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What are proteins made of?
Amino acid chains, protein structures, primary structure, secondary structure, tertiary structure, what are proteins, how amino acids are linked together to make proteins, what is the tertiary structure of proteins, what are some examples of globular proteins, further reading and references:.
- Proteins carry out the majority of the functions of the cell
- Proteins have hugely diverse components, sizes, structures, and functions
- Proteins are made up of chains of amino acids, which progressively fold to form the final structure of the protein
- Primary, secondary, tertiary and quaternary structures classify the distinct layers of polypepide folding structures, from the polypeptide sequence to the final 3D structure
Proteins are the building blocks of cells. They perform a variety of functions, and are the key executers of the instructions held within the DNA. Enzymes are examples of proteins, and are crucial in catalysing reactions within the cell and allowing cells to carry out their jobs. Proteins also regulate the transport of molecules within and outwith the cell, sense cellular environments and signal responses at the cell and organism level, and perform structural /scaffolding roles. The specialisation of proteins and diversification of their function relies on the unique and abundant structures that proteins can adopt.
All proteins in the cell are synthesised by the process of translation . The information coded within DNA is transmitted into a message RNA, which is translated into a sequence of amino acids , through the actions of tRNAs, a process covered in the topic of DNA and protein synthesis.
Amino acids have a basic amino group (NH2) and a carboxylic acid group (COOH) . Amino acids also possess a side chain called the ‘R’ group , which gives each amino acid its specificity. The R group is a different molecule in each amino acids, giving them their unique properties. This side chain can give the amino acid different 3D structures, charges or polarity.
The translated sequence of these amino acids creates a unique protein with specific structural and functional properties. The amino acids and their properties are summarised in the table shown.
Amino acids are linked together to form a chain – the carboxy group of one amino acid is joined to the amino group of another, forming a peptide bond , (also called an amine bond ). These are examples of covalent chemical bonds, and are stable . When two amino acids are joined, the reaction releases a molecule of water . This is type of reaction is called a condensation reaction. Hydrolysis is the reverse of the condensation reaction, involving breaking the peptide bond using a molecule of water.
The way scientists classify structures of proteins increases in complexity in a hierarchical manner, from the underlying chain of amino acids (the primary structure), right up to the overall 3D structure of the protein and the incorporation of other polypeptides and accessory molecules.
The most basic level of structure of a protein is the sequence of the polypeptide chain. This chain will be made up of a particular order of amino acids with their unique properties, forming the initial polypeptide chain. This chain is the first layer of structure, and is dictated by the information contained within the DNA.
The next layer of structural organisation is the local folding shapes that the polypeptide chain adopts. The two most common structures are the α-helix and the β-pleated sheet . Certain amino acid sequences tend to form particular secondary structures due to the properties of the peptide backbone. These structures are held together by hydrogen bonds .
The protein tertiary structure refers to the overall 3D structure of the polypeptide chain. This level of structure is principally due to the properties and interactions between the side chains of the amino acids, and depends on the nature of the chemical groups present on each amino acid. The properties of these side chains can attract or repel interactions with other side chains.
These interactions occur primarily through non-covalent bonds such as hydrogen and ionic bonds. Disulphide bonds are a unique example of a covalent bond that can form part of a tertiary structure, acting as strong bridges that form when two amino acids contain sulphur groups in their side chains. These stable bonds hold the tertiary structure in place.
Quaternary structure
Some proteins are made up of several polypeptide chains that form one structure. The final layer of structure is the way these polypeptides are arranged together, the quaternary structure. The quaternary structure is held together by interactions similar to those at the tertiary level.
Proteins can also have additional non-protein components that are incorporated into their structure and to help in the execution of their functions. These components are called prosthetic groups , and examples include vitamins, sugars and metal ions. A good example of a protein requiring a prosthetic group is the iron component of haemoglobin , which is essential for oxygen transport in the bloodstream
Frequently Asked Questions
Proteins are the polymers of amino acids. Hundreds or thousands of amino acids join together to make protein molecules.
Amino acids are joined together via peptide linkages to form long chains of amino acids. A peptide bond is formed between the amino group of one amino acid and the carboxylic group of another amino acid.
It refers to the overall three-dimensional structure of a protein molecule. The folding of the polypeptide chains to attain the final shape of the protein molecule is studied at this level of protein structure.
Some examples of globular proteins include enzymes, haemoglobin, albumin, ceruloplasmin, etc.
[1]. http://www.genome.gov/Pages/Hyperion//DIR/VIP/Glossary/Illustration/amino_acid.shtml Image primary protein structure
[2]. http://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/24-proteins/amino-acids.html Image amino acid tables
[3]. https://simple.wikipedia.org/wiki/Protein_structure#/media/File:Main_protein_structure_levels_en.svg Image protein structure
[4]. https://www.ncbi.nlm.nih.gov/books/NBK22364/
[5]. https://www.nature.com/scitable/topicpage/protein-structure-14122136
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AQA A Level Biology Essay
Subject: Biology
Age range: 16+
Resource type: Other
Last updated
11 June 2021
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This is an essay for AQA A Level Biology. The question was on ‘the importance of proteins in biology’ and was given 20 out of 25.
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The Role of Protein in Biology.
Balwant Flora 12SU 24/10/03
The Role of Protein in Biology
Proteins are an important molecule that plays a vital role in living organisms. More than 50% of dry mass of most cells is protein. Proteins have many different functions and some of them are:
- They are essential components of cell membranes.
- The oxygen carrying pigment (haemoglobin) is a protein.
- Antibodies are proteins.
- Most, if not all, enzymes are proteins.
- Collagen which adds strength to many parts of the body is a structural protein.
Despite having an enormous range of functions, proteins are made up from the same basic components. These are Amino acids.
Proteins are involved in a wide range of jobs in biology, some of which have been mentioned in the above list. Using amino acids bonds can be made such as a peptide bond. Also structures can be made by different types of bonds to make primary/secondary/tertiary/quaternary structures. Each of which have their own shape but they can be made up in so many different ways by changing the amino acids or replacing one amino acid with another and so on.
Collagen is probably the most important building block of the animal world as more than a third of the body's protein is collagen; it makes up 75% of our skin. Collagen acts as a sort of scaffolding for our bodies as it is a structural protein. Collagen controls cell shape and differentiation and is the reason why bones regenerate and wounds heal.
Collagen is a fibrous protein that is found in skin, tendons, cartilage, bones and the walls of blood vessels. It is an important structural protein for not only just us humans but almost all animals. Like all proteins collagen is made up of the basic components of amino acids.
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(b)
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In the above diagram there is a visual representation of a collagen molecule. The molecule consists of three polypeptide chains (it is not an Alpha-helix as it isn’t as tightly wound). The three helical polypeptides wind round each other to make a three stranded ‘rope’ shape. Inside each polypeptide chain there are amino acids and almost every third amino acid is glycine. This allows the three strands to lie close together because of its small size. The three strands that wind up are held together by hydrogen bonds. Each complete collagen molecule (three stranded) interacts with other collagen molecules which run parallel to it. Bonds form between the R groups of lysine in molecules lying next to each other. These cross-links made hold many collagen molecules together which are side by side, this forms fibres. The ends of these parallel molecules are staggered; if they weren’t there would be a weak spot running right across the collagen fibre. Collagen has tremendous tensile strength; it needs to be like this as it needs to withstand large pulling forces.
Protein has a countless amount of jobs and another one is transport . The most obvious transport protein in the human body is haemoglobin. Haemoglobin, the oxygen carrying pigment which is found in red blood cells, is a globular protein. It is made up of four polypeptide chains. Two of the four chains make an identical pair and they’re called ‘Alpha chains’. The other two make another identical pair but are different from the first two pair and are called ‘Beta chains’. The haemoglobin molecule is a near spherical shape.
The haemoglobin molecule contains
two α -globin chains (pattern A) and
two ß-globin chains (pattern B).
Two of the four haem molecules
are visible (pattern C).
The four polypeptide chains are packed closely together with their hydrophobic R groups pointing the centre and their hydrophilic ones pointing away from the centre. Each of the two Beta chains has a tertiary structure. The interactions between the hydrophobic R groups in the molecule are important in maintaining its correct 3-dimensional shape. The outward hydrophilic R groups play a part in keeping the solubility of the haemoglobin. It is important in having a polar amino acid on the outside of the molecule in the R group such as glutamine, by having a non-polar amino acid you make the haemoglobin less soluble and this causes unpleasant and hazardous symptoms in anyone whose haemoglobin is full of this ‘faulty’ type.
Each polypeptide chain contains a haem group which is an important and permanent part of protein molecules but it isn’t made up of amino acids. This is called a prosthetic group. Each of these heam groups contains an ion iron, Fe ². One oxygen molecule can bind with each iron ion. Because of this a complete haemoglobin molecule can carry four oxygen molecules on the four heam groups. It is the heam group which is responsible for the colour of haemoglobin. The colour changes depending on whether or not the ion irons are combined with the oxygen molecule.
Most Enzymes are proteins and can be described as catalysts. Most if not every metabolic reaction which takes place within a living organism is catalysed by enzymes.
Enzymes are globular proteins. Like all globular proteins, enzyme molecules are coiled into a specific three-dimensional shape with side chain hydrophilic R groups on the outside of the molecule. This ensures that the enzyme is soluble. Enzymes have a special feature and this is that they posses an active site. This is a region on the enzyme to which another molecule or molecules can bind onto it. This is the substrate of the enzyme. The shape of the specific shape allows the substrate to fit in just right. Also it is held by temporary bonds. This is called the enzyme-substrate complex as a simplified diagram below shows.
Each type of enzyme acts on a specific type of enzyme that the enzyme is fit to do as the shape of its active site has a specific shape that only allows that one type of substrate to fit in. The enzyme may catalyse a reaction causing the substrate molecule to split (2 or more) as shown in the diagram. Alternatively catalysing may cause a joining of two molecules. After this process the molecules leave the unchanged enzyme leaving it for another substrate molecule to go and bond onto it.
Hormones such as insulin are proteins. It is a small protein which brings blood sugar levels down from high levels. Disulphide bonds are found in hormones such as insulin. The hormone insulin in made by the pancreas and is released to bring sugar levels down. It turns glucose into glycogen which is a storage sugar in animals. Diabetic people use insulin injections to keep their sugar levels low.
Protection against viruses is important and antibodies help in getting rid of viruses. Antibodies are also proteins. Antibodies come from white blood cells and are in the blood stream. Any foreign molecule that is detected is an antigen and what antibodies do is detect these foreign molecules and isolates them. By engulfing them and dissolving the dangerous molecule. The virus or dangerous molecules are memorized by the antibodies so if the same virus or dangerous molecules appear, they can be gotten rid of quickly and efficiently.
Proteins are used in so many ways for many different things and there are so many ways of creating a chain of amino acids in numerous orders. This enables protein to do much more than just one thing and can take different 3-dimensional shapes to do the job that it needs to do whether it be a transport protein or an enzyme.
Bibliography: These are the sources that I used to do my essay:-
Cambridge: Advanced Sciences Biology 1 (OCR) Book
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- Word Count 1309
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