Unit 2 - BIO.pdf

Cells as the basic unit of life Cell theory ○ All living things are made of cells, the basic unit of life ○ Even unicellular organisms (single cells) come from other cells ex. Liver cells produce other cells ○ CELLS...

Cells as the basic unit of life Cell theory ○ All living things are made of cells, the basic unit of life ○ Even unicellular organisms (single cells) come from other cells ex. Liver cells produce other cells ○ CELLS Eukaryotes (plant cells, animal cells) Prokaryotes (bacteria) - Are the first forms of life and are structurally simpler than eukaryotes Includes: Archaebacteria ○ Bacteria that live in extreme environments that are often too extreme for humans, like in terms of temperature, salt concentrations, pH (acidity) etc. Eubacteria ○ Some are pathogenic (cause disease) EXCLUSIVE Components EXCLUSIVE Components Nucleus Nucleoid ○ Contains the cell’s DNA in ○ Just a region inside the cell with chromosomes DNA, a single chromosome. No clear boundaries the dna is just floating there Some have flagella ○ (the tail thingy) to help it move Pili ○ (hairy things on the outside of the ○ cell wall) to attach itself to things if it Nuclear membrane wants to infect them with disease ○ Wraps around the nucleus and etc or to help it with reproduction to protects it; has pores that allow do doggy style sexual reproduction molecules and ions to pass Plasmid through (ex: mRNA going out), but ○ Smaller bits of DNA that are circular, there are transport proteins that the genes provide the bacteria with only carry certain substances some protection, like antibiotic through resistance Nucleolus Capsule ○ The nucleolus contains the RNA ○ Outermost layer of a bacterial cell, it genes and proteins that are it prevents toxic stuff from entering, necessary for the construction of keeps the cell in, and is a physical ribosomes. These components are armor to stop the bacteria from assembled within the nucleolus being eaten by white blood cells  and then exported to the Cell wall cytoplasm, where they will be used ○ Right under the capsule, it also for protein synthesis. regulates what goes island out via Mitochondria diffusion and the transport proteins ○ You already know (produce ATP (like cell membrane) aka ENERGY) ○ mitochondria have their own DNA. Long ago, these structures may have originated as bacteria that were engulfed (eaten) by larger cells Vacuole/vesicle ○ A single membrane with fluid inside, store water, nutrients, waste products, and pigments. ○ Plant cells have really big vacuoles for all the water ○ Some vacuoles digest (lysosomes), and some vacuoles expel water ○ Vesicles are tiny vacuoles used to move around the substances within the cell Endoplasmic Reticulum ○ In general, used for manufacturing and transporting chemicals ○ Smooth endoplasmic reticulum Smooth because ribosomes aren’t attached to it Synthesizes lipids, phospholipids. Lipid synthesis is the process by which cells produce lipids, which are essential components/building blocks of cell membranes and other cellular structures. ○ Rough endoplasmic reticulum Has ribosomes attached to it, which do protein synthesis transporting proteins to the  Golgi apparatus for secretion When proteins are made in the ribosomes attached to it, they go to the cisterna (the membrane thingies) where it gets picked up by vesicles and moved to the Golgi Golgi Apparatus ○ Also composed of cisternae, the golgi processes proteins brought in from vesicles. Golgi apparatus modifies proteins by adding sugar groups (glycosylation) or phosphate groups (phosphorylation) so that the proteins can function properly and then be secreted from the cell membrane ○ Also sorts proteins (packaging) based on their destination within the cell or outside the cell. This helps to ensure that proteins are delivered to the correct locations in or outside the cell. Lysosomes ○ A kind of vesicle, sac filled with digestive chemicals, they break down waste products like ingested food from the vesicles ○ The Golgi packages digestive proteins/enzymes into the vesicles that are lysosomes. Centrioles ○ cylindrical structures, centrioles are bundles of microtubules, which are essential for cell division because it organizes the movement of the chromosomes ○ Microtubules form spindle fibers that pull chromosomes apart during cell division. Before cell division, there’s the cell’s DNA replication, creating two identical copies of each chromosome in the cell. During cell division, the two chromosomes need to be separated and distributed to the two daughter cells. This is where microtubules play a crucial role. Cilia  ○ Are small hair-like structures that extend from the surface of certain cells. They are composed of microtubules, which are protein filaments that aid movement and can create currents in the fluid that the cell is floating in Exclusive to plant cells: ○ Chloroplast Have their own dna Has stacks of thylakoids Does photosynthesis, aka converting sunlight into glucose into energy Contains chlorophyll, the pigment that absorbs the sunlight ○ (other) Plastids organelles that carry out functions for plant cells, they also have their own dna; chloroplast is a type of plastid ○ Cell Wall Surrounds the cell membrane, it provides protection and structural support for the cell COMMON COMPONENTS Cell membrane / plasma membrane ○ Encloses all the contents of a cell, not necessarily the outermost layer ○ Controls the entry and exit of substances (nutrients to intake, waste to excrete) Larger molecules and charged ions are too big to get through the membrane by itself, so transport proteins act as passageways to get them through. This is a whole other thing lol Ribosomes ○ The site of protein synthesis to create proteins for various uses; attract the tRNA, remember? ○ Quantified with Svedberg units (s). 70s for prokaryotes, 80s for eukaryotes ○ Created in the cytoplasm, from components from the nucleolus, kinda like protein synthesis but it produces ribosomes instead of proteins Cytoskeleton ○ Composed of microtubules and microfilaments, it gives the cell its shape and, for eukaryotes, is like the pathway for vesicles to move substances around Cytoplasm ○ Mainly composed of water ○ The liquid filling the cell that holds the organelles ○ Medium for chemical reactions, because it contains enzymes (proteins) that speed  up/catalyze reactions like metabolism DNA ○ Contains genetic information ○ Used to create proteins, which are used by the other cell organelles for division, etc Atypical cell structure (Eukaryotes) - Red blood cells - lose their nucleus and less organelles, making it easier to move/ more flexible. - Phloem sieve tube elements - Skeletal muscle cell - - Cells are not separated - One cell has no clear boundary with another cell, making each cell’s nucleus have odd placements in the cells so it looks like a mass of cell that has multiple nuclei - Processes of life in unicellular organisms (cells) - STUDY which parts of the cell are correlated with the below life processes in heterotrophs and autotrophs Homeostasis ○ Maintaining of internal balance/ a constant internal environment in an organism ○ Cell parts Contractile vacuoles ( a type of vacuole) can fill with water and then expel it through the plasma/cell membrane, which is water content regulation  Metabolism ○ The sum of all biochemical reactions that occur in a living organism ○ Includes digestion of food to produce energy ○ Or to create food (photosynthesis) for energy, for plant cells ○ Or building and repairing tissues ○ Cell parts The Cytoplasm has enzymes that catalyze (speed up) these metabolic reactions The Cell/Plasma membrane allows entry of oxygen for respiration Cellular respiration is an example of metabolism; it is when the cells convert glucose into ATP (adenosine triphosphate) aka energy that is released and used throughout the cell Nutrition ○ Definition: The process of obtaining and using nutrients for growth and energy. ○ Examples: Ingesting food, absorbing nutrients, and using nutrients for cellular processes. ○ Cell parts Vacuoles store and contain the food that the cells consume; Lysosomes, a type of Vesicle (and therefore a type of Vacuole), digest the food Because the golgi apparatus packages digestive enzymes/proteins into the vesicles, which become lysosomes. Lysosomes fuse with vesicles containing the nutrients, and the enzymes break down the molecules into smaller components that can be used by the cell. Excretion ○ Removal of metabolic wastes (substances become disruptive after a while) ○ Ex. sweat, food, CO2 ○ The Cell/Plasma membrane controls what enters and exits, so it also allows the exit of waste products via diffusion Growth ○ Maturation and development (size) of cell, or an increase in number Response to Stimuli ○ How the organisms react to changes in the environment ○ Cilia for eukaryotes, and flagellum for prokaryotes help the cells move in response to changes in the environment Reproduction ○ SEXUAL OR ASEXUAL ○ The nucleus divides and holds the DNA necessary to replicate when the cell reproduces, for eukaryotes. ○ The pili of a eukaryotic cell helps it physically do sexual reproduction (ick) Microscopes How to draw cells under microscope ○ Use a pencil to draw single hard and sharp lines. No shading ○ Make neat drawings with no overlaps ○ Use a ruler in labeling lines ○ Uncertainties in measurement The ruler is only accurate to its smallest division Developments in Microscopy Summary: Immunofluorescence is excellent for understanding the distribution and location of these molecules within the cell Freeze-fracture electron microscopy is best for studying the internal structure of membranes and the arrangement of its components. Better suited for examining the overall structure and arrangement of the membrane itself, doesn’t show you as clear location as immunofluorescence eh Cryo-EM is best for determining the 3D structure of biological molecules, especially those that are difficult to crystallize. ○ Fluorescent stains and immunofluorescence ○ Allows us to directly observe only parts of the cell and their locations within the cell fluorescent stains can be used to study antigens, which are often proteins or other molecules found on the surface of cells or within cellular compartments. Process: Because each antibody corresponds to one antigen An antibody is introduced to the cell, and locks on to the antigene of the cell The antibody has fluorescent dye (a fluorophore molecule) Since it locks on to the specific antigene of the cell, that specific antigene glows now and it can be directly observed There is a primary antibody, which recognizes and binds to the target molecule Then, they add a secondary antibody because it adds more light and allows for more detection. The secondary antibody can bind to the primary one ○ Freeze-fracture electron microscopy Was used to prove the theory of plasma membrane Used to produce images of surfaces (cell components) within cells immunofluorescence is better for looking at one specific part of the cell, while freeze fracture microscopy is better for looking at the arrangement of the parts of the cell Process: 1. Rapid freezing of the cell using liquefied propane  2. Fracturing (cutting) of the cell using a steel blade, revealing the components 3. Etching (+replication) of the cell components- since the liquidy stuff in the fractured cell is frozen, the ice is removed by vaporization, which forms a clearer texture of the surface. Then, to replicate it, some metal is fired onto the texture, which forms a replica of the surface. 4. Replica cleaning (processing of replica) the sample is removed using a strong oxidizing agent, such as chlorine gas. This process leaves behind a metal replica of the fractured surface. ○ Cryogenic electron microscopy Also called Cryo-EM Used to view structure of proteins which are super super small Some proteins are too fragile to view easily so we need to do this to view their shape and structure etc Process: Sample Preparation: The biological sample (e.g., protein, virus) is rapidly frozen in liquid ethane. This preserves the natural structure of the molecules. Imaging: The frozen sample is placed in an electron microscope. A beam of electrons is passed through the sample, creating a series of 2D images. Image Processing:Powerful computers are used to process the 2D images and reconstruct them into a 3D structure. This involves aligning and averaging thousands of images. Magnification ○ ○ All units should be the same ○ Magnification is unitless, so add x as its unit of measurement ○ ○ Types of microscopes Light microscope Can only see until 0.0002 millimeters Can be used for live specimens Gives color image Electron microscope Have high resolution than light microscopes (can see until 0.000001 millimeters) Cannot be live specimens.. It studies dead specimens Always black and white Types ○ TEM - high resolution of objects ○ SEM - display advanced depth to map objects at 3d, images are colorized for higher contrast