Protein Structure and Function PDF

8/27/24, 8:25 PM Platform | Study Fetch Introduction This lesson will cover: Amino acids The four levels of protein structure Enzymes and their kinetics Amino Acids (00:34 - 02:12) Proteins are one of t...

8/27/24, 8:25 PM Platform | Study Fetch Introduction This lesson will cover: Amino acids The four levels of protein structure Enzymes and their kinetics Amino Acids (00:34 - 02:12) Proteins are one of the most abundant molecules in nature and have a wide range of functions. Proteins are made up of carbon, hydrogen, oxygen, and nitrogen, which combine to form their 3D structure. There are 20 amino acids that make up proteins. Memorizing them can be challenging, but there are some strategies: Grouping the Amino Acids: Nonpolar (Hydrophobic) Amino Acids: Alanine, Glycine, Isoleucine, Leucine, Valine Aromatic Amino Acids: Phenylalanine, Tryptophan, Tyrosine Acidic Amino Acids: Aspartic Acid, Glutamic Acid Amide Amino Acids: Asparagine, Glutamine Sulfur-Containing Amino Acids: Cysteine, Methionine Hydroxyl-Containing Amino Acids: Serine, Threonine Positively Charged Amino Acids: Lysine, Arginine Unique Amino Acids: Proline (forms a ring) Histidine (can be protonated or deprotonated) Protein Structure (00:49 - 01:35) The structure of a protein affects its function. Proteins have four levels of structure: 1. Primary Structure: The sequence of amino acids 2. Secondary Structure: Local folding patterns (e.g., alpha helices, beta sheets) https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be88ab287f54e41f2b0/document?go=note 1/7 8/27/24, 8:25 PM Platform | Study Fetch 3. Tertiary Structure: The overall 3D shape of the protein 4. Quaternary Structure: The arrangement of multiple polypeptide chains Enzymes and Kinetics (01:35 - 02:12) Enzymes are proteins that catalyze chemical reactions, increasing the rate of the reaction. Enzyme kinetics describe the factors that affect enzyme activity, such as: Substrate concentration Enzyme concentration Temperature pH Amino Acids and Protein Structure (00:04:52 - 00:07:56) Amino Acid Structure Amino acids have an amino group (NH2) and a carboxylic acid group (COOH) attached to a central carbon The R-group (side chain) attached to the central carbon varies between different amino acids, providing diversity The amino and carboxylic acid groups form the "backbone" that links amino acids together into a polypeptide chain Proline is unique in that its R-group loops back to the amino group, creating a bend in the backbone Levels of Protein Structure 1. Primary Structure The sequence of amino acids in the polypeptide chain 2. Secondary Structure The local folding patterns of the polypeptide chain, such as alpha helices and beta sheets 3. Tertiary Structure The overall 3D shape of the protein, determined by interactions between R-groups 4. Quaternary Structure The arrangement of multiple polypeptide chains into a complete, functional protein Amino Acid Properties and Functions Amino acids can have acidic (e.g. aspartic acid, glutamic acid), basic (e.g. asparagine, lysine), or nonpolar (e.g. proline, leucine, isoleucine) side chains The side chain properties influence how the amino acid contributes to protein structure and function https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be88ab287f54e41f2b0/document?go=note 2/7 8/27/24, 8:25 PM Platform | Study Fetch Acidic and basic amino acids can form ionic interactions to stabilize protein structure Nonpolar amino acids can participate in hydrophobic interactions Specific amino acid sequences and side chain properties allow proteins to fold into shapes that enable their biological functions Protein Residues Each amino acid in a polypeptide chain is referred to as a "residue" For example, a sequence of methionine, aspartic acid, etc. would be described as individual residues (00:07:56 - 00:08:10) The primary structure is the simple linear sequence of amino acid residues (00:08:10 - 00:08:24) Secondary structure refers to local folding patterns like alpha helices and beta sheets Tertiary structure is the overall 3D shape of the protein Quaternary structure is the arrangement of multiple polypeptide chains into a complete protein Primary Structure of Proteins (00:08:10 - 00:08:32) The primary structure of a protein is simply the linear sequence of amino acids. This sequence is determined directly by the DNA code and is transcribed into mRNA, which is then translated into the protein. The primary structure alone does not give you the 3D shape or topology of the protein, it just provides the basic amino acid sequence. Secondary Structure of Proteins (00:08:32 - 00:09:22) The secondary structure refers to the local interactions between the amino acid side chains, forming higher- order structures like alpha helices and beta sheets. These secondary structures are stabilized by hydrogen bonding between the amino acid residues. The most common secondary structures are alpha helices and beta pleated sheets. There are also other less common secondary structures that can form. Tertiary Structure of Proteins (00:09:22 - 00:10:51) The tertiary structure is the overall 3D shape of the protein, formed by the interactions between the secondary structures. This is driven by longer-range interactions between the amino acid side chains, such as: Hydrophobic interactions Disulfide bridges Hydrogen bonds Ionic bonds These interactions cause the protein to fold into a specific 3D shape that gives it its function. https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be88ab287f54e41f2b0/document?go=note 3/7 8/27/24, 8:25 PM Platform | Study Fetch The tertiary structure represents the final, functional form of the protein. Quaternary Structure of Proteins (00:09:43 - 00:10:17) Quaternary structure refers to the assembly of multiple protein subunits into a larger, multi-unit complex. These subunits have discrete primary sequences but come together to perform a higher-level function. For example, hemoglobin is a quaternary structure made up of multiple protein subunits working together to transport oxygen. Hydrophobic Interactions and Protein Folding (00:11:28 - 00:12:10) Hydrophobic amino acid side chains, like phenylalanine, tend to orient themselves away from water and towards the interior of the protein. This hydrophobic packing helps drive the initial folding of the protein as it forms its tertiary structure. The water-fearing hydrophobic residues sequester themselves in the core of the protein, while the water-loving hydrophilic residues face outwards. This hydrophobic effect is a key force that stabilizes the final 3D shape of the protein. Disulfide Bridges (00:12:10 - 00:12:40) Disulfide bridges can form between cysteine residues in a protein. This occurs when cysteine releases a hydrogen molecule, allowing a covalent bridge to form between the sulfur atoms. Disulfide bridges help stabilize the tertiary structure of proteins. Protein Structure and Function Fibrous vs. Globular Proteins (00:12:40 - 00:12:55) Proteins have different structures, referring to their higher-order tertiary structure Fibrous proteins are long, cable-like chains that interact with the surrounding water Globular proteins are more spherical, with hydrophobic residues on the inside and hydrophilic residues on the outside Quaternary Structure (00:13:14 - 00:13:26) Quaternary structure refers to the interaction of multiple peptide sequences These sequences can have similar or different functions, but combine for a higher overall function https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be88ab287f54e41f2b0/document?go=note 4/7 8/27/24, 8:25 PM Platform | Study Fetch Protein Denaturation (00:13:37 - 00:13:59) Changes in heat, temperature, pH, or salt can cause the higher-order protein structure to unravel, leading to a loss of function This is why the body's temperature and pH must be maintained within precise ranges to preserve proper protein function Enzymes (00:14:19 - 00:17:17) Enzyme Function Enzymes catalyze chemical reactions, speeding them up by decreasing the activation energy required Substrates enter the enzyme's active site, causing a conformational change that forms an enzyme-substrate complex The enzyme then catalyzes the reaction and releases the final products, undergoing another conformational change Michaelis-Menten Model Plots enzyme activity (reaction rate) against substrate concentration Vmax is the maximum reaction velocity, the fastest the enzyme can work KM is the substrate concentration at which the enzyme reaches half its Vmax, indicating the enzyme's affinity for the substrate "So like I said, the Vmax is the maximum reaction velocity. So that is the maximum rate given the number of enzymes you have in solution, they cannot move any faster." Term Definition Vmax Maximum reaction velocity, the fastest the enzyme can work KM Substrate concentration at which the enzyme reaches half its Vmax, indicating affinity for substrate # Example Michaelis-Menten plotimport matplotlib.pyplot as pltimport numpy as np# Generate sample datasubstrate_conc = np.linspace(0, 10, 100)reaction_rate = [0.8 * x / (2 + x) for x in substrate_conc]# Plot the dataplt.figure(figsize=(8, 6))plt.plot(substrate_conc, reaction_rate)plt.xlabel('Substrate Concentration')plt.ylabel('Reaction Rate')plt.title('Michaelis-Menten Plot')plt.show() https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be88ab287f54e41f2b0/document?go=note 5/7 8/27/24, 8:25 PM Platform | Study Fetch Enzyme Kinetics and Inhibition (00:17:17 - 00:19:53) Enzyme Kinetics Km is the substrate concentration at which the enzyme reaches 50% of its maximum rate (Vmax) Enzymes can be inhibited in various ways, which can play a role in pharmaceuticals and endogenous reactions Enzyme Inhibition Enzymes can be modified to change their rate, often through the use of inhibitors Competitive Inhibition Inhibitor competes with the substrate for the enzyme's binding site Vmax remains the same, but Km increases This is because the inhibitor reduces the efficiency of the enzyme in producing the desired product Noncompetitive Inhibition Inhibitor binds to a different site on the enzyme, deactivating it Vmax decreases, as there is less functional enzyme in the solution Km remains the same, as the efficiency of the remaining functional enzymes is unchanged Uncompetitive Inhibition Combination of competitive and noncompetitive inhibition Vmax decreases and Km increases Summary Enzymes can be modified through inhibitors to change their kinetics Competitive inhibitors increase Km, noncompetitive inhibitors decrease Vmax, and uncompetitive inhibitors do both Understanding enzyme inhibition is important for studying proteins and their regulation (00:19:53 - 00:21:36) Enzyme Inhibition Graphs Graphs can be used to visualize the different types of enzyme inhibition The normal enzyme kinetics curve is shown, along with the effects of competitive, noncompetitive, and uncompetitive inhibitors These graphs help illustrate the changes in Vmax and Km for each type of inhibition Key Takeaways Competitive inhibition increases Km but leaves Vmax unchanged Noncompetitive inhibition decreases Vmax but leaves Km unchanged https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be88ab287f54e41f2b0/document?go=note 6/7 8/27/24, 8:25 PM Platform | Study Fetch Uncompetitive inhibition decreases both Vmax and Km Good luck on your exam! You've got this. https://www.studyfetch.com/platform/studyset/66cd116dd279f5220d947c66/material/66ce6be88ab287f54e41f2b0/document?go=note 7/7