Biochemistry LC3 Proteins PDF

A. BASIC STRUCTURE COURSE OUTLINE Elements: I. Amino Acids and Proteins Alpha Amino Acid...

A. BASIC STRUCTURE COURSE OUTLINE Elements: I. Amino Acids and Proteins Alpha Amino Acid A. Basic Structure Difference in R group B. Stereochemistry Alpha Amine C. Side Chain Chemistry II. Peptides A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure III. Protein Movement and Cell Signaling A. Structural Functions B. Fibrous Proteins C. Globular Structural Proteins Figure 2: Structure of Amino Acid D. Communication Signaling E. Proteins Involved in Movement Examples: IV. Protein Functions A. Antibodies B. Gene Expression C. Catalysis D. Transport Proteins E. Oxygen Transport F. Cooperativity G. Na/K ATPase PROTEINS Figure 3: Cysteine structure I. AMINO ACIDS AND PROTEINS Work Forces of the Cell Catalysis Signaling Structure Energy /Gradient Generation Utilization Amino acid - monomer of protein/polypeptide Essential amino acids are those that are Figure 4: Phenylalanine Structure not made in the human body but are needed in our cellular processes. Essential amino acids for humans- B. STEREOCHEMISTRY isoleucine, leucine, lysine, arginine, aspartic acid, cysteine. D and L isomers Essential amino acids differ from one organism to another. Figure 1: Essential and Non Essential Amino Acid Figure 5: D and L Isomers BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 Two Types of Isomers Enantiomers Diastereomers C. SIDE CHAIN CHEMISTRY - Hydrophobic, Hydrophilic, and Ionic amino acids - Figure 9: Aliphatic R groups cc. CARBOXYLATE R-GROUPS Charges at physiological pH Figure 6: Amino Acid Categories a. AROMATIC R-GROUPS Figure 10: Carboxylate R-Groups d. HYDROXYL R-GROUPS Charges at physiological pH Figure 7: Aromatic Groups Figure 11: Hydroxyl R-Groups e. SULFHYDRYL R-GROUPS Figure 8: Aromatic Groups (2) Hydrophobic amino acids have Aromatic side chains, those that contain the cyclic hydrocarbon structures, aliphatic or aromatic amino acid side chains. b. ALIPHATIC R-GROUPS Glycine - no chiral carbon Proline - inflexible, bending formation of Figure 12: Sulfhydryl R group (Cysteine) shape of proteins Aliphatic/Aromatic amino acid side chains - Cysteine ionizes and forms disulfide bonds alkane, alkenes, and alkynes. Disulfide bonds are covalent interactions Negatively charge due to the dissociation formed between the sulfur atoms of two of Hydrogen from the carboxyl group cysteine residues PREPARED BY: BATCH 2028 1D 2 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 f. CARBOXAMIDE R-GROUPS Figure 17: Charge changes due to ionization of Figure 13: Carboxamide R group Carboxyl Group g. IONIZABLE AMINE R-GROUPS Figure 18: Charge changes due to ionization of Carboxyl Group Figure 14: Ionizable Amine R group Lysine and arginine - abundant in Histones - Acetylation Histidine pKa = 6 readily ionize and deionize IONIZATION BINDING Figure 19: Charge changes due to ionization of Carboxyl Group Figure 15: pK Effect to Ionization of Carboxyl Group Figure 20: Charge changes due to ionization of Carboxyl Group 0 charge = isoelectric point (Zwitterion) Figure 16: pK Effect to Ionization of Carboxyl Group (2) PREPARED BY: BATCH 2028 1D 3 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 AMINO ACID AND PROTEINS CHEMICAL CHARACTER Figure 25: Chemical Hindrance STERIC HINDRANCE Figure 21: Amino Acid and Protein Properties II. PEPTIDES Adjacent (primary) Close (secondary) Distant (tertiary) Figure 26: Trans and Cis Amino Acid Separate units (quaternary) Physiology pH = 7.4 Alpha carbons can form trans or cis peptide group conformation. Trans is stronger due to steric hindrance. Steric Hindrance – declining speed of chemical reaction (Bonds is stronger if farther away from each other) Figure 22: Peptide Bond Carboxyl group of amino acid 1 forms a peptide bond with the Amine group of Figure 27: Alternating Orientation of R group amino acid number 2 via condensation/dehydration synthesis. FROM AMINO ACID TO PROTEINS Figure 23: Peptide bonds (Condensation) Figure 28: Multiple Peptide Bond Planes Figure 24: Peptide Bonds (Condensation 2) PREPARED BY: BATCH 2028 1D 4 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 B. SECONDARY STRUCTURE Regular structures arising from interactions nearby amino acids. A. ALPHA HELIX In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino Figure 29: Multiple Peptide Bond Planes (Rotation) acid chain. Alpha carboxyl group and amine group will undergo hydrogen POLYPEPTIDES bonding with each other. Alternating orientation of the side group (alpha amine group) would be able to for hydrogen bond from nearby amino acid forming helical structure Figure 30: Bond angles of stability PROTEIN STRUCTURE LEVELS Figure 32: Alpha Helix B. BETA STRANDS Beta stands are flat sheets that are formed by hydrogen bonds of the adjacent amino acid. Figure 31: Four Levels of Protein Structure A. PRIMARY STRUCTURE Linear sequence of amino acids Joined by peptide bonds Translated from mRNA using genetic code Synthesis begins at amino end and terminates at carboxyl end Figure 33: Beta Strands Carboxyl terminus contains 3 alpha carboxyl groups. C. REVERSE TURN Ultimately determines all properties of a Reverse turns occur in proteins protein and provide connections between There is no rotation in the peptide bonds different regions, often consisting due to its directional structure. of proline and glycine. Proline's cyclic structure lends bulkiness, while glycine’s simplicity allows for smooth turns in peptide chains. PREPARED BY: BATCH 2028 1D 5 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 Figure 36: High Propensity for Alpha Helices Figure 34: Reverse Turn D. SUPER SECONDARY STRUCTURE Figure 35: Motifs Figure 37: High Propensity for Beta Strands Motifs- combination of this glycine and proline structure would provide you a smooth turn of the peptide chain Super secondary motifs are the structures that are formed by the combination of secondary structures containing alpha-helices and beta-pleated sheets. These structures are found in the globular proteins and are joined by loop, turn, or hairpin (short amino acids sequences which are required to join the alpha helices and beta-pleated sheets) they are found in globular proteins Figure 38: High Propensity for Reverse Turns where the bend is required. C. TERTIARY STRUCTURE Examples: Folding of more complex structure of Collagen protein Keratin Different forces that stabilize the folding: Fibroin ○ Hydrogen bonds ○ Disulfide Bridges (Cysteine) TENDENCY OF AMINO ACID ○ Hydrophobic Interaction ○ Metallic Bonds The tendencies of specific amino acids to adopt various secondary structures can be quantified, with alanine and glutamic acid showing a high propensity for alpha helices, while isoleucine and valine favor beta sheets. Figure 39: Folding and Turns PREPARED BY: BATCH 2028 1D 6 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 III. PROTEIN MOVEMENT AND CELL SIGNALING Protein Functions Communication/signaling Protein Structural Consideration Chemistry Figure 40: Tertiary Structure Flexibility Geometry Polar, non-polar, charged D. QUATERNARY STRUCTURE Fibrous, globular, membrane Multi Subunit Proteins Quaternary structure exists in proteins consisting of two or more identical or different polypeptide chains (subunits). These proteins are called oligomers because they have two or more subunits. The quaternary structure describes the manner in which subunits are arranged in the native protein. Figure 42: Hemocyanin A. STRUCTURAL FUNCTIONS Fibrous and Filamentous Proteins Keratins – hair, nails Collagen – cartilage, connective tissues Elastin/Fibrillin – connective tissues Lamin (nuclear) – structure for nuclear envelope Actin – globular protein components of cytoskeleton filaments Tubulin – globular protein components of microtubules Figure 41:Multiple Subunits B. FIBROUS PROTEINS Repeated Sequences Mostly secondary structure Sequence repeats common SOLUBLE vs. MEMBRANE BOUND PROTEIN Glycine commonly present in abundance Hydroxyproline in collagen Figure 42: Proteins in Plasma Membrane Figure 43: Partial Collagen Sequence PREPARED BY: BATCH 2028 1D 7 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 Hydroxyproline (Hpr) - has an additional hydroxyl group that is formed from the oxidation of protein (will form hydrogen later on to form different strands of your collagen.) COLLAGEN Collagen is responsible for the strength (tensile strength) of different tissues. Figure 45: Collagen Binding Pattern Fibrous proteins – repeated sequence and mostly have secondary structure. Actin and fibrillin – polymerized globular protein Glycine – Most abundant in collagen and other fibrous proteins. Rough endoplasmic reticulum ribosomes produce various pro-alpha chains—precursors of collagen. These pro-alpha chains assemble into a helical structure, and post-translational modifications occur to hydroxylate specific proline residues, before the helical Figure 46: Collagen Chain structure is secreted outside of the cell to provide structural support. Clinical Correlation 1. SCURVY - To convert proline to hydroxyproline, you require ascorbic acid (vitamin C). A deficiency in vitamin C results in scurvy, characterized by weakened collagen structures. - In the synthesis of collagen, rough endoplasmic reticulum ribosomes produce various pro-alpha chains—precursors of collagen. These pro-alpha chains assemble into a helical structure, and post-translational modifications occur to hydroxylate specific proline residues, before the helical structure is secreted outside of the cell to provide structural support. Figure 44: Most Abundant Type of Collagen Type 1 – highest tensile strength. Network forming collagen – will not form fibrils but rather form a mesh. (base and Figure 47: Man with Scurvy membrane beneath the stratified squamous epithelia) PREPARED BY: BATCH 2028 1D 8 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 2. EHLERS DANLOS SYNDROME Type II is called osteogenesis imperfecta congenita, and is the most severe. Patients die of pulmonary hypoplasia in utero or during the neonatal period. Most patients with severe OI have mutations in the gene for either the pro-α1 or pro-α2 chains of type I collagen.’ The most common mutations cause the replacement of glycine residues (in –Gly–X–Y–) by amino acids with bulky side chains. The resultant structurally Figure 48: Ehlers Danlos Syndrome abnormal pro-α chains prevent the formation of the required triple-helical Connective tissue disorders that result conformation. from inheritable defects in the metabolism of fibrillar collagen molecules. EDS can result from a deficiency of ELASTIN collagen-processing enzymes (for example, lysyl hydroxylase or procollagen peptidase), or from mutations in the amino acid sequences of collagen types I, III, or V. Collagen containing mutant chains is not secreted, and is either degraded or accumulated to high levels in intracellular compartments.Because collagen type III is an important component of the arteries, potentially lethal vascular problems occur Figure 50: Elastin 3. OSTEOGENESIS IMPERFECTA Stretchy fibers that are found in the lungs, walls of large artery and elastic ligaments. Tropoelastin - linear polypeptide precursor composed of about 700 amino acids primarily small and nonpolar. Rich in proline and lysine, contains only a little hydroxyproline and hydroxylysine. Secreted and interacts with specific glycoprotein microfibrils, such as fibrillin, which function as a scaffold onto which it is deposited. 1 lysyl side chain and 3 alkyl side chains and will form a desmosine cross-link. Figure 49: Lethal Form of Osteogenesis Imperfecta Retarded wound healing and a rotated and twisted spine leading to a “humped-back” (kyphotic) appearance Type I is called osteogenesis imperfecta tarda. Consequence of decreased production of α1 and α2 chains. It presents in early infancy with fractures secondary to minor trauma, and may be suspected if prenatal ultrasound detects bowing or fractures of long bones. PREPARED BY: BATCH 2028 1D 9 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 Cellular signal transduction: Kinases and many others Transcription factors: Bind specific DNA sequences to control gene expression Responding to the environment Figure 51: Desmosine Cross Link in Elastin C. GLOBULAR STRUCTURAL PROTEINS Figure 54: Protein Response to Environment Tubulin can self assemble in the presence of ATP to form active molecules in the E. PROTEINS INVOLVED IN MOVEMENT skeleton Movement by rotation caused by the binding of ATP. Figure 52: Self Assembly Structural Proteins Actin: Activation Required (polymerize to form F actin) Figure 55: Movement of Protein IV. PROTEIN FUNCTIONS A. ANTIBODIES Proteins of the Immune System Produced by adaptive immune system Figure 53: Assembly Structural Proteins Soluble forms Membrane bound forms D. COMMUNICATION SIGNALING Anti bodies will be able to bind to antigen in order to neutralize them. Membrane Receptors where molecules bind: Integral proteins Many 7TMs Respond to outside signal; start second messenger formation Peptide Hormones: Endocrine system Insulin, oxytocin, many other Figure 56: Antibodies PREPARED BY: BATCH 2028 1D 10 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 Reaction products induce structural B. GENE EXPRESSION change, resulting in release of products DNA methylation state helps determine if process occurs The combination of transcription and translation is known as gene expression Figure 60: Induced Fit Catalysis Figure 57: Controlling the Expression of Cellular Proteins D. TRANSPORT PROTEINS C. CATALYSIS Cellular Organismal - LDL/HDL/chylomicron, Enzymatic Function hemoglobin, serum albumin Membrane transport: active and passive Figure 58: Enzymatic Function Speeds up chemical reaction without itself being consumed in the process. Shape of substrate and enzymes should Figure 61: Transport Proteins be complementary in shape. E. OXYGEN TRANSPORT - Oxygen and hemoglobin Figure 59: Enzyme Substrate Interaction Figure 62: Oxygen transport of Hemoglobin and Myoglobin Induced Fit- Another View Substrate binding induces structural change, bringing substrates together to react PREPARED BY: BATCH 2028 1D 11 BIOCHEMISTRY LC 3: PROTEINS DR. ESPIRITU, A. DATE: 08/28/2024 F. COOPERATIVITY - Multisubunit Interactions Figure 63: Multisubunit interactions Hemoglobin can have T state or R state: T state- tight state (do not allow binding of oxygen) R state- relax state (allows binding of oxygen) High concentration of oxygen in the lungs binds to T state causing conformational change to adjacent globin cells. G. NA/K ATPASE Figure 64:Transmembrane Iron Transport Reference(s): 1. Dr. A. Espiritu (2024). Lecture and Powerpoint Presentation.. 2. Protein Quaternary Structure. Retrieved from https://www.sciencedirect.com/topics/biochemistry-gen etics-and-molecular-biology/protein-quaternary-structur e#:~:text=Quaternary%20structure%20exists%20in%2 0proteins,arranged%20in%20the%20native%20protein. PREPARED BY: BATCH 2028 1D 12