Lecture 1: Biomolecules And Cells (Cells-Cytology) PDF

BIOMOLECULES AND CELLS: BIO 111 Mr. Derrick Banda MSc, BSc  How to get in touch with Mr Derrick Banda Office: Mulungushi University, Main Campus, SSET Offices E-mail: [email protected] or [email protected] Phone Number: +260974420585 : +260955556060  ME...

BIOMOLECULES AND CELLS: BIO 111 Mr. Derrick Banda MSc, BSc  How to get in touch with Mr Derrick Banda Office: Mulungushi University, Main Campus, SSET Offices E-mail: [email protected] or [email protected] Phone Number: +260974420585 : +260955556060  METHODS OF TEACHING Lectures: Four (4) hours per week ( Two (2) hours each lecture session) Tutorials: One (1) hour of tutorials per week Laboratory sessions: Three (3) hours per week  ASSESSMENT METHODS Continuous Assessment (CA): 40% Theory Quizzes : 5% Two (2) tests 20% Laboratory experiments 15% Final Examination 60% Maximal Score (CA + Final Exams) 100%  COURSE GRADINGS GRADE PERCENTAGE A+ 86 and above A 76-85 B+ 66-75 B 60-65 C+ 55-59 C 50-54 D Below 50  LECTURE 1: CELLS - CYTOLOGY  Introduction to Cells The living material of most organisms is organized into discrete units called cells. The study of cell and their features is known as cytology. The earliest phase of cytology began with the English scientist Robert Hooke’s microscopic investigations of cork (plant) in 1665.  How Did Cells Originate? In general terms, life can only have come from one of two possible places: 1. Spontaneous creation - Random chemical processes created the first living cell. This is the theory that most scientists today believe in today. It is believed by some scientists that the accidental creation of a single molecule of self-replicating RNA (similar to DNA) in the oceans of the world led to the eventual creation of cells. 2. Supernatural creation - God or some other supernatural power created the first living cell.  Levels of Organization of Living Things The biological levels of organization of living things arranged from the simplest to most complex are: atom, molecules, macromolecules, organelles, cells, tissues, organs, organ systems and organisms. HUMAN BEING  The Cell Theory The history of cell theory is a history of the actual observation of cells, because early prediction and speculation about the nature of the cell were generally unsuccessful. The decisive event that allowed the observation of cells was the invention of the microscope in the 16th century, after which interest in the “invisible” world was stimulated. The remarkable structural complexity of the cell is more fully revealed at the higher magnifications attainable with the electron microscope.  The Cell Theory English physicist Robert Hooke, who described cork and other plant tissues in 1665, introduced the term cell because the cellulose walls of dead cork cells reminded him of the blocks of cells occupied by monks. The term cells was coined by Hooke in this work, describing the pores observed in the cork.  The Cell Theory The magnifying powers of the microscope and the inadequacy of techniques for preparing cells for observation precluded a study of the intimate details of the cell contents. The inspired Dutch microscopist Antonie van Leeuwenhoek, beginning in 1673, discovered blood cells, spermatozoa, and a lively world of “animalcules.”  The Cell Theory German physiologist Theodor Schwann and German biologist Matthias Schleiden clearly stated in 1839 that cells are the “elementary particles of organisms” in both plants and animals and recognized that some organisms are unicellular and others multicellular.  The Cell Theory The cell theory was later extended by Rudolf Virchow to include the idea that all cells arise from existing cells. Rudolf Virchow, a German pathologist (1821–1902), famously wrote “omnis cellula e cellula”—all cells come from other cells.  Summary of the Cell Theory The generally accepted modern Cell Theory is as follows: 1. The cell is the fundamental unit of structure and function in living things. 2. All living organisms are made up of one or more cells. 3. All new cells arise only from pre-existing cells 4. All biochemical processes are carried out by cells. The cell theory established forms one of the unifying principles of biology.  Types of Cells Cells are of two types: eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular. Eukaryotic and Prokaryotic Cells  Prokaryotic Cells Prokaryotes are unicellular organisms that lack membrane-bound structures, the most noteworthy of which is the nucleus. They have cell membrane, cytoplasm and ribosomes. Prokaryotic cells tend to be small, simple cells, measuring around 1-10 μm in diameter. In prokaryotic cells, DNA bundles together in a region called the nucleoid. Prokaryotic organisms include bacteria and archea.  Prokaryotic Cells Prokaryotic cells tend to be small, simple cells, measuring around 1-10 μm in diameter.  Eukaryotic Cells Eukaryotic cells have a nucleus and other organelles enclosed by a plasma membrane. Organelles are internal structures responsible for a variety of functions, such as energy production and protein synthesis. Eukaryotic cells are large (around 10-100 μm) and complex. While most eukaryotes are multicellular organisms, there are some single-cell eukaryotes. Eukaryotic organisms include: Protozoans, Algae, Fungi, Plants and Animals  Eukaryotic Cells Eukaryotic cells are large (around 10-100 μm) and complex. While most eukaryotes are multicellular organisms, there are some single-cell eukaryotes.  Prokaryotic versus Eukaryotic Cells Prokaryotic cells and eukaryotic cells differ in a number of key features, including:  Organelles An organelle is a subcellular structure that has one or more specific jobs to perform in the cell, much like an organ does in the body. Cells organelles are found in the Cytoplasm. Within cells, each structure carries out specific cellular functions. Cell organelles are embedded in the cytoplasm and are divided into: Membrane-bounded organelles (rough and smooth endoplasmic reticulum, Golgi apparatus, mitochondria, chloroplasts (in plant cells) ,lysosomes, peroxisomes) Non-membrane-restricted organelles such as ribosomes or centrioles Cell Organelles  Cytoplasm The cytoplasm is the site in which the biochemical reactions of the cell take place. It is mainly composed of water, salts, and proteins. The primary semi-fluid component of the cytoplasm is known as the Cytosol. All of the organelles in eukaryotic cells, such as the nucleus, endoplasmic reticulum, and mitochondria, are located in the cytoplasm.  Cytoplasm In prokaryotes the cytoplasm encompasses everything within the plasma membrane, including the cytoskeleton and genetic material. In eukaryotic cells, the cytoplasm comprises everything between the plasma membrane and the nuclear envelope, including the organelles.  Nucleus The word 'nucleus' can mean the control centre of a cell or the centre of an atom. It is responsible for determining and controlling what a cell look like and what it does. The nucleus is the largest membranous organelle of the cell. It contains the chromosomes together with the machinery for DNA replication and RNA transcription and processing. The nucleus directs the process of protein synthesis in the cytoplasm by informational macromolecules (RNAs) formed in the nucleus and transported to the cytoplasm.  Parts of the Nucleus Parts of the nucleus includes; i. The nucleus envelope with nuclear pores encloses the nucleus and keeps it separated from the rest of the cell. ii. It contains chromatin, which is a substance within a chromosome consisting of DNA and protein (histones). iii. In the middle of the cell is the nucleolus which produces ribosomes, which are key in protein synthesis.  Nucleoid In contrast, the smaller prokaryotic cells have no nucleus. The materials are already fairly close to each other and there is only a "nucleoid" which is the central open region of the cell where the DNA is located.  Nucleoid Nucleoid is an area in the cytoplasm which houses the prokaryotes’ genetic material (DNA). It is an irregular-shaped region. The nucleoid is not surrounded by nuclear membranes, unlike eukaryotic nucleus. A single, circular chromosome can be found in the nucleoid of prokaryotes.  Mitochondria The mitochondria is the power house of the cell. Its only found in eukaryotic cell. It carries a process called aerobic respiration, which is breaking down of food and provide energy with the help of oxygen. They produce energy molecules called ATP (adenosine triphosphate) which is used as an energy currency powering everything the cell needs to do.  Mitochondria The mitochondrion has a fluid that fills the organelle containing enzymes and other compounds called the matrix. Inside the mitochondrion is the inner membrane which has folds called cristae. Mitochondria contain their own DNA and ribosomes.  Mitochondria Each mitochondrion is surrounded by two membranes: outer and inner, which define two mitochondrial compartments; 1. The intermembrane space, the compartment located between the two membranes. 2. The matrix space, the compartment enclosed by the inner membrane.  Chloroplasts The chloroplast in an organelle that is unique to plants. It contains chlorophyll, which is what make a plant green. Chloroplasts convert light energy into chemical energy via the photosynthetic process.  Structure of Chloroplast Thylakoids are small compartments found inside the chloroplast, it contain all the chlorophyll and its main role is to absorb sunlight and allow photosynthesis to occur. The thylakoids are surrounded by a liquid portion of the chloroplast called stroma.  The origin of mitochondria and chloroplasts Mitochondria and chloroplasts likely evolved from engulfed prokaryotes that once lived as independent organisms. At some point, a eukaryotic cell engulfed an aerobic prokaryote, which then formed an endosymbiotic relationship with the host eukaryote, gradually developing into a mitochondrion. Eukaryotic cells containing mitochondria then engulfed photosynthetic prokaryotes, which evolved to become specialized chloroplast organelles.  Ribosomes Ribosomes are granules found in both eukaryotic and prokaryotic cells, consisting of one third proteins and two thirds ribosomal RNA (rRNA). There are two types of ribosomes - free ribsomes and attached ribosomes. The attached ribosomes are bound to the surface of the endoplasmic reticulum and they are the site for protein synthesis. They are present in all cells especially abundant in cells where protein synthesis is taking place.  Ribosomes Each ribosome is formed of two subunits, a small subunit, and a large subunit. The ribosomes of the eukaryotic cells are larger than prokaryotic ribosomes i.e. 80S compared to 70S.  Peroxisomes Peroxisome, membrane-bound organelle occurring in the cytoplasm of eukaryotic cells.They are mainly located in the liver and kidney. Peroxisomes contain enzymes peroxidase and catalase that oxidize fatty acids and amino acids. Those oxidation reactions produce hydrogen peroxide, which is the basis of the name peroxisome. Hydrogen peroxide is toxic to the cell. Peroxisome’s also catalase that convert hydrogen peroxide to water and oxygen, thereby neutralizing the toxicity.  Endoplasmic reticulum The endoplasmic reticulum forms the most extensive membrane system in the cytoplasm.The ER has two types: 1. Rough endoplasmic reticulum (rER). 2. Smooth endoplasmic reticulum (sER). Both types form a single membrane system but their histological appearance, relative proportions, and functions vary in different cell types.  Endoplasmic reticulum (ER) The Endoplasmic Reticulum has two types: 1. Rough endoplasmic reticulum (rER). 2. Smooth endoplasmic reticulum (sER).  Rough endoplasmic reticulum Abundant in liver cells and protein-synthesizing and secreting cells e.g. pancreatic acini, fibroblasts, and plasma cells The function of Rough endoplasmic reticulum includes; 1. Synthesis of secretory proteins e.g. hormones and enzymes. 2. Synthesis of lysosomal proteins, enzymes, and proteins inserted into the cytoplasmic membranes. 3. Modification of the newly-formed protein including folding, initial glycosylation and sulfation. 4. Transport the newly-synthesized protein to the Golgi body by transport vesicles.  Smooth endoplasmic reticulum The smooth ER is where the synthesis of lipids, phospholipids and steroids take place and it is also where the metabolism of carbohydrate take place.  Smooth endoplasmic reticulum Abundant in liver cells and steroid-secreting cells e.g. the adrenal cortex, testis, and ovary. The functions of smooth endoplasmic reticulum includes: 1. Synthesis of membrane lipids, phospholipids, and cholesterol. 2. Synthesis of steroid hormones. 3. Detoxification of toxic substances e.g. alcohol and drugs. 4. Stores and regulate calcium ions during muscle contraction.  Golgi Apparatus The Golgi apparatus also called the Golgi body, is a membrane bound organelle within the cytoplasm. It is composed of flattened membranes called cisternae. The Golgi apparatus works closely with the rough endoplasmic reticulum. It receives protein from the rough endoplasmic reticulum. They process and package proteins and other macromolecules, especially proteins destined to be exported from the cell.  Golgi Apparatus Proteins produced in the Rough ER, reach the cis-Golgi by means of transport vesicles, after which they are then modified and processed (phosphorylation, sulfation, glycosylation) within the Golgi apparatus and sorted with regards to their destination. At the trans-site, the packaging in secretory granules or vesicles takes place.  The function of the Golgi apparatus 1. Post-translational modifications of proteins previously-synthesized in rER through removal, addition or modification of sugars. 2. Packaging of different proteins in the membrane-bounded vesicles. 3. Sorting and targeting of vesicles to the right destination 4. Formation of lysosomes (in clathrin-coated vesicles) to remain inside the cell.  Lysosomes A lysosome is a membrane-bound cell organelle that contains digestive enzymes. A lysosome are packaged by Golgi Body. They have an acidic pH (4.5 – 5) as well as a high content of hydrolytic enzymes such as hydrolases, proteases, lipases, nucleases and amylases among other things.  Functions of Lysosomes Lysosomes serve two major functions: 1. Intracellular Digestion To digest food, the lysosome membrane fuses with the membrane of food vacuole and squirts the hydrolytic enzymes inside. The digested food then diffuses through the vacuole membrane and enters the cell to be used for energy and growth. 2. Autolytic Action Cell organelles that need to be get ridden are covered by vesicles or vacuoles by the process of autophagy to form autophagosome. The autophagosome is then destroyed by the action of lysosomal enzymes.  Functions of Lysosomes Processes in which lysosomes play crucial roles include: a. Autophagy A normal physiological process that deals with the destruction of cells in the body. It is essential for maintaining homeostasis, for normal functioning by protein degradation, turnover of destroyed cell organelles for new cell formation. b. Heterophagy The taking into the cell of exogenous material by phagocytosis or pinocytosis and the digestion of the ingested material after fusion of the newly formed vacuole with a lysosome.  Vacuoles A vacuole is a membrane-bound cell organelle. Vacuoles are more prominent in plant cells than that of the animal cells. A plant cell has only one centrally placed vacuole which helps to maintain the cell shape.The membrane of the vacuole is called tonoplast.  Types of Vacuoles There are mainly four types of vacuoles based on their contents.They are: 1. Sap vacuoles: Sap (fluid) consists of water, inorganic molecules, organic molecules and enzymes.They maintain turgidity or turgor of the plant cells. 2. Contractile vacuoles: They prevent too much water from accumulating in a cell and swelling it to bursting point. This process is called osmoregulation. E.g fresh water protozoans like amoeba and paramecium. 3. Food vacuoles: They help in internalization and digestion of food. E.g in protozoan protists and sponges. 4. Gas vacuoles: They store gases and regulate buoyancy of the cell. E.g in bacteria.  Functions of vacuoles Functions of vacuolar system of the cell are as below: 1. The main function of the vacuole is to store both nutrient and non- nutrient chemicals and also break down complex molecules. 2. Isolation of harmful material from the cytoplasm of the cell. 3. Export unwanted substances from the cell 4. Maintains the pH of the cell. 5. Maintains the osmotic pressure within a cell  Cell wall Cell wall is specialized form of extracellular matrix that surrounds every cell of a plant. It is responsible for many of the characteristics that distinguish plant cells from animal cells. The cell wall is mainly composed of cellulose, hemicellulose, glycoproteins, pectins, chitin and lignin. Certain prokaryotes, algae, slime molds, water molds, and fungi also have cell walls.  Functions of the Cell wall The cell wall actually has a multitude of functions upon which plant life depends. Such functions include: 1. Providing a protective layer outside the cell membrane. 2. Providing shape and support for the cell's structure. 3. Providing a porous medium for the circulation and distribution of water, minerals, and other small nutrient molecules. 4. Providing rigid building blocks from which stable structures such as leaves and stems, can be produced. 5. Playing a vital role in cell to cell communication.  Cytoskeleton This three-dimensional cytoskeleton network is generated by microtubules, intermediate filaments and actin filaments. The cytoskeleton is located within the cytoplasm and is responsible for the stabilization, intracellular transport of substances as well as migration of the cell.  Functions of Cytoskeleton The cytoskeleton functions includes; 1. Maintaining cell shape 2. Providing internal organization. 3. Providing mechanical support. 4. It is also paramount in movement and cell division. 5. Provide intracellular transport of substances  Animal cell vs plant cell They are both eukaryotic cells which contain membrane-bound organelles, including a clearly defined nucleus, mitochondria, chloroplasts (unique to plant cells), a Golgi apparatus, an endoplasmic reticulum, lysosomes, and peroxisomes.  Cell membrane or Plasma membrane The cell membrane forms a barrier between the cytoplasm inside the cell and the environment outside the cell. The principal components of the plasma membrane are lipids (phospholipids and cholesterol), proteins, and carbohydrate groups that are attached to some of the lipids and proteins.  Phospholipid molecule of cell membrane Phospholipids make up the basic structure of a cell membrane. A single phospholipid molecule has two different ends: a head and a tail. The head end contains a phosphate group and is hydrophilic. This means that it likes or is attracted to water molecules. The tail end is made up of two strings of hydrogen and carbon atoms called fatty acid chains. These chains are hydrophobic, or do not like to mingle with water molecules.  Protein and carbohydrate molecules of cell membrane The cell membrane contains proteins, lipid and carbohydrate groups in its structure. 1. Proteins are the second major component of plasma membranes. There are two main categories of membrane proteins: integral and peripheral. 2. Carbohydrates are the third major component of plasma membranes. In general, they are found on the outside surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids). 3. Lipids such as phospholipids and cholesterol. Cholesterol is embedded among the phospholipids of the membrane, helps to minimize the effects of temperature on fluidity.  Protein molecules of the cell membrane i. Integral proteins are embedded in the plasma membrane and may span all or part of the membrane. Integral proteins may serve as channels or pumps to move materials into or out of the cell. ii. Peripheral proteins are found on the exterior or interior surfaces of membranes, attached either to integral proteins or to phospholipid molecules. Both integral and peripheral proteins may serve as enzymes, as structural attachments for the fibers of the cytoskeleton, or as part of the cell’s recognition sites.  Carbohydrate molecules of the cell membrane Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids). Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other.  Lipid (cholesterol) molecules of the cell membrane Cholesterol is embedded among the phospholipids of the membrane. Cholesterol molecules are important for maintaining the consistency of the cell membrane. They strengthen the membrane by preventing some small molecules from crossing it. Cholesterol molecules also keep the phospholipid tails from coming into contact and solidifying.This ensures that the cell membrane stays fluid and flexible.  The Phospholipid Bilayer Cell Membrane The phospholipids of a cell membrane are arranged in a double layer called the lipid bilayer. The hydrophilic phosphate heads are always arranged so that they are near water. Watery fluids are found both inside a cell (intracellular fluid) and outside a cell (extracellular fluid). The hydrophobic tails of membrane phospholipids are organized in a manner that keeps them away from water.  Properties of the Phospholipid Bilayer i. The hydrophobic tail regions face inwards and are shielded from the surrounding polar fluids, while the two hydrophilic head regions associate with the cytosolic and extracellular fluids respectively ii. The bilayer is held together by weak hydrophobic interactions between the tails iii. Hydrophilic and hydrophobic layers restrict the passage of many substances iv. Individual phospholipids can move within the bilayer, allowing for membrane fluidity and flexibility v. This fluidity allows for the spontaneous breaking and reforming of membranes (endocytosis / exocytosis)  Fluid mosaic model of cell membrane The fluid mosaic model describes the structure of a cell membrane. It indicates that the cell membrane is not solid. Membrane a fluid character refers to flexibility, and that all the individual molecules are just floating in a fluid medium, and they are all capable of moving sideways within the cell membrane. Mosaic refers to something that contains many different parts. The plasma membrane is a mosaic of phospholipids, cholesterol molecules, proteins and carbohydrates.  Functions of the cell membrane The cell membrane’s functionality is decisively determined by its membrane proteins, which include: ion channels, cell adhesion molecules, aquaporins, membrane pumps, carrier proteins and receptor proteins. The membrane is semi-permeable (also referred to as selective permeability), which means it is well permeable for small-molecular substances like water, which are able to diffuse osmotically. Higher molecular substances such as proteins require specific transport systems in order to by-pass the cell membrane.  Functions of the cell membrane The cell membrane functions include: 1. The plasma membrane provides protective barrier for a cell. 2. Regulate transport in and out of the cell (selectively permeable). 3. The cell membrane also provides structural support for a cell. 4. Provides anchoring sites for filaments of cytoskeleton. 5. Balances the internal environment of cells plasma by controlling what enters and leaves the cell. 6. Allow cell recognition – including recognition of signalling molecules, adhesion proteins and other host cells. END OF LECTURE THANK YOU