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GenBio Week 3 Notes

by: Selen Nehrozoglu

GenBio Week 3 Notes 01:119:115

Marketplace > Rutgers University > 01:119:115 > GenBio Week 3 Notes
Selen Nehrozoglu

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These notes cover material from lectures 5-6.
General Biology I
Dr. Gregory Transue
Class Notes
Cell, Multicellularity, Ediacaran, animals, Microscopy, SEM, TEM, Cambrian, fractionation, prokaryotes, eukaryotes, nucleus, ribosomes, DNA, RNA, Endomembrane, nucleoid, golgi, Lysosomes, Vacuoles, membrane, phospholipid, bilayer, peripheral, integral, Diffusion, Osmosis, tonicity, Isotonic, hypertonic, hypotonic, ATP, exocytosis, endocytosis, phagocytosis, pinocytosis
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This 10 page Class Notes was uploaded by Selen Nehrozoglu on Tuesday September 27, 2016. The Class Notes belongs to 01:119:115 at Rutgers University taught by Dr. Gregory Transue in Fall 2016. Since its upload, it has received 4 views.


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Date Created: 09/27/16
Lecture 5 – Cell Structure D. Origins of Multicellularity  Multicellularity emerged around 1.2 bya, but may have even been present at around 1.8 bya  Early animals emerged around 700 mya  Ediacaran Period o Around 600 mya o Large and diverse multicellular eukaryotes roamed the earth o Almost nothing from this period is still alive, we do not see specimens like the Ediacaran organisms in the current time period  Cambrian Explosion o Lasted around 20 million years ago o Time during which the most extant animal groups appeared in fossil record o Cambrian period: ~542-488 mya o First appearance of offensive and defensive armaments that were specialized to protect the animals from their environment  Colonization of land: Land animals finally start to emerge o ~500 mya o Around the end of the Cambrian period o Plants and fungi first, animals later o Applications: prevent desiccation  Animals on land o Arthropods (such as crustaceans, arachnids, insects, etc.) were the first animals on land around 450 mya o Tetrapods came later, around 365 mya, from lobe-finned fish o Human lineage appeared ~67 mya o Modern humans appeared ~200 thousand years ago (kya) Cell Structure The Cell is the smallest unit that carries out all activities associated with life It can do everything or be specialized to each area it belongs to All cells share common features and evolutionary history I. How we study cells Microscopy: we didn’t know cells existed until invention of microscope Leeuwenhoek helped develop the modern microscope in the 1670s that we use today Microscopes improved over time, we have much more sophisticated technology, and now our understanding of cells has improved A. Parameters of Microscopy  Magnification: ratio of size of image to size of actual specimen o Higher magnification means you can see smaller things  Resolution: Measure of clarity; minimum distance between two objects at which they can be seen separately o Function of wavelength of radiation passing through specimen o The longer the wavelength, the lower (worse) the resolution is  Contrast: Making things that can be resolved stand out o Stains: color the specimens so you can distinguish them better o Optics: manipulate wavelength of light to achieve higher optical contrast B. Types of Microscopes  Light Microscope (LM) o Uses visible light, putting through one or more lenses to magnify o At best: ~1000 x magnification, 0.2μm resolution o Flaw: there is little internal information  Electron microscopy (EM) o Focuses beam of electrons through or reflect off specimen o Magnification: >250,000x o The best microscopes can show the individual atoms o Resolution: ~1nm o 2 kinds of EM: Transmission EM (TEM), Scanning EM (SEM) o TEM  Specimen embedded in plastic, cut into very thin slices, 50-100 nm  Electron beam passes through  Stained with heavy metals, improves contrast o SEM  Better to look at surfaces, textures, and larger structures in general  Electron beam does not pass through  Specimen coated with gold film, emits electron when struck o Electron microscopy drawbacks  Cells killed; you can’t study living specimens or processes  Many times, they alter the specimen structure  Expensive equipment  Tedious preparation o Microscopy Summary  Parameters: magnification, resolution, contrast  Light microscope vs. Electron microscope  TEM vs SEM C. Cell Fractionation  Separate cell contents  Using centrifuge, spins very fast, separate materials by mass  The higher the mass, the more it’s going to move as you spin your specimen around really fast  Homogenize tissues, make uniform mixture  Put it on centrifuge, spin specimen, the g-forces that affect the sample are going to move the bigger materials to the bottom of the tube, and the smaller ones rise to the top  The more you spin, the smaller the organelles rise to the top II. Diversity and Characteristics of Cells A. Mainly Classified by Structure/Morphology  Prokaryotes o Literally means “before nucleus” o Break life into three domains: The two domains are bacteria and archaea o ~3.7 bya o Size: 1-10 μm o Nucleoid: DNA restricted in this region, there is no nucleus o Includes ribosomes, Plasma membrane, and cell wall  Eukaryotes o Literally means “true nucleus” o Domain: Eukarya o ~1.8 bya o Size: 10-100 μm; much bigger than prokaryotes o Includes (but isn’t limited to) nucleus, endoplasmic reticulum, and golgi apparatus B. Common Features of Eukaryotic Cells  Surrounded by plasma membrane  Distinct internal environment  Store and replicate genetic info  Divide/reproduce  Metabolism: energy transformations  Interact with response to external environment  Generally limited in size (also true for prokaryotes)  Most cells are microscopic C. Cell Size  Most cells are very small (see fig. 6.2)  Limits to cell size o Plasma membrane  All material must pass to enter cell  With large cells, there is a limit to how much material can enter the cell; it is easier for that material to travel through smaller cell, so there is a smaller distance o Advantageous to maximize surface area over volume ratio  Surface area increases while total volume remains constant III. Eukaryotic Cell Structure A. Nucleus  The nucleus is a membrane-bound region that… o Contains most DNA o Is often highly visible (under the microscope, that is) o Surrounded by nuclear envelopes, which have a double membrane and separate nucleoplasm from cytoplasm  When the membranes are fused, nuclear pores form  Protein completes: two proteins stick together to form channels between the inside and outside of the nucleus  These regulate the passage between the cytoplasm and the nucleus o Nucleolus: Region of ribosome production within nucleus; high activity occurs  Dense in RNA and proteins B. Ribosomes  Structures responsible for protein synthesis  Not membrane bound, not considered organelles because they are surrounded by membrane, they are just considered structures  Made of protein and RNA  Found in cytoplasm (just floating freely about) as well as in endoplasmic reticulum C. Endomembrane System  Internal membrane system  Membrane: lipid bilayer, closed  Divides the cell into compartments, known as membrane-bound organelles  Membrane communication o Direct continuity: compartment connected to another compartment through a channel; looks something like this:  Vesicular transport is the transfer of membrane segments. Tiny bit of cell is pinched off and fuses with another:  Plasma membrane o Selectively permeable phospholipid bilayer  Some materials can go right through it, others cannot o Encloses cell content o Controls flow of materials in and out o Is NOT the cell wall  Endoplasmic Reticulum (ER) o Internal membrane complex o The inside is a single contiguous lumen (unit of internal space) o Connected to the outer membrane of nuclear envelope o 2 types of ER:  Rough ER (RER)  Ribosomes attached to outer surface, distinguishing its ‘texture’ from that of SER  Protein is made at the ribosomes, which then travels through the translocon (ER Pore) into the ER lumen, which is then folded and modified in ER  It is then transferred to other locations via transport vesicle  Smooth ER (SER)  Contain no ribosomes  It is the primary site of lipid synthesis and metabolism  Lots of SER in liver-blood glucose regulation, and detoxification  Golgi Apparatus o Contain many membranes: modify and transport proteins o No contiguous lumen  Lysosomes o Compartments containing hydrolytic or digestive enzymes that break things down o Lys- means to “break down”, -Some means “body” o Primary lysosome: Made by RER, processed in golgi apparatus, contains enzymes but is inactive; in its storage state o Secondary lysosome: Appears when primary lysosome fuses with a vacuole o If released in cytoplasm, the enzymes would not be active, which is bad for the cell, but cells have a mechanism that will ensure the enzyme is not destructed if it enters cytoplasm  Vacuoles o Large vesicles derived from endomembrane system o Has many functions  Contain Food  Contractiles in plant cells or aquatic environments that pump water out of the cell  Plant cells with vacuoles: associated with storage o Protein synthesis occurs through endomembrane system  Proteins are going to move to golgi where they’re going to be modified  Exported through vesicular transport o Membranes can divide the environment into two regions  Cytoplasmic Region: in cytoplasm, stays inside cell  Extracellular Region: connected through vesicular transport to inside of lumen and golgi. Contents go in and out of cell Lecture 6 – Membranes and T ransport I Membrane Structure D. Membrane components  Primary phospholipids o Hydrocarbons are hydrophobic o Phosphate group is hydrophilic  Bilayer formation o Forms spontaneously o Due to phospholipid shape, it has an amphipathic nature (having both hydrophobic and hydrophilic parts)  Membrane proteins o Proteins determine many membrane functions o Tend to be amphipathic o Peripheral  Associated with one side of membrane but not within membrane  Hydrophilic o Integral  Goes into the membrane  Amphipathic  Transmembrane within integral span the membrane  You can have integral membranes that do not go all the way through the membrane o Some membrane proteins can move within the membrane itself  Example: scientists fused a mouse cell with a human cell to make a hybrid cell. When they were fused, the proteins mixed together and spread evenly throughout the membrane  Even though the membrane proteins can move side to side, they cannot flip, because that would require moving through the center part of the membrane, which is hydrophobic. The hydrophilic region of the proteins cannot interact with the hydrophobic part of the membrane. o Some proteins can neither move nor flip  Typically, these are on the outside of the cell  Located on what’s known as the extracellular side of membrane  Connected to cytoskeleton  Underside and inside the cell membrane o Functions of membrane proteins  Transport  Involved in moving things from one side of membrane to other  Enzymatic activity  Many enzymatic pathways involve enzymes that are embedded in the membranes  It’s beneficial to have all of the proteins close to each other rather than spread out  Signal transduction  Proteins embedded in membrane  Take signal from outside the cell and translate it into a signal on the inside of the cell  Cell-cell recognition  Proteins that have ID tags for the cell  Intercellular joining  Cells need to be held together  Membrane proteins are responsible for direct connections between cells  Attachment to the cytoskeleton and extracellular matrix (ECM)  Pulls the cell in place within a multicellular organism o Carbohydrates  Polysaccharides attached to protein (glycoprotein)  Glycolipids: Polysaccharides attached to lipid  Cell identification E. Fluid Mosaic model  Membrane components can move laterally within one layer of the membrane; not locked in place  Fluidity depends on characteristics of the fluid: o Temperature: if warmer, it is more likely to break bonds, and more fluid o Chain length: Longer chains mean less fluid membrane and more Van der Waals interactions o Saturation: When something is saturated, it is packed together very tightly and more viscous than unsaturated. When something is unsaturated, there are kinks in the proteins, so the molecules cannot pack tightly together  Cholesterol: Steroid based on a 4-ring structure. It is mostly hydrophobic except for its hydrophilic head o There is a complex relationship between cholesterol and temperature o At a moderate temperature, cholesterol will reduce fluidity o As the temperature drops, cholesterol will promote membrane fluidity o If the temperature is high, the influence of cholesterol becomes less and the temperature becomes the main factor of fluidity  Mosaic: Small components coming together to create a bigger system. It is the same concept as artistic mosaic pieces, but instead of colorful tiles it consists of little components of the membrane, that, if you look at it from above, it will be a whole entity. IV. Membrane Transport The plasma membrane is selectively permeable There are two basic types of transport: Passive (does not use metabolic energy like ATP), and Active (does use metabolic energy) A. Passive transport  Spontaneous, does not require any energetic input  Includes simple diffusion, osmosis, and facilitated diffusion  Net movement is down, towards, or with the concentration gradient. No ATP required  Dynamic equilibrium is the end result  Dynamic equilibrium o While there is movement in the system, there is no net movement of concentrations o Different substances diffuse independently from one another  Diffusion o Tendency for molecules of a substance to fill available space o All molecules in constant random motion, eventually are evenly distributed in available space o Example: Gas molecules in a closed bottle are forced to be closer to one another, but when the bottle opens, the gas molecules will disperse over time  What can diffuse across a membrane? o Two determining factors:  Membrane fluidity  Solute hydrophobicity o Gases: O 2 CO 2 N2 o Small nonpolar molecules (hydrophobic) including hydrocarbons o Small polar uncharged molecules (hydrophilic) including H 2  Osmosis o Diffusion of water across selectively permeable membrane (special case of diffusion) o Solvent: A substance capable of dissolving other substances o Solute: A dissolved substance  Direction of osmosis is determined by a difference in total concentration of the solute o Type of solute does not affect osmosis o Water diffuses from lower to higher concentration of solute, which also means that the concentration of the solvent, H 2, is going from higher to lower  Tonicity o Ability of a solution to cause a cell to gain or lose water o Isotonic soil  Concentration of solution outside the cell = concentration of solution inside cell  No net H 2 movement o Hypertonic solution  Concentration of solute outside cell > concentration of solute inside cell  Loses H 2 o Hypotonic  Concentration of solute outside cell < concentration of solute inside cell  Cell gains H2O o If system A is hypotonic to system B, then it is less dense, and vice versa  Osmosis and cells o In hypotonic solution, without cell wall, water rushes inwards into cell, eventually the cell will break o In isotonic solution, water moves in and out at dynamic equilibrium. o Hypertonic solution: water moving outwards to stabilize solute concentration, cells will shut off because they have water deficiency  Simple diffusion can be insufficient o Large molecules are just too big, even if hydrophobic o Small polar molecules are hydrophilic, cannot get across membrane o Ions are charged, anything that has a net charge can’t just diffuse across a membrane. It doesn’t matter the size.  Carrier-mediated transport o Transport using transport proteins o Span membrane (integral) o Can be passive or active o Specific: a protein, no matter what type of transport, is specific, moving only one specific type of ion or molecules o Diameter of channel affects what molecules are allowed to move through  Facilitated diffusion o Passive transport through a transport protein o Does not require ATP o 2 Types  Channel  Carrier protein  Passive transport summary o Does not require ATP o Movement down concentration gradient o Simple diffusion B. Active Transport  Transport through membrane protein, changes shape  Requires ATP  Moves from lower concentration to higher concentration  Works against concentration gradient  Uses energy  Sodium-potassium pump: generating two different gradients at same time o Establishes general electrical gradient o Uses energy from ATP to change shape, sodium ions can move outside cell, pick up K , comes back into cell + + o Each cycle requires 3 Na out, 2 K in, and 1 ATP V. Bulk Transport Transport of a large number of molecules at once Moving in and out of cell without crossing membrane A. Exocytosis  Vesicle containing same material that fuses with plasma membrane  Releases contents from cell  Also the primary mechanism for growing plasma membrane B. Endocytosis  Taking material in by forming vesicles derived from plasma membrane  Phagocytosis o “cellular eating” o Cell engulfs large particle o Fuses with 1 lysosome o Particle is digested  Pinocytosis o Ingestion of fluid and dissolved material o Cellular drinking o Forms vesicle, slowly transferred to cytoplasm o Non-specific  Receptor-Mediated endocytosis o Receptors attach to something specific o Form coated pits in surface of membrane o Pinched inward to form vesicles o Main mechanism for uptake of macromolecules  Active transport summary o Requires ATP o Against concentration gradient o Includes bulk transport


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