Protein Structure, Function, Secretion PDF

Protein Structure & Function Cellular & Molecular Biology MD105 Dr. V. E. Kalodimou  instrumental in about everything that an Made up of chains of amino acids organism does....

Protein Structure & Function Cellular & Molecular Biology MD105 Dr. V. E. Kalodimou  instrumental in about everything that an Made up of chains of amino acids organism does. Transport of other Structural Support substances Intercellular signaling Storage defense against foreign Introduction: substances What are Movement Proteins intercellular signaling main enzymes in a cell and regulate metabolism by selectively accelerating chemical reactions. Structural Differences Between Carbohydrates, Lipids, and Proteins  Structure of Proteins Classified by number of amino acids in a chain Peptides: fewer than 50 amino acids Dipeptides: 2 amino acids Tripeptides: 3 amino acids Polypeptides: more than 10 amino acids Proteins: more than 50 amino acids Typically 100 to 10,000 amino acids linked together Chains are synthesizes based on specific bodily DNA Amino acids are composed of carbon, hydrogen, oxygen, and nitrogen  Essential, Nonessential, and Conditional Non- Essential Essential must be consumed in the Conditional diet can be synthesized in the body cannot be synthesized due to illness or lack of necessary precursors  Protein synthesis 1. mRNA copy is made of one of the DNA strands. 2. mRNA copy moves out of nucleus into cytoplasm. 3. tRNA molecules are activated as their complementary amino acids are attached to them. 4. mRNA copy attaches to the small subunit of the ribosomes in cytoplasm. A tRNA bonds complementarily with the mRNA via its anticodon. 5. The ribosome moves along. The first tRNA leaves the ribosome. 6. The process is repeated with 2nd and 3rd tRNA 7. Eventually a stop codon is reached on the mRNA. The newly synthesised polypeptide leaves the ribosome. Protein Synthesis: Overview  Elements in a protein Carbon Hydrogen Oxygen Nitrogen (sometimes sulphur)  Protein Secretion Golgi bodies especially numerous and active in secretory cells -gastric gland cells in stomach walls -mucus -pancreas -insulin  Proteins Make up about 15% of the cell. Have many functions in the cell: – Enzymes – Structural – Transport – Motor – Storage – Signaling – Receptors – Gene regulation – Special functions  Fibrous proteins Several spiral-shaped polypeptide molecules. Linked in parallel by disulphide bridges. Protein has a rope-like structure.  Proteins – Multiple Peptides Non-covalent bonds can form interactions between individual polypeptide chains: – Binding site – where proteins interact with one another. – Subunit – each polypeptide chain of large protein. – Dimer – protein made of 2 subunits, Can be same subunit or different subunits.  Protein Domains A domain is a basic structural unit of a protein structure – distinct from those that make up the conformations. Part of protein that can fold into a stable structure independently. Different domains can impart different functions to proteins. Proteins can have one or many domains depending on protein size.  Globular proteins Several polypeptide chains. folded roughly into a spherical shape like a tangled ball of string. Enzymes are globular proteins. Also vital component in cell and sub-cellular membranes.  Hormones Chemical messengers. Globular protein. Exert a specific effect on tissues.  Antibodies Y-shaped globular proteins. Made by lymphocytes. Defend body against antigens.  Conjugated proteins Globular protein associated with a non-protein chemical. Glycoprotein, -protein and carbohydrate - e.g mucus  Different Subunit Proteins Oxygen-transporting pigment in blood. Conjugated protein, -globular protein globin, -haem (non-protein containing iron). Hemoglobin – 2  globin subunits – 2  globin subunits  Protein Assemblies Proteins can form very large assemblies. Can form long chains if the protein has 2 binding sites – link together as a helix or a ring. Actin fibers in muscles and cytoskeleton – is made from thousands of actin molecules as a helical fiber.  Stabilizing Cross-Links Cross linkages can be between 2 parts of a protein or between 2 subunits. Disulfide bonds (S-S) form between adjacent -SH groups on the amino acid cysteine.  Proteins at Work The conformation of a protein gives it a unique function. To work proteins must interact with other molecules, usually 1 or a few molecules from the thousands protein available. Ligand – the molecule that a protein can bind. Binding site – part of the protein that interacts with the ligand, – Consists of a cavity formed by a specific arrangement of amino acids.  Formation of Binding Site The binding site forms when amino acids from within the protein come together in the folding. The remaining sequences may play a role in regulating the protein’s activity.  Prosthetic Groups Occasionally the sequence of the protein is not enough for the function of the protein. Some proteins require a non-protein molecule to enhance the performance of the protein, – Hemoglobin requires heme (iron containing compound) to carry the O2. When a prosthetic group is required by an enzyme it is called a co-enzyme, – Usually a metal or vitamin. These groups may be covalently or non-covalently linked to the protein. Regulation of Enzymes Regulation of enzymatic pathways prevent the deletion of substrate. Regulation happens at the level of the enzyme in a pathway. Feedback inhibition is when the end product regulates the enzyme early in the pathway.  Feedback Regulation Negative feedback – pathway is inhibited by accumulation of final product. Positive feedback – a regulatory molecule stimulates the activity of the enzyme, usually between 2 pathways, –  ADP levels cause the activation of the glycolysis pathway to make more ATP.  Allostery Conformational coupling of 2 widely separated binding sites must be responsible for regulation – active site recognizes substrate and 2nd site recognizes the regulatory molecule. Protein regulated this way undergoes allosteric transition or a conformational change. Protein regulated in this manner is an allosteric protein.  Allosteric Regulation Enzyme is only partially active with sugar only but much more active with sugar and ADP present.  Phosphorylation Some proteins are regulated by the addition of a PO4 group that allows for the attraction of + charged side chains causing a conformation change. Reversible protein phosphorylations regulate many eukaryotic cell functions turning things on and off. Protein kinases add the PO4 and protein phosphatase remove them. Phosphorylation/Dephosphorylation Kinases induce the PO4 on 3 different amino acid residues, – Have a –OH group on R group: Serine, Threonine or Tyrosine. Phosphatases remove the PO4. Motor Proteins Proteins can move in the cell, say up and down a DNA strand but with very little uniformity: – Adding ligands to change the conformation is not enough to regulate this process. The hydrolysis of ATP can direct the movement as well as make it unidirectional: – The motor proteins that move things along the actin filaments or myosin.  Cytoskeleton The cytoskeleton is a network of fibers extending throughout the cytoplasm. The cytoskeleton organizes the structures and activities of the cell.  The cytoskeleton also plays a major role in cell motility: – This involves both changes in cell location and limited movements of parts of the cell. The cytoskeleton interacts with motor proteins: – In cilia and flagella motor proteins pull components of the cytoskeleton past each other. – This is also true in muscle cells.  Motor molecules also carry vesicles or organelles to various destinations along “monorails’ provided by the cytoskeleton. Interactions of motor proteins and the cytoskeleton circulates materials within a cell via streaming. Recently, evidence is accumulating that the cytoskeleton may transmit mechanical signals that rearrange the nucleoli and other structures. There are three main types of fibers in the cytoskeleton: microtubules, microfilaments, and intermediate filaments.  Microtubules, the thickest fibers, are hollow rods about 25 microns in diameter: – Microtubule fibers are constructed of the globular protein, tubulin, and they grow or shrink as more tubulin molecules are added or removed. They move chromosomes during cell division. Another function is as tracks that guide motor proteins carrying organelles to their destination.  In many cells, microtubules grow out from a centrosome near the nucleus: – These microtubules resist compression to the cell. In animal cells, the centrosome has a pair of centrioles, each with nine triplets of microtubules arranged in a ring. During cell division the centrioles replicate.  Microtubules are the central structural supports in cilia and flagella: – Both can move unicellular and small multicellular organisms by propelling water past the organism. – If these structures are anchored in a large structure, they move fluid over a surface. For example, cilia sweep mucus carrying trapped debris from the lungs. cilia flagella  Intermediate filaments Intermediate filaments, intermediate in size at 8 - 12 nanometers, are specialized for bearing tension: – Intermediate filaments are built from a diverse class of subunits from a family of proteins called keratins. Intermediate filaments are more permanent fixtures of the cytoskeleton than are the other two classes. They reinforce cell shape and fix organelle location.  Microfilaments Microfilaments, the thinnest class of the cytoskeletal fibers, are solid rods of the globular protein actin: – An actin microfilament consists of a twisted double chain of actin subunits. Microfilaments are designed to resist tension. With other proteins, they form a three-dimensional network just inside the plasma membrane.  In muscle cells, thousands of actin filaments are arranged parallel to one another. Thicker filaments, composed of a motor protein, myosin, interdigitate with the thinner actin fibers: – Myosin molecules walk along the actin filament, pulling stacks of actin fibers together and shortening the cell.  Proteins involved in muscle contraction. Role of Calcium in Cross-Bridge Formation. Sliding Filament Mechanism. Following muscle contraction Changes in Banding Pattern During Shortening Muscle Contraction Power Stroke Cross-Bridge Cycling: Actin links with Myosin to form Contractile Structures  Muscle Fatigue Muscle fatigue is a condition in which the muscle is no longer able to generate or sustain the expected power output. Its thought to mainly arise from failure in excitation-contraction coupling within the muscle than from presynaptic factors. Central fatigue include subjective feelings of tiredness and a desire to cease activity. Its thought that central fatigue precedes physiological fatigue in the muscle. Acidosis of lactic acid dumped into the bloodstream may influence the sensation of fatigue perceived in the brain.  Muscle Disorders Muscle overuse resulting in muscle fatigue. Trauma may also cause tearing of the tissue. Muscle disuse could be just as bad as overuse, resulting in muscle atropy. e.g. muscle immobilized in a cast for long periods. The blood supply to the muscle diminishes and muscle fibres get smaller. Atropy longer than a year is permanent. Acquired disorders, such as weakness resulting from infectious diseases, such as, influenza, poisoning by toxins such as that producing botulism (botulinum toxin) and tetanus (tetanus toxin). Inherited disorders are the hardest to treat. e.g. muscular dystrophy as well as biochemical defects in glycogen and lipid storage.  Duchenne muscular dystrophy Duchenne muscular dystrophy is due to the absence of a cytoskeletal protein known as dystrophin. These muscle fibres have tiny tears which allow Ca2+ ions to enter them and activate enzymes that break down fibre components. Patients usually die before 30.  Diseases associated with motor protein defects The importance of motor proteins in cells becomes evident when they fail to fulfill their function. e.g Dynein deficiencies can lead to chronic infections of the respiratory tract as cilia fail to function without dynein. Defects in muscular myosin predictably cause myopathies and damaged muscle tissue. Misfolded Proteins and Neurodegenerative Diseases Accumulation of misfolded proteins can cause disease, and unfortunately some of these diseases, known as amyloid diseases, are very common. The most prevalent one is Alzheimer's disease, which affects about 10 percent of the adult population. Parkinson's disease and Huntington's disease have similar amyloid origins. Misfolded Proteins and Neurodegenerative Diseases.  Summary 1. Protein structural support, storage, movement. 2. Protein synthesis & elements in a protein. 3. Protein secretion. 4. Proteins – Multiple Peptides. 5. Phosphorylation/Dephosphorylation. 6. There are three main types of fibers in the cytoskeleton: microtubules, microfilaments, and intermediate filaments. 7. Interactions of motor proteins and the cytoskeleton circulates materials within a cell via streaming. 8. Diseases associated with motor protein defects.