Biochemistry, Proteins Enzymes (2023)


Every day, trillions upon trillions of chemical reactions occur in our body to make essential metabolic processes occur.Enzymes are proteins that act upon substrate molecules and decrease the activation energy necessary for a chemical reaction to occur by stabilizing the transition state. This stabilization speeds up reaction rates and makes them happen at physiologically significant rates. Enzymes bind substrates at key locations in their structure called active sites. They are typically highly specific and only bind certain substrates for certain reactions. Without enzymes, most metabolic reactions would take much longer and would not be fast enough to sustain life.


There are six main categories of enzymes: oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. Each category carries out a general type of reaction but catalyzes many different specific reactions within their own category. Some enzymes, called apoenzymes, are inactive until they are bound to a cofactor, which activates the enzyme. A cofactor can be either metal ions (e.g., Zn) or organic compounds that attach, either covalently or noncovalently, to the enzyme. The cofactor and apoenzyme complex is called a holoenzyme. Enzymes are proteins comprised of amino acids linked together in one or more polypeptide chains. This sequence of amino acids in a polypeptide chain is called the primary structure. This, in turn, determines the three-dimensional structure of the enzyme, including the shape of the active site. The secondary structure of a protein describes the localized polypeptide chain structures, e.g.,α-helices or β-sheets.

The complete three-dimensional fold of a polypeptide chain into a protein subunit is known as its tertiary structure. A protein can be composed of one (a monomer) or more subunits (e.g., a dimer). The three-dimensional arrangement of subunits is known as its quaternary structure. Subunit structure is determined by the sequence and characteristics of amino acids in the polypeptide chain. The active site is a groove or crevice on an enzyme in which a substrate binds to facilitate the catalyzed chemical reaction. Enzymes are typically specific because the conformation of amino acids in the active site stabilizes the specific binding of the substrate. The active site generally takes up a relatively small part of the entire enzyme and is usually filled with free water when it is not binding a substrate.[1][2]

Molecular Level

There are two different models of substrate binding to the active site of an enzyme. The first model called the lock and key model, proposes that the shape and chemistry of the substrate are complementary to the shape and chemistry of the active site on the enzyme. This means when the substrate enters the active site, it fits perfectly, and the two binds together, forming the enzyme-substrate complex. The other model is called the induced fit model, and it hypothesizes that the enzyme and the substrate don’t initially have the precise complementary shape/chemistry or alignment, but rather, this alignment becomes induced at the active site by substrate binding. Substrate binding to an enzyme is generally stabilized by local molecular interactions with the amino acid residues on the polypeptide chain. There are four common mechanisms by which most of these interactions are formed and alter the active site to create the enzyme-substrate complex: covalent catalysis, general acid-base catalysis, catalysis by approximation, and metal ion catalysis.

  1. Covalent catalysis occurs when one or multiple amino acids in the active site transiently form a covalent bond with the substrate. This reaction usually takes the form of an intermediate through a nucleophilic attack of the catalytic residues, which helps stabilize later transition states.

    (Video) Enzymes (Updated)

  2. General acid-base catalysis takes place when a molecule other than water acts as a proton donor or acceptor. Water can be one of the proton donors or acceptors in the reaction, but it cannot be the only one. This characteristic can sometimes help make catalytic residues better nucleophiles, so they will more easily attack substrate amino acids.

  3. Catalysis by approximation happens when two different substrates work together in the active site to form the enzyme-substrate complex. A common example of this involves water entering the active site to donate or receive a proton after a substrate has already bound to form better nucleophiles that can form and break bonds easier.

  4. Metal ion catalysis involves the participation of a metal ion at the active site of the enzyme, which can help make the attacking residue a better nucleophile and stabilize any negative charge in the active site.

Enzymes can be either be a single subunit or comprised of multiple subunits. The subunits in a multisubunit enzyme can sometimes work together in a mechanism called “cooperativity,” in which one subunit influences another for either positive, activity boosting effects or negative, inhibiting effects. Through cooperativity between subunits, an enzyme can either take on a T-state or an R-state. The T-state, or “tense” state, results in less affinity for binding substrate than regular state enzyme would. The R-state, or “relaxed” state, results in higher affinity and increased substrate binding for the enzyme as a whole. There are also two different models for the relationship between these two states of a multisubunit enzyme. The concerted model states that when an enzyme is in the T-state, if one subunit changes to the R-state, then all of the other subunits will change to the R-state at the same time, resulting in increased binding and affinity for other effectors. This model is also reversible, for if all subunits are in the R-state and an effector dissociates, then they will all go towards the T-state. On the other hand, the sequential model states that once one effector binds to one of the subunits, the rest of the subunit’s affinity for the effector increases, but they all do not necessarily change from one state to the other. They are merely more likely to change as well.[3][4][5][6]



The initial step occurs when an enzyme binds to a substrate to form an enzyme-substrate [ES] complex (reaction 1). Increasing the concentration of a substrate [S] will, in turn, increase the rate of reaction until it reaches maximum velocity.After forming the ES, a product forms that dissociates from the enzyme, and the enzyme is then ready to repeat the catalysis steps.

Enzymes do not alter or shift the equilibrium of a given reaction but instead affect the free energy required to initiate a conversion, which affects the reaction rate. The energy hump that must be surmounted for a reaction to progress is called the activation energy; this is the highest energy on a reaction diagram. It is the most unstable conformation of the substrate in the reaction. Enzymes generally do not add energy to the reaction but instead lower the transition state energy to require less activation energy.

(Video) Proteins and Enzymes

Inhibitors are regulators that bind to an enzyme and inhibit its functionality. There are three types of models in which an inhibitor can bind to an enzyme: competitive, non-competitive, and uncompetitive inhibition.

  1. Competitive inhibition occurs when the inhibitor binds to the active site of an enzyme where the substrate would usually bind, thereby preventing the substrate from binding. For enzymes obeying Michaelis-Menten kinetics, this results in the reaction having the same max velocity but less affinity for the binding substrate.

  2. Non-competitive inhibition occurs when the inhibitor binds to a site on the enzyme other than the active site but results in a decreased ability of the substrate to bind to the active site. The substrate is still able to bind in this model, but the active site functions less effectively. The max velocity under non-competitive inhibition decreases, but the affinity for substrate stays the same.

  3. Uncompetitive inhibition (also called anti-competitive inhibition) occurs when an inhibitor binds only to the enzyme-substrate (ES in reaction 1). This reaction usually occurs when there are two or more substrates or products in a reaction. In uncompetitive inhibition, the max velocity and binding affinity both decrease.

Another kind of inhibition occurs with allosteric enzymes. These can bind a molecule called an allosteric effector, which will affect either the Vmax of the catalytic reaction or the substrate binding affinity.[7][8][9]

Clinical Significance

Knowledge about enzymes is essential in medicine for diagnosing many diseases. In clinical studies, enzymes can act as markers that identify disease states within the body. Doctors can often determine what kind of disease is affecting a patient and which organ is damaged by characterizing the enzymes released into circulation. Enzymes can also be a component in a tissue biopsy and provide detailed diagnostic information.[10]

Review Questions

(Video) Chapter 3 - Amino Acids, Peptides, and Proteins



Robinson PK. Enzymes: principles and biotechnological applications. Essays Biochem. 2015;59:1-41. [PMC free article: PMC4692135] [PubMed: 26504249]


Cutlan R, De Rose S, Isupov MN, Littlechild JA, Harmer NJ. Using enzyme cascades in biocatalysis: Highlight on transaminases and carboxylic acid reductases. Biochim Biophys Acta Proteins Proteom. 2020 Feb;1868(2):140322. [PubMed: 31740415]

(Video) Proteins & Amino Acids | Biochemistry


Ohmatsu K, Ooi T. Cationic Organic Catalysts or Ligands in Concert with Metal Catalysts. Top Curr Chem (Cham). 2019 Oct 25;377(6):31. [PubMed: 31654245]


Weitzner BD, Kipnis Y, Daniel AG, Hilvert D, Baker D. A computational method for design of connected catalytic networks in proteins. Protein Sci. 2019 Dec;28(12):2036-2041. [PMC free article: PMC6863703] [PubMed: 31642127]


Wagner T, Boyko A, Alzari PM, Bunik VI, Bellinzoni M. Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts. J Struct Biol. 2019 Nov 01;208(2):182-190. [PubMed: 31476368]


Chang S, Mizuno M, Ishikawa H, Mizutani Y. Tertiary dynamics of human adult hemoglobin fixed in R and T quaternary structures. Phys Chem Chem Phys. 2018 Jan 31;20(5):3363-3372. [PubMed: 29260810]


Lorsch JR. Practical steady-state enzyme kinetics. Methods Enzymol. 2014;536:3-15. [PubMed: 24423262]


Vo NNQ, Nomura Y, Muranaka T, Fukushima EO. Structure-Activity Relationships of Pentacyclic Triterpenoids as Inhibitors of Cyclooxygenase and Lipoxygenase Enzymes. J Nat Prod. 2019 Dec 27;82(12):3311-3320. [PubMed: 31774676]


Onder S, Biberoglu K, Tacal O. The kinetics of inhibition of human acetylcholinesterase and butyrylcholinesterase by methylene violet 3RAX. Chem Biol Interact. 2019 Dec 01;314:108845. [PubMed: 31593690]


Hemalatha T, UmaMaheswari T, Krithiga G, Sankaranarayanan P, Puvanakrishnan R. Enzymes in clinical medicine: an overview. Indian J Exp Biol. 2013 Oct;51(10):777-88. [PubMed: 24266101]

(Video) Protein Structure and Folding


Are enzymes considered as proteins explain your answer? ›

Enzymes are proteins comprised of amino acids linked together in one or more polypeptide chains. This sequence of amino acids in a polypeptide chain is called the primary structure. This, in turn, determines the three-dimensional structure of the enzyme, including the shape of the active site.

What level of protein structure is needed for enzyme function? ›

Tertiary structure is the most important of the structural levels in determining, for example, the enzymatic activity of a protein.

Which sentence is correct why all enzymes are proteins or most enzymes are proteins? ›

Only few proteins have the capability to bind the substrate with the help of their active sites in such a manner that allows the reaction to take place in an efficient manner. Hence, all enzymes are proteins but all proteins are not enzymes.

Are enzymes not classified as proteins True or false? ›

Answer and Explanation: The given statement is true. All enzymes are proteins but all proteins are not enzymes. Enzymes are the proteins that act as biological catalysts or biocatalysts and are required for almost every reaction in the body.

Is it true that all enzymes are proteins? ›

With the exception of ribozymes, all enzymes are protein-based.

Are all enzymes made from protein? ›

Posted July 1, 2022. All enzymes are proteins. Enzymes are made up of long chains of proteins called amino acids. These chains are held together by peptide bonds to form a 3-dimensional type of structure.

Why are all proteins not enzymes? ›

Enzymes are proteins made up of amino acids that help reduce reactive activation energy. Only a few proteins, with the help of their active sites, have the ability to bind the substrate in a way that allows the reaction to take place efficiently.

How many enzymes break down proteins? ›

From the Stomach to the Small Intestine

The two major pancreatic enzymes that digest proteins are chymotrypsin and trypsin. The cells that line the small intestine release additional enzymes that finally break apart the smaller protein fragments into the individual amino acids.

How do proteins become enzymes? ›

Enzymes are made from amino acids, and they are proteins. When an enzyme is formed, it is made by stringing together between 100 and 1,000 amino acids in a very specific and unique order. The chain of amino acids then folds into a unique shape.

Why is enzyme the most important protein in the body? ›

Enzymes are proteins that help speed up chemical reactions in our bodies. Enzymes are essential for digestion, liver function and much more. Too much or too little of a certain enzyme can cause health problems.

Why are there three enzymes to digest proteins? ›

Why are there three enzymes to digest proteins? The digestive system produces three different proteases, pepsin, trypsin, and chymotrypsin, to function under different conditions and on different substrate proteins. Pepsin is produced in the stomach and helps break down proteins into amino acids at an acidic pH.

Do enzymes only break down proteins? ›

These digestive enzymes are categorized based on the reactions they help catalyze: Amylase breaks down starches and carbohydrates into sugars. Protease breaks down proteins into amino acids. Lipase breaks down lipids, which are fats and oils, into glycerol and fatty acids.

Which two enzymes are not proteins? ›

  • The enzyme which does not have any protein component is RNA based enzyme called Ribozymes.
  • Ribozymes are composed of RNA that has catalytic activity.
  • These act as a catalyst during protein synthesis.
  • RNase P is an example of ribozymes.

What is an example of all proteins are not enzymes? ›

Growth hormone, insulin, collagen, and keratin are four examples of proteins that are not enzymes. Pepsin, trypsin, amylase, and carbonic anhydrase are four enzymes that are proteins, but as others have already said, some RNA also has enzymatic properties.

What are some enzymes that are not proteins? ›

Enzymes that are not proteinaceous in nature are exemplified by ribozymes. A ribozyme is an enzyme made of RNA rather than a protein. An example of a ribozyme is in the ribosome, which is a complex of protein and catalytic RNA units.

Can we live without enzymes? ›

Enzymes are proteins

They act as catalysts, which means that they make biochemical reactions happen faster than they would otherwise. Without enzymes, those reactions simply would not occur or would run too slowly to sustain life. For example, without enzymes, digestion would be impossible.

Which is protein only part of enzyme? ›

So, the correct answer is 'Apoenzyme'

What happens if there are no enzymes to process protein? ›

With no enzymes to break down food, much of the protein, fat and carbohydrate in food is not absorbed for use in the body. This is called malabsorption.

What six enzymes digest proteins? ›

The six primary digestive enzymes are amylase, lactase, lipase, maltase, sucrase, and protease. Each enzyme has its unique function, yet all are essential for optimal digestion. They include: Amylase: Found in saliva, pancreatic, and stomach juices, it breaks down carbs and starches into simple sugars.

What are the 7 types of enzymes? ›

Enzymes can be classified into 7 categories according to the type of reaction they catalyse. These categories are oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, and translocases. Out of these, oxidoreductases, transferases and hydrolases are the most abundant forms of enzymes.

What helps absorb protein? ›

Complex Carbohydrates

By consuming carbohydrates with your protein, your body releases insulin. Elevated insulin levels help your muscles absorb amino acids, especially during muscle-building exercises. That means eating carbohydrates right before a high-intensity workout yields the best protein-absorbing results.

What activates protein enzymes? ›

The phosphorylation of a protein can make it active or inactive. Phosphorylation can either activate a protein (orange) or inactivate it (green). Kinase is an enzyme that phosphorylates proteins. Phosphatase is an enzyme that dephosphorylates proteins, effectively undoing the action of kinase.

What organs produce protein enzymes? ›

Your stomach, small intestine and pancreas all make digestive enzymes. The pancreas is really the enzyme “powerhouse” of digestion. It produces the most important digestive enzymes, which are those that break down carbohydrates, proteins and fats.

How do proteins affect enzymes? ›

A fundamental task of proteins is to act as enzymes—catalysts that increase the rate of virtually all the chemical reactions within cells. Although RNAs are capable of catalyzing some reactions, most biological reactions are catalyzed by proteins.

What are the 7 functions of proteins? ›

Proteins have multiple functions, including: acting as enzymes and hormones, maintaining proper fluid and acid-base balance, providing nutrient transport, making antibodies, enabling wound healing and tissue regeneration, and providing energy when carbohydrate and fat intake is inadequate.

Why are all enzymes made of proteins? ›

Only few proteins have the capability to bind the substrate with the help of their active sites in such a manner that allows the reaction to take place in an efficient manner. Hence, all enzymes are proteins but all proteins are not enzymes.

What is the key to a proteins function? ›

The Bottom Line

It helps repair and build your body's tissues, allows metabolic reactions to take place and coordinates bodily functions. In addition to providing your body with a structural framework, proteins also maintain proper pH and fluid balance.

Why are enzymes so important? ›

Enzymes help speed up chemical reactions in the human body. They are essential for respiration, digesting food, muscle and nerve function, among thousands of other roles. Each cell in the human body contains thousands of enzymes. Enzymes provide help with facilitating chemical reactions within each cell.

What enzyme breaks down fat? ›

Lipase is an enzyme the body uses to break down fats in food so they can be absorbed in the intestines.

What makes an enzyme different from other proteins? ›

Essentially, an enzyme is a specific type of protein that performs a very specific function. Enzymes function to regulate biochemical reactions in living things, in this sense, they operate solely as a functional protein, while a protein can be either functional or structural.

What is an enzyme but not a protein? ›

The enzyme which does not have any protein component is RNA based enzyme called Ribozymes. Ribozymes are composed of RNA that has catalytic activity. These act as a catalyst during protein synthesis. RNase P is an example of ribozymes.

How are enzymes classified? ›

According to the International Union of Biochemists (I U B), enzymes are divided into six functional classes and are classified based on the type of reaction in which they are used to catalyze. The six kinds of enzymes are hydrolases, oxidoreductases, lyases, transferases, ligases and isomerases.

What is the enzyme for protein? ›

Protease (made in the pancreas; breaks down proteins)

What is an example of an enzyme protein? ›

Trypsin: These enzymes break proteins down into amino acids in the small intestine. Lactase: Lactase breaks lactose, the sugar in milk, into glucose and galactose. Acetylcholinesterase: These enzymes break down the neurotransmitter acetylcholine in nerves and muscles.

What is an example of an enzyme not a protein? ›

Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes.

What are the 4 functions of enzymes? ›

What do enzymes do?
  • Breathing.
  • Building muscle.
  • Nerve function.
  • Ridding our bodies of toxins.
May 12, 2021

Where are enzymes created? ›

Digestive enzymes are mostly produced in the pancreas, and help your body break down foods and extract nutrients.

Where are protein enzymes found? ›

The pancreas secretes digestive juices into the small intestine, and these contain more enzymes to further break down polypeptides. The two major pancreatic enzymes that digest proteins in the small intestine are chymotrypsin and trypsin .

What breaks down proteins? ›

The two major pancreatic enzymes that digest proteins are chymotrypsin and trypsin. The cells that line the small intestine release additional enzymes that finally break apart the smaller protein fragments into the individual amino acids.

How do enzymes function? ›

Enzymes (and other catalysts) act by reducing the activation energy, thereby increasing the rate of reaction. The increased rate is the same in both the forward and reverse directions, since both must pass through the same transition state.

What do proteins do? ›

Proteins are the building blocks of life. Every cell in the human body contains protein. The basic structure of protein is a chain of amino acids. You need protein in your diet to help your body repair cells and make new ones.

How do you get enzymes? ›

Digestive enzymes can be obtained from supplements or naturally through foods. Foods that contain natural digestive enzymes include pineapples, papayas, mangoes, honey, bananas, avocados, kefir, sauerkraut, kimchi, miso, kiwifruit and ginger.


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