Sinai University Biochemistry 1: Cell Biology PDF

Biochemistry 1 Cell Biology Dr. Esraa M. Elnshar Lecturer of Chemistry, Sinai university 2 Quizzes: 2 x 7.5 = 15 marks assignment = 15 marks Midterm exam = 20 Marks Final Exam = 50 Marks Biochemistry Study of the chemical processes occurring in living organisms. Combinati...

Biochemistry 1 Cell Biology Dr. Esraa M. Elnshar Lecturer of Chemistry, Sinai university 2 Quizzes: 2 x 7.5 = 15 marks assignment = 15 marks Midterm exam = 20 Marks Final Exam = 50 Marks Biochemistry Study of the chemical processes occurring in living organisms. Combination of Biology and chemistry. gives an idea about structure and interactions of biological macromolecules with the cells. Biomolecules are included macromolecules like Carbohydrates, protein, lipid and nucleic acids. Biochemistry and medicine are related. Health depends on a balance of biochemical reactions occurring in the body, and disease reflects abnormalities in biomolecules and biochemical processes.  Cell Biology The branch deals with the structure and functions of cells in living organisms. The cell biology branch of biochemistry is also called Cytology. Cell biology is essential to understand the cellular processes that cells carry out during their life cycle, like respiration, nutrition, cell division, defense mechanisms, cell death, etc.  The cell is the smallest unit of all living organisms. Tissue is a group of cells with similar structure and function. Tissues are grouped to form organ. Group of organs work together to form organism. Organisms can be classified as unicellular (consisting of a single cell including most bacteria) or multicellular (including plants and animals).  Composition of cell Cells are composed of micromolecules as water, inorganic ions [including sodium (Na+), potassium (K+), magnesium (Mg2+), calcium (Ca2+)] and carbon-containing molecules [including macromolecules]. Water is the main component in cells, accounting for 70% or more of total cell mass. The cell structure comprises individual components included cell membrane, cytoplasm, nucleus, and cell organelles [Chromosomes, Endoplasmic Reticulum, Ribosome, Mitochondria, Lysosomes,….].  Types of cell prokaryotic and eukaryotic cells  prokaryotes eukaryotes Type of Cell Always unicellular Unicellular and multi-cellular much larger than prokaryote Very small (size from 0.2 μm Cell size [Size from 10 μm – 100 μm in – 2.0 μm) in diameter diameter] No nucleus, No nuclear True nucleus with nuclear Nucleus membrane, they have membrane a nucleoid region in the cell Cell Membrane present present Present. Smaller in size and Present. Comparatively larger Ribosomes spherical in shape in size and linear in shape DNA arrangement Single chromosome, Circular Linear Cytoplasm Present Present Organelles (Endoplasmic Absent present reticulum, Mitochondria) Only in plant cells and fungi Cell wall Usually chemically complex (chemically simpler) Cell division Through binary fission Through mitosis The flagella are smaller in Flagella The flagella are larger in size size Reproduction Asexual Both asexual and sexual Example Bacteria Plant and human cell  Cell Membrane The cell membrane (also known as the plasma membrane) separates the inner contents of a cell from its exterior environment. Under the electron microscope it is seen to consist of two outer dark layers, with a clearer inner layer.  Molecular structure and composition of Cell membrane Membranes consist of a lipid bilayer, which is a double layer of phospholipid, sterol (cholesterol), and glycolipid molecules. Embedded in the lipid bilayer are large proteins. Attached to proteins on the outside of the plasma membrane are long carbohydrate molecules.  Cell membrane lipids Phospholipids are the most abundant lipid in the plasma membrane Phospholipids consist of two fatty acid chains make lipid tails (hydrophobic) linked to glycerol and a phosphate group with negative charge, making the head polar (hydrophilic). Phospholipids are amphipathic molecules, containing hydrophobic and hydrophilic region The cell membrane consists of two adjacent layers of phospholipids. The lipid tails of one layer face the lipid tails of the other layer, meeting at the interface of the two layers. The phospholipid heads face outward, as the phosphate groups are polar and hydrophilic, they are attracted to water in the intracellular fluid (the fluid interior of the cell). The phosphate groups are also attracted to the extracellular fluid (the fluid environment outside the enclosure of the cell membrane) by H-bonds. Because the lipid tails are hydrophobic, they meet in the inner region of the membrane, excluding watery intracellular and extracellular fluid from this space.  In this way, they form a barrier of a double layer of phospholipids that separates the interior and exterior of the cell, because water and other polar or charged substances cannot easily cross the hydrophobic core of the membrane. So phospholipid is impermeable membrane.  Phospholipids heated in an aqueous solution tend to spontaneously form small spheres or droplets (called micelles or liposomes), with their hydrophilic heads forming the exterior and their hydrophobic tails on the inside. Lipid bilayer Lipid single-layer Cholesterol is another lipid component of animal cell membranes. Cholesterol molecules are selectively dispersed between membrane phospholipids (hydrophobic rings interact with hydrophobic tails). This helps to keep cell membranes rigid. Cholesterol is not found in the membranes of plant cells. Glycolipids are located on cell membrane surfaces and have a carbohydrate sugar chain attached to them. They help the cell to recognize other cells of the body (marker).  Proteins Proteins are the second major component of plasma membranes that may extend partway into the plasma membrane, cross the membrane completely, or be loosely attached to its inside or outside face. Two different types of proteins that are commonly associated with the cell membrane are the integral protein and peripheral protein.  Integral protein is embedded in the membrane. a) Completely hidden: they have at least one hydrophobic region that anchors them to the hydrophobic core of the phospholipid bilayer. b) Partly hidden: stick only partway into the membrane, the hydrophobic part and partly attached to the hydrophilic heads c) while others hydrophilic stretched from one side of the membrane to the other and are exposed on either side. Proteins that extend all the way across the membrane are called transmembrane proteins. Some integral membrane proteins form a channel that allows ions or other small molecules to pass is known as a channel protein. Peripheral proteins are typically found on the inner or outer surface of the lipid bilayer attached either to integral proteins or to phospholipids by hydrophilic interactions. Functions of membrane proteins: 1.Enzymes activity. 2. Acting as antigens, or receptors for hormones. 3. Acting as transport proteins (channels) for transport of small molecules. 4. Glycoproteins (recognizing the cell and Develop cell adhesion to other neighboring cells by means of interaction between their surface glycoproteins).  Carbohydrates The third component of the plasma membrane are carbohydrates. They are generally found on the exterior surface of membrane and linked either to lipids to form glycolipids or proteins to form glycoproteins. On the exterior surface of cells, these carbohydrates, their components of both glycolipids and glycoproteins are together known as glycocalyx, which is extremely hydrophilic in nature attracting huge quantities of water on the cell surface. Functions: Identify the cell as marker that is important in the immune system, allowing immune cells to differentiate between body cells, which they shouldn’t attack, and foreign cells or tissues, which they should. Receptor helps the cell to acquire substances dissolved in water. Cell adhesion to other neighboring cells by means of interaction.  Fluid mosaic model S.J. Singer and Garth L. Nicolson This model explains the structure of the plasma membrane of animal cells as a mosaic of components such as phospholipids, proteins, cholesterol, and carbohydrates. These components give a fluid character to the membranes. Membrane fluidity The fluidity of the cell membrane is influenced by three factors: 1) The structure of the fatty acid tails of the phospholipids. Saturated fatty acid chains have a single bond between the carbon atoms whereas, unsaturated fatty acid chains have double bonds between the carbon atoms. Unsaturated double bonds make it harder for the chain to pack tightly by creating kinks. These kinks increase the fluidity of the membrane. And saturated with straight tails, make the membrane less fluid. 2) Temperature when it is cold, the straight tails of saturated fatty acids can pack tightly together, making a dense and fairly rigid membrane. When it’s hot, unsaturated fatty acid tails cannot pack together as tightly because of the kink structure of the tails So a membrane will stay fluid. 3) Cholesterol The cholesterol molecules are randomly distributed along the phospholipid bilayer and hold it preventing it from separating too far, or compact too tightly. minimize the effects of temperature on fluidity. An increase in its ratio decrease fluidity Functions of cell (biological) membranes: (1) Support the cell organelles and help maintain its shape. (2) This cell membrane provides a protective barrier around the cell and regulates which materials can pass in or out. (3) exhibits selective permeability, allowing some molecules to enter or leave the cell while restricting the passage of others [ lipid make the cell impermeable to all hydrophilic molecules while proteins allow the movement of hydrophilic molecules through the membrane] (4) contain receptors and channels that allow specific molecules, such as ions, nutrients, wastes, and metabolic products, that mediate cellular and extracellular activities between the cell and the outside environment (5) regulate the concentration of substances inside the cell. These substances include ions such as Ca++, Na+, K+, and Cl–, nutrients including sugars, fatty acids, and amino acids, and waste products, particularly carbon dioxide (CO2), which must leave the cell.  Membrane transport 1. Transport of small molecules either by passive diffusion or by active transport. 2. Transport of large molecules either by endocytosis or exocytosis. Transport of small molecules Passive transport is the movement of substances across the membrane without consumption of any cellular energy. In contrast, active transport is the movement of substances across the membrane using energy from adenosine triphosphate (ATP)  passive diffusion Passive transport is a naturally occurring phenomenon and does not require the cell to exert any of its metabolic energy to accomplish the movement. substances move from an area of higher concentration to an area of lower concentration to reach equilibrium (down concentration gradient). A concentration gradient is the difference in concentration of a substance across a space. (simple diffusion or facilitated diffusion)  Simple diffusion Small substances that can easily diffuse through the lipid bilayer of the cell membrane, such as the gases oxygen (O2) and carbon dioxide (CO2) or other small lipid soluble molecules that can dissolve in the membrane and enter or exit the cell following their concentration gradient. O2 diffuses into cells because it is more concentrated outside of them, and CO2 typically diffuses out of cells because it is more concentrated inside of them.  Facilitated diffusion The diffusion process used for substances that cannot cross the lipid bilayer due to their charge, and polarity. Solutes dissolved in water on either side of the cell membrane will tend to diffuse down their concentration gradients, but because most substances cannot pass freely through the lipid bilayer of the cell membrane, their movement is restricted to facilitated transport protein in the membrane shield these materials from the repulsive force of the membrane, allowing them to diffuse into the cell. Two classes of proteins that mediate facilitated diffusion are generally: carrier proteins and channel proteins. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids; they additionally have a hydrophilic channel through their core that provides a hydrated opening through the membrane layers. Passage through the channel allows polar compounds to avoid the nonpolar central layer of the plasma membrane that would otherwise slow or prevent their entry into the cell. Carrier proteins bind a substance to specific sites on the carrier protein and undergo conformational changes that allow the molecule to pass through the membrane depending on the gradient. Each carrier protein is specific to one substance. Substance → binding site → substance protein complex →conformational changes → release of substance.  Active transport The movement of particles through a transport protein from low concentration to high concentration required metabolic energy. Molecules are moved across the cell membrane against their concentration gradient (away from equilibrium). The sodium–potassium (Na+, K+) pump is an integral membrane protein that pumps Na+ out of a cell and K+ in. One molecule of ATP moves two K+ and three Na+ ions. The most common energy source used by cells is adenosine triphosphate or ATP required to change the nature of transporter proteins. Transport of macromolecules (Large molecules) (1) endocytosis moves particles, such as large molecules from extracellular space into a cell, Require energy. The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created intracellular vesicle formed from the plasma membrane. The three types of endocytosis are phagocytosis, pinocytosis, and receptor-mediated endocytosis. Exocytosis The reverse process of moving material into a cell (require energy). The purpose of exocytosis is to release material from the cell into the extracellular fluid. Waste material is enveloped in vesicle, which fuses with the interior of the plasma membrane, expelling the waste material into the extracellular space. Cells also use exocytosis to secrete proteins such as hormones, neurotransmitters.  Cytoplasm They are jelly-like substances, found between the cell membrane and nucleus. It composed of water, organic and inorganic compounds and holds all the cell organelles. These cell organelles contain enzymes, mainly responsible for controlling all metabolic activity taking place within the cell and are the site for most of the chemical reactions within a cell.  Nucleus It is located in the center of the cell and is usually spherical in shape, contain most of cell’s genetic information (DNA). It consists of nuclear envelop, nucleolus and chromatin suspended is the nucleoplasm. The nuclear envelop separated nucleus from the cytoplasm. This membrane contains 2 membranes, porous and allows the movement of selective materials between the cytoplasm and the inside of the nucleus. Chromatin is a combination of DNA and other helper proteins (Histones) found inside the nucleus. Nucleolus is small spherical body in the nucleus, produces ribosomes, the cell's protein-producing structures Function of nucleus: The nucleus controls and regulates the activities of the cell (e.g., cell growth, protein synthesis and metabolism) and carries the genes, structures that contain the genetic information.  Mitochondria Mitochondria are membrane- bound cell organelles found in the cytoplasm of almost all eukaryotic cells that comprises an outer membrane, an inner membrane, and a gel-like material called the matrix. The two membranes are made of proteins and phospholipid layers separated by the intermembrane space. The outer membrane has a large number of special proteins known as porins. The inner membrane contains folds that form a layered structure called cristae. Matrix, the space within the inner membrane. Containing enzymes, it is important in the production of ATP. Function of Mitochondria  generate most of the chemical energy in the form of adenosine triphosphate (ATP) needed to power the cell's biochemical reactions (called power of the cell)  Responsible of cellular respiration  Regulates the metabolic activity of the cell  Controlling cell growth and death.