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Proteins and Amino Acids: An Introduction (A-level Biology)

Proteins and amino   acids: an introduction.

Proteins are biological molecules that are made up of small monomers i.e. amino acids.

Table of Contents

Structure of Amino Acids

• Amino acids are the monomers of proteins .
• There are 20 amino acids and they all have very similar structures . On one end, they contain an amine group (-NH2). This is known as the N-terminus . On the opposite end they contain a carboxyl group (-COOH) which makes them an acid. This is known as the C-terminus .
• The amine group and carboxyl group are covalently bonded to a central carbon atom . The central carbon atom is bonded to one hydrogen (H) atom, and a variable “R” group.
• The variable “R” group is different for each amino acid . This variable group is what gives each amino acid its unique chemical and physical properties. This group is also commonly known as the side chain.
• Different amino acids can be grouped together based on their “R” groups .

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CIE 1 Cell structure

Roles of atp (a-level biology), atp as an energy source (a-level biology), the synthesis and hydrolysis of atp (a-level biology), the structure of atp (a-level biology), magnification and resolution (a-level biology), calculating cell size (a-level biology), studying cells: confocal microscopes (a-level biology), studying cells: electron microscopes (a-level biology), studying cells: light microscopes (a-level biology), life cycle and replication of viruses (a-level biology), cie 10 infectious disease, bacteria, antibiotics, and other medicines (a-level biology), pathogens and infectious diseases (a-level biology), cie 11 immunity, types of immunity and vaccinations (a-level biology), structure and function of antibodies (a-level biology), the adaptive immune response (a-level biology), introduction to the immune system (a-level biology), primary defences against pathogens (a-level biology), cie 12 energy and respiration, anaerobic respiration in mammals, plants and fungi (a-level biology), anaerobic respiration (a-level biology), oxidative phosphorylation and chemiosmosis (a-level biology), oxidative phosphorylation and the electron transport chain (a-level biology), the krebs cycle (a-level biology), the link reaction (a-level biology), the stages and products of glycolysis (a-level biology), glycolysis (a-level biology), the structure of mitochondria (a-level biology), the need for cellular respiration (a-level biology), cie 13 photosynthesis, limiting factors of photosynthesis (a-level biology), cyclic and non-cyclic phosphorylation (a-level biology), the 2 stages of photosynthesis (a-level biology), photosystems and photosynthetic pigments (a-level biology), site of photosynthesis, overview of photosynthesis (a-level biology), cie 14 homeostasis, ectotherms and endotherms (a-level biology), thermoregulation (a-level biology), plant responses to changes in the environment (a-level biology), cie 15 control and co-ordination, the nervous system (a-level biology), sources of atp during contraction (a-level biology), the ultrastructure of the sarcomere during contraction (a-level biology), the role of troponin and tropomyosin (a-level biology), the structure of myofibrils (a-level biology), slow and fast twitch muscles (a-level biology), the structure of mammalian muscles (a-level biology), how muscles allow movement (a-level biology), the neuromuscular junction (a-level biology), features of synapses (a-level biology), cie 16 inherited change, calculating genetic diversity (a-level biology), how meiosis produces variation (a-level biology), cell division by meiosis (a-level biology), importance of meiosis (a-level biology), cie 17 selection and evolution, types of selection (a-level biology), mechanism of natural selection (a-level biology), types of variation (a-level biology), cie 18 biodiversity, classification and conservation, biodiversity and gene technology (a-level biology), factors affecting biodiversity (a-level biology), biodiversity calculations (a-level biology), introducing biodiversity (a-level biology), the three domain system (a-level biology), phylogeny and classification (a-level biology), classifying organisms (a-level biology), cie 19 genetic technology, cie 2 biological molecules, properties of water (a-level biology), structure of water (a-level biology), test for lipids and proteins (a-level biology), tests for carbohydrates (a-level biology), protein structures: globular and fibrous proteins (a-level biology), protein structures: tertiary and quaternary structures (a-level biology), protein structures: primary and secondary structures (a-level biology), protein formation (a-level biology), phospholipid bilayer (a-level biology), cie 3 enzymes, enzymes: inhibitors (a-level biology), enzymes: rates of reaction (a-level biology), enzymes: intracellular and extracellular forms (a-level biology), enzymes: mechanism of action (a-level biology), enzymes: key concepts (a-level biology), enzymes: introduction (a-level biology), cie 4 cell membranes and transport, transport across membranes: active transport (a-level biology), investigating transport across membranes (a-level biology), transport across membranes: osmosis (a-level biology), transport across membranes: diffusion (a-level biology), signalling across cell membranes (a-level biology), function of cell membrane (a-level biology), factors affecting cell membrane structure (a-level biology), structure of cell membranes (a-level biology), cie 5 the mitotic cell cycle, chromosome mutations (a-level biology), cell division: checkpoints and mutations (a-level biology), cell division: phases of mitosis (a-level biology), cell division: the cell cycle (a-level biology), cell division: chromosomes (a-level biology), cie 6 nucleic acids and protein synthesis, transfer rna (a-level biology), transcription (a-level biology), messenger rna (a-level biology), introducing the genetic code (a-level biology), genes and protein synthesis (a-level biology), synthesising proteins from dna (a-level biology), structure of rna (a-level biology), dna replication (a-level biology), dna structure and the double helix (a-level biology), polynucleotides (a-level biology), cie 7 transport in plants, translocation and evidence of the mass flow hypothesis (a-level biology), the phloem (a-level biology), importance of and evidence for transpiration (a-level biology), introduction to transpiration (a-level biology), the pathway and movement of water into the roots and xylem (a-level biology), the xylem (a-level biology), cie 8 transport in mammals, controlling heart rate (a-level biology), structure of the heart (a-level biology), transport of carbon dioxide (a-level biology), transport of oxygen (a-level biology), exchange in capillaries (a-level biology), structure and function of blood vessels (a-level biology), cie 9 gas exchange and smoking, lung disease (a-level biology), pulmonary ventilation rate (a-level biology), ventilation (a-level biology), structure of the lungs (a-level biology), general features of exchange surfaces (a-level biology), understanding surface area to volume ratio (a-level biology), the need for exchange surfaces (a-level biology), edexcel a 1: lifestyle, health and risk, phospholipids – introduction (a-level biology), edexcel a 2: genes and health, features of the genetic code (a-level biology), gas exchange in plants (a-level biology), gas exchange in insects (a-level biology), edexcel a 3: voice of the genome, edexcel a 4: biodiversity and natural resources, edexcel a 5: on the wild side, reducing biomass loss (a-level biology), sources of biomass loss (a-level biology), transfer of biomass (a-level biology), measuring biomass (a-level biology), net primary production (a-level biology), gross primary production (a-level biology), trophic levels (a-level biology), edexcel a 6: immunity, infection & forensics, microbial techniques (a-level biology), the innate immune response (a-level biology), edexcel a 7: run for your life, edexcel a 8: grey matter, inhibitory synapses (a-level biology), synaptic transmission (a-level biology), the structure of the synapse (a-level biology), factors affecting the speed of transmission (a-level biology), myelination (a-level biology), the refractory period (a-level biology), all or nothing principle (a-level biology), edexcel b 1: biological molecules, inorganic ions (a-level biology), edexcel b 10: ecosystems, nitrogen cycle: nitrification and denitrification (a-level biology), the phosphorus cycle (a-level biology), nitrogen cycle: fixation and ammonification (a-level biology), introduction to nutrient cycles (a-level biology), edexcel b 2: cells, viruses, reproduction, edexcel b 3: classification & biodiversity, edexcel b 4: exchange and transport, edexcel b 5: energy for biological processes, edexcel b 6: microbiology and pathogens, edexcel b 7: modern genetics, edexcel b 8: origins of genetic variation, edexcel b 9: control systems, ocr 2.1.1 cell structure, structure of prokaryotic cells (a-level biology), eukaryotic cells: comparing plant and animal cells (a-level biology), eukaryotic cells: plant cell organelles (a-level biology), eukaryotic cells: the endoplasmic reticulum (a-level biology), eukaryotic cells: the golgi apparatus and lysosomes (a-level biology), ocr 2.1.2 biological molecules, introduction to eukaryotic cells and organelles (a-level biology), ocr 2.1.3 nucleotides and nucleic acids, ocr 2.1.4 enzymes, ocr 2.1.5 biological membranes, ocr 2.1.6 cell division, diversity & organisation, ocr 3.1.1 exchange surfaces, ocr 3.1.2 transport in animals, ocr 3.1.3 transport in plants, examples of xerophytes (a-level biology), introduction to xerophytes (a-level biology), ocr 4.1.1 communicable diseases, structure of viruses (a-level biology), ocr 4.2.1 biodiversity, ocr 4.2.2 classification and evolution, ocr 5.1.1 communication and homeostasis, the resting potential (a-level biology), ocr 5.1.2 excretion, ocr 5.1.3 neuronal communication, hyperpolarisation and transmission of the action potential (a-level biology), depolarisation and repolarisation in the action potential (a-level biology), ocr 5.1.4 hormonal communication, ocr 5.1.5 plant and animal responses, ocr 5.2.1 photosynthesis, ocr 5.2.2 respiration, ocr 6.1.1 cellular control, ocr 6.1.2 patterns of inheritance, ocr 6.1.3 manipulating genomes, ocr 6.2.1 cloning and biotechnology, ocr 6.3.1 ecosystems, ocr 6.3.2 populations and sustainability, related links.

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Functions of Proteins

All enzymes are proteins, functions of proteins: they act as receptors on cell membranes, some hormones are also proteins, proteins act as transport channels in cell membranes, proteins maintain the shape and structure of a cell, proteins are involved in cell division, proteins are required for transport within a cell, proteins are necessary for the transport of various substances in the blood, proteins are involved in muscle contraction, proteins prevent edema, proteins protect our body against diseases, proteins are needed for digestion, proteins also act as storage substances, proteins control the expression of genes, what are some examples of proteins, what are the functions of albumin, what are the functions of collagen, what are the functions of antibodies.

Proteins are the most abundant organic molecules present on earth. They are present abundantly in every living cell. Proteins are the polymers made up of thousands of amino acids linked via peptide bonds. Long chains of amino acids known as polypeptides fold around themselves in several ways to form complex structures called proteins. 

Functions performed by proteins can be divided into different categories. Some functions are essential at the cellular level while others are required for the better performance of the body as a whole. Here, we will try to understand different functions performed by proteins in our body through various examples. 

Enzymes are the proteins that are required for any chemical reaction to take place in our body. They catalyze the biochemical reaction so that life can proceed. 

An example of enzymatic reaction in our body is glycolysis. This is the process by which energy is released from a glucose molecule. This energy is required to carry out several processes taking place within a cell. The process of glycolysis involves around 10 steps each requiring a particular enzyme. The absence of a single enzyme stops the process and energy from glucose cannot be obtained. 

Synthesis of proteins also requires specific enzymes. Protein synthesis involves transcription of DNA into mRNA and then translation of mRNA by ribosomes. Both these steps require enzymes that are proteins. For example;

• RNA polymerase is an enzyme required to join RNA nucleotides in the process of transcription. 
• Aminoacyl tRNA synthetase is an enzyme that attaches specific amino acids to tRNA so that it can be used in protein synthesis. 

Thus, from obtaining energy to making proteins, all chemical processes in living organisms need enzymes, and all enzymes are proteins. The role of proteins as enzymes is the most important and crucial function performed by proteins. 

Proteins are essential components of all the cell membranes and membranes of the organelles. One of the functions of these membrane proteins is that they act as receptors. Hormones, neurotransmitters, and other signalling molecules bind to these receptors and convey signals to cells. In this way, proteins play a role in cell signalling that is essential for the coordinated function of all the cells present in our body.  Take the following example to understand the role of proteins as receptors. 

• Insulin is a hormone that controls the glucose levels in our blood. It performs its function by binding to its receptor that is a protein. Insulin binds to its receptor that sends signals for the opening of glucose channels so that glucose can be taken up from the blood into the liver and muscle cells. If the insulin receptors are not present, the blood glucose levels cannot be regulated. 

This and various other examples in our body prove why proteins are necessary for cell signalling and coordination of cellular functions. 

Read more about Tests for Proteins

Proteins not only act as cellular receptors but also hormones. Insulin and Glucagon are the two hormones that are protein in nature. Both these hormones are required for the regulation of blood glucose levels. They control the uptake and release of glucose by the cells, glycolysis and gluconeogenesis, as well as the synthesis and degradation of glycogen. The roles of these hormones in our body are listed below;

• Insulin is released by the pancreas when blood glucose levels are high. It promotes glucose uptake by the cells, its breakdown as well as its storage in the form of glycogen. It also inhibits the synthesis of new glucose molecules from non-carbohydrate sources (gluconeogenesis). 
• Glucagon is released by the pancreas when the blood glucose levels are low. It promotes the breakdown of glycogen to release glucose. It also promotes gluconeogenesis. 

Proteins present in cell membranes also act as transport channels. Substances that are not permeable through membranes due to their size or charge can enter the cell through these protein channels. One protein channel is specific for one or more substances. Examples of protein channels are given below;

• Aquaporins are the protein channels that allow the passage of water molecules through cells
• GLUT (glucose transporter) are the transporters for glucose molecules
• Sodium channels allow the passage of sodium ions within the cell
• Potassium channels allow only potassium ions to pass through them
• Calcium channels are specific for calcium ions only

These are the few examples of protein channels present in membranes.

This is another important cellular function performed by proteins. Cytoskeleton is made up of several interlinked protein filaments. The proteins in the cytoskeleton are organized in the form of microtubules, microfilaments, and intermediate filaments. All these components of the cytoskeleton are arranged in a particular fashion that maintains the shape of a cell. Important proteins that make cytoskeleton include actin and tubulin. In the absence of these proteins, it would not be possible for a cell to maintain its structure. 

Cell division is the process by which a mature adult parent cell divides into daughter cells. Proteins are required for this process also. 

During cell division, the chromosomes of a cell are divided into two halves by pulling apart. This separation of chromosomes is done by proteins known as spindle fibers. 

Proteins are also required for the division of cytoplasm that occurs after the chromosomes have been divided. 

Specific transport proteins are needed for intracellular transport of different substances. The different proteins that are involved in intracellular proteins are known as motor proteins. These proteins use energy in the form of ATP and travel along the microtubules to transport various substances within the cytoplasm of a cell. An example of motor proteins is kinesin protein. It is involved in the transport of various substances in axons of neurons. 

Proteins are needed for oxygen transport

This function of proteins is essential for the survival of the body as a whole. Two proteins are involved in this process, hemoglobin and myoglobin. 

It is a protein present in the red blood cells. Hemoglobin is made up of four polypeptide chains, two alpha chains and two beta chains,  that are coiled around each other. Each of these polypeptide chains carries one heme group (containing an iron atom). 

This protein is responsible for the transport of oxygen from the lungs to the tissue fluid. One molecule of oxygen can bind to four molecules of oxygen. It binds to oxygen molecules present in the air while passing through the lungs. These oxygen molecules are released when the blood passes through the tissues. 

Any deficiency or abnormality of hemoglobin impairs the oxygen transport by the blood. Our cells cannot survive in the absence of oxygen. Any interruption in oxygen supply will result in cell death in the affected tissues. 

Myoglobin is another protein involved in the transport of oxygen. It is made up of a single polypeptide chain having a heme group. It is a cytoplasmic protein having a higher affinity for oxygen molecules meaning that it can bind to oxygen even when the concentration of oxygen is high. Its function is to transport oxygen from tissue fluid to the cells.

Because of its high affinity for oxygen, myoglobin releases oxygen at very low concentrations. This feature of myoglobin is responsible for storing oxygen in tissues. 

Although blood acts as a transport medium, proteins are necessary to hold and transport some substances that cannot dissolve in blood. This function of proteins is also essential for the proper functioning of the body. Some examples of transport proteins present in blood are as follows.

• Albumin is the major transport protein in blood. It acts as a carrier for fatty acids, steroids, thyroid hormones, lipophilic drugs, heavy metals, calcium ions, and bilirubin
• Prealbumin is another transport protein in blood that carries steroid hormones, thyroxine, and vitamin A
• Haptoglobin is a transport protein that carries any free hemoglobin that is present in plasma
• Thyroxine binding protein is specific for thyroid hormone
• HDL is a lipoprotein that transports cholesterol from tissues to the liver
• LDL is another lipoprotein that transports cholesterol from the liver to the tissues

Muscle contraction is the process that enables us to perform our daily life tasks such as walking, running, sitting, standing, writing and even speaking. This process of muscle contraction is also because of proteins. Contractile proteins are present in muscle fibers. These proteins interact in a particular fashion that enables contraction and relaxation of muscles. The most important contractile present are;

Edema is a condition in which excess fluid leaks from the blood vessels and collects in the tissue spaces. The loss of fluid from blood results in decreased blood pressure. It is a potentially lethal condition that can compromise the effective delivery of blood to body tissues. 

Proteins present in blood known as plasma proteins prevent the leakage of fluid through capillaries due to their osmotic effects. The oncotic pressure due to plasma proteins keeps water inside the blood vessels preventing its leakage into the tissue fluids, thus preventing edema. If these proteins are absent, edema develops in different parts of the body. 

This function is performed by antibodies. Antibodies or immunoglobulins are the plasma proteins that are produced in response to various disease-causing agents entering our body. They fight against these pathogens and prevent our bodies from their harmful effects. If antibodies are already present in our body against a pathogen, they destroy the pathogen before it causes any disease. This process is known as immunity. 

The process of digestion involves breaking down the complex substances present in our diet into simpler ones so that they can be absorbed into the blood. The breakdown of various dietary substances into simpler molecules takes place in our digestive system by enzymes that are proteins in nature. 

Proteins are the polymers of amino acids. They act as storage substances that store thousands of amino acids. These amino acids are released from proteins when needed in the body. Examples of storage proteins are;

• Casein present in milk
• Albumin present in egg

These proteins provide the essential amino acids needed in the body to make several proteins. Moreover, in time of starvation, the proteins present in the body can also be used as an energy source to provide the calories needed for carrying out various body functions. 

Gene expression is a process by which the information in a particular gene is copied in the form of mRNA and later, this mRNA is used by ribosomes to make the protein coded by that gene. 

This process of gene expression is controlled by transcription factors. These transcription factors allow the transcription of genes of only those proteins that are currently required in the body. 

The transcription factors are also proteins in nature. Thus, proteins regulate their own synthesis by regulating gene expression. 

Proteins are the polymers made up of amino acids. They are involved in almost all the processes taking place in our body. A summary of the functions performed by proteins is as follows;

• As enzymes, proteins are required for all chemical processes in living organisms
• As hormones and cellular receptors, they are needed for cellular signalling and co-ordination
• As transport channels, protein are needed for the entry of ions and larger-sized particles into the cells
• Being components of cytoskeleton, they maintain the shape of cells
• Spindle fibers are protein fibers that are needed for cell division
• Hemoglobin and myoglobin are the proteins required for oxygen transport
• Albumin and other plasma proteins are needed for the transport of lipids, drugs and other substances in the blood
• Contractile proteins are needed for muscle contraction
• Antibodies are the proteins that protect our bodies from harmful disease
• Plasma proteins maintain fluid balance in our body 
• They regulate gene expression
• Proteins also provide energy to the body in times of starvation

Frequently Asked Questions

Some examples of proteins include albumin, globulins, collagen, elastin, haemoglobin, etc. 

Albumin is the most abundant plasma protein. Its main function is to provide oncotic pressure. It also acts as a carrier for the transportation of hydrophobic substances in the blood. It transports lipids, fatty acids, bilirubin, calcium, heavy metals, etc.

Collagen is a structural protein found in bones, cartilage, ligaments, etc. It provides strength and support to these structures. 

Antibodies or immunoglobulins are found in the plasma. They identify antigens and bind to them. They are an essential component of humoral immunity.

• Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J (2004). Molecular Cell Biology (5th ed.). New York, New York: WH Freeman and Company
• Zhang C, Kim SH (February 2003).  “Overview of structural genomics: from structure to function” . Current Opinion in Chemical Biology.  7  (1): 28–32.  doi : 10.1016/S1367-5931(02)00015-7 .  PMID   12547423
• Sleator RD (2012). “Prediction of protein functions”. Functional Genomics. Methods in Molecular Biology.  815 . pp. 15–24.  doi : 10.1007/978-1-61779-424-7_2 .  ISBN   978-1-61779-423-0 .  PMID   22130980

Syllabus Edition

First teaching 2020

Last exams 2024

The Four Levels of Protein Structure ( CIE A Level Biology )

Revision note.

Biology Lead

Proteins: Structures

• There are four levels of structure in proteins, three are related to a single polypeptide chain and the fourth level relates to a protein that has two or more polypeptide chains
• Polypeptide or protein molecules can have anywhere from 3 amino acids (Glutathione) to more than 34,000 amino acids (Titan) bonded together in chains
• The sequence of amino acids bonded by covalent peptide bonds is the primary structure of a protein
• DNA of a cell determines the primary structure of a protein by instructing the cell to add certain amino acids in specific quantities in a certain sequence. This affects the shape and therefore the function of the protein
• The primary structure is specific for each protein (one alteration in the sequence of amino acids can affect the function of the protein)

The primary structure of a protein. The three-letter abbreviations indicate the specific amino acid (there are 20 commonly found in cells of living organisms)

• The secondary structure of a protein occurs when the weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms to form hydrogen bonds
• β-pleated sheet
• The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond (between the oxygen of the carboxyl group and the hydrogen of the amine group)
• The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other enabling hydrogen bonds to form between parallel peptide bonds
• Most fibrous proteins have secondary structures (e.g. collagen and keratin)
• The secondary structure only relates to hydrogen bonds forming between the amino group and the carboxyl group (the ‘protein backbone’)
• The hydrogen bonds can be broken by high temperatures and pH changes

The secondary structure of a protein with the α-helix and β-pleated sheet shapes highlighted. The magnified regions illustrate how the hydrogen bonds form between the peptide bonds

• Further conformational change of the secondary structure leads to additional bonds forming between the R groups (side chains)
• Hydrogen (these are between R groups)
• Disulphide (only occurs between cysteine amino acids)
• Ionic (occurs between charged R groups)
• Weak hydrophobic interactions (between non-polar R groups)
• This structure is common in globular proteins

The tertiary structure of a protein with hydrogen bonds, ionic bonds, disulphide bonds and hydrophobic interactions formed between the R groups of the amino acids

• Occurs in proteins that have more than one polypeptide chain working together as a functional macromolecule, for example, haemoglobin
• Each polypeptide chain in the quaternary structure is referred to as a subunit of the protein

The quaternary structure of a protein. This is an example of haemoglobin which contains four subunits (polypeptide chains) working together to carry oxygen

Summary of bonds in proteins table

Familiarise yourself with the difference between the four structural levels found in proteins, noting which bonds are found at which level. Remember that the hydrogen bonds in tertiary structures are between the R groups whereas in secondary structures the hydrogen bonds form between the amino and carboxyl groups.

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Author: Lára

Lára graduated from Oxford University in Biological Sciences and has now been a science tutor working in the UK for several years. Lára has a particular interest in the area of infectious disease and epidemiology, and enjoys creating original educational materials that develop confidence and facilitate learning.