Cell Biology PDF

Cell Biology - Cells are the structural and functional units of all living organisms. They are primarily formed from the elements carbon, oxygen, hydrogen and nitrogen - Cells not only function as individual units, but also as a part of larger structures, namely tissues and o...

Cell Biology - Cells are the structural and functional units of all living organisms. They are primarily formed from the elements carbon, oxygen, hydrogen and nitrogen - Cells not only function as individual units, but also as a part of larger structures, namely tissues and organs, where they communicate with other cells, forming co-ordinated functional units - New cells are created by cell division. Once divided, they differentiate into cells specialized for their purpose. These qualities allow them to respond to the body’s constantly changing internal and external environments - The human body is composed of many different types of cells, which are generally classified by size, shape, and function - There are two main types of cells, germ cells, and somatic cells; germ cells consist of the sperm in the male, and oocyte in the female, and somatic cells include all other cells in the body Human Germ Cells - Germ line o Refers to the sex cells (eggs and sperm) that sexually reproducing organisms use to pass on their genomes from one generation to the next (parents to offspring). o Egg and sperm cells are called germ cells, in contrast to the other cells of the body, which are called somatic cells  ^Somatic Cells^ - Somatic cells are the cells in the body other than sperm and egg cells (which are called germ cells.) In humans, somatic cells are diploid, meaning they contain two sets of chromosomes, one inherited from each parent. DNA mutations in somatic cells can affect an individual, but they cannot be passed on to their offspring. Blood Cells - Red blood cells, or erythrocytes, are the most common type of blood cell. These cells bind oxygen in the lungs, and carry it to tissues throughout the body, where it is exchanged for the waste product carbon dioxide. - White blood cells, or leukocytes, function by identifying, capturing, and eliminating invading pathogens, or foreign particles. There are many types of white blood cells, including neutrophils, eosinophils, basophils, monocytes, and lymphocytes. Plasma Membrane - The plasma membrane is a flexible membrane that surround all cells, forming a barrier between the intracellular fluid (inside the cell), and extracellular fluid (outside the cell) - All living cells, prokaryotic and eukaryotic, have a plasma membrane that encloses their contents and serves as a semi-porous barrier to the outside environment. The membrane acts as a boundary, holding the cell constituents together and keeping other substances from entering. The plasma membrane is permeable to specific molecules, however, and allows nutrients and other essential elements to enter the cell and waste materials to leave the cell. Small molecules, such as oxygen, carbon dioxide, and water, are able to pass freely across the membrane, but the passage of larger molecules, such as amino acids and sugars, is carefully regulated. - The fluid mosaic model, the plasma membrane is composed of a double layer (bilayer) of lipids, oily substances found in all cells - Most of the lipids in the bilayer can be more precisely described as phospholipids, that is, lipids that feature a phosphate group at one end of each molecule - Phospholipids are characteristically hydrophilic (water loving) at their phosphate ends and hydrophobic (water fearing) along their lipid tail regions - In each layer of a plasma membrane, the hydrophobic lipid tails are oriented inwards and the hydrophilic phosphate groups are aligned so they face outwards, either toward the aqueous cytosol of the cell or the outside environment. Phospholipids tend to spontaneously aggregate by this mechanism whenever they are exposed to water. Membrane proteins - Are proteins that are part of or interact with cell membranes, and they are responsible for carrying out the majority of the functions of these membranes. Membrane proteins account for approximately one-third of human proteins and are responsible for regulating processes that help biological cells survive. Intrinsic vs Extrinsic Proteins - Membrane proteins are classified into two groups known as intrinsic and extrinsic proteins based on the nature of the interaction between proteins and the membrane - Intrinsic membrane proteins are embedded in the membrane. They are permanently attached to the membrane - Extrinsic proteins are attached to membrane from the outside. They are held by weak molecular attractions such as ionic, hydrogen, or Van der Waals bonds. This is the difference between intrinsic and extrinsic proteins What are Intrinsic Proteins? - Intrinsic proteins are a type of membrane proteins which are important in transporting ions or molecules across the cell membrane - Intrinsic proteins are embedded in the membrane. Some intrinsic proteins span completely through the membrane to the both sides of the membrane while some intrinsic proteins are only partially embedded in the membrane - Intrinsic proteins that extend from one side of the membrane to the other side are referred as transmembrane proteins - Transmembrane proteins work as channel proteins to move molecules and ions across the membrane in and out the cell. These proteins have pores inside their structure What are Extrinsic Proteins? - Extrinsic proteins are a type of membrane proteins which are loosely bound to the membrane from the outside. They are bound with weak molecular interactions such as ionic, hydrogen and/or Van der Waals bonds. - Extrinsic proteins are also known as peripheral proteins. These proteins are hydrophilic in nature. They interact with integral proteins or with polar heads of the lipid molecules - Peripheral proteins on the extracellular membrane work as receptors in cell to cell signaling or interactions. Peripheral proteins which are in the cytosolic face work as cytoskeletal proteins such as spectrin, actin, protein kinase C, etc. Some peripheral proteins are involved in signal transduction. Transport Across a Cell Membrane - In order to function normally, a cell must allow substances to move into and out from its plasma membrane. Some substances may be nutrients, which are required to help essential chemical reactions take place within the cell, others may be waste materials of these reactions, which must leave the cell to be used by other cells, or be excreted from the body - The cell membrane is one of the great multi-taskers of biology. It provides structure for the cell, protects cytosolic contents form the environment, and allows cells to act as specialized units. A membrane is the cell’s interface with the rest of the world- it’s gatekeeper, if you will. This phospholipid bilayer determines what molecules can move into or out of the cell, and so is in large part responsible for maintaining the delicate homeostasis of each cell  - Sodium is more than ten times more concentrated outside of cells rather than inside. If our cells couldn’t control what crossed their membranes, either no molecule would make it across, or they’d be traveling willy-nilly and the internal environment would always be in flux. It’d be like taking every item on a menu and blending it together before serving (not the tastiest idea) - So how do cells maintain different concentrations of proteins and molecules despite the pressure on them to be homogenous? Cell membranes are semipermeable, meaning they have control over what molecules can or cannot pass through. Some molecules can just drift in and out, others require special structures to get in and out of a cell, while some molecules even need an energy boost to get across a cell membrane. Each cell’s membrane contains the right mix of the these structures to help that cell keep its internal environment just right Gradients across a membrane - The difference in concentration of substances on one side of a membrane compared with the other can occur in the direction of the gradient, or against it. If substances move in the direction of a gradient, energy may not be required. However, substances move against a gradient, energy is always needed to facilitate the process. Movement Across a Membrane and Energy - There are two major ways that molecules can be moved across a membrane, and the distinction has to do with whether or not cell energy is used. Passive mechanisms like diffusion use no energy, while active transport requires energy to get done.  - Mode of transport o Molecules moved ▪ Uses energy Example - Simple Diffusion o Small, nonpolar ▪ No Pulmonary edema - Facilitated diffusion o Polar molecules, larger ions ▪ No GLUT4/ Diabetes Mellitus Type 2 - Primary Active Transport o Molecules moving against their gradient coupled to the hydrolysis of ATP ▪ Yes Sodium-potassium pump, proton pump/ atrial fibrillation, acid reflux - Secondary Active Transport o Molecule going with + molecule going against ▪ Yes Sodium-calcium exchanger, SGLT2 How does a macrophage “eat” a pathogen or a piece of cellular debris? - Vesicular transport o It is another form of active transport, where adenosine triphosphate (ATP) is required to move larger substances into and out of a cell - The bulk transport mechanisms o In which large particles (or large quantities of smaller particles) are moved across the cell membrane. These mechanisms involve enclosing the substances to be transported in their own small globes of membrane, which can then bud from or fuse with the membrane to move the substance across. For instance, a macrophage engulfs its pathogen dinner by extending membrane “arms” around it and enclosing it in a sphere of membrane called a food vacuole (where it is later digested). - There are 3 main types of vesicular transport: o Endocytosis, where substances are moved into a cell o Exocytosis, where substances are moved out of a cell o Transcytosis, where substances are moved into, across, and out of a cell Endocytosis - Endocytosis (Endo= internal, cytosis= transport mechanism) is a general term for the various types of active transport that move particles into a cell by enclosing them in a vesicle made out of plasma membrane. - There are variations of endocytosis, but all follow the same basic process. First, the plasma membrane of the cell invaginates (folds inward), forming a pocket around the target particle  or particles. The pocket then pinches off with the help of specialized proteins, leaving the particle trapped in a newly created vesicle or vacuole inside the cell. - Endocytosis can be further subdivided into the following categories: phagocytosis, pinocytosis, and receptor-mediated endocytosis - Phagocytosis (literally, “cell eating”) is a form of endocytosis in which larger particles, such as cells or cellular debris, are transported into the cell - Pinocytosis (literally, “cell drinking”) is a form of endocytosis in which a cell takes in small amounts of extracellular fluid. - Receptor-mediated endocytosis o Is a form of endocytosis in which receptor proteins on the cell surface are used to capture a specific target molecule. o When the receptors bind to their specific target molecules are taken into the cell in a vesicle. o The coat proteins participate in this process by giving the vesicle its rounded shape and helping it bud off from the membrane. o Receptor-mediated endocytosis allows cells to take up large amounts of molecules that are relatively rare (present in low concentrations) in the extracellular fluid Exocytosis - Cells must take in certain molecules, such as nutrients, but they also need to release other molecules, such as signaling proteins and waste products, to the outside environment - Exocytosis (exo=external, cytosis= transport mechanism) is a form of bulk transport in which materials are transported from the inside to the outside of the cell in membrane- bound vesicles that fuse with the plasma membrane. Transcytosis - Is the active movement of substances into one side of a cell via endocytosis, across the cell, and then out from the other side by exocytosis - Transcytosis is a form of specialized transport through which an extracellular cargo is endocytosed, shuttled across the cytoplasm in membrane-bound vesicles, and secreted at a different plasma membrane surface. - This important process allows membrane-impermeable macromolecules to pass through a cell and become accessible to adjacent cells and tissue compartments Endocytosis vs exocytosis - Endocytosis: o Definition: ▪ Refers to the transportation of macromolecules, large particles, and polar substances into the cell from the external environment o Process: ▪ Involved with up taking nutrients into the cell o Involvement in cell wall formation: ▪ Not involved in cell wall formation o Types: ▪ Clathrin-mediated endocytosis, caveolae, micropinocytosis, and phagocytosis o Fate of the vesicle: ▪ Vesicle fuses with the membrane bound organelles at the end of the process o Definition: ▪ Endocytosis is a cellular process in which substances are brought into the cell o Transporting molecules: ▪ Small molecules, macromolecules, suspended molecules, pathogens, etc. o Involvement of exocytosis: ▪ No o Forms: ▪ Phagocytosis, pinocytosis and receptor mediated endocytosis  - Exocytosis o Definition: ▪ Refers to the transportation of molecules or particles from the cell to the outside of the cell o Process: ▪ Involved in removing waste from the cell o Involvement in cell wall formation ▪ Involved in cell wall formation o Types: ▪ Ca2+ triggered non-constitutive (regulated exocytosis) and non-Ca2+ triggered constitutive (non-regulated) o Fate of the vesicle: ▪ Vesicle connects with the cell membrane at the end of the process o Definition: ▪ Transcytosis is a type of transcellular transport that transports various macromolecules across the interior of a cell o Transporting molecules: ▪ Various macromolecules such as enzymes, proteins and antibodies, etc. o Involvement of exocytosis: ▪ Yes o Forms: ▪ None Cytoplasm - The cytoplasm is the term used to describe everything that resides between the plasma membrane surrounding the cell, and the nucleus. - It is made up of many tiny organelles suspended in a fluid known as cytosol Nucleus - The nucleus is commonly found in the center of most cells - It is the control center of the cell, and contains most of the cell’s genetic material encoded within DNA molecules  - These DNA molecules are arranged and folded into chromosomes - The nucleus controls a cell’s activities by regulating gene expression in response to signals acting upon it - All of the cells in the body have a nucleus, except for red blood cells - Without a nucleus, red blood cells do not have the necessary codes and instructions for the synthesis of new proteins essential for reproduction and regeneration - As a result, red blood cells have short life cycles, living only for a few months before degenerating Nuclear Envelope - The nuclear envelope separates the contents of the nucleus from the cytoplasm and provides the structural framework of the nucleus - The nuclear envelope forms a double membrane around the nucleus - It exhibits ribosomes on its outer surface and has nuclear pores spanning the inner and outer membrane - Ribosomes are attached to the surface of the outer membrane. They link amino acids together to produce proteins Nucleoplasm - The nucleoplasm is a jelly-like fluid similar to the cytosol but contained within the nucleus - It contains dissolved ions, nutrients, and other solutes - Nuclear elements suspended in the nucleoplasm include nucleoli and chromatin Nucleolus - The nucleolus is the largest structure in the nucleus of eukaryotic cells - The plural of nucleolus is nucleoli Nucleoli - Are spherical bodies with no surrounding membrane, and are composed of DNA, RNA and protein. There are usually one or two nucleoli within a nucleus. They are particularly large in growing cells active in protein synthesis - Nucleoli are present in almost every eukaryotic cell type and represent the most prominent compartment of the cell nucleus - The primary function of the nucleolus consists in ribosomal RNA (rRNA) transcription, rRNA processing and ribosome subunit assembly - Ribosomal subunits are assembled from ribosomal RNA within the nucleoli, they then pass out of the nucleus through nuclear pores, before being joined together and commencing protein synthesis Chromatin - As cells prepare to divide, chromatin threads coli, condense, and shorten to form chromosomes; a structure less likely to become damaged during cell division - Chromatin contains the cell’s genetic material in the form of DNA, which when active, is transcribed into proteins - The function of chromatin is to determine which proteins the cell produces Cell Organelles - Organelle o Function - Nucleus o Contains genetic material for the cell - Ribosomes o Small complex proteins that assemble proteins from mRNA - Golgi Apparatus o Packages proteins into membrane-bound vesicles for excretion from the cell - Endoplasmic Reticulum o Synthesizes cellular materials. Subdivided into SER and RER - Nucleolus o Substructure of nucleus that synthesizes ribosomal RNA - Mitochondria o Powerhouse of the cell that performs cellular respiration - Vacuoles o Empty “bags” within the cell - Vesicles o A scaffolding of tubes providing internal support for the cell - Cytoskeleton o A scaffolding of tubes providing internal support for the cell - Flagella/Cilia/Pili  o Protein filaments that allow cells to move - Cell Wall (plant only) o Cellulose structure supporting the cell - Chloroplasts o Photosynthesizing organelles - Central Vacuole o Large water-filled sac in the middle of plant cells - Lysosomes (Animal only) o Structures containing enzymes that break down unwanted materials - Centrosomes o Organelle containing centrioles DNA vs RNA DNA - Definition o It’s a lengthy polymer, It has 4 bases: adenine, guanine, thymine, and cytosine, with a deoxyribose and phosphate backbone - Location o DNA is found in a cell’s nucleus as well as its mitochondria - Sugar portion o It has 2-deoxyribose - Function o The transfer of genetic information is made possible by DNA. It takes the shape of a long-term storage medium  - Predominant Structure o DNA is a nucleotide-rich double-stranded molecule with a long chain of nucleotides - Propagation o Self-replicating DNA replicates on its own - Nitrogenous Bases and Pairing o The base pairing is as follows: GC (Guanine pairs with Cytosine) A-T (Adenine pairs with Thymine) RNA - Definition o It is a ribose and phosphate-based polymer having four different bases: uracil, guanine, adenine, and cytosine - Location o The cytoplasm, nucleus, and ribosome all consist of RNA - Sugar portion o It has ribose - Function o The transmission of the genetic code required for protein production from the nucleus to the ribosome is accomplishes by RNA - Predominant Structure o RNA is a single-stranded molecule with a shorter nucleotide chain than DNA - Propagation o RNA does not have the ability to reproduce on its own. When it’s needed, it’s made from DNA - Nitrogenous Bases and Pairing o The base pairing is as follows: GC (Guanine pairs with Cytosine) A-U (Adenine pairs with Uracil) Types of RNA - Messenger RNA (mRNA) o Carries information from DNA in the nucleus to ribosomes in the cytoplasm - Ribosomal RNA (rRNA) o Structural component of ribosomes - Transfer RNA (tRNA) o Carries amino acids to the ribosome during translation to help build amino acid chain From Gene to protein - DNA serves as the molecular basis of heredity through replication, expression, and translation processes - DNA Replication o Creates identical DNA strands - Transcription o Converts DNA into messenger RNA (mRNA) - Translation o Then decodes mRNA into amino acids, forming proteins essential for life functions DNA Replication GO back to slide 43 Transcription - In Transcription, a DNA sequence is rewritten, or transcribed, into a similar RNA “alphabet.” - In eukaryotes, the RNA molecule must undergo processing to become a mature messenger RNA mRNA) Translation - In translation, the sequence of the mRNA is decoded to specify the amino acid sequence of a polypeptide. - The name translation reflects that the nucleotide sequence of the mRNA sequence must be translated into the completely different “language: of amino acids Transcription vs. Translation Review - Transcription o Process by which genetic information encoded in DNA is copied onto messenger RNA o Occurs in the nucleus o DNA>mRNA - Translation o Process by which information encoded in mRNA is used to assemble a protein at a ribosome o Occurs on a ribosome o mRNA>protein Come back to slide 46 Protein Synthesis What is the difference between DNA Polymerase and RNA Polymerase? - DNA polymerase is an enzyme that synthesizes new DNA molecules in the process of DNA replication  - RNA polymerase is an enzyme that synthesizes RNA molecules form DNA in the process of transcription - DNA polymerase produces a double-stranded DNA molecule - RNA polymerase produces a single-stranded RNA molecule - Both enzymes form phosphodiester bonds between nucleotides and function in the direction of 5’ to 3’. What is DNA Polymerase? - DNA polymerase is an enzyme that synthesizes new DNA molecules in the process of DNA replication - New DNA gets synthesized from DNA nucleotides at the S phase of the interphase of cell division to form a double-stranded DNA molecule - DNA polymerase uses a primer sequence to synthesize the complementary daughter strand during DNA replication - In addition to its main function, DNA polymerase also takes part in proofreading and DNA repair functions What is RNA Polymerase? - RNA polymerase is an enzyme that synthesizes RNA molecules from DNA in the process of transcription - Here, RNA polymerase adds RNA nucleotides in the direction of 5’ to 3’ - The synthesizing RNA could be either mRNA, rRNA, or tRNA\ - RNA polymerase does not need a synthetic DNA primer to start adding RNA nucleotides; hence it works independently - It recognizes the promoter region of the template strand of DNA to commence transcription - In eukaryotic cells, RNA polymerase is of five types (I to V) - Out of the five types, RNA polymerase I is responsible for 50% of transcription process - Prokaryotes consist of only a single type of RNA polymerase A Cell Cycle - It is a series of events that takes place in a cell as it grows and divides - A cell spends most of its time in what is called interphase, and during this time it grows, replicates its chromosomes, and prepares for cell division - The cell then leaves interphase, undergoes mitosis, and completes its division - The resulting cells, known as daughter cells, each enter their own interphase and begin a new round of the cell cycle - The cell cycle is a repeating series of events that include growth, DNA synthesis, and cell division - In prokaryotes is quite simple: the cell grows, its DNA replicates, and the cell divides>> This form of division in prokaryotes is called asexual reproduction - In eukaryotes, the cell cycle is more complicated - The eukaryotic cell cycle has several phases - The mitotic phase (M) includes both mitosis and cytokinesis - This is when the nucleus and then the cytoplasm divide - The other three phases (G1, S, and G2) are generally grouped together as interphase - During interphase, the cell grows, performs routine life processes, and prepares to divide ^Prokaryotes Cell cycle^ - Binary fission o Asexual reproduction in unicellular organisms in which a single cell divides to form two new cells. It is like mitosis Eukaryotes Cell Cycle Go to slide 54 video Mitosis - A process of cell division that results in two genetically identical daughter cells from a single parent cell - It’s critical for growth, repair, and asexual reproduction  - Mitosis is classically divided into either four or five stages: prophase, prometaphase (sometimes included in prophase), metaphase, anaphase, and telophase - Each phase features unique events concerning chromosomal alignment, spindle formation, and the division of cellular contents Go to Slide 57 video Meiosis - The process where a cell replicates DNA once but divides twice, producing four cells that have half the genetic information of the original cell - It is how organisms produce gametes or sex cells, which are eggs in females and sperm in males - In meiosis one cell divides twice, forming four cells - The daughter cells are haploid (n), having half of the chromosome number of the original cell, which is diploid (2n) - Meiosis produces sex cells, while mitosis replicates cells from growth and repair - Both begin with DNA replication, but mitosis involves one division step, while meiosis has two divisions - Steps of Meiosis o Meiosis is a type of cell division that reduces the chromosome number by half (2n to n), leading to the formation of four non-identical daughter cells o It is crucial for sexual reproduction in eukaryotes o Meiosis involves two divisions> meiosis 1 and meiosis 2 Why do males have the ability to produce 4 viable sperms while females can only produce one egg? - In male meiosis, four equal spermatids are produced from one spermatocyte cell (A) - In contrast, female meiosis undergoes asymmetric and produces only one egg from one oocyte cell - Chromosomes that are extended out to the polar body will degrade, and therefore, not be transmitted to the next generation Video slide 65 Mitosis vs. Meiosis