular bonding between separate polypeptide chains.
Disulfide bridges can form between cysteine residues separated by more than 20 amino acid residues in the linear sequence. Disulfide bonds form between the thiolate anion and the disulfide atom of another cysteine residue through an S N 2 reaction.
A functional protein forms when eleven to one hundred polypeptide chains combine, forming what is known as a quaternary structure. The quaternary structure of a protein is dependent on the interactions between the nonpolar groups and hydrogen bonds. The quaternary structure of a protein can be found in two ways.
The first is through X-ray crystallography, which reveals the quaternary structures if the protein has been crystallized. The other way is to identify and use a specific amino acid sequence region that changes little throughout many interactions in the quaternary structure.
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Intrinsically Disordered Proteins (IDPs)
Some proteins are not structured enough to be part of a specific, stable structure and are classified as intrinsically disordered proteins (IDPs). The lack of structure in these IDPs is caused by the high flexibility of their polypeptide chains.
A frameshift is when an insertion or a deletion in a DNA sequence causes the reading frame to shift. The bases before and after a gap will be read differently because of the insertion or deletion, which will change the amino acid sequence that is translated from it.
The sequence change causes a mutation, which is a permanent change in the DNA sequence. This mutation tells the cell to read the sequence differently, which causes a change in the amino acid sequence.
Characteristics of Proteins
Proteins demonstrate a wide range of chemical, physical and structural properties that help their bodies function. The most important characteristics include:
- Proteins are made from chains of amino acids
- They are the structural components of all cells, tissues, and organs in the body.
- They play an important role in communication between cells.
- They carry out virtually all of the functions necessary for life to exist and continue.
- They are very diverse in their structure and function.
- Each protein functions as a machine made up of many different molecules working together to achieve a specific goal.
- They can be tuned in their interaction with other molecules to form a specific structure at a particular time and place.
- Proteins are water-insoluble
- They can store and transfer information.
- The identity of a protein comes from its amino acid makeup; this determines its biological activity. The sequence of amino acids that makes proteins have a distinct identity, structure, and function.
- Protein molecules are the fundamental building blocks that make up our cells, tissues, and organs. This characteristic makes them essential to all living systems.
Depending on their different structures and compositions, proteins play different roles in living organisms. The functions of proteins can be categorized into five different groups: structural, biochemical, catalytic, regulatory, and signaling.
Structural proteins are required for building cells, tissues, and organs. They make up the structural framework of living things and tend to be quite large.
The different building blocks of molecules, including amino acids and sugars, are used when the protein is synthesized or created. These amino acids come from different sources, including proteins and carbohydrates, which are both made up of amino acids.
An example of structural protein is the human growth hormone required for long-term cell and tissue growth.
Biochemical proteins are enzymes, which catalyze metabolic reactions within the cells. Proteins also perform many of the functions involved with metabolism in living organisms. These reactions include the synthesis, breakdown, and transportation of molecules.
Proteins that are capable of accelerating chemical reactions without themselves being destroyed in the process are known as enzymes. These catalytic proteins are responsible for speeding up and often controlling metabolic reactions within cells. Moreover, they are important for the proper functioning of all living organisms.
Examples of enzymes are:
- Enzyme Amylase. It breaks carbohydrates down into smaller sugars.
- Enzyme Peptidase. It cleaves peptide bonds and is responsible for the digestion of proteins in the stomach.
Enzymes are often considered catalysts or machines that speed up a process in which they do not undergo any chemical change. They are key to carrying out reactions necessary for life.
Another set of proteins crucial to the study of living organisms are those with regulatory functions; they carry out important duties for the cells, tissues, and organs.
Protein molecules include hormones like insulin, which allows certain cells to respond to the presence of glucose in the blood.
- Regulatory proteins also include antibodies and other immune system components that attack invading microbes and other harmful substances.
- Antibodies are used for immune reactions and are critical to the body’s defense system. They attack foreign substances that enter the body and attempt to protect it from infections.
- Glucagon causes the liver to break down glycogen into glucose and release it into the bloodstream.
Proteins that can send information are called signaling proteins. These include hormones, which are chemical messengers that carry out important functions in the body.
Hormones exist as part of a cell or gland and are dispersed into the body through the bloodstream. Once a protein hormone enters a cell, it can bind to specific target sites on other proteins. When it binds, the message that it carries will be delivered to the target cell.
Examples of signaling proteins in the body are:
- Antigens in the immune system. Antigens are molecules that cause an immune reaction in the body and trigger the release of antibodies.
- Hormones. They regulate growth and metabolism. Hormones control various actions in the body, including reproductive functions and processes involved in growth.
- Hormones are also used as messages to control emotions and stress responses. They can either work to reduce or increase these feelings.
- Insulin controls the amount of glucose in the bloodstream by increasing the rate at which glucose is absorbed into cells.
Protein denaturation refers to the disruption of a protein’s normal three-dimensional structure. Denatured proteins cannot perform their functions and have lost some or all of their biological activity.
Some causes of protein denaturing include:
- Excessive heat. Extremely high temperatures can cause proteins to lose their function and change their structure.
- Destructive binding. Denaturation will occur of the protein molecule binds with chelating agents and other destructive compounds.
- Varying pH levels. Changes in pH levels can cause structural proteins to lose their function. This effect happens because the pH levels directly influence the conformation of a protein.
- Exposure to organic compounds and other substances can change the protein’s structure by binding with it. One of the most common causes is exposure to heavy metals.
When proteins are denatured, their secondary and tertiary structures can be destroyed.
Some denaturing processes are reversible, while others are irreversible. Examples of reversible processes include:
Heating milk to set it. In this process, the three-dimensional structure of a protein will be changed, and the denatured milk proteins will be able to return to their original state when cooled.
Irreversible denaturation, on the other hand, destroys protein structure. The artificial sweetener aspartame is an example of a substance that can cause irreversible denaturation in proteins such as those in living cells.
A common example of irreversible denaturation is pasteurization, in which milk is heated to destroy any harmful microorganisms that might exist in the milk.
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Your Take Away
Proteins are composed of many different amino acids arranged in a specific manner to form a particular function. The arrangement or sequence of amino acids is what gives each protein its unique three-dimensional structure. This structure allows the proteins to work properly with other molecules and to perform many functions.
If the protein cannot fold into its three-dimensional structure, it will be useless to the cell. This inability is an example of a misfolded protein in which the three-dimensional structure is disrupted, thus preventing the protein from performing its function.