Module 2.2 Cellular Basis of Life PDF

MODULE 2.1 CELLULAR BASIS OF LIFE The cell is the basic unit of structure and function of a living organism. Take note that living organisms could either be unicellular (consist of a single cell) or multicellular (made of two or mor...

MODULE 2.1 CELLULAR BASIS OF LIFE The cell is the basic unit of structure and function of a living organism. Take note that living organisms could either be unicellular (consist of a single cell) or multicellular (made of two or more cells). Cells, on the other hand, could be prokaryotic or eukaryotic. Prokaryotic cells (bacteria) do not have membrane-bound nucleus and organelles. Other living organisms are eukaryotic, their nucleus and cell organelles are enclosed in a membrane. In Biochemistry, our study of cells focuses on the animal cell. The Cell: Parts and Functions The cell is the basic unit of life. All organisms are made up of cells (or in some cases, a single cell). Most cells are very small; most are invisible without using a microscope. Cells are covered by a cell membrane and come in many different shapes. The contents of a cell are called the protoplasm. I. Plasma Membrane The plasma membrane serves as the interface between the interior of the cell and the extracellular fluid (ECF) that bathes all cells.   The cell membrane regulates the exchange of vital substances between the content of the cells and it external environment.  it communicates with other cells to help the body function.  It is extremely thin (you could stack 10,000 plasma membranes to equal the thickness of a piece of paper). Made up of: 1. Phospholipids are amphiphilic with the hydrocarbon tail of the molecule being hydrophobic; its polar head hydrophilic. - As the plasma membrane faces watery solutions on both sides, its phospholipids accommodate this by forming a phospholipid bilayer with the hydrophobic tails facing each other. - Serves as "gateway + barrier for cell". The cell membrane isolate's the contents of the cell from the external environment. 2. Membrane proteins: One role of proteins in cells is for transport of molecules/ions into or out of cells. Three methods of doing this are through active, facilitated or passive transport. Other roles of membrane proteins are in cell recognition, receptors, cell to cell communication. 3. Cholesterol. Cholesterol breaks up the Van der Waals interactions and close packing of the phospholipid tails. This disruption makes the membrane more fluid. Therefore, one way for a cell to control the fluidity of its membrane is by regulating its level of cholesterol in the cell. Transport System in Cell Membrane Movement of small molecules across membranes can involve simple diffusion or protein- mediated transport Cell membranes are selectively permeable. 1. Passive Transport. a. Diffusion. A process of passive transport in which molecules move from an area of higher concentration to one of lower concentration until equilibrium in concentration is achieved. Substances move within the cell by diffusion, and certain materials move through the plasma membrane by diffusion, too. Lipophilic solutes cross the membrane freely by dissolving in the lipid bilayer. Examples: ethanol (alcohol, contains both polar and non-polar regions); also fatty acids, glycerol, steroids, etc. Also nonpolar gases like O=O (O2) b. Osmosis. The movement of water through a semipermeable membrane from areas of high to low concentration. When solutions of different osmolarities are separated by a membrane permeable to water, but not to solute, water will move from the side with lower osmolarity to the side with higher osmolarity. Three terms—hypotonic, isotonic, and hypertonic—are used to compare the osmolarity of a cell to the osmolarity of the extracellular fluid around it.  The solution is hypotonic when the extracellular fluid has lower osmolarity than the fluid inside the cell. (hypo means less than—to the cell, and the net flow of water will be into the cell).  The solution is hypertonic when the extracellular fluid has a higher osmolarity than the cell’s cytoplasm. (hyper means greater than—to the cell, and water will move out of the cell to the region of higher solute concentration).  In an isotonic solution there will be no net movement of water into or out of the cell. (iso means the same) 2. Selective transport by protein carriers = "permeases". Polar or ionic small solutes may be transported across membranes if specific protein carriers are in the membrane. Examples: sugars, amino acids, ions. Many substances cannot cross the membrane. Examples: large molecules such as proteins, nucleic acids. Also small polar molecules or ions for which there is no protein carrier. Some protein transporters require energy; others do not. 2 possible situations: a. facilitated diffusion. Membrane has specific protein carrier, will bind to molecule and bring it across cell membrane. No energy required. No preferential direction. If molecule is more concentrated outside than inside cell, net movement will be out of cell. i. Channel-mediated - a solute moves down its concentration gradient across the lipid bilayer through a membrane channel  - membrane channels are ion channels, integral transmembrane proteins that allow passage of small, inorganic ions that are too hydrophilic to penetrate the nonpolar interior of the lipid bilayer. ii. Carrier-mediated - a carrier (also called a transporter) is used to move a solute down its concentration gradient across the plasma membrane - solute binds to a specific carrier on one side of the membrane and is released on the other side after the carrier undergoes a change in shape b. active transport. Membrane has specific protein carrier, also a requirement for energy (ATP or other form of energy). Will move solute against a concentration gradient, so can concentrate material even if diffusion would favor opposite direction of flow. Example: Na+, K+ ATPase in nerve cells. Pumps Na+ to outside, K+ in, maintains electrical potential against diffusion. When nerve cell "fires", momentary gates open to let diffusion occur. Then pumps are turned back on to restore potential. Movement of Large Molecules: Endocytosis, Exocytosis, Phagocytosis, Carrier-Mediated Endocytosis 1. Large molecules (proteins, nucleic acids, polypeptides larger than a few amino acids, polysaccharides larger than a few sugars) are not carried by transport proteins. 2. There are mechanisms for moving larger molecules, but they don't enter into cytoplasm. - Exocytosis: membrane vesicle fuses with cell membrane, releases enclosed material to extracellular space. Ex: release of digestive enzymes from pancreatic cells; mucus, milk, hormones, etc - Endocytosis: cell membrane invaginates, pinches in, creates vesicle enclosing contents. Three common situations: i. Phagocytosis: Typically works on debris, bacteria, other particulate matter. Contents of the "phagosome" are usually fused with lysosome to create "phagolysosome", where material is broken down. Especially common in white blood cells such as macrophages and other leukocytes. ii. Pinocytosis: similar to phagocytosis, but ingests fluid rather than particulate matter. "Cell drinking". Ex. cells lining blood capillaries take fluid from blood (but not red cells), move fluid across their cytoplasm, release into extracellular space surrounding cells outside the capillary. iii. Carrier-mediated endocytosis (CME), aka receptor-mediated endocytosis: very specialized system. Certain important molecules or ions are not brought into cell by transport processes, but by CME. Ex. iron is carried through blood tightly bound to transferrin protein carrier. To get iron into cells, cell membrane contains special receptor proteins that bind transferrin, move towards special regions of membrane under which lie clathrin proteins. Endocytosis occurs inside clathrin "cage", moves inside cell. Cage eventually recycles back to cell surface, returning transferrin proteins to cell exterior. However, iron is released inside cell, exits from vesicles, becomes bound to ferritin. Molecule Mode of Transportation O2 Diffusion CO2 Diffusion H2O Osmosis Glucose (C6H12O2) Facilitated Diffusion Ions Special Transport Large Solids (starch) Phagocytosis Large Liquids (oils Pinocytosis Hormones Receptor-Mediated II. Protoplasm B. The Cytoplasm  made up of all of a cell's internal contents, so all the organelles except the nucleus.  composed of 65% water, with as much as a billion molecules contained within the cytoplasm of one single cell.  contains enzymes, and dissolved nutrients like amino acids and sugars.  The water allows for reactions to occur within the cell Cellular structures and organelles: 1. Ribosomes  for synthesizing proteins  Large assemblies of RNA + dozens of different proteins, synthesized in nucleolus in eukaryotes  Proteins are synthesized through the formation of peptide bonds between amino acids. POLYPEPTIDES are long chains of amino acids  found free in the cytoplasm in both eukaryotes and prokaryotes or bound to endoplasmic reticulum in eukaryotes ==> rough ER 2. Endoplasmic Reticulum:  A network of flattened, interweaving tubules which are formed by membranes within the cell. They create mazes of narrow channels.   ER is continuous with the Nuclear Envelope -- nuclear membrane is part of the endomembrane syst.  Rough ER -- contains many bound ribosomes which bind to the ER after beginning synthesis of proteins which are to be secreted into the lumen. The proteins are then carried through the ER membrane as they are synthesized.  Smooth ER -- connected to rough ER; no ribosomes 3. Golgi Complex  The Golgi body consists of layers of sacs. These sacs have a very thin membrane. Vesicles are pinching off the edges of the sacs.  it acts in the modification of lipids and proteins.  it serves to store and package materials for exportation from the cell. The Golgi body works together with the vesicles. They move back and forth from the organelle to the cell membrane carrying the packaged materials to the outside of the cell.  Golgi modifies products of ER 4. Lysosomes  Made from ER: ---> Golgi ---> Lysosomes  Compartment surrounded by membrane which contains enzymes to digest (hydrolyze) macromolecules, proteins polysaccharides, fats, nucleic acids. - membrane keeps enzymes from digesting functional parts of the cell - maintains low pH (approx. 5) where these digestive enzymes are most active  Used to digest: - external material by engulfing into vesicles (Phagocytosis) which then fuse with lysosomes - digest and recycle cellular materials -- engulfs damaged organelles 5. Peroxisomes  Some of the functions of the peroxisomes in the human liver: - Breakdown (by oxidation) of excess fatty acids. - Breakdown of hydrogen peroxide (H2O2), a potentially dangerous product of fatty-acid oxidation. It is catalyzed by the enzyme catalase. - Participates in the synthesis of cholesterol - Participates in the synthesis of bile acids. - Participates in the synthesis of the lipids used to make myelin. - Breakdown of excess purines (AMP, GMP) to uric acid 6. Mitochondria  Function: Cellular Respiration -- oxidize intermediate products of metabolism to CO2 and H2O; excess free energy transformed into synthesis of ATP  Structure - Approximately 1 μ in diameter; may be very long in some cells - 2 membranes - inner membrane and outer membrane - inner membrane has large surface area and folds inward forming cristae; contains membrane proteins responsible for respiration and ATP synthesis - outer membrane is a sieve permeable to small molecules; intermembrane space is similar to cytoplasm in concentration of small molecules - matrix - contains enzymes responsible for many steps of metabolism - contains DNA molecule 7. The Cytoskeleton  Cells contain elaborate arrays of protein fibers that serve such functions as: - establishing cell shape - providing mechanical strength - locomotion - chromosome separation in mitosis and meiosis - intracellular transport of organelles  The cytoskeleton is made up of three kinds of protein filaments: 1. Actin filaments (also called microfilaments). Monomers of the protein actin polymerize to form long, thin fibers. These are about 8 nm in diameter and, being the thinnest of the cytoskeletal filaments: - form a band just beneath the plasma membrane that  provides mechanical strength to the cell  links transmembrane proteins (e.g., cell surface receptors) to cytoplasmic proteins  anchors the centrosomes at opposite poles of the cell during mitosis  pinches dividing animal cells apart during cytokinesis - generate cytoplasmic streaming in some cells - generate locomotion in cells such as white blood cells and the amoeba - interact with myosin ("thick") filaments in skeletal muscle fibers to provide the force of muscular contraction  2. Intermediate filaments. These cytoplasmic fibers average 10 nm in diameter (and thus are "intermediate" in size between actin filaments (8 nm) and microtubules (25 nm) (as well as of the thick filaments of skeletal muscle fibers). 3. Microtubules are straight, hollow cylinders - have a diameter of about 25 nm; are variable in length but can grow 1000 times as long as they are thick - built by the assembly of dimers of alpha tubulin and beta tubulin. - Microtubules participate in a wide variety of cell activities. Most involve motion. The motion is provided by protein "motors" that use the energy of ATP to move along the microtubule. C. Nucleus 1. Nuclear Envelope - double membrane surrounding the nucleus separating it from the rest of the cell - nuclear pores - pores through both membranes; formed by protein molecules; controls traffic of molecules between the cytoplasm and the nucleus - nuclear lamina - layer of proteins inside the nuclear membrane; may be responsible for stabilizing the nuclear membrane. - Nucleolus--where ribosomes are made 2. Chromosomes - DNA + proteins (histones) ==> chromatin which is dispersed through most of the nucleus. The proteins keep the very long DNA molecules organized. Chromatin is divided into individual units called chromosomes. - during cell division chromatin segregates into individual chromosomes - number of chromosomes depends upon type of cell; e.g. what organism and whether it is somatic or germ (reproductive) form. 3. Nucleolus - part of the nucleus responsible for synthesis of ribosomes needed for protein synthesis in the cytoplasm. Nucleolar Organizers are regions of chromosomes which contain multiple copies of genes for ribosome synthesis. FIVE TYPES OF METABOLIC REACTIONS Metabolism is a complex set of biochemical processes that occur within living organisms to maintain life. These processes can be categorized into several types of metabolic reactions. 1. Anabolic Reactions (Anabolism) - involve the synthesis of complex/large molecules from smaller molecules - requires energy - e.g. protein synthesis (protein biosynthesis), DNA replication, and the formation of polysaccharides 2. Catabolic Reactions (Catabolism) - involve the breakdown of complex/large molecules from smaller molecules - releases energy, which can be used for various cellular processes or stored for future use - e.g. breakdown of glucose through glycolysis, the digestion of food in the gastrointestinal tract, and the breakdown of fats (lipolysis) for energy production 3. Oxidation-Reduction Reactions (Redox Reactions) - involve the transfer of electrons between molecules - oxidation refers to the loss of electrons, while reduction involves the gain of electrons - crucial for energy production in cellular respiration and photosynthesis, as well as for the functioning of various enzymes and metabolic pathways 4. Hydrolysis Reactions - involve the cleavage of chemical bonds through the addition of water molecules - used to break down complex molecules, such as carbohydrates, proteins, and fats, into their constituent monomers - e.g. hydrolysis of sucrose into glucose and fructose and the digestion of proteins into amino acids 5. Phosphorylation and Dephosphorylation Reactions - Phosphorylation involves the addition of a phosphate group (usually from ATP) to a molecule, often to activate or deactivate it - Dephosphorylation is the removal of a phosphate group from a molecule - play a central role in the regulation of metabolic pathways and the control of enzyme activity FUNCTIONAL GROUPS IMPORTANT IN BIOMOLECULES The structures and reactions of organic compounds depend on the properties of the functional groups. These are groups of atoms, covalently attached to the relatively inert carbon backbone. Behavior of biomolecule may contain more than one functional group. Functional groups are distinct arrangements of atoms within biomolecules that confer unique chemical properties and reactivity. These groups are integral components of biomolecules, serving critical roles in biological processes. Hydroxyl groups (-OH) impart water solubility and hydrogen bonding capacity, while carbonyl groups (C=O) contribute to molecular reactivity. Carboxyl groups (-COOH) are both acidic and hydrophilic, and amino groups (-NH2) act as basic functional groups. Phosphate groups (-PO4) are central in energy storage and cell signaling, while sulfhydryl groups (-SH) participate in protein stabilization. Methyl groups (-CH3) are key in epigenetic modifications, and ester groups (-COO-) play a role in lipid structure. Amide groups (- CONH2) are crucial in the formation of proteins and nucleic acids, while alkyl groups contribute to hydrophobic interactions. The presence and arrangement of these functional groups dictate the biological functions and chemical reactivity of biomolecules, making them essential for life's processes.