Unit 1 Facts of Life PDF

What is Science? Study of the physical and natural world using theoretical models and data from experiments or observations. 1 Why do you do Science? To understand the world better!...

What is Science? Study of the physical and natural world using theoretical models and data from experiments or observations. 1 Why do you do Science? To understand the world better! 2  The five components of the scientific method are:  Observations  Questions  Hypothesis  Methods  Results 3 4 5  Velcro The Fly Wall Velcro fastening was invented in 1941 by Swiss engineer George de Mestral, who took the idea from the burrs that stuck to his dog's hair. Under the microscope he noted the tiny hooks on the end of the burr's spines that caught anything with a loop - such as clothing, hair or animal fur. The 2-part Velcro fastener system uses strips or patches of a hooked material opposite strips or patches of a loose-looped weave of nylon that holds the hooks. HUMAN GENOME PROJECT  Computational biology Anne Carpenter, a computational biologist and senior director of the Imaging Platform of the Broad Institute of MIT and Harvard. She developed CellProfiler, a widely used open- source software for measuring phenotypes (sets of observable traits) from cell images. It has been cited in more than 12,000 publications since its release in 2005. https://www.youtube.com/watch?v=KDQFUmDJ3nY https://www.youtube.com/watch?v=gFuEo2ccTPA – Introduction to cells https://www.youtube.com/watch?v=URUJD5NEXC8 - Biology of cell structure 1 metre = 100 cm 1 cm = 10 mm 1mm = 1000 micrometers (µm) 1 µm = 1000 nanometers (nm) 1 nanometer = 1000 picometers (pm) 1 picometer = 1000 femtometers (fm)  UNIT - 1 THE FACTS OF LIFE  Cell : The Unit of Life The smallest functional unit of life is cell, discovered by Robert Hooke in 1665. A cell can independently perform all necessary activities to sustain life. Hence cell is the basic unit of life. There are two types of cells → plant cell and animal cell. Cells have different organelles, each one with a distinct function. Size of cells vary greatly Generally small and seen only with microscope Relative sizes of the cells 13  Size and Geometry of cells The standard cells. (A) A schematic bacterium revealing the characteristic size and components of E. coli. (B) A budding yeast cell showing its characteristic size, its organelles, and various classes of molecules present within it. (C) An adherent human cell. (adapted from Alberts B, Johnson A, Lewis J et al. Molecular Biology of the Cell, 6th ed. Garland Science.) Both plant and animal cells show diverse shapes such as –  Cells as Chemical Factories media-cache-ec0.pinimg.com Cells get raw materials — including water, oxygen, minerals and other nutrients — from the foods. Nutrients are transported through the cell membrane: the thin, elastic structure that forms the border of each cell.  Nucleus - it controls cell function. It contains DNA (deoxyribonucleic acid), the master organizer for how cells work. Mitochondria are the “batteries” in your cells. Chemical reactions within the mitochondria create the energy that powers cell functions. Lysosomes are fluid-filled vesicles, or sacs, that act as a waste-disposal system for cells. Ribosomes are the cell’s molecule makers. They assemble proteins from amino acids. The endoplasmic reticulum is a system of tubelike structures that’s essential for the production of proteins and lipids (fats). The Golgi apparatus is like a conveyor belt (iStock images/The Washington Post illustration) that “wraps” proteins inside vesicles so they can be “shipped” out of the cell. Cell Organelles/Compartments - Plasma membrane – Boundary, Protection and transport Nucleus - hereditary data essential for multiplication and cell development. Endoplasmic Reticulum & Golgi apparatus- Protein processing and Lipid biosynthesis Mitochondria - Energy factories of cells Lysosomes - digest undesirable materials present in the cell Chloroplast (only Plant cells) – Photosynthesis Ribosomes – Protein synthesis Cell Theory Cells were discovered in 1665 by Robert Hooke. Early studies of cells were conducted by - Mathias Schleiden (1838) - Theodor Schwann (1839) Schleiden and Schwann proposed the Cell Theory. 20 Cell Theory Cell Theory 1. All organisms are composed of cells. 2. Cells are the smallest living things. 3. Cells arise only from pre-existing cells. All cells today represent a continuous line of descent from the first living cells. 21 Cell Theory Microscopes are required to visualize cells. Cell size is limited. -As cell size increases, it takes longer for material to diffuse from the cell membrane to the interior of the cell. Light microscopes can resolve structures that are 200nm apart. Electron microscopes can resolve structures that are 0.2nm apart. 22 Cell Theory All cells have certain structures in common. 1. genetic material – in a nucleoid or nucleus 2. cytoplasm – a semifluid matrix 3. plasma membrane – a phospholipid bilayer 23 Why are cells so small? Cells need to produce chemical energy (via metabolism) to survive and this requires the exchange of materials with the environment The rate of metabolism of a cell is a function of its mass / volume (larger cells need more energy to sustain essential functions) The rate of material exchange is a function of its surface area (large membrane surface equates to more material movement) As a cell grows, volume (units3) increases faster than surface area (units2), leading to a decreased SA:Vol ratio If metabolic rate exceeds the rate of exchange of vital materials and wastes (low SA:Vol ratio), the cell will eventually die Hence growing cells tend to divide and remain small in order to maintain a high SA:Vol ratio suitable for survival Cell Theory 25 Cells are Us Cells are Us A person contains about 100 trillion cells. That’s 100,000,000,000,000 or 1 x 1014 cells. There are about 200 different cell types in mammals (one of us). Red and Cells are tiny, measuring on average about white blood 0.002 cm (20 um) across. That’s about cells above 1250 cells, “shoulder-to-shoulder” per vessel- forming cells. inch. nerve cell A Sense of Scale and Abundance – Bacteria on the Head of a Pin Prokaryotic Cells Prokaryotic cells lack a membrane-bound nucleus. -genetic material is present in the nucleoid Two types of prokaryotes: -archaea -bacteria 29  Prokaryotic Cells: Bacteria  Either classified as eubacteria or archaea.  Eubacteria: commonly found  Archaea: Live in extreme environments Prokaryotic Cells Prokaryotic cells possess -genetic material in the nucleoid -cytoplasm -plasma membrane -cell wall -ribosomes -no membrane-bound organelles 31  Prokaryotic Cells: Bacteria  Reproduction: Usually Asexual  Binary Fission: an organism duplicates its DNA and then divides into two parts, with each new organism receiving one copy of DNA.  Conjugation: Exchange of DNA between bacteria (not Asexual)  Prokaryotic Cells: Bacteria“The Good”  Bioremediation: organisms are added to water to convert toxic pollutants, such as oil, into harmless substances.  Food Production: Butter, Cheese, Yogurt, Sauerkraut, Beer, Pickles, Olives, Chocolate, Coffee, Soy sauce, meats, etc.  Decompose dead organisms  Digesting food  Fix Nitrogen for Plants Prokaryotic Cells: Bacteria“The Bad”  Food Spoilage  Can cause disease in plants and animals  Produce Toxins  Prokaryotic Cells: Bacteria“The Ugly”  Must be dealt with every day.  People die each year from infections.  Bubonic Plague:  Killed 2 out of 3 patients in 2-6 days without treatment  Yersina pestis  Anthrax  Cell Movement  Flagella: tail-like projections – prokaryotes and eukaryotes  Pseudopodia: false-foot in eukaryotes  Cilia: finger-like projections (some non-motile) in eukaryotes Prokaryotic Cells Flagella -present in some prokaryotic cells -used for locomotion -rotary motion propels the cell 38  Main Types of Cells  Eukaryotic (YOU!)  More complex & larger than prokaryotes  Have membrane bound organelles  Has a nucleus  Has more DNA than prokaryotes  DNA is linear  Animal, plant, fungi  NOT BACTERIA Eukaryotic Cells Eukaryotic cells -possess a membrane-bound nucleus -are more complex than prokaryotic cells -compartmentalize many cellular functions within organelles and the endomembrane system -possess a cytoskeleton for support and to maintain cellular structure 40 Cellular Anatomy Animal Cell 42 Plant cell 43 It’s Crowded In There A micrograph showing cytoskeleton (red), ribosomes (green), and membrane (blue) Eukaryotic Cells Nucleus -stores the genetic material of the cell in the form of multiple, linear chromosomes -surrounded by a nuclear envelope composed of 2 phospholipid bilayers -in chromosomes – DNA is organized with proteins to form chromatin 45 The Nucleus Think of the nucleus as the cell’s control center. Two meters of human DNA fits into a nucleus that’s 0.000005 meters across. Eukaryotic Cells 47 Eukaryotic Cells Ribosomes -the site of protein synthesis in the cell -composed of ribosomal RNA and proteins -found within the cytosol of the cytoplasm and attached to internal membranes 48 Endomembrane System Endomembrane system -a series of membranes throughout the cytoplasm -divides cell into compartments where different cellular functions occur 1. endoplasmic reticulum 2. Golgi apparatus 3. lysosomes 49 Endomembrane System Rough endoplasmic reticulum (RER) -membranes that create a network of channels throughout the cytoplasm -attachment of ribosomes to the membrane gives a rough appearance -synthesis of proteins to be secreted, sent to lysosomes or plasma membrane 50 Ribosomes and the Endoplasmic Reticulum  The Rough Endoplasmic Reticulum Functions: Protein synthesis (about half the cell’s proteins are made here). Protein movement (trafficking) Protein “proofreading” Endomembrane System Smooth endoplasmic reticulum (SER) -relatively few ribosomes attached -functions: -synthesis of membrane lipids -calcium storage -detoxification of foreign substances 53 Endomembrane System 54 Endomembrane System Golgi apparatus -flattened stacks of interconnected membranes -packaging and distribution of materials to different parts of the cell -synthesis of cell wall components 55 56 Endomembrane System Lysosomes -membrane bound vesicles containing digestive enzymes to break down macromolecules -destroy cells or foreign matter that the cell has engulfed by phagocytosis 57  The Lysosome Functions: Digesting food or cellular invaders Recycling cellular components Cell suicide (suicide is bad for cells, but good for us!)  The Lysosome This bacterium about to be eaten by an immune system cell will spend the last minutes of its existence within a lysosome. 60 Endomembrane System Microbodies -membrane bound vesicles -contain enzymes -not part of the endomembrane system -glyoxysomes in plants contain enzymes for converting fats to carbohydrates -peroxisomes contain oxidative enzymes and catalase – detoxification of reactive oxygen species, metabolism (fatty acid oxidation),cell signalling, bile acid synthesis. 61 Endomembrane System Vacuoles -membrane-bound structures with various functions depending on the cell type There are different types of vacuoles: -central vacuole in plant cells -contractile vacuole of some protists -vacuoles for storage 62 Mitochondria Mitochondria -organelles present in all types of eukaryotic cells -contain oxidative metabolism enzymes for transferring the energy within macromolecules to ATP -found in all types of eukaryotic cells -surrounded by 2 membranes -smooth outer membrane -folded inner membrane with layers called cristae -matrix is within the inner membrane -intermembrane space is located between the two membranes -contain their own DNA 63 Mitochondria 64  The Mitochondrion A class of diseases that causes muscle weakness and neurological disorders (Alziehmers, Huntington’s, Parkinson’s) are due to malfunctioning mitochondria. Worn out mitochondria may be an important factor in aging.  Chloroplasts of Mitochondria of Prokaryotes Eukaryotes Photosynthetic Eukaryotic cells eukaryotes Multiple linear 1 single, circular chromosomes 1 single, circular 1 single, circular DNA chromosome compartmentalized in chromosome chromosome a nucleus Binary Fission Binary Fission Binary Fission Replication Mitosis Ribosomes "70 S" "80 S" "70 S" "70 S" Found in the plasma Not found in the Found in the plasma Found in the Electron Transport membrane around plasma membrane membrane around plasma membrane Chain cell around cell mitochondrion around chloroplast Size (approximate) ~1-10 microns ~50 - 500 microns ~1-10 microns ~1-10 microns Anaerobic bacteria: ~3.8 Billion years Appearance on Photosynt.bacteria: ~1.5 billion years ~1.5 billion years ~1.5 billion years ago Earth ~3.2 Billion years ago ago Aerobic bacteria: ~2.5 Billion years 66 Mitochondria & Chloroplasts Much evidence supports this endosymbiosis theory. Mitochondria and chloroplasts: -have 2 membranes -possess DNA and ribosomes -are about the size of a prokaryotic cell -divide by a process similar to bacteria 67 Mitochondria & Chloroplasts Endosymbiosis -proposal that eukaryotic organelles evolved through a symbiotic relationship -one cell engulfed a second cell and a symbiotic relationship developed -mitochondria and chloroplasts are thought to have evolved this way 68 Chloroplasts Chloroplasts -organelles present in cells of plants and some other eukaryotes -contain chlorophyll for photosynthesis -surrounded by 2 membranes -thylakoids are membranous sacs within the inner membrane -grana are stacks of thylakoids 69 Chloroplasts 70 Cytoskeleton Cytoskeleton -network of protein fibers found in all eukaryotic cells -supports the shape of the cell -keeps organelles in fixed locations -helps move materials within the cell 71 Cytoskeleton Cytoskeleton fibers include -actin filaments – responsible for cellular contractions, crawling, “pinching” -microtubules – provide organization to the cell and move materials within the cell -intermediate filaments – provide structural stability 72 Cytoskeleton 73 The Cytoskeleton The name is misleading. The cytoskeleton is the skeleton of the cell, but it’s also like An animal cell cytoskeleton the muscular system, able to change the shape of cells in a flash. A Cytoskeleton Gallery Cell Movement Cell movement takes different forms. -Crawling is accomplished via actin filaments and the protein myosin. -Flagella undulate to move a cell. -Cilia can be arranged in rows on the surface of a eukaryotic cell to propel a cell forward. 76 Cell Movement The cilia and flagella of eukaryotic cells have a similar structure: 9+2 structure: 9 pairs of microtubules surrounded by a 2 central microtubules Cilia are usually more numerous than flagella on a cell. 77 Cell Movement 78  Detailed structure of eukaryotic cilia/flagellum A schematic diagram of the axoneme of a eukaryotic cilium or flagellum as viewed in cross- section. The component parts are labeled for the convenience of the reader. Reproduced with permission from Lindemann, CB & Lesich KA 2010. Flagellar and ciliary beating: the proven and the possible. Journal of Cell Science 123 519–528. (doi:10.1242/jcs.051326) q Company of Biologists.  Bacterial Flagella Flagella -present in some prokaryotic cells -used for locomotion -rotary motion propels the cell Extracellular Structures Extracellular matrix (ECM) -surrounds animal cells -composed of glycoproteins and fibrous proteins such as collagen -may be connected to the cytoplasm via integrin proteins present in the plasma membrane 81 Extracellular Structures 82 83  How cells are constructed? ▪ New cells are created from existing cells through a process referred to as the cell cycle. One cell can make a copy of itself and form two new daughter cells. ▪ There are two major tasks that have to happen every cell cycle. First, cells have to make an exact copy of their DNA. DNA is like the instruction manual for a cell. It encodes genes for characteristics and dictates things like eye color and blood type. ▪ The second major task of every cell cycle is for the replicated chromosomes to be organized and separated into opposite sides of the cell. This happens during mitosis, or M phase of the cell cycle. ▪ The cell then grows longer, further separating those masses of chromosomes. The middle of the cell then pinches off in a process known as cytokinesis, splitting the cell into two cells. A new cell has been created and that completes the cell cycle. Mitosis Mitosis is a process of cell division in which each of two identical daughter cells receives a diploid complements of chromosomes same as the diploid complement of the parent cell. It is usually followed by cytokinesis in which the cell itself divides to yield two identical daughter cells. The basics in mitosis include: 1. Each chromosome is present as a duplicated structure at the beginning of nuclear division (2n). 2. Each chromosome divides longitudinally into identical halves and become separated from each other. 3. The separated chromosome halves move in opposite directions, and each becomes included in one of the two daughter nuclei that are formed.  How cells build Organisms ? Organizational control mechanism allows cells to form tissues and anatomical structures in the developing embryo Spatial and Temporal organization Cell Census An order-of-magnitude census of the major components of the three model cells Importance of cell census Realistic physical picture of any biological phenomenon demands a precise, quantitative understanding of the individual molecules involved and the distance between them You will find the cell interior is extremely crowded in contrast to the dilute and homogeneous environment of the biochemical test tube. We will see that the mean spacing between protein molecules within a typical cell is less than 10 nm. This is extremely useful to estimate the rates of macromolecular synthesis during the cell cycle. E Coli: a model organism which has led to astounding discoveries Is easy to isolate present in human fecal matter E. coli is able to grow well in the presence of oxygen Easy to culture in lab, has high growth rate Genome has been sequenced 1997 It carries plasmids extra-chromosomal DNA which can be manipulated easily by molecular biology techniques. Molecular biology techniques are easy to apply for creation of mutants Often, we will have recourse to E. coli because of particular experiments that have been performed on this organism. Further, even when we speak of experiments on other cells or organisms, often E. coli will be behind the scenes coloring our thinking.  Size of an E. coli cells and molecular composition E. coli. are made up of an array of different macromolecules as well as small molecules and ions. To estimate the number of proteins in an E. coli cell We begin by noting that with its 1 fL volume, the mass of such a cell is roughly 1 pg, where we have assumed that the density of the cell is that of water which is 1 g/mL. Measurements reveal that the dry weight of the cell is roughly 30 percent of its total and half of that mass is protein. As a result, the total protein mass within the cell is roughly 0.15 pg We can also estimate the number of carbon atoms in a bacterium on the grounds that roughly half the dry mass comes from the carbon content of these cells, a figure that implies 1010 carbon atoms per cell Revealing the extent of crowding within a bacterium, we can estimate the number of proteins by assuming a mean protein of 300 amino acids with each amino acid having a characteristic mass of 100 Da. Using these rules of thumb, we find that the mean protein has a mass of 30,000 Da. Using the conversion factor that 1 Da 1.6 × 10−24 g, we have that our typical protein has a mass of 5 × 10−20 g.  How big is an E. coli cell ? ▪ The size of a typical bacterium such as E. coli serves as a convenient standard ruler for characterizing length scales in molecular and cell biology ▪ Diameter ≈1μm, a length of ≈2μm, and a volume of ≈1μm3 ▪ The shape can be approximated as a spherocylinder—that is, a cylinder with hemispherical caps. ▪ Inferences can vary with cell types under various conditions. Relation between cell volume and growth rate. Using microscopy and microfluidic devices, cell volume can be measured at the single-cell level under various conditions, confirming that the average cell volume grows exponentially with growth rate.  =10- 3Pa⋅sec =147b p 1 Da = (mass of one carbon-12)/12  VE ≈ 1μm3 = 1 fL m.Coli E.Coli ≈ 1pg ρE.Coli ≈ 1g / mL ≈ ρwater 1molecule / 1 fL = 1mol ≈ 2nM 6 × 1023 × 10−15 L Thermal energy scale (at 300K) k B T = 4.14 × 10−21 J = 4.14 pN ⋅ nm AB  A + B  0.59kcal / mol [A][B] ΔG = k BT log K d = k BT log ≈ k BT log10 −9 2.3 × 9k B T ≈ −20k BT [AB] =− ≈ 20k T (Kd = 1nM )[1molecule cell] Typical protein-protein ≈ 14k BT (K = 1μM )[103 molecules / cell] interaction energy B ≈ 7kBTd (Kd = 1mM )[10 6 molecules / cell] Water is 70 % of the cell mass (mE.Coli = 1pg) Dry mass of the cell (30% of 1pg) = 0.3 pg Half of the dry mass (=0.15 pg) = proteins 1 1 Da = mass of a hydrogen atom = g = 1.6 × 10−24 g 6 × 1023 1 amino acid = 100 Da average protein size = 300 a.a. → 30,000 Da 0.15 0.15 pg Nprot = ≈ 3, 000, 000 30,pg 30, 000 × 1.6 × 10−24 1 N 000Da g =⎧ → membrane prot proteins mwater = ⎪ 3 0.7 pg → ⎨ ⎪ 2N → cytoplasmic proteins 0.7 3 prot N water ≈ 2 × 1010 pg× 10 g / Da) 18Da × (1.6 −24 = There are 2 × 106 proteins in cytoplasm cprot = 2 × 106 / 1μm3 (10 nm) 3 3 d prot − prot = c −1/ 3 = 1/ 3 = (500nm)1/ 3 ≈ 2 ×8nm 106 4 nm 4 nm 8 nm Mean spacing between the macromolecules in cell ~ size of macromolecules themselves Cell is very crowded... 28 Membrane Surface area of E.Coli A ≈ (2πR) × L ≈ 6μm2 E.Coli E. coli has double (inner and outer) membranes and each membrane is made of bilayer. Half of the surface area is covered with membrane proteins 4 × 0.5 × 6μm2 N lipid E ≈ ≈ 2 × 107.Coli 0.5nm2 Taking the molecular census to set criteria for the judgement Measurement of protein census of E. Coli using 2D polyacrylamide gel electrophoresis Experimental determination of biomolecular content Large and negatively charged proteins 1.Protein mixture loaded at one end of the gel and an electric field is applied across the gel. (F=qE=ζv) 2.A charged detergent binding to proteins is added. (charge of detergent ~ protein size; q ~ R~v) 3. Proteins are stained using dye. Conc ~ Intensity of the spot. 4.Cut each spot, elute the proteins and determine the size and amino acid content using mass spectroscopy. small and positively charged proteins  RIBOSOME 20% of the protein complement of a cell = ribosomal proteins Ribosome (70S) = Large subunit + small subunit Large subunit (50S) = 23S r-RNA + r-proteins Small subunit (30S) = 16S r-RNA + r-proteins S : Svedberg constant (sedimentation constant) - A heavier particle sediments faster in the centrifugation, thus have a larger S value. dr m(1 − ρν )rω = ξ 2 dt M (1 − ρν )D = d log r ≡ S RT ω 2 dt ⎧ r − RNA : 2/3 of the mass ribosome (2.5MDa) ⎨ r − protein : 1/3 of the mass ⎪ ⎪ ⎩ Mr − prot N ribosome = = 0.2 × 0.15 pg = 20, 000 mr − protein = 830, 000Da mr − prot 830, 000Da Mr − protein = 20% × M protein ≈ 19, 000 Conversion : Number ➯ Concentration ➯ Average distance * 1 molecule in a bacterium ~ 2 nM. Example : Ribosome 1L = 10−3 m3 no. of ribosome = 19,000 (Table 2.1) Concentration = 19,000/1fL ~ 32 μM Average distance ~ 37 nm. Cellular crowding and its implications The Cellular Interior Is Highly Crowded With Mean Spacings Between Molecules That Are Comparable to Molecular Dimensions Increase in the effective concentration of macromolecules alters the rates and equilibrium constants of their reactions Alters dissociation constants by favoring the association of macromolecules, such as when multiple proteins come together to form protein complexes, or when DNA-binding proteins bind to their targets in the genome Crowding may also affect enzyme reactions involving small molecules if the reaction involves a large change in the shape of the enzyme. The size of the crowding effect depends on both the molecular mass and shape of the molecule involved,  Cellular crowding and its implications the increase in the strength of interactions between proteins and DNA is importance in processes such as transcription and DNA replication involved in processes as diverse as the aggregation of hemoglobin in sickle-cell disease, and the responses of cells to changes in their volume. the crowding effect can accelerate the folding process, crowding can reduce the yield of correctly folded protein by increasing protein aggregation.[ increase the effectiveness of chaperone proteins such as GroEL in the cell, Crystallins fill the interior of the lens. These proteins have to remain stable and in solution for the lens to be transparent; precipitation or aggregation of crystallins causes cataracts Crystallins are present in the lens at extremely high concentrations, over 500 mg/ml, and at these levels crowding effects are very strong. The large crowding effect adds to the thermal stability of the crystallins, increasing their resistance to denaturation This effect may partly explain the extraordinary resistance shown by the lens to damage caused by high temperatures. Crowding may also play a role in diseases that involve protein aggregation, such as sickle cell anemia, alzheimer's disease, Biological Structures exist over a huge range of scales Hierarchy of spatial scales Number of proteins in an E.coli cell 3,000,000 Number of ribosomes in an E.coli cell 20,000 Number of lipids in an E.coli cell 20,000,000 Size of genome in an E.coli cell 5,000,000 bp  yeast cell : useful representative to study eukaryotes Tremendous diversity in living cells... Protist Cells Biological Structures exist over a huge range of scales Hierarchy of spatial scales yeast cell : model system to study a single eukaryote cell V 4= π 3(2.5μm) Lyeast  yeast 3 ≈ 60VE 5μYeast m 3≈ 60μm.Coli N protein ≈ 60 × N protei E.Coli n 2 × 0.5 × 80μm2 N Yeast lipid ≈ ( ) ≈ 2 × 10 8 0.5nm2 1.2 × 107 bp N genome ~ 1.2 × 107 bp N nucleosome  = 60, 000 200bp / nucleosome  Video resources https://www.youtube.com/watch?v=URUJD5NEXC8 https://dnalc.cshl.edu/resources/3d/08-how-dna-is-packaged-advanced.html https://www.youtube.com/watch?v=jOhNyVjkChM 43 VIRUSES A virus is an infectious microbe consisting of a segment of nucleic acid (either DNA or RNA) surrounded by a protein coat. A virus cannot replicate alone; instead, it must infect cells and use components of the host cell to make copies of itself. Often, a virus ends up killing the host cell in the process, causing damage to the host organism. Well-known examples of viruses causing human disease include AIDS, COVID-19, measles and smallpox. ▪ Viruses are much smaller than the cells they infect. ▪ They could pass through filters small enough to remove pathogenic bacterial cells. ▪ These genomes can be DNA or RNA, single- stranded or double-stranded (that is, ssDNA, dsDNA, ssRNA, or dsRNA) with characteristic sizes ranging from 103–106 bases (A) Electron microscopy image of phi29 and T7 bacteriophages as revealed by electron microscopy. (B) Schematic of the structure of a bacteriophage. (A, adapted from Grimes S, Jardine PJ & Anderson D Adv Virus Res 58:255–280.)  Viral infection A B A virus infection. ( a ) Micrograph showing a late stage in the infection of a bacterial cell by a bacteriophage. Virus particles are being assembled within the cell, and empty phage coats are still present on the cell surface. ( b ) Micrograph showing HIV particles budding from an infected human lymphocyte. Cellular building blocks ▪ Cells of all organisms consist of four fundamental macromolecular components: nucleic acids (including DNA and RNA), proteins, lipids and glycans. ▪ From the construction, modification and interaction of these components, the cell develops and functions. ▪ DNA and RNA are produced from the 8 nucleosides. Although deoxyribose (d) and ribose (r) are saccharides, they are an integral part of the energetically charged nucleoside building blocks that are used to synthesize DNA and RNA. ▪ There are 20 natural amino acids used in the synthesis of proteins. ▪ Glycans derive initially from 32, and possibly more, saccharides used in the enzymatic process of glycosylation and are often attached to proteins and lipids. ▪ Lipids are represented by 8 recently classified categories and contain a large repertoire of hydrophobic and amphipathic molecules.  What are Carbohydrates ? : Carbohydrates are defined as polyhydroxy aldehyde or ketone with empirical formula (CH2O)n., the simplest being glyceraldehyde or dihydroxy acetone. Carbohydrates include sugars, starches, cellulose and many other compounds found in living organisms.  What are saccharides? : Saccharide is a term derived from the Latin for sugar (origin = "sweet sand”).The term carbohydrate is most common in biochemistry where it is a synonym of saccharide. Carbohydrates are often classified according to the number of saccharide units they contain. They are divided into four chemical groupings: monosaccharides, disaccharides, oligosaccharides and ploysaccharides. In their basic form, carbohydrates are simple sugars or monosaccharides. These simple sugars can combine with each other to form more complex carbohydrates. The combination of two simple sugars is a disaccharide. Carbohydrates comprising of 2-10 monosaccharide units are called oligosaccharides, and those with a larger number are called polysaccharides. Classification of carbohydrates :  Simple Carbohydrates : These are made up of a single basic sugar. Simple carbohydrates are responsible for the sweet taste in our food. Fruit sugar, table sugar or corn sugar are all simple sugars. On consumption, these sugars are directly absorbed in the blood and generally used for energy requirements of the body. Glucose provides instant energy and reaches different parts of the body via blood, by being quickly metabolized. Simple sugars are occur in plenty in natural foods like fruits, vegetables, milk and milk products. Additionally, honey, molasses, corn and maple syrup are also rich sources of simple sugars. Monosaccharides : 'Mono' refers to single. These are the basic compounds consisting of carbon, hydrogen and oxygen in the ratio 1:2:1 having the emperical formula of (CH2O)n. Monosaccharides are sweet to taste, colourless crystalline solids, freely soluble in water but insoluble in nonpolar solvents. Glucose, fructose and galactose are types of monosaccharides.  Properties of monosaccharides : Simple monosaccharides are reducing agents because of their ability to reduce potential oxidising agents like Cu2+ and hydrogen peroxide.They are thus called "reducing sugars". This reaction forms the basis of Bendict’s test for qualitative analysis of simple sugars. Glucose, the "blood sugar“ and an immediate source of energy for cellular respiration.  Disaccharides : When two monosaccharides bond together by a condensation reaction, thereby releasing a molecule of water, a disaccharide is formed. The two monosaccharide units are linked by glycosidic bond in α or β anomeric carbon. Commonly available disaccahrides are sucrose, maltose and lactose. Disaccharides cannot be absorbed through the wall of the small intestine into the bloodstream. They are therefore hydrolyzed to respective monosaccharides by carbohydares present in small intestine, specifically sucrase or invertase, maltase and lactase (β - galactosidase). Major Disaccharides : Sucrose : Major carbohydrate present in canesugar, commonly called table sugar. Glucose +fructose are linked by α(1 --> 1) glycosidic bonds.  Lactose : A major sugar in milk and milk products. Glucose + galactose units linked by α(1 --> 4) glycosidic bonds. Maltose : Simplest sugar; present in barley malt and also a product of starch digestion. Glucose + glucose linked by α (1 --> 4) glycosidic bonds. Cellobiose : The molecule is derived from the condensation of two glucose molecules linked in a β(1 --> 4) fashion. It can be obtained by enzymatic or acidic hydrolysis of cellulose and cellulose rich materials such as cotton, jute or paper.  Oligosaccharides : Carbohydrates having more than two or up to ten monosaccharide units are termed as oligosaccharides. Raffinose and stachyose are two major examples of oligosaccharides which consist of repetitive chains of fructose, galactose and glucose. Fats and oils Steroids and waxes Structure of Cell membrane  What are lipids? : Lipids are one among the four major biomolecules of living systems. By definition, these are the class of biomolecules which are insoluble or sparingly soluble in aqueous solutions and soluble in organic solvents. Fatty acids are major constituents of lipids. Fatty acids are mono carboxylic acid containing short/ long-chain hydrocarbon molecules. Some important fatty acids are enlisted below. The numbering of carbons in fatty acids begins with the carbon of the carboxylate group. Fatty acid represented by the total number of carbons e.g, palmitic acid a 16- carbon fatty acid CH3(CH2)14COOH is designated as C16. It is customary to write it as C 16:0 where zero represent that there is no double bond in the fatty acid). If there is one double bond, then it will be written as C:16:1  Types of fatty acids : Saturated fatty acids : All sets of examples in the previous table were fatty acids that contained no carbon-carbon double bonds. These are called saturated fatty acids. Saturated fatty acids having short carbon chain are liquid at room temperature, whereas long carbon chain fatty acids are solid. Unsaturated fatty acids : These have carbon-carbon double bonds in between, thus leading to unsaturation. The representations for these fatty acids consists of the number of carbon atoms, followed by the number double bond and the place of unsaturation. The place of unsaturation in a fatty acid is indicated by the symbol (Δ) and the number of the first carbon of the double bond in superscript form. Thus oleic acid a 16-carbon fatty acid with one site of unsaturation between carbons 9 and 10, and will be represented by C16:1Δ9.  Biological functions of lipids : Lipids perform and are involved in variety of important cellular functions. However, following are some of the major physiological functions attributed to lipids : Energy source in animals, insects, birds and high lipid seeds e.g. triacyl glycerols. Activators of enzymes namely glucose-6-phosphatase, stearoyl CoA desaturase, monooxygenases which are important mitochondrial enzymes. Some of the lipids derivatives serve as vitamins and hormones e.g. Prostaglandins. Essential components of biological membranes e.g. shingolipids and glycoloipids. As lipoproteins in protein modification and recognitions. Components of the electron transport system in the inner membrane of mitochondria. The central dogma of Life  Functions of proteins : Proteins carry out most diverse and possibly the largest volumes of cellular functions. Some of the key functions are summarized as below : Biocatalysis- Almost all the biological reactions are catalyzed by the enzymes. These are substrate specific and carry out reactions at very high rates under mild physiological conditions. Several thousand enzymes have been identified to date. Membrane are constitute of lipoprotein and some proteins are integral part of membrane. Receptors found on the membrane are also protein in nature. Transport and storage proteins - small molecules are often carried by proteins in the physiological setting e.g. haemoglobin is responsible for the transport of oxygen to tissues. Muscle are made up of proteins and their contraction is done by actin and myosin protein. Mechanical support - skin and bone are strengthened by the protein collagen. Antibodies of immune system are protein structures. Many of the hormones and growth factors such as insulin or thyroid stimulating hormone are proteins. Signals: Key Models, Cells & Organisms  SIGNAL TRANSDUCTION Cells can exist as single celled organisms or be part of a multi-cellular organism How do they know what is happening around them? Cells do not have ‘eyes’, ‘noses’, or ‘ears’ SIGNAL TRANSDUCTION Cells communicate with others and have mechanisms to sense their environments using a variety of methods as we will uncover - whichever method is used it involves a very important principle.  Signal Transduction The conversion of a signal, of some type, from one physical form to another. 16_02_Signal_transduct.jpg Electrical impulses are Signal molecules are received by converted to sound waves target cells via receptors and that we hear converted to other intracellular forms Cell Signaling types Endocrine - hormones, long distance Paracrine - local vicinity Neuronal - very short distances Contact-dependent - physical contact Autocrine - act on self **Contact signaling involves communication between cells that are in direct contact with each other. This communication is often mediated by gap junctions in animal cells and plasmodesmata in plant cells. One example of contact-dependent signaling is the Delta- Notch pathway used in embryonic development. 16_03_signal_various.jpg The same signal molecule may interact with different cells with entirely different effects. Here is an example of acetylcholine 16_05_target_cells.jpg Acetylcholine has a role in both branches of your nervous system It has a half-life of about 2 minutes.  Cells generally respond to a combination of signals. The same cell may have different outcomes to various signal combinations 16_06_extracellular_sig.jpg Cells that DO NOT RECEIVE The default pathway= SIGNALS DIE How do these signals work At which level? Where? How many? General Plan of Action 16_07_change_behavior.jpg  Each cell responds to a limited set of signals - why? These signals change the activity of internal cellular proteins which changes the behavior of the cell These signals follow a chain of events known as the signal cascade A system of relaying information from the site of reception to the point of action Normally the signal is amplified too - a small input is quickly converted to a large response  General Overview 2 16_08_cascades.jpg Some signal molecules act at the cell surface whilst others can enter the cell readily and act inside such as steroids. 16_09_molecules_bind.jpg The red signal molecule has a target receptor to which it binds and that’s that. Note that it is usually hydrophilic. Other receptors enter the cell and they must pass through the membrane. A simple example of how a steroid works. -The signal can enter the cell through the membrane and bind to its target protein. 16_12_cortisol.jpg -This is now able to enter through the nuclear pore and control transcription directly of certain target genes Ion-channel linked receptors All nerve impulses are generated via ion-channel linked receptors The release of neurotransmitter causes the ion-channel on the target neuron to allow the passage of ions (which?) into the cell. This action is propagated through the nerve cell along its axon. Many interactions taking place within the cell act to turn on or off proteins. These are known as molecular switches. 16_15_molec_switches.jpg  Some cellular responses are quick, whilst others are slow. 16_23_slowly_rapidly.jpg Fertilization Calcium has a very important role to play as an intercellular messenger. As we know the concentration of calcium is extremely low in the cytoplasm of a typical cell, compared to the outside and to that of the ER. In this example fertilization results in the wave of receptors opening up to permit the influx of calcium into the cell. This results in a change in the cell surface which both initiates cell division and prevents other sperm from entering the cell.  The speed at which Photoreceptor signaling cascades operate is clearly illustrated by the photoreceptors of the eye. The human eye has two forms of receptors - rods and cones The cones are further divided depending on the wavelength of light they respond to - red, green, and blue 16_29_amplifies_light.jpg