B1.2 Proteins IB DP SL Biology PDF

2.4 Proteins Essential idea: Proteins have a very wide range of functions in living organisms. One of the central ideas in Biology is that structure dictates function. Above you can see insulin in its secondary, tertiary and quaternary struct...

2.4 Proteins Essential idea: Proteins have a very wide range of functions in living organisms. One of the central ideas in Biology is that structure dictates function. Above you can see insulin in its secondary, tertiary and quaternary structures. Polypeptides vary hugely in the combination and number of amino acids that they are composed from. Even if we consider a single polypeptide it's properties, and hence it's function, would http://www.biotopics.co.uk/as/insulinproteinstructure.html vary greatly depending on it's level of structure. Insulin can exist in all these forms, By Chris Paine but the active form, which controls blood glucose levels, is a the tertiary structure. https://bioknowledgy.weebly.com/  B1.2. Proteins Theme B: Form and Function FirstLevel of organization: Molecules 2023-2024 IBDP SL Biology  Statement Guidance Understandings B1.2.1 Generalized structure of an amino acid. B1.2.2 Condensation reactions forming dipeptides and longer chains of amino acids. B1.2.3 Dietary requirements for amino acids. B1.2.4 Infinite variety of possible peptide chains. B1.2.5 Effect of pH and temperature on protein structure. B1.2.6 Chemical diversity in the R-groups of amino acids as a basis for the immense diversity in protein form and function. B1.2.7 Impact of primary structure on the conformation of proteins. B1.2.8 Pleating and coiling of secondary structure of proteins. B1.2.9 Dependence on tertiary structure on hydrogen bonds, ionic bonds, disulfide covalent bonds and hydrophobic interactions. B1.2.10 Effect of polar and non-polar amino acids on tertiary structure of proteins. B1.2.11 Quaternary structure of non-conjugated and conjugated proteins. B1.2.12 Relationship of form and function in globular and fibrous proteins. A little about proteins….. Key words: amino acids, polypeptide, protein Amino Acids Polypeptide Protein Activity: Using the beads provided, show me a few examples of amino acids One polypeptide chain One protein molecule made up of one polypeptide chain One protein molecule made up of two polypeptide chains A little about proteins….. Every protein contains one or more polypeptides. The 20 different amino acids that can be used to assemble polypeptides are chemically diverse (each one is different) This idea is very similar to the linking of letters of the alphabet to form words: any length and sequence is possible, but only a small proportion of the possibilities are used. A difference is that polypeptides are much longer than words—most have hundreds or even thousands of amino acids. How does the sequence of amino acids in polypeptides determine their three-dimensional shape? We shall see later! How is the shape of a protein related to its function? We shall see later! Activity: On your worksheet, please draw the generalized structure of an amino acid. B1.2.1. Generalized structure of an amino acid. Amino acids are the building blocks of proteins Each amino acid molecule has central carbon atom known as the alpha Carbon This alpha carbon connects with 4 other elements by single covalent bonds One atom is the Nitrogen from the amine group –NH2 One atom is the Carbon from the carboxyl group -COOH The third atom is a Hydrogen atom Finally, the alpha carbon is also covalently bonded to an R group or radical group (R) B1.2.1. Generalized structure of an amino acid. Important note: The carboxyl group is acidic because it can donate a proton The amine group is basic because it can accept a proton So the amino acid molecule is amphiprotic Meaning it is a molecule that can act as an acid or base B1.2.2. Condensation reactions forming dipeptides and longer chains of amino acids. To form a dipeptide, two amino acids are linked together by peptide bonds (another special kind of covalent bond) By a condensation reaction (loss of water) More amino acids can be linked by further condensation reactions to create a longer chain. Polypeptides can contain any number of amino acids, though chains of fewer than 20 amino acids are usually referred to as oligopeptides rather than polypeptides Polypeptides are the main component of proteins 2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules B1.2.2. Condensation fromforming reactions monomers by condensation dipeptides reactions. and longer chains of amino acids. Example of anabolism by condensation http://commons.wikimedia.org/wiki/File:Peptidformationball.svg B1.2.2. Condensation reactions forming dipeptides and longer chains of amino acids. The peptide bond forms b/w the amine group of one amino acid Peptide bond and the carboxyl group of the next amino acid After eliminating/losing/producing water (OH lost from carboxyl group and H from the amine group) The newly formed bond is called a peptide bond ( a special covalent bond) The new molecule consisting of 2 amino acids is called a dipeptide B1.2.2. Condensation reactions forming dipeptides and longer chains of amino acids. Q: Where does the formation of polypeptides occur within the cell? Peptide bond The reaction is catalysed in cells by ribosomes It is a directional process: the amine group of a free amino acid is linked to the carboxyl group at the end of the growing chain. The R group does not change anything about this process However, R-groups can be non-polar or polar, linear or in ringed form, providing each amino acid with distinct chemical and physical properties. Activity: Drawing dipeptides and oligopeptides Continue Activity on WorkSheet Let’s Recap: 1. Five Important Facts to Remember about this whole process: Two __________ _________form a dipeptide. The _____ _________of one amino acid reacts with the _________ ___________of another amino acid. A ___________ molecule is eliminated in a condens ation reaction. A __________ _______ is formed between N and C. This is a __________ bond. Let’s Recap: 1. Five Important Facts to Remember about this whole process: Two amino acids form a dipeptide. The carboxyl group of one amino acid reacts with the amine group of another amino acid. A water molecule is eliminated in a condensation reaction. A peptide bond is formed between N and C. This is a covalent bond. Know your vocabulary 1. The condensation reaction involves… a. The ______ group of one aa and the _____ group of the other aa 2. __________ is produced 3. The newly formed bond is called _______ 4. A ______ is a molecule made up of 2 aa linked together by a ______ 5. A ______ is a molecule consisting of ______ aa linked together by ____________ Know your vocabulary 1. The condensation reaction involves… a. The amine group of one aa and the carboxyl group of the other aa 2. Water is produced 3. The newly formed bond is called peptide bond 4. A dipeptide is a molecule made up of 2 aa linked together by a peptide bond 5. A polypeptide is a molecule consisting of many aa linked together by peptide bonds Computer Modelling Please go to chemagic.org Build the following molecules (call me over when you finish each one)—3 min for each diagram! Serine Glutamic Acid Alanine Glycine Recap Question 1: True or false? When three amino acids join together in succession, a total of one water molecule is released. False! Recap Question 1: True or false? When three amino acids join together in succession, a total of one water molecule is released. False! Explanation: When two amino acids join together through a condensation reaction, one water molecule is released. If a third amino acid joins the growing strand, another water molecule will be released as a new peptide bond is formed. Therefore, when three amino acids join together, two water molecules are released. Recap Question 2: Identify which of the following chemical groups binds directly to the central carbon of an amino acid. I –OH II –NH2 III –COOH IV –H A. II, III and IV only B. I, II and III only C. II and III only Recap Question 2: Identify which of the following chemical groups binds directly to the central carbon of an amino acid. I –OH II –NH2 III –COOH IV –H A. II, III and IV only B. I, II and III only C. II and III only Recap Question 3: A. --COOH B. --NH2 C. --COH D. --R group Recap Question 3: A. --COOH B. --NH2 C. --COH D. --R group B1.2.3. Dietary requirements for amino acids. The ______ different amino Peptide bond acids are used by __________ to make polypeptides Most plants can make all of these by ____________ Animals obtain amino acids from their _________. The amino acids are divided into two types: ________ and ________ B1.2.3. Dietary requirements for amino acids. The 20 different amino acids Peptide bond are used by ribosomes to make polypeptides Most plants can make all of these by photosynthesis Animals obtain amino acids from their food/diet The amino acids are divided into two types: essential and non-essential B1.2.3. Dietary requirements for amino acids. Nutrients are chemical substances, found in foods, that are used in the human body An essential amino acid is one that cannot be synthesized in sufficient quantities or at all by the animal Therefore, it’s essential, because it has to be included in the diet Essential amino acids are necessary for proper growth, maintenance and repair of the body’s tissues and organs Failure to include them in diet can lead to malnutrition and certain diseases Non-essential amino acids can be synthesized by the animal body by the metabolic pathway that transforms one amino acid into another or by the breakdown of proteins B1.2.3. Dietary requirements for amino acids. _______ of the 20 amino acids in proteins are essential in humans because _________________________________________ __ in the body Without them, the production of proteins at _______________ cannot continue Though several become essential in special circumstances B1.2.3. Dietary requirements for amino acids. 9 of the 20 amino acids in proteins are essential in humans because They cannot be synthesized in sufficient quantities in the body Without them, the production of proteins at ribosomes cannot continue Though several become essential in special circumstances What is happening in this diagram? Which is the essential amino acid/non-essential amino acid? Why? B1.2.3. Dietary requirements for amino acids. Example of essential/non-essential amino acid: Phenylalanine is essential because it cannot be synthesized by the human body Tyrosine is non-essential because it can be made from phenylalanine However, for people whose body cannot produce the enzyme phenylalanine hydroxylase, both amino acids become________ Essential! Do Now: Where do we get our essential amino acids from? What happens to these amino acids in our body? Protein Digestion/Hydrolysis Rxn Protein synthesis/Condensation Reaction B1.2.3. Dietary requirements for amino acids. Foods vary in their amino acid content It is possible to eat a protein-rich diet and still be deficient in an essential amino acid How is that possible? Animal-based foods (fish, meat, milk, eggs) have a balance of amino acids that is similar to what is needed in the human diet However, plant-based foods have a different balance and some are deficient in specific amino acids B1.2.3. Dietary requirements for amino acids. Example: Cereals such as wheat have a low lysine content Peas and beans are low in methionine Both lysine and methionine are essential amino acids for humans So, people eating a vegan diet, must ensure that enough of each essential amino acid is consumed Traditional plant-based diets in successful civilizations do provide such a balance At any time, when one or more of these essential amino acids is in short supply in the food eaten, the body cannot make sufficient amounts of the proteins it requires - a condition known as protein deficiency malnutrition. B1.2.3. Dietary requirements for amino acids. Vegan diets can provide all the essential amino acids necessary for a healthy diet through plant-based protein sources like: Beans Tofu Lentils Nuts Seeds However, adequate amounts of these protein sources must be consumed for optimal health. B1.2.4. Infinite variety of possible peptide chains. Ribosomes link amino acids together one at a time, until a polypeptide is fully formed The ribosome can make peptide bonds between any pair of amino acids, so all sequences are possible Ribosomes do not make random sequences of amino acids Q: So what determines the sequence of amino acids? Questions to Consider: 1. What determines the amino acid sequence of a polypeptide? They receive instructions in the form of genetic code (Genes). 20 different amino acids are included in the code 2. Where are the genes found? In your DNA (inside the nucleus of every cell in your body) 3. Where are polypeptides made? By what? In the cytoplasm by ribosomes B1.2.4. Infinite variety of possible peptide chains. If there are only 20 amino acids, how do organisms make thousands of different polypeptides? The sequence of amino acids is the key! The number of possible amino acid sequences can be calculated starting with dipeptides Remember this formula for calculating polypeptide diversity: 20n where n is equal to the number of amino acids in the dipeptide/peptide/polypeptide For a dipeptide, Both amino acids in a dipeptide can be any of the 20, so there are 20 × 20 possible sequences (400). B1.2.4. Infinite variety of possible peptide chains. Calculating polypeptide diversity: Number of amino Number of possible acids amino acid sequences 2 400 3 8, 000 4 206 64 million 2.4.U3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides. B1.2.4. Infinite variety of possible peptide chains. The number of amino acids in a polypeptide can be anything from 20 to tens of thousands. For example, if a polypeptide has 400 amino acids, there 20400 possible amino acid sequences. This is an incredibly large number, and some online calculators simply express it as infinity. Given that the number of amino acids in a polypeptide can be tens of thousands, the number of possible sequences is infinite But only an extremely small proportion are made by an organism. This is the organism’s proteome (all of the proteins produced by a cell, a tissue or an organism) More on a person’s proteome….. Whereas the genome of an individual is fixed, the proteome is variable b/c different cells in an organism make different proteins Sometimes the proteins made by a cell varies over time depending on the cell’s activities It reveals what is actually happening in an organism, not what potentially could happen Within a species, there are strong similarities in the proteome of all individuals, but also differences The proteome of each individual is unique b/c of differences in activity and small differences in aa sequences of proteins No two individuals have the same proteome – Proteome of identical twins can vary over time Seeing an individuals Proteome? How to find out how many different proteins are being produced? Proteins that are extracted from a tissue can be separated in a sheet of gel by electrophoresis and identified How to check for the production of a certain protein? To identify whether or not a particular protein is present, antibodies to the protein that have been fluorescently marked can be used If the cell fluoresces, the protein is present Examples of Polypeptides: 1. Beta-endorphin is natural pain killer secreted by the pituitary gland that is a polypeptide of 31 amino acids 2. Insulin is a small protein that contains two short polypeptides, one with 21 amino acids and the other with 30 (it is a hormone released by the pancreas to regulated blood glucose levels) 3. Alpha amylase is the enzyme in saliva that starts the digestion of starch. It is a single polypeptide of 496 amino acids, with one chloride ion and one calcium ion associated. 4. Titin is the largest polypeptide discovered so far. It is part of the structure of muscle. In humans, titin is a polypeptide of 34,350 amino acids, but in mice it is even longer with 35,213 amino acid More examples of Polypeptides: 5. collagen Structural protein (rope-like proteins ) Made of three polypeptides wound together About a quarter of all protein in the human body is collagen (most common) Forms a mesh of fibres in skin and in blood vessel walls that resists tearing. Gives strength to tendons, ligaments, skin and blood vessel walls. Forms part of teeth and bones, helps to prevent cracks and fractures to bones and teeth https://en.wikipedia.org/wiki/Tooth_(human)#mediaviewer/File:Teeth_by_David_Shankbone.jpg http://chempolymerproject.wikispaces.com/file/view/collagen_%28alpha_chain%29.jpg/34235269/collagen_%28alpha_chain%29.jpg Collagen in the skin…. B1.2.5. Effect of pH and temperature on protein structure. The conformation (arrangement/structure) of a protein is its three-dimensional structure The shape (conformation) is determined by the amino acid sequence of a protein The function of a protein is determined by the _______ of its molecule – Shape So the shape of the protein is very important to its function!! B1.2.5. Effect of pH and temperature on protein structure. The three-dimensional conformation of proteins is stabilized by bonds or interactions between the R-groups of amino acids within the molecule Most of these bonds and interactions are relatively weak and they can be disrupted or broken. This results in a change to the conformation of the protein and is called denaturation A denatured protein does not normally return to its former structure — the denaturation is permanent After the amino acids are bonded together…. B1.2.5. Effect of pH and temperature on protein structure. Q: what factors affect protein functions? Factors that can denature proteins Deviation of optimum Heat pH vibrations within the molecule breaks Breaks bonds intermolecular bonds or interactions B1.2.5. Effect of pH and temperature on protein structure. Soluble proteins often become insoluble and form a precipitate This is due to the hydrophobic R-groups in the centre of the molecule becoming exposed to water by the change in conformation Heat Impact: Heat denatures proteins because it causes vibrations within the molecule that break intermolecular bonds/interactions Proteins vary in their heat tolerance, though. Some organisms that live in volcanic springs or in hot water near geothermal vents have high heat tolerance, up to 80C or higher Example: DNA polymerase from Thermus aquaticus, a prokaryote that lives in the hot springs in Yellowstone National Park B1.2.5. Effect of pH and temperature on protein structure. pH Impact: Extremes of pH, both acidic and alkaline, can cause denaturation. This is because positive and negative charges on R-groups are changed, breaking ionic bonds within the protein or causing new ionic bonds to form. The three-dimensional structure of the protein is altered and proteins that have been dissolved in water often become insoluble There are exceptions: the contents of the stomach are normally acidic, with a pH as low as 1.5, but this is the optimum pH for the protein-digesting enzyme pepsin that works in the stomach Application Techniques: Using a colorimeter to measure turbidity: denaturation experiments Instruments used: Colorimeter or spectrophotometer Purpose: to measure the amount of light that passes through a sample. If a colorimeter is used, set at 500 nm Functions: 1. Transmittance to measure how much light has passed through the sample 2. Absorbance to measure how much light is being absorbed Application Techniques: Using a colorimeter to measure turbidity: denaturation experiments Possible steps of the experiment: Albumen is one of the main proteins in egg white A solution of egg albumen in a test tube can be heated in a water bath to find the temp at which it denatures The effects of pH can be investigated by adding acids and alkalis to the test tubes of egg albumen solution To quantify denaturation extent, a colorimeter can be used, as denatured albumen absorbs more light than dissolved albumen (the solution becomes more turbid) Q: What are the IV and DV? Which factors should be controlled? Quick Summary of B1.2 Proteins so far: In a nutshell: A polypeptide is an unbranched chain of amino acids (aa) Ribosomes link aa together one at a time, until a polypeptide is fully formed The ribosomes can make peptide bonds b/w any pair of aa, so any sequence of aa is possible The number of aa in a polypeptide is variable and can be over 10,000, most have b/w 50 and 2,000 amino acids Chains of fewer than 20 aa are usually called oligopeptides (rather than polypeptides or proteins) Amino acids can be linked together in any sequence, giving a huge range of possible polypeptides If we consider a polypeptide with 100 aa, the number of possible sequences is 20100 However, only a small proportion of the possible sequence of aa are ever made by living organisms Over 2 million have been discovered in all living organisms Review Questions 1. 2. What differentiates b/w amino acids? The R group! Review Questions 3. How peptide bonds form b/w a.a. Review Questions 4. How does the peptide bond form? By removing the OH of the carboxyl group and the H of the Amine group of 2 different amino acids 5. What is the name of the newly formed molecule? Dipeptide