Case 5 - The Cells Inside PDF

Case 5 - The cells inside 1. What is the structure and function of the cell itself? Scale of cells - Water molecule is ~ 0.275 nm (1 billionth of a meter) - Hemoglobin 5 nm - Virus (HIV) 120 nm - Red blood cell + T-cell roughly same size ~ 6-8 μm Red blood cells contain...

Case 5 - The cells inside 1. What is the structure and function of the cell itself? Scale of cells - Water molecule is ~ 0.275 nm (1 billionth of a meter) - Hemoglobin 5 nm - Virus (HIV) 120 nm - Red blood cell + T-cell roughly same size ~ 6-8 μm Red blood cells contain about 280 million hemoglobin molecules - Pseudomonas bacteria width 1 μm and length 5 μm - Human egg cell → some of the largest Diameter 100 μm (upper bound) - Smallest cell discovered 300 nm (lower bound) - Cell has to be able to take in nutrients and excrete waste fast enough So it can’t have a to large volume Volume to surface ratio can’t be to large Eukaryotic cells Function The functions of a eukaryotic cell are responsible for the healthy shape and functioning of all living things. - Production of food and energy. - Growth. - Development. - Reproduction. - Regulation of cell growth and death. Structure A thin, flexible membrane encloses every living cell. The structure of a group of cells is called a tissue, and the group of tissues constitutes an organ. Cells also have a centrosome. consists of two centrioles in the middle and has microtubules branching out. Organelles have membranes, salty solutions (inside organelle) can be different Non polar is in the middle → water can not flow through it To let things though you have proteins, channels, filaments Cytoskeleton → shape, movement 30 % of proteins will end up in the membrane, to make it stronger, to allow molecules to pass through, receptors, protect etc. The ability to maintain different environments inside a single cell allows eukaryotic cells to carry out complex metabolic reactions that prokaryotes cannot. In fact, it’s a big part of the reason why eukaryotic cells can grow to be many times larger than prokaryotic ones. - Cytosol is about 54% of the cell - Mitochondria 22% of the cell - ER (mainly rough) 9% of the cell - Smooth ER and golgi 6% of the cell - Nucleus 6% of the cell Diagram of typical animal cell: Prokaryotes Components of prokaryotic cells A prokaryote is a simple, single-celled organism that lacks a nucleus and membrane-bound organelles The majority of prokaryotic DNA is found in a central region of the cell called the nucleoid, and it typically consists of a single large loop called a circular chromosome. The nucleoid and some other frequently seen features of prokaryotes are shown in the diagram below of a cut-away of a rod-shaped bacterium. (Not every bacteria has these features) Most bacteria are, however, surrounded by a rigid cell wall made out of peptidoglycan, a polymer composed of linked carbohydrates and small proteins. The cell wall provides an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. Many bacteria also have an outermost layer of carbohydrates called the capsule. The capsule is sticky and helps the cell attach to surfaces in its environment. Some bacteria also have specialized structures found on the cell surface, which may help them move, stick to surfaces, or even exchange genetic material with other bacteria. - Flagella are whip-like structures that act as rotary motors to help bacteria move - Fimbriae are numerous, hair-like structures that are used for attachment to host cells and other surfaces. - Bacteria may also have rod-like structures known as pili, which come in different varieties. For instance, some types of pili allow a bacterium to transfer DNA molecules to other bacteria, while others are involved in bacterial locomotion—helping the bacterium move. Archaea may also have most of these cell surface features, but their versions of a particular feature are typically different from those of bacteria. For instance, although archaea also have a cell wall, it's not made out of peptidoglycan—although it does contain carbohydrates and proteins. 2. Function and structure of the organelles The plasma membrane Both prokaryotic and eukaryotic cells have a plasma membrane, a double layer of lipids that separates the cell interior from the outside environment. This double layer consists largely of specialized lipids called phospholipids. - Amphiphilic → hydrophilic outside and hydrophobic inside Phospholipids spontaneously arrange themselves in a double-layered structure with their hydrophobic tails pointing inward and their hydrophilic heads facing outward. This energetically favorable two-layer structure, called a phospholipid bilayer, is found in many biological membranes. As shown below, proteins are also an important component of the plasma membrane. Some of them pass all the way through the membrane, serving as channels or signal receptors, while others are just attached at the edge. Different types of lipids, such as cholesterol (temperature buffer), may also be found in the cell membrane and affect its fluidity. The plasma membrane is the border between the interior and exterior of a cell. As such, it controls passage of various molecules—including sugars, amino acids, ions, and water—into and out of the cell. - How easily these molecules can cross the membrane depends on their size and polarity. Some small, nonpolar molecules, such as oxygen, can pass directly through the phospholipid portion of the membrane. Larger and more polar, hydrophilic, molecules, such as amino acids, must instead cross the membrane by way of protein channels, a process that is often regulated by the cell. Glycolipids are lipids with a carbohydrate attached by a glycosidic (covalent) bond. Their role is to maintain the stability of the cell membrane and to facilitate cellular recognition, which is crucial to the immune response and in the connections that allow cells to connect to one another to form tissues. Glycolipids are found on the surface of all eukaryotic cell membranes, where they extend from the phospholipid bilayer into the extracellular environment. Glycocalyx is a surface layer that covers the cell membrane of many bacteria, epithelial cells or other cells. It is made up of proteoglycans, glycoproteins and glycolipids. This acts as a barrier for a cell from its surroundings and provides protection. It helps in maintaining the integrity of cells. It is involved in cell-cell interactions such as signaling, adhesion, etc. The glycocalyx layer also provides mechanical strength to tissues. Nerve cell to increase connectivity → cell membrane can suck up or excrete different ions The cytoplasm The part of the cell referred to as cytoplasm is slightly different in eukaryotes and prokaryotes. In eukaryotic cells, which have a nucleus, the cytoplasm is everything between the plasma membrane and the nuclear envelope. In prokaryotes, which lack a nucleus, cytoplasm simply means everything found inside the plasma membrane. One major component of the cytoplasm in both prokaryotes and eukaryotes is the gel-like cytosol, a water-based solution that contains ions, small molecules, and macromolecules. In eukaryotes, the cytoplasm also includes membrane-bound organelles, which are suspended in the cytosol. The cytoskeleton, a network of fibers that supports the cell and gives it shape, is also part of the cytoplasm and helps to organize cellular components. Even though the cytosol is mostly water, it has a semi-solid, Jello-like consistency because of the many proteins suspended in it. The cytosol contains a rich broth of macromolecules and smaller organic molecules, including glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, and fatty acids. Ions of sodium, potassium, calcium, and other elements are also found in the cytosol. Many metabolic reactions, including protein synthesis, take place in this part of the cell. The nucleus The nucleus (plural, nuclei) houses the cell’s genetic material, or DNA, and is also the site of synthesis for ribosomes, the cellular machines that assemble proteins. Inside the nucleus, chromatin (DNA wrapped around proteins, described further below) is stored in a gel-like substance called nucleoplasm. Enclosing the nucleoplasm is the nuclear envelope, which is made up of two layers of membrane: an outer membrane and an inner membrane. Each of these membranes contains two layers of phospholipids, arranged with their tails pointing inward (forming a phospholipid bilayer). There’s a thin space between the two layers of the nuclear envelope, and this space is directly connected to the interior of another membranous organelle, the endoplasmic reticulum. Nuclear pores, small channels that span the nuclear envelope, let substances enter and exit the nucleus. Each pore is lined by a set of proteins, called the nuclear pore complex, that control what molecules can go in or out. The nuclear lamina is a dense (~30 to 100 nm thick) fibrillar network inside the nucleus of eukaryotic cells. It is composed of intermediate filaments and membrane associated proteins. Besides providing mechanical support, the nuclear lamina regulates important cellular events such as DNA replication and cell division. If you look at a microscope image of the nucleus, you may notice – depending on the type of stain used to visualize the cell – that there’s a dark spot inside it. This darkly staining region is called the nucleolus, and it’s the site in which new ribosomes are assembled. Endoplasmic Reticulum Basically, an endoplasmic reticulum is a plasma membrane found inside the cell that folds in on itself to create an internal space known as the lumen. This lumen is actually continuous with the perinuclear space, so we know the endoplasmic reticulum is attached to the nuclear envelope. There are actually two different endoplasmic reticuli in a cell: the smooth endoplasmic reticulum and the rough endoplasmic reticulum. The rough endoplasmic reticulum is the site of protein production (where we make our major product) while the smooth endoplasmic reticulum is where lipids (fats) are made. Rough Endoplasmic Reticulum The rough endoplasmic reticulum is so-called because its surface is studded with ribosomes, the molecules in charge of protein production. When a ribosome finds a specific RNA segment, that segment may tell the ribosome to travel to the rough endoplasmic reticulum and embed itself. The protein created from this segment will find itself inside the lumen of the rough endoplasmic reticulum, where it folds and is tagged with a (usually carbohydrate) molecule in a process known as glycosylation that marks the protein for transport to the Golgi apparatus. - Glycoproteins are proteins containing glycans attached to amino acid side chains. Glycans are oligosaccharide chains; which are saccharide polymers, that can attach to either lipids (glycolipids) or amino acids (glycoproteins). Typically, these bonds are formed through a process called glycosylation. The rough endoplasmic reticulum is continuous with the nuclear envelope, and looks like a series of canals near the nucleus. Proteins made in the rough endoplasmic reticulum are destined to either be a part of a membrane, or to be secreted from the cell membrane out of the cell. Without a rough endoplasmic reticulum, it would be a lot harder to distinguish between proteins that should leave the cell, and proteins that should remain. - Thus, the rough endoplasmic reticulum helps cells specialize and allows for greater complexity in the organism. Smooth Endoplasmic Reticulum The smooth endoplasmic reticulum makes lipids and steroids, instead of being involved in protein synthesis. The smooth endoplasmic reticulum is also responsible for detoxifying molecules, by adding a hydroxyl group. It is more tubular than the rough endoplasmic reticulum, and is not necessarily continuous with the nuclear envelope. Every cell has a smooth endoplasmic reticulum, but the amount will vary with cell function. For example, the liver, which is responsible for most of the body’s detoxification, has a larger amount of smooth endoplasmic reticulum. Stores calcium ions in muscle cells, a specialized sarcoplasmic reticulum releases Ca+ once an action potential from a motor neuron arrives. Golgi apparatus It is responsible for packing proteins from the rough endoplasmic reticulum into membrane-bound vesicles (tiny compartments of lipid bilayer that store molecules) which then translocate to the cell membrane. At the cell membrane, the vesicles can fuse with the larger lipid bilayer, causing the vesicle contents to either become part of the cell membrane or be released to the outside. (exocytosis/endocytosis) - Attached to microtubules Different molecules actually have different fates upon entering the Golgi. This determination is done by tagging the proteins with special sugar molecules that act as a shipping label for the protein. The shipping department identifies the molecule and sets it on one of 4 paths: 1. Cytosol: the proteins that enter the Golgi by mistake are sent back into the cytosol 2. Cell membrane: proteins destined for the cell membrane are processed continuously. Once the vesicle is made, it moves to the cell membrane and fuses with it. Molecules in this pathway are often protein channels which allow molecules into or out of the cell, or cell identifiers which project into the extracellular space and act like a name tag for the cell.  3. Secretion: some proteins are meant to be secreted from the cell to act on other parts of the body. Before these vesicles can fuse with the cell membrane, they must accumulate in number, and require a special chemical signal to be released. 4. Lysosome: The final destination for proteins coming through the Golgi is the lysosome. Vesicles sent to this acidic organelle contain enzymes that will hydrolyze the lysosome’s content. Cisternae A cisterna is any membrane-bound sac found in both the Golgi apparatus and the Endoplasmic Reticulum. Cisterna play an important role in the Golgi protein packaging and modification processes. Cis side (the side facing the ER) → entrance Trans side (the side facing the plasma membrane) → ships Proteins are packaged and modified for transport throughout the cell as they travel through the cisterna. The number of cisterna in the Golgi stack varies according to organism and cell type. - Around 60 to 100 cisternae are in a golgi apparatus. Each cisterna’s structure, composition, and function may differ within the Golgi stack. There are three types of Golgi cisternae: cis golgi networks, medial Golgi networks, and trans Golgi networks. - The cisternae are moving to the trans side, there they are broken down in vesicles The cytoskeleton of the cell shapes the cisternae via a lipid bilayer. The Golgi undergoes post-translational modifications such as glycosylation, phosphorylation, and cleavage. Lysosome The lysosome is the cell’s recycling center. These organelles are spheres full of enzymes ready to hydrolyze whatever substance crosses the membrane, so the cell can reuse the raw material. These disposal enzymes only function properly in environments with a pH of 5, two orders of magnitude more acidic than the cell’s internal pH of 7. Lysosomal proteins only being active in an acidic environment acts as a safety mechanism for the rest of the cell - if the lysosome were to somehow leak or burst, the degradative enzymes would inactivate before they chopped up proteins the cell still needed. - Everything they get is through vesicles, so endocytosis - Phagocytosis → process by which certain living cells called phagocytes ingest or engulf other cells or particles - Autophagy → recycling process - Cell damage → lysosome discrete enzymes to kill itself, apoptose Peroxisome The peroxisome is a spherical organelle responsible for destroying its contents. Unlike the lysosome, which mostly degrades proteins, the peroxisome is the site of fatty acid breakdown. - Beta oxidation → convert fatty acid into acetyl-coa Detoxify alcohol and other toxins in the liver by by transferring their H atoms to to form hydrogen peroxide → converted to water It also protects the cell from reactive oxygen species (ROS) molecules which could seriously damage the cell. ROSs are molecules like oxygen ions or peroxides that are created as a byproduct of normal cellular metabolism, but also by radiation, tobacco, and drugs. They cause what is known as oxidative stress in the cell by reacting with and damaging DNA and lipid-based molecules like cell membranes. These ROSs are the reason we need antioxidants in our diet. Mitochondria ATP (adenosine triphosphate) is the energy currency of the cell, and is produced in a process known as cellular respiration. The bulk of the energy produced comes from later steps that take place in the mitochondria. - About 0.5 to 2 micrometers Like we saw with the nuclear envelope, there are actually two lipid bilayers that separate the mitochondrial contents from the cytoplasm. We refer to them as the inner and outer mitochondrial membranes. If we cross both membranes we end up in the matrix, where pyruvate is sent after it is created from the breakdown of glucose (this is step 1 of cellular respiration, known as glycolysis). The space between the two membranes is called the intermembrane space, and it has a low pH (is acidic) because the electron transport chain embedded in the inner membrane pumps protons (H+) into it. Energy to make ATP comes from protons moving back into the matrix down their gradient from the intermembrane space. Cristae A crista is a fold in the inner membrane of a mitochondrion. The name is from the Latin for crest or plume, and it gives the inner membrane its characteristic wrinkled shape, providing a large amount of surface area for chemical reactions to occur on. This aids aerobic cellular respiration, because the mitochondria require oxygen. Cristae are studded with proteins, including ATP synthase and a variety of cytochromes. Cytoskeleton Within the cytoplasm there is a network of protein fibers known as the cytoskeleton. This structure is responsible for both cell movement and stability. The major components of the cytoskeleton are microtubules, intermediate filaments, and microfilaments. - Control shape, guidance through intracellular environment Microtubules (largest) Microtubules are small tubes made from the protein tubulin. These tubules are found in cilia and flagella, structures involved in cell movement. They also help provide pathways for secretory vesicles to move through the cell, and are even involved in cell division as they are a part of the mitotic spindle, which pulls homologous chromosomes apart. Intermediate Filaments Smaller than the microtubules, but larger than the microfilaments, the intermediate filaments are made of a variety of proteins such as keratin and/or neurofilament. They are very stable, and help provide structure to the nuclear envelope and anchor organelles. Microfilaments (Smallest) Microfilaments are the thinnest part of the cytoskeleton, and are made of actin. Actin is both flexible and strong, making it a useful protein in cell movement. In the heart, contraction is mediated through an actin-myosin system. - Only found in eukaryotes not prokaryotes 3. Difference between eukaryotes and prokaryotes Prokaryotes and eukaryotes Main difference is the membrane bound structures that eukaryotes have but prokaryotes don't have - Main one is the nucleus → genetic information inside → extra dense part is the nucleolus → ribosomal rRNA produced - Prokaryotic DNA is not membrane bound - DNA in eukaryotes multiple molecules of double strand DNA, prokaryotes mostly circular - Eukaryote: mitochondria + golgi apparatus Prokaryote: no mitochondria + golgi apparatus - Ribosomes both - Eukaryotes mostly larger than prokaryotes - Prokaryotes have a cell wall, eukaryotes plants do animals not - Prokaryotes range from 0.1 to 5.0 μm in diameter and are significantly smaller than eukaryotic cells, which usually have diameters ranging from 10 to 100 μm. - In prokaryotes, glycocalyx is often involved in adherence and protection from host defenses. It can be a capsule or a slime layer. In eukaryotes, glycocalyx is generally less structured than in prokaryotes. In animal cells, it's known as the extracellular matrix. All cells have 4 key components: 1. The plasma membrane is an outer covering that separates the cell’s interior from its surrounding environment.  2. Cytoplasm consists of the jelly-like cytosol inside the cell, plus the cellular structures suspended in it. In eukaryotes, cytoplasm specifically means the region outside the nucleus but inside the plasma membrane. 3. DNA is the genetic material of the cell. 4. Ribosomes are molecular machines that synthesize proteins. Unlike prokaryotic cells, eukaryotic cells have: - A membrane-bound nucleus, a central cavity surrounded by membrane that houses the cell’s genetic material. - A number of membrane-bound organelles, compartments with specialized functions that float in the cytosol. - Multiple linear chromosomes, as opposed to the single circular chromosome of a prokaryote. The Cell division in prokaryotes occurs through binary fission whereas in eukaryotes it may occur through mitosis or meiosis leading to the formation of the new cells. The cell division in prokaryotes through the binary fission is an example of asexual reproduction in prokaryotic organisms as there is only one parent involved and there is no fusion of gametes whereas the cell division in eukaryotes involves meiosis and mitosis that are relatively complex process are an example of vegetative reproduction and sexual reproduction in the eukaryotic organisms.