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Classifying Polypeptides (and/or Proteins)


Since polypeptides are a linear chain of twenty amino acids, each having a single letter abbreviation (e.g. Alanine = A). So can a polypeptide be represented as just the sequence (say: ADN for an Alanine, Aspartic acid, Asparagine polypeptide)?

This method of classifying polypeptides would lead to a possible 8000 (20**3) variations just for 3-amino-acid-polypetides (3200000 for 5-amino-acid-polypeptides, etc.) and that there would be many variations; and for longer polypeptides - that is, proteins - there would be even more variations.

Or are only the important polypeptides and proteins named, since not every variation of polypeptides and proteins are found in the body? I would've thought that many proteins (and enzymes, etc.) are incredibly specific and so they could be classified in some methodological way, as opposed to just 'lipase' or 'carbohydrase' which provides no structural information (though it would have a long methodological name).


You can certainly refer to short peptides by their sequence. I don't know of any exact boundaries, but I've seen tripeptides referred to by either their three letter codes (Ala-Asp-Asn) or even the chemical name (alanylaspartylasparagine) although obviously that gets ridiculous pretty quickly.

As the largest known protein, titin also has the longest IUPAC name of a protein. The full chemical name of the human canonical form of titin, which starts methionyl… and ends… isoleucine, contains 189,819 letters and is sometimes stated to be the longest word in the English language, or any language. However, lexicographers regard generic names of chemical compounds as verbal formulae rather than English words

For more than around 5 amino acids, just the sequence makes more sense. It would be interesting to analyse scientific paper abstracts to see how many have the sequence as the 'name', but anyway.

When we get to proteins, it would be unhelpful to refer to them by their sequence. They usually have names - enzymes are often named by what they act on (like 'alcohol') and how they act on them (like 'dehydrogenase'). In addition, there are structured names called E.C. numbers - sarcosine dehydrogenase is 1.5.8.2, for example.

As you point out, there are a very large number of sequences that do not correspond to proteins found in an organism. To name one of these is tricky, and if someone synthesises one then they would have to come up with some naming scheme to refer to it.


Protein Shake

Figure 3.6.1 Protein shakes vary in quality based on which amino acids they contain.

Drinks like this shake contain a lot of protein. Muscle tissue consists mainly of protein, so such drinks are popular with people who want to build muscle. Making up muscles is just one of a plethora of functions of this amazingly diverse class of biochemicals.


Twenty amino acids form the building blocks for proteins. Amino acids chemically stick together by forming peptide bonds. You can call any string of two or more amino acids a peptide. Thus, a polypeptide is a type of peptide. Further, dipeptides, tripeptides and tetrapeptides respectively hold two, three and four amino acids. An oligopeptide is the general term for peptides containing 12 to 20 amino acids. Peptides also rarely contain strings of more than 30 amino acids.

Biochemists generally use the term polypeptide to describe medium-size peptide chains consisting of 10 or more amino acids. In biochemistry, the term protein is nonspecific, because it includes amino acid chains of any length. However, polypeptides refer to proteins of a particular size. Therefore, the term polypeptide refers to a general size of peptide chains. The pancreatic hormone insulin is an example of a polypeptide. Insulin helps your body to use and store sugar.


Proteins: Definition, Classification and Structure | Biochemistry

In this article we will discuss about:- 1. Definition of Proteins 2. Classification of Proteins 3. Composition of Protein Molecule 4. Primary Structure 5. Secondary Structure 6. Quaternary Structure.

Definition of Proteins:

Proteins may be defined as high molar mass compounds consisting largely or entirely of chains of amino acids. The general formula of a naturally occurring amino acid may be repre­sented with the following Fischer projection formula (Fig. 8.60). In this structure an amino group is present on the carbon atom adjacent to carboxyl group.

The amino acids having this general formula are known as alpha (α) amino acids. In its structure four bonds of a carbon atom (Cα) are occupied by NH2, COOH, H and R molecules. R may be any compound which determine the properties of an amino acid and is referred to as the amino acid side chain:

Classification of Proteins:

Like carbohydrates and lipids, proteins could not be classified only on the basis of structural similarities. Because protein molecules posses great structural comple­xities.

In earlier days, a convention of classi­fying proteins was under two headings:

(1) Fibrous—elongated proteins, e.g., silk fibroin, keratin etc.

(2) Globular—spher­ical, compact proteins, e.g., egg albumin, caesin and most enzymes. Fibrous proteins tend to be insoluble in water and other sol­vents, whereas globular proteins are soluble in water and in solutions of salt and water.

Nowadays, there are two alter­native methods of protein classification:

(1) According to the composition of the protein and

(2) According to the function of the protein.

These two classifications are given here:

1. Classification according to the compo­sition:

In this process, proteins are classified into two groups:

A simple protein is composed of only α-amino acids. Thus, produces exclusively α-amino acids upon hydrolysis. These proteins are further sub­divided according to their solubility in various solvents. Different simple proteins are described here.

These are soluble in water and in dilute salt solutions. Albumins constitute the most important and the most common group of simple pro­teins. These are present in egg white (egg albumin) and in blood (serum albumin).

These are insoluble in water but are soluble in dilute salt solutions. They are widely distributed group of simple proteins. They are present as antibodies in blood serum and as blood fibrinogen.

They are soluble in water and insoluble in dilute ammonium hydroxide. Histones contain a high proportion of basic amino acids (lysine and/or arginine). These are found in association with nucleic acids in the nucleoprotein of the cell.

(iv) Scleroproteins (albuminoids):

These are characterised by their insolubility in water and other solvents. Scleroproteins have structural and protective functions in the body. The examples of scleroproteins are keratin (present in hair, skin and nails), colla­gen (present in bone, tendon and car­tilage) and elastin (elastic fibers of connective tissues).

B. Conjugated proteins:

These are formed of a-amino acids and a non-protein material. The non-protein material of the con­jugated protein is called prosthetic group. Different types of conjugated proteins are subdivided on the basis of their prosthetic group.

Different conjugated proteins are as follows:

These are composed of α-amino acids and phosphoric acids. So, their prosthetic group is phosphoric acid. Caesin, present in milk, is an important member of this group.

They contain a carbo­hydrate or a carbohydrate derivative as prosthetic group. Mucin, a constituent of saliva, is a glycoprotein.

Their prosphetic group is a pigment compound. Example: Haemoglobin. Its possesses the iron-containing pigment haemeco-ordinated to the simple protein globin.

Here prosthetic groups are complex polymers of high molar masses and are called nucleic acids (DNA and RNA). Nucleo-proteins are present in all the cells of plants and animals.

They consist of choles­terol esters and phospholipids attached to the protein molecules. They are frequently classified as compound lipids. Most of the lipid in mam­malian blood is transported in the form of lipoprotein complexes. The electron transport system in the mito­chondria contains large amount of lipoproteins. These are also found in egg yolk, myelin sheath of nerves and different cell organelles.

2. Classification on the basis of functions:

Proteins are classified into six groups on the basis of their functions:

A. Structural proteins:

These proteins participate in the formation of different body parts. More than half of the total protein of the mammalian body is collagen found in skin, cartilage and bone.

B. Contractile proteins:

These special types of proteins are responsible for the con­traction and relaxation of muscle cells, e.g., actin and myosin. These proteins are also present in the unicellular animals.

They represent the largest class of proteins. Nearly 2,000 different kinds of enzymes are known. The enzymes are called biological catalyst and are vital for any activity in the living organism.

Many of the hormones are protein in nature, e.g., insulin. Some other hormones are steroid.

Higher organisms (birds, mammals, etc.) produce antibodies to destroy any foreign material (antigen) released into the body by an infectious agent. Gamma globulins are example of antibodies in mammals.

The albumins, globulins and fibrinogen are the three major protein constituents of blood.

Composition of Protein Molecule: Conden­sation of Amino Acids:

In favourable conditions amino acids polymerize. The a-amino group of one molecule joins to the carboxyl group of another in a condensation reaction. This results in the formation of peptide linkage (Fig. 8.65). The peptides containing two, three and four amino acids are called dipeptides, tripeptides and tetra-peptides, respec­tively. The amino and carboxyl groups at opposite end of the depeptide can form peptide linkages with other amino acid molecules.

The term polypeptide is generally applied to the relatively small molecules of proteins containing from five to thirty-five amino acids. The term protein is arbitrarily used for longer polypeptides (i.e., having molecular mass above 5,000). However, this is not the fact that protein is composed of only one long polypeptide chain.

There are also many instances that a protein is com­posed of two or more polypeptide chains. Example—enzymes lysozyme (Fig. 8.66) and ribonuclease (Fig. 8.67) contain 129 and 124 amino acids, respectively, in only one chain. Hormone insulin (Fig. 8.68) contains two polypeptide chains (one chain having 21 amino acids and the other 30) joined by disulfide linkages. The haemoglobin molecule contains four polypeptide chains.

Primary Structure of Protein:

The primary structure of the protein is the number and sequence of amino acids in a polypep­tide chain. The only form of bonding in a protein’s primary structure is the peptide linkage. By convention, we represent the struc­ture of peptides beginning with the amino acid whose amino group is free and this end is called as N-terminal end (Fig. 8.69).

The other end, therefore, contains a free carboxyl group and is referred to as C-terminal end. Each amino acid in the peptide, with the exception of the C-terminal amino acid, is named as an acyl group in which the suffixine is replaced by-yl (e.g., alanine → alanyl, glycine → glycyl etc.). Oxytocin and vaso­pressin are peptides produced by pituitary gland. These are with primary structural con­figuration.

At present protein research yields a large number of sequences. This number is rapidly growing day by day. So instead of recording them on paper these are deposited in elec­tronic media. There are several protein sequence databases that can be accessed via internet.

Important continuously updated protein databases include EMBL (European Molecular Biology Laboratory Data Library), Gen Bank (Genetic sequence Databank), and PIR (Protein Identification Resource Sequence Database).

Secondary Structure of Protein:

The primary structure describes only the sequence of amino acids in the protein chain. But from the primary structure one cannot understand about the shape (conformation) of the protein molecule. Now it is established that each protein occurs in nature in a single, particular, three dimensional conformations. The fixed configuration of the polypeptide back­bone is referred to as the secondary structure of the protein.

Configuration and Conformation of Proteins:

Two considerations are involved in the secondary structure of proteins. The first one is configuration, which refers to the geo­metric relationship between a given set of atoms. Inter-conversion of configurational alternatives (e.g., conversion of D- to L-alanine) can be achieved only by breaking and reforming covalent bonds.

The second is con­formation, which refers to the three dimen­sioned architecture of the protein, the spatial relationships of all the atoms to all the others. The inter-conversion of conformers involves not the rupture of covalent bonds but the rupture and reformation of non-covalent forces (hydrogen bonds) that stabilise a given conformation.

The particular conformation of a protein is of immense importance in bio­logical activities. There may be different conformational species for a particular protein, but all cannot equally participate in biologi­cal actions.

Quaternary Structure of Protein:

Primary, secondary and tertiary struc­tures, described so far, deals with a single helix or one polypeptide chain. The quater­nary structure of a protein defines the struc­ture resulting from interactions between separate polypetide units of a protein con­taining more than one submit.

Example, the enzyme phosphorylase A contains two iden­tical submits that alone are catalytically inac­tive but when joined as a dimer it becomes an active enzyme (Fig. 8.72A).


Difference between polypeptide and protein

Definition of polypeptide and protein

A polypeptide is a polymer formed by a defined sequence of amino-acids linked together through covalent peptide bonds.

A protein is a structurally and functionally complex molecule formed by the folding of one or many polypeptide chains.

Structural differences in polypeptide and protein

A polypeptide presents a simple structure and consists of the polypeptide backbone formed by the repeating sequence of atoms at the core of the linked amino-acids chain. Attached to the polypeptide backbone are the amino-acids specific side chains, the R group

A protein, on the other side, is a complex molecule consisting of one or more polypeptide chains folding into secondary, tertiary or quaternary structure.

The protein shape is held stable by three types of weak non covalent bonds: hydrogen bonds, ionic bonds, and van der Waal bonds.

Function of polypeptide and protein

The main function of a polypeptide is being the primary structure of more complex proteins. Polypeptides lack the three-dimensional structure which enables a protein to bind to a ligand and be functional.

On the other side, the structural complexity of a protein, its stable shape with its ligand-binding sites enables it to bind specifically and with high affinity to particular ligands, to be regulated, and to participate in many vital cellular metabolic pathways.

Polypeptide versus Protein: Comparioson Table


Protein

Large molecule or multimolecular complex, consisting of amino acids, polypeptides, and other substances, that serves as the key component that implements the functions encoded by hereditary material.

Proteins consist of polymers of amino acids (polypeptides) along with other, non-amino acid substances, such as the found in the proteins and . Proteins are the primary facilitators of phenotype, as viewed both at cellular and organismal levels.

The following video is a nice introduction to different types and representations of protein structure, shown both in static and dynamic forms:

It is important to not confuse the concept of protein with that of polypeptides since the two terms, though related, are not identical. Indeed, much discussion of proteins, such as the many details of (particularly, the process of translation) are actually more correctly viewed as discussions of the synthesis of polypeptides rather than, strictly, of proteins.

Proteins can be differentiated into a number of components including polypeptide (or polypeptides) along with cofactors (and coenzymes). For the subset of proteins known as enzymes, the polypeptide portion alone is called an apoenzyme whereas the combination of polypeptide(s) and cofactor(s), forming an active enzyme, is known as the holoenzyme. Polypeptides often are functional within proteins in combination with other polypeptides, forming , , etc.

Many and in our serve as cofactors or coenzymes. Proteins requiring these substances are unable to function without them. You can think of these other substances as supplying more chemical properties, that is, chemistry to proteins that is other than what individual amino acids can provide. In proteins that employ these other substances there will be amino acids that together form structures which hold on to them, and typically these cofactors and coenzymes will be held at what is known as an enzyme's or protein's active site.

The following is a list of terms associated with proteins generally (but not necessarily with enzymes also):

The following are examples of different types of proteins (see also enzymes):


Difference Between Polypeptide and Protein

Amino acid is a simple molecule formed with C, H, O, N and may be S. It has the following general structure.

There are about 20 common amino acids. All the amino acids have a –COOH, -NH 2 groups and a –H bonded to a carbon. The carbon is a chiral carbon, and alpha amino acids are the most important in the biological world. The R group differs from amino acid to amino acid. The simplest amino acid with R group being H is glycine. According to the R group, amino acids can be categorized into aliphatic, aromatic, non polar, polar, positively charged, negatively charged, or polar uncharged, etc. Amino acids present as zwitter ions in the physiological pH 7.4. Amino acids are the building blocks of proteins. When two amino acids join together to form a dipeptide, the combination takes place in a -NH 2 group of one amino acid with the –COOH group of another amino acid. A water molecule is removed, and the formed bond is known as a peptide bond.

Polypeptide

The chain forms when a large number of amino acids are joined together is known as a polypeptide. Proteins consist of one or more of these polypeptide chains. The primary structure of a protein is known as a polypeptide. From the two terminals of the polypeptide chain, N-terminus is where the amino group is free, and the c- terminus is where the carboxyl group is free. Polypeptides are synthesized at ribosomes. The amino acid sequence in the polypeptide chain is determined by the codons in mRNA.

Proteins are one of the most important types of macromolecules in living organisms. Proteins can be categorized as primary, secondary, tertiary and quaternary proteins depending on their structures. The sequence of amino acids (polypeptide) in a protein is called a primary structure. When polypeptide structures fold into random arrangements, they are known as secondary proteins. In tertiary structures proteins have a three dimensional structure. When few three dimensional protein moieties bound together, they form the quaternary proteins. The three dimensional structure of proteins depends on the hydrogen bonds, disulfide bonds, ionic bonds, hydrophobic interactions and all the other intermolecular interactions within amino acids. Proteins play several roles in living systems. They participate in forming structures. For example, muscles have protein fibers like collagen and elastin. They are also found in hard and rigid structural parts as nails, hair, hooves, feathers, etc. Further proteins are found in connective tissues like cartilages. Other than the structural function, proteins have a protective function too. Antibodies are proteins, and they protect our bodies from foreign infections. All the enzymes are proteins. Enzymes are the main molecules which control all the metabolic activities. Further, proteins participate in cell signaling. Proteins are produced on ribosomes. Protein producing signal is passed onto the ribosome from the genes in DNA. The required amino acids can be from the diet or can be synthesized inside the cell. Protein denaturation results in the unfolding and disorganization of the proteins’ secondary and tertiary structures. This can be due to heat, organic solvents, strong acids and bases, detergents, mechanical forces, etc.

What is the difference between Polypeptide and Protein?

• Polypeptides are amino acid sequence, whereas proteins are made by one or more polypeptide chains.

• Proteins have a higher molecular weight than polypeptides.

• Proteins have hydrogen bonds, disulfide bonds and other electrostatic interactions, which governs its three dimensional structure in contrast to polypeptides.


Lysosomes

Lysosomes are organelles that digest macromolecules, repair cell membranes, and respond to foreign substances entering the cell.

Learning Objectives

Describe how lysosomes function as the cell’s waste disposal system

Key Takeaways

Key Points

  • Lysosomes breakdown/digest macromolecules (carbohydrates, lipids, proteins, and nucleic acids), repair cell membranes, and respond against foreign substances such as bacteria, viruses and other antigens.
  • Lysosomes contain enzymes that break down the macromolecules and foreign invaders.
  • Lysosomes are composed of lipids and proteins, with a single membrane covering the internal enzymes to prevent the lysosome from digesting the cell itself.
  • Lysosomes are found in all animal cells, but are rarely found within plant cells due to the tough cell wall surrounding a plant cell that keeps out foreign substances.

Key Terms

  • enzyme: a globular protein that catalyses a biological chemical reaction
  • lysosome: An organelle found in all types of animal cells which contains a large range of digestive enzymes capable of splitting most biological macromolecules.

Lysosomes

A lysosome has three main functions: the breakdown/digestion of macromolecules (carbohydrates, lipids, proteins, and nucleic acids), cell membrane repairs, and responses against foreign substances such as bacteria, viruses and other antigens. When food is eaten or absorbed by the cell, the lysosome releases its enzymes to break down complex molecules including sugars and proteins into usable energy needed by the cell to survive. If no food is provided, the lysosome’s enzymes digest other organelles within the cell in order to obtain the necessary nutrients.

In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are considered to be parts of the endomembrane system. Lysosomes also use their hydrolytic enzymes to destroy pathogens (disease-causing organisms) that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis or endocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen.

Lysosomes digest foreign substances that might harm the cell: A macrophage has engulfed (phagocytized) a potentially pathogenic bacterium and then fuses with a lysosomes within the cell to destroy the pathogen. Other organelles are present in the cell but for simplicity are not shown.

A lysosome is composed of lipids, which make up the membrane, and proteins, which make up the enzymes within the membrane. Usually, lysosomes are between 0.1 to 1.2μm, but the size varies based on the cell type. The general structure of a lysosome consists of a collection of enzymes surrounded by a single-layer membrane. The membrane is a crucial aspect of its structure because without it the enzymes within the lysosome that are used to breakdown foreign substances would leak out and digest the entire cell, causing it to die.

Lysosomes are found in nearly every animal-like eukaryotic cell. They are so common in animal cells because, when animal cells take in or absorb food, they need the enzymes found in lysosomes in order to digest and use the food for energy. On the other hand, lysosomes are not commonly-found in plant cells. Lysosomes are not needed in plant cells because they have cell walls that are tough enough to keep the large/foreign substances that lysosomes would usually digest out of the cell.


What Is the Difference Between a Peptide and a Protein?

Proteins and peptides are fundamental components of cells that carry out important biological functions. Proteins give cells their shape, for example, and they respond to signals transmitted from the extracellular environment. Certain types of peptides play key roles in regulating the activities of other molecules. Structurally, proteins and peptides are very similar, being made up of chains of amino acids that are held together by peptide bonds (also called amide bonds). So, what distinguishes a peptide from a protein?

The basic distinguishing factors are size and structure. Peptides are smaller than proteins. Traditionally, peptides are defined as molecules that consist of between 2 and 50 amino acids, whereas proteins are made up of 50 or more amino acids. In addition, peptides tend to be less well defined in structure than proteins, which can adopt complex conformations known as secondary, tertiary, and quaternary structures. Functional distinctions may also be made between peptides and proteins.


Ring-Opening Polymerization and Special Polymerization Processes

4.16.4.2 Mesogen-Functionalized Polypeptides

The polypeptide materials field has grown tremendously in recent years. However, a drawback of polypeptides has been the difficulty in using melt processing with these materials, since the abundant H-bonds and consequent poor chain flexibility prevent melting before decomposition. Although solution-based methods allow processing of these materials for most applications, 84 melt processing, or even capability for thermal annealing, would greatly expand the utility of polypeptides.

Pioneering studies on thermotropic polypeptides were done by Watanabe’s group, where poly(glutamates) were derivatized either with long alkyl chains 85 or by end-on attachment of biphenyl mesogens (eqn [21] ). 86 Polypeptides with short alkyl side chains were not thermotropic, yet side chains greater than 10 carbons long gave melting transitions from –26 to 54 °C. These samples formed cholesteric liquid crystalline phases above the melting transition, but formed layered structures at low temperatures driven by crystallization of the side chains. Furthermore, poly(γ-octadecyl- l -glutamate) was found to form a columnar hexagonal phase at temperatures above 200 °C, where the rodlike helices make up the two-dimensional (2D) lattice. 85 When biphenyl mesogens were attached end-on to poly(glutamate) side chains by six carbon alkyl spacers, layered structures were observed in the crystalline and liquid crystalline states, followed by transition into a cholesteric structure at higher temperatures. 86 Similar results were found when mesogens were attached end-on to poly(lysine) chains. 87 In these examples, the liquid crystalline mesophases were dominated either by the side-chain group (layered structure) or by the rodlike nature of the polypeptide backbone (hexagonal phase), but in no case was coexistence of both types of ordering observed.

Deming developed mesogen-functionalized polypeptides in which liquid crystalline ordering exists concurrently with backbone ordering. To obtain this coexistence between mesogen and main-chain ordering, ‘side-on’ mesogen 88 modification of the polypeptides was used to allow facile parallel orientation of mesogens and the peptide backbones. Since it is known that varying the length of flexible spacers connecting polymer backbones and mesogens affects the mesophase behavior of side-chain liquid crystalline polymers, 89 NCA monomers with spacers of 3, 5, and 10 methylene units between the lysine side chains and the mesogens were prepared. The mesogen used for this study was a well-known three-ring aromatic ester molecule, 90 which was derivatized from a central carboxylic acid group by ester coupling to attach linkers of 3, 5, and 10 methylene units to enable attachment to l -lysine ( Scheme 9 ). Mesogen-derivatized polypeptides were prepared by polymerization of the corresponding NCAs using (PMe3)4Co initiator in THF solvent in high yield. 91 The polypeptides were soluble in THF and were found to adopt α-helical conformations in solution by CD and Fourier transform infrared (FTIR) spectroscopy. These polymers displayed an unusual thermotropic mesophase where both side-chain mesogens and polymer backbones are ordered and coexist in a nematic hexagonal structure.


Watch the video: Classification of amino acids. Chemical processes. MCAT. Khan Academy (December 2021).