2A - Protein Structure 2025 PDF

2A - PROTEIN STRUCTURE  STUDY DESIGN POINT amino acids as the monomers of a polypeptide chain and the resultant hierarchical levels of structure that give rise to a functional protein proteins as a diverse group of molecules that collectively make an organism’s proteome, including...

2A - PROTEIN STRUCTURE  STUDY DESIGN POINT amino acids as the monomers of a polypeptide chain and the resultant hierarchical levels of structure that give rise to a functional protein proteins as a diverse group of molecules that collectively make an organism’s proteome, including enzymes as catalysts in biochemical pathways  BIOMACROMOLECULES – CLICK HERE OR PLAY THE VIDEO GIVEN BELOW Proteins make up all living materials EXAMPLES OF PROTEINS RECAP - PROTEIN SYNTHESIS PROTEOME In living organisms, proteins are involved in one way or another in virtually every chemical reaction. They may be the enzymes involved, they may be the reactants or the products, or they may be all three. The complete array of proteins produced by a single cell or organism in a particular environment is called the proteome of the cell or organism. The study of the proteome is called proteomics. CAN YOU EXPLAIN THE PROCESS OF PROTEIN SYNTHESIS, BRIEFLY? PROTEIN STRUCTURES PLAY THE VIDEO OR CLICK HERE STRUCTURE OF AMINO ACID (Imp) Amino group carboxyl group Formation of a polypeptide chain Proteins are assembled from amino acids that are joined by peptide bonds. Each peptide bond forms by the linkage of an amino group from one amino acid and a carboxyl group of another amino acid. A number of amino acids joined by peptide bonds form a polypeptide chain. This process requires an input of energy. LEVELS OF PROTEIN ORGANIZATION Protein structure https://youtu.be/wvTv8TqWC48 Primary-linear sequence of amino acids that makes a polypeptide chain Secondary- folding or coiling of polypeptide chain, hydrogen bonds are formed between the amine and carboxyl groups to form the secondary structure-alpha helix, beta pleated sheets or random coil. Tertiary- further folding of polypeptides to form more stable fibrous or globular 3D shapes. This is the shape that can denature and cause a permanent change to its shape. Quaternary-two or more polypeptide chains join together to form a single functional protein. DIFFERENCE BETWEEN A POLYPEPTIDE AND A PROTEIN A polypeptide is a string of covalently bonded amino acids which are not folded into any specific structure. whereas a protein is a string of covalently bonded amino acids that has folded into its correct shape. A protein is a polypeptide but there can be other polypeptides.  PRIMARY STRUCTURE The unique sequence of amino acids that makes up a protein or polypeptide chain. Proteins are made up of polypeptide chains, which are amino acids joined together with peptide bonds. The unique sequence of amino acids that make up a protein or polypeptide chain is called the Primary Structure. Peptide bonds are created by enzyme catalysed condensation reactions and broken down by enzyme catalysed hydrolysis reactions. Breaking down proteins is important in many areas of the body, not merely in digestion. For example, in hormone regulation, cells that are targeted by hormones contain enzymes to break down those hormones. This stops their effects from being  SECONDARY STRUCTURE Secondary structure refers to regular, local structure of the protein backbone, stabilised by intramolecular and sometimes intermolecular hydrogen bonding of amide groups.  SECONDARY STRUCTURE The next level of protein structure is the secondary structure, where three different folds can occur in amino acid chains, depending on the R groups in the different amino acids. Hydrogen bonds form between segments of the folded chain that have come close together and help stabilise the three- dimensional shape of the protein. The following are some examples of secondary structure. 1. Alpha helix: the major proteins of wool are keratins that have a spiral secondary structure, known as an alpha helix. If the fibre is stretched and the hydrogen bonds are broken, the fibre becomes extended. If the fibre is then ‘let go’, the hydrogen bonds reform and the fibre returns to its original length. The secondary structure of myoglobin, the oxygen-binding protein of muscle, consists mainly (75%) of a coiled alpha helix structure. 2. Beta-pleated sheet: the major protein of silk is fibroin, which is fully extended and lacks the coiling found in the structure of wool. The silk molecules form a beta-pleated sheet. The polypeptide chains of silk are already extended and cannot be extended further. 3.Random coiling: the secondary structure of portions of a protein is called random coiling if the portions do not conform to the shape of an alpha helix or a beta-pleated sheet. SECONDARY STRUCTURE  TERTIARY STRUCTURE The final 3D structure of a protein is its Tertiary Structure, which pertains to the shaping of the secondary structure. This may involve coiling or pleating, often with straight chains of amino acids in between. Tertiary structure can be broken by the action of heat. Increasing the kinetic energy of protein with a tertiary structure makes it vibrate more, and so the bonds that maintain its shape (which are mainly weak, non-covalent bonds) will be more likely to break. When a protein loses its shape in this way it is said to be Denatured. Even when it’s  QUATERNARY STRUCTURE The structure formed when two or more polypeptide chains join together, sometimes with an inorganic component, to form a protein. Some proteins are made up of multiple polypeptide chains, sometimes with an inorganic component (for example, a haem group in haemoglogin) called a Prosthetic Group. These proteins will only be able to function if all subunits are present. EXAMPLE: Haemoglobin Haemoglobin is a water-soluble globular protein which is composed of two α polypeptide chains, two β polypeptide chains and an inorganic prosthetic haem group. Its function is to carry oxygen around in the blood, and it is facilitated in doing so by the presence of the haem group which contains a Fe2+ ion, onto which the oxygen molecules can bind. PROSTHETIC GROUPS Prosthetic groups are typically other molecules (like metal ions or organic compounds) that bind to proteins and enhance their function. Some proteins are made up of multiple polypeptide chains, sometimes with an inorganic component (for example, a haem group in haemoglogin) called a Prosthetic Group. For example: Heme, the prosthetic group in hemoglobin, helps in oxygen transport. Biotin, a prosthetic group in enzymes, helps with carboxylation reactions. Click here for some notes and explanations Hemoglobin CLICK HERE OR PLAY THE VIDEO Watch this video and write key points to share with the class. PROTEIN STRUCTURE - Play the video or click here  REAL WORLD APPLICATION Here are some examples of how you could connect protein synthesis to its applications in the real world: Role of protein synthesis in the development of protein-based vaccines against COVID-19 and hepatitis B. Protein synthesis using recombinant DNA technology helps in the treatment of diseases like diabetes and cancer. LETS’S PRACTICE!!! Label the basic structure of an amino acid: Fill the blanks using words given below:  SOME EXAMPLES: MEMBRANE PROTEINS RECEPTOR PROTEINS Receive signal molecules (ligands) from other cells These proteins are usually just called receptors For example, some receptors receive signals from other cells in the form of hormones, which triggers the cell to do something Each receptor is specific for the signal molecule it receives  RECOGNITION PROTEINS Called MHC proteins Act as markers to identify the cell as belonging to the individual This prevent the body’s immune system from attacking the cell More on that in AOS 2…  ADHESION PROTEINS In multicellular organisms, adhesion proteins link cells together  CHANNEL PROTEINS Allow for transport across the cell membrane Form narrow passageways within the cell membrane through which molecules can move Cross the plasma membrane They do not change shape while moving the substances CARRIER PROTEINS Also allow for transport across the cell membrane Bind to a specific molecule on one side of the plasma membrane After binding, the protein changes its shape and releases the molecule on the other side MOTOR PROTEINS CLICK HERE TO PLAY THE VIDEO  THINK AND ANSWER!! DISCUSS IN YOUR TABLE GROUP: Why does raw egg white dissolve in water but the cooked egg white doesn’t? In your own words, describe how the chemical properties of amino acids affect the tertiary structure of a protein.  THINK AND ANSWER!! Why does raw egg white dissolve in water but the cooked egg white doesn’t? Raw egg white (albumen) is composed mainly of proteins, and one of these proteins is called ovalbumin. When the egg white is raw, ovalbumin is in its native, folded state. This folded structure is held together by weak interactions, such as hydrogen bonds. When you cook the egg white, the heat denatures the proteins. Denaturation involves the unfolding or alteration of the protein's native structure. In the case of egg white, the heat disrupts the weak interactions that held the protein in its folded form, causing it to unfold and form new, more stable structures. The denatured proteins in the cooked egg white are no longer soluble in water to the same extent as the native proteins in raw egg white. In your own words, describe how the chemical properties of amino acids affect the tertiary structure of a protein. The chemical properties of amino acids, specifically their side chains, play a crucial role in determining the tertiary structure of a protein. Interactions such as hydrogen bonding, disulphide bridges, hydrophobic interactions, and electrostatic attractions between these side chains contribute to the folding and three- dimensional arrangement of the protein. These interactions stabilize the protein's tertiary structure, influencing its overall shape and function. LET’S PRACTICE EXAM QUESTIONS!! LET’S PRACTICE EXAM QUESTIONS!! LET’S PRACTICE EXAM QUESTIONS!! LET’S PRACTICE EXAM QUESTIONS!!  Homework – 2A: Edrolo back exercise questions: Q10 to 19 (Hand-written in notebook)