Human Physiology- Chapter 3 summary
Human Physiology- Chapter 3 summary BIOL 2213
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This 11 page Class Notes was uploaded by Celine Notetaker on Thursday January 21, 2016. The Class Notes belongs to BIOL 2213 at University of Arkansas taught by Dr. Hill in Fall 2014. Since its upload, it has received 27 views. For similar materials see Human Physiology in Biology at University of Arkansas.
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Date Created: 01/21/16
Chapter 3 – Cellular Structure, Proteins, and Metabolism Mitochondria: The function of mitochondria is to facilitate the chemical processes that transfer energy from the chemical bonds of nutrient molecules to newly created adenosine triphosphate. Mitochondria are spherical and elongated that have an inner and outer membrane which is folded into sheets. Ribosomes: The function of ribosomes is to synthesize proteins from amino acids, using genetic information carried by RNA messenger molecules from DNA. Ribosomes are large particles that are composed of 7080% protein and several ribosomal RNA molecules. They consist of 2 subunits that are either free floating in the cytoplasm or bound to rough ER. Rough Endoplasmic Reticulum: The function of rough ER is to package proteins that are created by the ribosomes. Rough ER is an extensive network of membranes that has ribosomes attached to its surface and has a flattenedsac appearance. Smooth Endoplasmic Reticulum: The function of smooth ER is to synthesize certain lipid molecules, detoxify certain hydrophobic molecules, and store and release calcium ions involved in controlling various cell activities. Smooth ER is a network of membranes that has a flattened sac appearance. Unlike rough ER, it has no ribosomes attached to the surface. Golgi apparatus: The function of the Golgi apparatus is to modify proteins, such as forming glycoproteins, and sorting proteins into discrete classes of transport vesicles that travel to various cell organelles or the plasma membrane. The Golgi apparatus is a series of closely apposed, flattened membranous sacs that are slightly curved, forming a cupshaped structure. Spherical vesicles surround the Golgi apparatus. Cell Membrane: All membranes consist of a double layer of phospholipids and other minor lipids which contain embedded proteins. Membranes, since nothing is chemically bonded together, have considerable lateral movement of both membrane lipids and proteins. Therefore, the lipid bilayer has fluid characteristics. Functions of the plasma membrane include: 1. Regulating the passage of substances into and out of cells and between cell organelles. 2. Detect chemical messengers arriving at the cell surface. 3. Link adjacent cells together by membrane junctions. 4. Anchor cells to the extracellular matrix. Cell Membranes contain 2 types of protein: 1. Integral Membrane Proteins – these cannot be extracted from the membrane without disrupting the phospholipid bilayer. They are amphipathic, which means they have both a polar amino acid side chains and nonpolar side chains in different regions. Most integral proteins span the entire membrane and cross the bilayer several times. Functions of integral proteins include forming channels in which ions can pass through the membrane, transmission of chemical signals across the membrane, and anchoring extracellular and intracellular protein filaments to the plasma membrane. Integral proteins that span the entire membrane are called transmembrane proteins. 2. Peripheral Membrane Proteins – these proteins are not amphipathic. They are bound to the polar surface of the bilayer. Most of these proteins reside on the cytosolic surface and aid in influencing the cell’s shape and motility. Membrane Junctions – plasma membrane are involved in the interaction between other cells to form tissues. Integrins are the transmembrane proteins that bind to proteins in the extracellular matrix that are linked to integrins on adjacent cells. If integrins are not involved, certain junctions are responsible for physically joining together 2 cells. 1. Desmosomes Desmosomes are composed of “dense plaque” protein on the cytoplasmic side of adjacent cells. The dense plaque is held to the cytoskeleton by keratin filaments. The dense plaque serves as an anchoring point for cadherins, proteins that extend from the cell into the extracellular space, where they bind with cadherins of adjacent cells. Desmosomes are very strong and provide structural integrity to areas subject to stretching, such as the skin. Desmosomes are diskshaped. 2. Tight Junctions Tight Junctions from when the extracellular surfaces of two adjacent cells combine, so that no extracellular space remains between them. Tight junctions form a band around the entire cell. Tight junctions are the main junction in the apical portion of epithelial cells. The tight junctions serve to not let anything pass in between the cells in the extracellular space. This is apparent in the small intestine, where organic nutrients must pass through the plasma membranes of the epithelial cells themselves to enter the bloodstream. However, ions and water can pass between the cells. 3. Gap Junctions Gap junctions are protein channels that link the cytosols of adjacent cells. These proteins are called connexons. These protein channels are very small so that only small molecules are ions can pass through. Gap junctions are apparent in the muscle cells of the heart, where they transmit electrical activity. Nucleus: The function of the nucleus is to store and transmit genetic information to the next generation of cells. This genetic information is encoded in DNA that creates proteins that determine the structure and function of the cell. The nucleus is surrounded by a double membrane, called the nuclear envelope. At certain points, the two membranes join together to form nuclear pores. mRNA leaves the nucleus through the nuclear pores while proteins enter to help regulate gene expression. Within the nucleus is a dense structure called the nucleolus, which contains specific DNA that code for ribosomal RNA formation. In addition, the nucleolus forms ribosomes. Cytoskeleton: This is a filamentous network that is associated with maintaining and changing cell shape and producing cell movements. There are 3 classes of cytoskeleton filaments made of proteins. 1. Actin – these proteins are made of the monomer, Gactin, which assemble into a polymer of 2 twisting chains, known as Faction. Actin have roles in determining cell shape, moving the cell with amoeboidlike movements, cell division, and muscle cell contraction. 2. Intermediate Filaments – these are composed of twisted strands of several different proteins, including keratin, desmin, and lamin. These filaments help determine cell shape and anchor the nucleus. They provide considerable strength and are therefore associated with desmosomes. 3. Microtubules – these are composed of the protein, tubulin. They are the most rigid filament and are present in neurons, which help maintain the cylindrical shape. Microtubules make up centrioles, which exist in pairs to form the centrosome, which can control the lengths of its radiating microtubules during cell division. Microtubules help control the movement of cell organelles. Finally, microtubules are present in cilia along with contractile protein to move items through lumens or the esophagus. Proteins: Proteins have a lot of different functions so protein synthesis is occurring all the time. Protein is synthesized through the following steps: DNATranscription RNATranslationProtein → → A gene is a specific sequence of DNA nucleotides that code for a specific sequence of amino acids to form a single polypeptide chain. Each DNA molecule has many genes and is packed, along with histones, into a single chromosome. 1. Transcription (mRNA synthesis) – This takes place in the nucleus. DNA unzips. Free ribonucleotides pair with their respective nucleotides in DNA. The aligned ribonucleotides are joined together by RNA polymerase. Once the RNA has been formed, it leaves the nucleus and binds to ribosomes in the cytoplasm. However, right before it leaves, it undergoes splicing to remove any sequences corresponding to DNA introns. Once this occurs, it becomes mRNA. Each 3base sequence of mRNA is called a codon, which codes for a specific amino acid. 2. Translation (Polypeptide Synthesis) – mRNA passes through the nuclear pores where it binds to a ribosome. The process of assembling a polypeptide chain is a 3step process: a. Initiation – tRNA binds to the small ribosomal subunit based on the codon anticodon pairing. The large ribosomal subunit then encloses the mRNA. b. Elongation – the tRNA continues pairing up with mRNA based on the anticodons. The tRNA carries an amino acid specific to the anticodon. Ribosomal enzymes facilitate the linking of the amino acids through peptide bonds. The ribosome continues moving down the mRNA strand as tRNA continues providing amino acids. Once the ribosome has moved on, cytoplasmic enzymes break down mRNA to reform free floating nucleotides. c. Termination – a termination sequence is reached, and the completed protein is released from the ribosome. Mutations: a mutation is any alteration in the nucleotide sequence of DNA. If DNA is mutated, a nonfunctional protein forms, which could lead to the death of the cell because proteins are needed for the cell’s survival. A mutation may have 1 of 3 effects: 1. It may cause no noticeable change in cell function 2. It may modify the cell function but still be compatible with cell growth and replication 3. It may lead to cell death Ligands: A ligand is any molecule or ion that is bound to a protein by one of the following forces: 1) electrical attraction between oppositely charged ionic or polarized covalent groups on the ligand and protein or 2) weaker attractions due to hydrophobic forces between nonpolar regions on the 2 molecules. Neither of these bonds are covalent bonds. Ligands bind to proteins on the proteins’ binding sites. Factors that affect binding include: 1. Affinity – the strength of the ligandprotein binding. This determines how likely it is that a ligand will leave the protein site. Different proteins can bind to the same ligand, but have different affinities for those ligands. 2. Saturation – refers to the fraction of total binding sites that are occupied at any given time. This is determined by 1) the concentration of unbound ligand in solution and 2) the affinity of the binding site for the ligand. 3. Competition – more than one ligand can bind to certain binding sites. My drugs produce their affects by competing with the body’s natural ligands for binding sites. Regulation of Binding Sites: 2 mechanisms found in cells that can alter protein shape are known as allosteric modulation and covalent modulation. 1. Allosteric Modulation – When a ligand binds to a protein, the attractive forces change the proteins shape. This change in shape at the binding site alters the protein shape at other sites, especially if it has a 2 binding site. So, allosteric proteins are ones which have 2 binding sites, a functional site, and a regulatory site. The ligand that binds to the regulatory site is called the modulator molecule and makes the protein’s regulatory site functional for a specific ligand. The ligand binding to the regulatory site changes the activity of the functional site. 2. Covalent Modulation – Certain chemical groups covalently bond to the protein’s side chains. The most common chemical reaction is the addition of phosphorus, called phosphorylation. Kinase is the enzyme that phosphorylates the protein, using ATP. Phosphatase is the enzyme that removes the phosphate from protein using water. The difference between covalent and allosteric modulation is that allosteric modulation has 2 specific binding sites. Metabolism: metabolism involves the synthesis and breakdown of organic molecules. Anabolism is the synthesis of organic molecules while catabolism is the breakdown of organic molecules. Chemical Reactions: involve breaking down chemical bonds of reactants and making new chemical bonds to form a new product. Factors that affect chemical reactions include: 1. Reversible Reaction – Reactions that reach a chemical equilibrium 2. Irreversible Reaction – Reactions that release large quantities of energy. Since the reactants are going to a much more stable product, a large amount of energy is released. Law of Mass Action: The direction of a chemical reaction is determined in part by the concentrations of reactant and product. Enzymes: enzymes are protein molecules that come into contact with substrates at the active site. The substrate binds to the enzyme which then breaks down to release products. The enzyme can be used over and over again. For example, the enzyme responsible for breaking down carbonic acid into carbon dioxide and water is carbonic anhydrase. 1. Cofactors – substances that activate the enzyme, which is a form of allosteric modulation. 2. Coenzymes – a cofactor that is an organic molecule which directly participates as one of the substrates. Coenzymes, like normal enzymes and unlike substrates, can act over and over again. Factors that affect enzyme catalyzed reactions are: 1. Substrate Concentration – increases in substrate concentration increase reaction rate 2. Enzyme Concentration – increases in enzyme concentration increase reaction rate 3. Enzyme Activity – changes in allosteric or covalent modulation affect reaction rate Multienzyme Reaction (Metabolic Pathway): The metabolic pathway is a sequence of enzyme mediated reactions leading to the formation of a particular product. Cellular Respiration: Cells use 3 distinct but linked metabolic pathways to transfer energy released from the breakdown of nutrient molecules to form ATP. 1. Glycolysis 2. Krebs Cycle 3. Oxidative Phosphorylation and the Electron Transfer Chain Glycolysis Characteristics of Glycolysis Entering Substrate Glucose + Coenzyme Production 2 NADH + 2 H Aerobic Products 2 Pyruvate Anaerobic Products 2 Lactate Net ATP Produced 2 Krebs Cycle Characteristics of the Krebs Cycle Pyruvate to Entering Substrate Acetyl Coenzyme A (Produces 2 CO 2 1 for each Pyruvate) 3 NADH Coenzyme Production 3 H + 2 FADH 2 Important Ketoglutarate (5C) Intermediates Oxaloacetate (4C) Final Products 4 CO 2 Oxidative Phosphorylation Oxidative Phosphorylation Entering NADH + H + Substrates FADH 2 2 – 3 ATP from each NADH + H + ATP Production 1 – 2 ATP from each FADH 2 Final Products H 2 for each pair of hydrogens entering pathway C H O +6O →6 H O+6CO +686kcal/mol Carbohydrate Metabolism: 6 12 6 2 2 2 Glycogen Storage: Glucose can be stored in the body as an energy reserve. It is stored in the body as glycogen. To form glycogen, ATP provides one phosphate to phosphorylate glucose. Thus, after the first step of glycolysis, glucose can be either used to produce ATP or to form glycogen. When an abundance of glucose is available, enzymes in a glycogen synthesis pathway are activated and those enzymes that break down glycogen are inhibited and vice versa. Glycogenolysis is the process that breaks down glycogen to glucose6phosphate. Glucose Synthesis: As described above, glucose can be formed in the liver from the breakdown of glycogen in glycogenolysis. However, it can also be synthesized in the liver and kidneys from intermediates derived from the catabolism of glycerol (sugar alcohol) and amino acids. This process is known as gluconeogenesis. 1. Substrate is pyruvate/lactate/glycerol and amino acids Fat Metabolism: 1. Fat Catabolism: Triglycerides consist of 3 fatty acids and a glycerol. Most fat is stored in adipocytes, which form adipose tissue. a. Coenzyme A links to the carboxyl end of the fatty acid, breaking down ATP to AMP in the process. b. The coenzyme A derivative goes through beta oxidation, which splits a molecule of acetyl coenzyme A from the fatty acid and transfers 2 pairs of hydrogen atoms + to the coenzymes, FAD and NAD . c. FADH and2 ADH then enter oxidativephosphorylation to form ATP. The coenzyme A shortens the fatty acid chain by 2 carbons every time it attaches, and then splits off. 2. Fat Anabolism (Synthesis) a. Acetyl coenzyme A links to another molecule to form a 4carbon chain. So, fatty acids are built up 2 carbons at a time. Then, triglycerides are formed by linking the fatty acids to the hydroxyl groups on glycerol. b. In this process, acetyl coenzyme A can be formed from pyruvate, the end product of glycolysis. Protein Metabolism: 1. Protein Catabolism: Protein anabolism is a straightforward process. Protein catabolism makes use of a few enzymes that are collectively called proteases. Proteases break the peptide bonds between amino acids. These amino acids can either be used to provide energy for ATP synthesis or can be part of other reactions, such as gluconeogenesis. a. Oxidative Deamination – Amino acids contain a nitrogen group. Once this is removed, the organic molecule can be metabolized to intermediates that can enter glycolysis or the Krebs cycle. Oxidative deamination is the process of removing this nitrogen to form NH 3nd a keto acid. i. The NH i3 highly toxic to cells so the liver makes it into urea, which is the major nitrogenous waste product of protein catabolism. b. Transamination – Transamination is the second process that can remove an amino acid. The amino group is transferred from the amino acid to a keto acid, which then becomes an amino acid. 2. Protein Anabolism: During the Krebs cycle, one of the intermediates is ketoglutarate, which can be transaminated to form glutamate alanine. Therefore, glucose can be used to form certain amino acids, provided that other amino acids are available for transamination to occur. Only 11 of the 20 amino acids can be formed this way. The other 9 are called essential amino acids that must be obtained through the diet. Therefore, in summary, amino acid pool in the body can accumulate in 3 ways: a. Ingested protein which is degraded by proteases into amino acids in the small intestine. b. The synthesis of nonessential amino acids from keto acids derived from carbohydrates and fat in the Krebs cycle. c. The continuous breakdown of body proteins.
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