Protein Notes 2024 - PDF

BIOCHEMISTRY: INTRODUCTION TO PROTEINS Video: What is a Protein – PDB101 THINK, PAIR, SHARE: What is a Protein? What I Learned from the Video: What is a Protein What are Amino Acids Levels of Protein Structure Ways to Represent Pr...

BIOCHEMISTRY: INTRODUCTION TO PROTEINS Video: What is a Protein – PDB101 THINK, PAIR, SHARE: What is a Protein? What I Learned from the Video: What is a Protein What are Amino Acids Levels of Protein Structure Ways to Represent Proteins How Protein Shape Relates to Function Examples of Proteins in the Video MAWANI Biology 12: Biochemistry - Proteins – Notes WHAT ARE PROTEINS? 1. Proteins are the most abundant molecules in living cells, constituting 40% - 70% of their dry weight. 2. They are large, complex organic molecules that perform the following functions in our bodies, and in nature: Catalyze Reactions (_________________) Chemical signals (____________________, and cytokines). Cells communicate with each other via direct contact (juxtacrine signaling), over short distances (paracrine signaling), or over large distances (endocrine signaling). Storage (e.g., myoglobin stores oxygen in muscle) Structural (e.g., elastin and collagen in skin, tendons, and bone, cytoskeleton of cells, hair, nails, cartilage) Protective (antibodies, skin) Movement (e.g., actin and myosin in muscle) Transport (e.g., hemoglobin for oxygen, and proteins which let substances in and out of cells.) Cell to cell communication (e.g., glycoproteins) FUNCTION FORM EXAMPLE USE Collagen Cartilage & skin Structural Fibres Keratin hair & nails Fibrin blood clotting Metabolism Enzymes protease break down proteins Sodium- Excitable membranes potassium Membrane Pump Channels transport Aquaporins Water transport through cell membranes MHC proteins; “self” recognition; Cell surface Cell recognition antigens ABO blood group Identifies red blood cells Osmotic Albumin Serum albumin Maintains osmotic concentration of blood concentration MAWANI Biology 12: Biochemistry - Proteins – Notes  FUNCTION FORM EXAMPLE USE Regulation of Repressors Lac repressors Regulates transcription of a gene into RNA genes Insulin Controls blood glucose levels Regulation of body Hormones Vasopressin; Increases water retention by kidneys function Oxytocin Regulates milk production Hemoglobin Carries O2 and CO2 in blood Transport Globins Myoglobin Carries O2 and CO2 in muscle throughout body Cytochromes Electron transport Actin Contraction of muscle fibres Contraction Muscle Myosin Immunoglobins Antibodies Mark foreign proteins for elimination Defense Toxins Snake venom Blocks nerve function Molecular motor proteins are proteins that power much of the movement performed by living organisms within Kinesin Movement within the cell itself. Motor proteins Dynein the cell Myosin https://www.youtube.com/watch?v=9RUHJhskW00 HOMEWORK Name a protein which: a. Breaks down starch b. Breaks down lipids c. Breaks down proteins Name three proteins which function as hormones Which interleukin stimulates B-cells Name the storage protein for iron in our body Protein which protects cells from stress like heat, cold, U.V. MAWANI Biology 12: Biochemistry - Proteins – Notes  What molecule provides the energy for actin and myosin? Which protein is used to transport in the blood? 1. Lipids 2. Testosterone 3. Thyroxin At what stage in your life was the Notch trans-membrane receptor protein important? https://embryo.asu.edu/pages/notch-signaling-pathway- embryogenesis What are proteins which neurons use to communicate with each other called? Is Spider Silk the Next Bulletproof Material Close-up Spider Spinning Web Videos: Rare Spider Silk on Exhibit at AMNH Spider Silk violin strings WHAT ARE PROTEINS MADE OF? 1. All proteins are composed of amino acid monomers joined together in a chain by peptide bonds (like a train is made up of individual railway cars). What is the name of the chemical process which cells use to join monomers together called? ____________________________________________ 2. Amino acids are organic compounds that contain a __________________ group (which contains nitrogen), and a ______________________ group (Which acts like an acid) 4. The R-group can be a hydrogen atom, hydrocarbon, or various other groups of bonded atoms. Amino acids are named based on their R-groups. 5. It is the different R-groups which give the amino acids their identities and different biological properties  Note the "amino" group on left, and the "acid" group on the right (COOH = organic acid) of the central carbon.  All amino acids have this formula.  Difference is in "R" (= Remainder) group -- different for each amino acid. MAWANI Biology 12: Biochemistry - Proteins – Notes  There are 20 STANDARD AMINO ACIDS that make up all of the proteins in plants and animals. These twenty amino acids are called the Standard Amino Acids. MAWANI Biology 12: Biochemistry - Proteins – Notes 6. There are 20 standard amino acids that make up all of the proteins in plants and animals. These twenty amino acids are called the standard amino acids. Nine of these amino acids are called Essential Amino Acids. An essential amino acid for an organism is an amino acid that cannot be synthesized by the organism from other available resources, and therefore must be supplied as part of its diet. Essential amino acids may also differ between species. Most plants and microorganisms are able to use inorganic compounds to make all the amino acids necessary for the normal growth. Why do you think they evolved to make all 20 standard amino acids, whereas most animals did not? The nine amino acids regarded as essential for humans are: PVT TIM HALL: Phenylalanine, Valine, Tryptophan Threonine, Isoleucine, Methionine Histidine, Lysine, Leucine Limiting Amino Acid Content: The essential amino acid found in the smallest quantity in the foodstuff. Protein source Limiting amino acid Wheat lysine Rice lysine and threonine Maize lysine and tryptophan Pulses methionine Beef methionine and cysteine Whey none Milk none HOMEWORK What are some foods that are good sources of the essential amino acids? MAWANI Biology 12: Biochemistry - Proteins – Notes 7. Scientists have recently discovered two new amino acids in nature, and are also beginning to experiment with adding R-groups not found in nature: Expanding the Genetic Code: Discovery of Two New Amino Acids: http://www.yalescientific.org/2009/10/expanding-the-genetic- code-discovery-of-two-new-amino-acids/ Engineered genetic machinery derived from E. coli delivers new amino acids to proteins: https://phys.org/news/2018- 08-genetic-machinery-derived-coli-amino.html Recoded organisms engineered to depend on synthetic amino acids: https://www.nature.com/articles/nature14095 8. In addition to being the building blocks to make proteins, amino acids can also have other biological functions: In the human brain, glutamate (glutamic acid) is the main excitatory neurotransmitters. Hydroxyproline, a major component of collagen, is synthesized from proline. Glycine is a biosynthetic precursor to porphyrins used in red blood cells. Carnitine is used in lipid transport. Ornithine, citrulline, argininosuccinate are amino acids that are found in the urea cycle. Aspartame is one of the most common artificial sweeteners in use today. It is sold under the brand names NutraSweet® and Equal®. Aspartame is made by joining together the amino acids aspartic acid and phenylalanine. Amino acids are the building blocks of proteins and are found naturally in many foods. 5-HTP (5-hydroxytryptophan) has been used to treat neurological problems associated with PKU (phenylketonuria), as well as depression. L-DOPA (L-dihydroxyphenylalanine) is a drug used to treat Parkinsonism. Monosodium glutamate is a food additive to enhance flavor. MAWANI Biology 12: Biochemistry - Proteins – Notes HOW ARE PEPTIDES AND PROTEINS ASSEMBLED FROM AMINO ACIDS? Peptides are short amino acid chains (less than fifty amino acids) that are also biologically important. They are generally not classified as proteins, and are referred to by the size of their chain: Dipeptide: 2 aa’s joined together Tripeptide: 3 aa’s joined together Oligopeptide: 5-50 aa’s joined together Polypeptide: >50 amino acids joined together. Protein: a folded and complete polypeptide chain or chains MAWANI Biology 12: Biochemistry - Proteins – Notes Proteins, which are large folded chains of amino acids called polypeptides, are assembled by ribosomes and in the cytoplasm in the following steps: I. Ribosomes join different amino acids in the correct order to form a polypeptide chain. II. The polypeptide chain is folded in the cytoplasm into either an α-helix, or a β-pleated sheet. III. This α-helix or β-pleated sheet is folded into its correct 3-D shape by hydrogen bonds. IV. Multiple folded polypeptides are assembled together (if necessary) to form the final quaternary protein 1. Forming the Polypeptide Chain: Peptides and proteins consist of amino acids joined by ____________________ bonds. Peptide bonds are polar bonds, which leads to H-Bonding when the protein is folded into its correct shape. Peptide bonds from through a dehydration reaction, when the ___________________ of one amino acid reacts with the _______________________ acid of another amino acid, releasing a molecule of _____________________ H H O H H O Circle the peptide bond on the dipeptide: H N C C N C C O H R R Now, do it for this “polypeptide” MAWANI Biology 12: Biochemistry - Proteins – Notes Step 1: At the ribosome, two amino acids are placed side- by-side. The –OH group is removed from the carboxylate group on the left-most amino acid. A hydrogen atom is removed from the amine group on the rightmost amino acid. The –OH group and the hydrogen atom combines to form a water molecule. Step 2: A new bond is made between the carbonyl carbon and the nitrogen. The peptide formed in this example is called a _________________________ because it contains two amino acid residues. The new bond between the two amino acids is called a peptide bond. Larger peptides are formed by adding more amino acids, one by one, to the C-terminus of a growing peptide. MAWANI Biology 12: Biochemistry - Proteins – Notes  HOW DO PROTEINS GET THEIR SHAPE(S)? Proteins are amino acid chains that fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state, which is determined by its sequence of amino acids and interaction of groups. The properties of proteins depend not only on their sequence of amino acid residues, but also on how they are folded, twisted, and bent. The structure and shape of proteins is understood in terms of four levels of organization: 1) __________________________ 2) __________________________ 3) __________________________ 4) __________________________ 1. Primary Protein Structure The ________________ of amino acids in a peptide or protein is referred to as its primary structure. Here are two polypeptide chains that are 12 amino acids long. Note however, that they have different primary structures (different sequences of the 20 amino acids). A) 7 3 8 20 3 14 9 12 16 7 17 11 B) 8 14 9 1 5 11 19 16 4 2 15 10 The primary structure is analogous to the arrangement of letters in a word. Having the letters in the correct order is crucial to the meaning of the word! COOL MATH! o Different proteins typically contain from about 40 to over 4000 amino acids o There are 400 distinct dipeptides (202). o There are 8000 distinct tripeptides (203). o When there are 100 amino acids in the chain, there are 20100 = 1.27 × 10130 distinct peptides! To determine the number of unique tripeptides that can be formed from 3 amino acids, we need to consider the different possible arrangements. A tripeptide consists of three amino acids linked together, and the order in which they are arranged matters. Given 3 amino acids (let's call them A, B, and C), the number of unique tripeptides can be calculated using permutations. For each position in the tripeptide, you have 3 choices, and since there are 3 positions, the total number of unique tripeptides is: 3! = 3 × 2 × 1 = 6 So, there are 6 unique tripeptides possible from 3 amino acids. MAWANI Biology 12: Biochemistry - Proteins – Notes 2. Secondary Protein Structure Secondary protein structure describes the geometric patterns that occur when individual peptide chains “fold” back on themselves. Since peptide bonds are polar, H-bonding occurs between amino acids in the polypeptide chain. This will cause the chain to either coil up into an α-helix, fold into a β-pleated sheet. A key feature of secondary protein structure is that it only involves hydrogen bonding between peptide groups within an individual peptide chain. The R-groups are not involved. 3. Tertiary Protein Structure Alpha helices and/or beta sheets, along with the unorganized sections of a peptide chain, “fold” into a more compact shape. Although it may look randomly formed, the final 3-D shape is very exact and precise. The shape is due to the original sequence of amino acids (the primary structure); and the folding will be determined by the R-group interactions of the specific amino acid sequence. Since the sequence of amino acids (primary structure) ultimately determines which folding pattern is selected, so both secondary and tertiary structure ______________________on primary structure Different types of bonding (covalent, ionic, hydrogen) between -R groups make the alpha helix bend and turn, forming "globs" of protein of all shapes. This three-dimensional arrangement of the amino acid chain is called the “tertiary structure.” It is only the final shape that will determine the protein’s specific function. Of the many folding patterns (conformations) possible for a protein, there is usually only one that leads to a functioning molecule. MAWANI Biology 12: Biochemistry - Proteins – Notes  SOME OF THE INTERACTIONS THAT ARE INVOLVED IN TERTIARY STRUCTURE ARE ILLUSTRATED BELOW: I. Hydrophobic Interactions Nonpolar side-chains are attracted to other nonpolar side-chains and form “water-free pockets” in the interior region of the folded and compacted peptide (see the illustration above). II. Hydrogen Bonding Hydrogen bonding in tertiary structures can occur between polar side chains and/or peptide groups. III. Salt Bridges A salt bridge is an attraction between the positive charge on an amino acid, and a negative charge on another amino acid. IV. Disulfide Bridges Disulfide (covalent) bridges can be formed between two (SH) groups. Each cysteine residue contains a thiol group in its side-chain that is capable of forming a disulfide bridge with another cysteine residue, as shown above. MAWANI Biology 12: Biochemistry - Proteins – Notes 4. Quaternary Protein Structure A large number of native proteins are a combination of more than one polypeptide chain. Quaternary protein structure is the overall shape that occurs when two or more tertiary folded peptide chains assemble to make a protein. In proteins composed of two or more peptide chains, the individual peptide chains are referred to as “subunits.” The forces that hold the subunits together in quaternary structures are the same as those involved in tertiary structures. Example: Hemoglobin Haemoglobin is a water soluble, globular quaternary protein consisting of 4 polypeptides. The subunits of hemoglobin are α polypeptide chains, two β polypeptide chains, and an inorganic heme group. Two of the polypeptides (α subunits) contain 141 amino acids, while the other two (β subunits) contain 146 amino acids Found in RBCs, its function is to carry oxygen to your cells f or respiration. Scientists believe the protein dates back 4 billion years to the start of life on earth. Video: Bozeman Science – Proteins What is a Protein – PDB 101 HOMEWORK: Visit the site: www.chemistry.wustl.edu/~edudev/LabTutorials/Hemoglobin/MetalComplexinBlood.html Complete the The Many Colours of Blood (get the handouts from me) assignment: Further Reading: If you are interested in learning more about globular, fibrous and membrane proteins and how muscle fibers work, then ask me to print the handout for you. Excellent websites for review: https://www.ncbi.nlm.nih.gov/books/NBK26830/ http://www.nature.com/scitable/topicpage/protein-structure-14122136 PIPE-CLEANER PROTEINS ACTIVITY MAWANI Biology 12: Biochemistry - Proteins – Notes HOW DO PROTEINS GET DENATURED, AND WHY IS THIS IMPORTANT? Denaturation of Proteins Protein Denaturation: A protein that is not in its native state and shape which allows for optimal activity. 1. The shape of a protein is the key factor in its ability to perform its biological role. Protein shape is critical to its function. Prions in Mad Cow Disease Tau proteins in Alzheimer’s Why do we get a fever? 2. Proteins denature when they lose their characteristic three- dimensional folded structure (their chemical conformation). Proteins may be denatured at secondary, tertiary, quaternary structural levels, but not at the primary structural level 3. Protein shape is maintained by the attractive forces involved in secondary, tertiary, and quaternary structures. Some of these forces include: ________________________________________________________________________________________ When these attractive forces are disrupted, the native shape of proteins can be changed enough that a partial or complete loss of bioactivity (function) occurs. When a protein loses some or all of its biological activity in such a manner, this is referred to as “protein _______________________.” 5.. This change is usually caused by heat, acids, bases, detergents, alcohols, heavy metal salts, reducing agents or certain chemicals such as urea. Any mechanical or chemical agent that causes the denaturation of a protein is called a ______________ _____________. 4. In most cases, unless the shape change is very minor, the denaturation is irreversible. 5. Proteins, therefore, operate within a limited range of pH, temperature, and ionic balance. This is why it is important for the body to maintain homeostasis – so that its proteins do not become denatured! MAWANI Biology 12: Biochemistry - Proteins – Notes WAYS TO DENATURE PROTEINS Some of the most common denaturing agents are listed and described below: 1) ________________ The non-covalent attractive forces (i.e., _________________________________) involved in secondary, tertiary, and quaternary structures in proteins are easily disrupted by heating. The cooking of an egg is an example of heat denaturation. 2) _________________ _____________, which can disrupt the noncovalent attractive forces involved in secondary, tertiary, and quaternary structures. An example of denaturation of protein by mechanical agitation is the foaming that occurs during beating of raw egg (yolks removed). Chefs use this process to make meringue. 3) _________________ ______________ Some amphipathic compounds can cause denaturation by inserting their nonpolar ends into an association of hydrophobic side chains and thereby displacing some of the side chains. For example, detergents are capable of denaturing proteins. 4) ____________ _______________ Some polar solvents, such as acetone or ethanol, can interfere with hydrogen bonding, dipole-dipole, and ion-dipole interactions by competing for a protein’s existing interactions. 70% alcohol solution is used as a disinfectant on the skin. This concentration of alcohol penetrates the bacterial cell wall and denatures proteins and enzymes inside the cell. A 95% alcohol solution merely coagulates proteins on the outside of the cell wall and prevents any alcohol from entering the cell. Alcohol denatures proteins by disrupting the side chain intra-molecular hydrogen bonding. New hydrogen bonds are formed instead between the new alcohol molecule and the protein side chains. 5) ______ _________________, which can disrupt a protein’s salt bridges and ion-dipole interactions. The charged R-groups of polar amino acids help proteins maintain their tertiary and/or quaternary structure because they participate in salt bridges and ion-dipole interactions. As might be expected, acids and bases disrupt salt bridges held together by ionic charges. A type of double replacement reaction occurs where the positive and negative ions in the salt change partners with the positive and negative ions in the new acid or base added. This reaction occurs in the digestive system, when the acidic gastric juices cause the curdling (coagulating) of milk. This process is also used to curdle milk for making yoghourt and cheese. An example of the denaturation of proteins by a pH change is the use of citric acid in the marinating (soaking) of fish and shellfish in a dish called ceviche. The citric acid comes from citric juices such as lemon, lime, orange, or grapefruit juice. 6) ____________ __________. Heavy metals denature proteins in the same manner as acids and bases. Heavy metal salts usually contain Hg+2, Pb+2, Ag+1 Tl+1, Cd+2, ions, and other metals with high atomic weights. Since salts are ionic, they disrupt salt bridges in proteins. MAWANI Biology 12: Biochemistry - Proteins – Notes  The reaction of a heavy metal salt with a protein usually leads to an insoluble metal protein salt. This same reaction is used in reverse - in cases of acute heavy metal poisoning. In such a situation, a person may have swallowed a significant quantity of a heavy metal salt. As an antidote, a protein such as milk or egg whites may be administered to precipitate the poisonous salt. Then an emetic is given to induce vomiting so that the precipitated metal protein is discharged from the body. Heavy metals may also disrupt disulfide bonds because of their high affinity and attraction for sulfur and will also lead to the denaturation of proteins. Conformational Stability - Khan Academy Protein Denaturation - Food Science Videos: How to unboil an egg - Eleanor Nelsen Why Unboil an Egg - Gregory Weiss - UC Irvine The Science of BBQ!!! MAWANI Biology 12: Biochemistry - Proteins – Notes