CELL BIO MODULE 1&2

8. Why are chemical stains required for visualizing cells and tissues with the basic light microscope?

Because cells on their own are mostly transparent, they are oftentimes stained with dyes so that structures can be more readily observed

20. What types of data could be obtained using flow cytometry on a blood sample?

Flow Cytometry is a technique used to detect and measure physical and chemical characteristics of a population of cells or particles. In this process, a sample containing cells or particles is suspended in a fluid and injected into the flow cytometer instrument.

During which cell cycle phase does the cell increase in size as cell constituents are made?

The cell cycle phase in which Eukaryotic cells increase in size and create new constituents for cell division is the Interphase. The Interphase encompasses 3 different cycles, or phases named G1, S, and G2, in which cell will double in size as it prepares for cell division. The G1 phase is the first step, and it is where the cell will duplicate several internal components such as RNA, lipids, proteins, and other cell components, except for the chromosomes. Once the cell is committed to duplicating, which occurs late in the G1 phase, the S phase begins, in which the cell cannot terminate its duplication, despite if the required resources are no longer present. In the S phase, the cell duplicates its chromosomes. Finally, the cell enters the G2 phase, where additional proteins and components are synthesized and the DNA sequence is verified for errors, this is the last step before Mitosis, where the cell divides to create 2 daughter cells.

7. The magnification possible with any type of microscope is an important property, but its resolution, the ability to distinguish between two very closely apposed objects, is even more critical. Describe why the resolving power of a microscope is more important for seeing finer details than its magnification. What are the limitations of microscopy that uses light to visualize a specimen? (Hint: Consider the wavelengths of light. In theory, which wavelengths of light could provide the highest resolving power - longer or shorter?)

The limit of resolution of a light microscope using visible light is about 200nm. No matter how many times you amplify a specimen, a conventional light microscope will never resolve or provide a clear resolution of structures that are closer than 0.2nm to one another in size. This is discussed and established by solving for the resolution of a microscope lens using the equation: D= 0.61λ /N sin α α is the angular aperture N is the refractive index of the medium and λ is the wavelength of incident light Owing to the limitations of those values, and the properties of the visible light spectrum, 200µm is the limit of resolution. While all of these variables can be manipulated to improve the limit of resolution, one to notice is that by using shorter wavelengths of light, resolution can be improved.

6. The DNA double helix is stabilized by weak hydrogen bonds between: a. G and C bases only b. A and T bases only c. A and U bases only d. A and T bases and between G and C bases e. A and U bases and between G and C bases

d. A and T bases and between G and C bases Discussion: DNA has the nucleotide bases adenine, thymine, guanine, and cytosine (A, T, G, and C). Because of the structure of these nucleotide bases, A bases hydrogen bond only with T bases in DNA and G bases hydrogen bond only with C bases in DNA.

4. Phospholipid bilayers contain: a. cholesterol b. transmembrane proteins c. hydrophobic fatty acyl chains d. hydrophilic head groups e. all of the above

e. all of the above

15. What is the difference between a cell strain, a cell line, and a clone?

A 'cell line' refers to the lineage of cells derived from a primary culture in which a single transformed cell takes over the culture, dividing rapidly with an indefinite life span given the proper nutrients. A 'cell strain' refers to passaged cells derived from one initial primary culture with a finite life span. The 'cell strain' differs from the 'cell line' in that a strain both has a finite life span and is not composed of a single transformed rapidly diving cell taking over the culture A 'clone' refers to a colony of genetically homogenous cells grown from a single cell of a specific type in a controlled environment. The difference comes from a 'clone' line being derived from a single specific cell instead of a primary culture.

15. What does the term "common ancestor" mean, as it relates to evolution?

All living organisms are descended from a common ancestral cell. The term "common ancestor" means the most recent ancestral form or species from which two different species evolved. Through evolution, all organisms are related in a family tree extending from primarily single celled organisms that lived in the distant past to the diverse plants, animals, and microorganisms of the present era

What advantage do fluorescent dyes and fluorescence microscopy provide in comparison to the chemical dyes used to stain specimens for light microscopy?

Allows labelling of features/molecules of interest and tracking the dynamics of processes involving these features real-time and in vivo. Allows 1-2 magnitude increase in the resolving power of conventional light microscopy, an aspect known as super-resolution microscopy. Allows the micro-detection and identification of elements/compounds of interest within an unknown substance, via Raman spectroscopy. Also employed in micro-geology for this same reason. Provides insight into studies of structural and association dynamics via fluorescence anisotropy & FRET, as well as other fluorescence-related techniques (including FLIM & FRAP). Allows evaluation and analysis of molecular interactions via techniques such as fluorescence correlation spectroscopy (FCS) or fluorescence cross-correlation spectroscopy (FCCS).

17. What is a reading frame, as it relates to a gene sequence?

Answer: A reading frame is a sequence of nucleotide triplets that are read as codons specifying amino acids in messenger RNA (or deduced from DNA).

Both light and electron microscopy are commonly used to visualize cells, cell structures, and the location of specific molecules. Explain why a scientist may choose one or the other microscopy technique for use in research.

Answer: Both light microscopy and the more modern electron microscopy have their advantages and disadvantages. Some of the pros of using light microscopes are that they are small, easy to use, and inexpensive. They are also great for examining live cells, bacteria, and other living organisms (Anonymous, 2021). However, visible light still is not conducive for examining cell structures in fine detail since anything smaller than 700 nanometers is not visible (Anonymous, 2021). Electron microscopy, on the other hand, provides substantially higher resolution. A major limitation of electron microscopy is that cells must be fixed and sectioned, which prevents the observation of live specimens Biological interactions can't be adequately observed and are only visible in black and white, not color

What advantages do confocal and deconvolution microscopy provide in comparison to conventional fluorescence microscopy?

Confocal microscopy removes the out of focus light by obtaining fluorescent images from only a specific focal plane and excluding light from other planes. This will yield optical sections through thick cells or tissue samples. As you can see, the confocal microscopy image on the right is much clearer than the conventional fluorescence microscopy image on the left Compared to other forms of 3D light microscopy, like confocal microscopy, the advantage of deconvolution microscopy is that it can be accomplished at very low light levels, thus enabling multiple focal-plane imaging of light-sensitive living specimens over long time periods.

What are the functions of the cytoskeletal fibers?

Cytoskeletal fibres can be divided into three separate sub-categories: microtubules, intermediate filaments, and microfilaments (listed in descending size) Structure: When I think of cytoskeletal fibres, I always flashback to my early biology education that analogized them to the framework of sport center ceilings, maintaining shape and helping to resist outside forces pressing into the cell. This was our introduction to intermediate filaments and a section of their function which can be boiled down to that core concept, keeping the ceiling strong. While they do play a major role in the other points on this list, intermediate filaments also help to reinforce the plasma membrane of the cell by forming various linkages bordering the cell cortex, depending on the need of that cell Organization: The organization of sub-components within the cytoplasm is also handled by cytoskeletal fibres, and here a major contributor is the microtubules. By being able to quickly alter their length to accommodate the cell's needs they can not only assist the intermediate filaments with maintaining the cell's form, but they can also sequester different organelles. The microtubules also help the cell throughout its dividing process as they are able to lengthen and shorten themselves as the cell stretches and pinches off to form the daughter cells Motility: To continue the thought of microtubules, mitosis, and a moving/changing cell, the third major function of cytoskeletal fibres is that of cell movement. Whether this be the rudder of a single celled organism or the tethering of cells to docking stations, these fibres utilize mechanical energy to help move the cell. Within the cell, these filaments also serve as railway tracks for structures moving from one organelle to another

Much of what we know about cell function depends on experiments using specific cells and specific parts (e.g., organelles) of cells. What techniques do scientists commonly use to isolate cells and organelles from complex mixtures, and how do these techniques work

Differential centrifugation Differential centrifugation is the technique used to separate different cell parts. After first breaking open cells, you can use differential centrifugation to sediment or pellet organelles based upon their size. Fractions obtained by differential centrifugation can then be further separated by equilibrium density-gradient centrifugation.

18. What is a frameshift mutation?

Frameshift mutation is a type of genetic mutation that involves the deletion or addition/insertion of any bases or nucleotides which could modify the reading frame of the gene.

Liquid chromatography is an analytical method used to separate proteins. Describe the principles for separating proteins by gel filtration, ion-exchange, and affinity chromatography

Gel-filtration chromatography separates proteins based upon their size. A mixed sample is loaded at the top, and then each protein flows out of the bottom of the column at different times, with larger proteins flowing through more quickly. The total volume of liquid required to separate a protein from a gel filtration column depends on the proteins mass -- the smaller the mass, the longer it is trapped on the beads, the longer it takes to traverse the column, and the greater dilution volume. Ion-exchange chromatography the proteins are separated on the basis of differences in their charges. After the sample is loaded at the top of the column, proteins with the same charge as the beads repel one another and flow through the column, whereas proteins with the opposite charge bind to the beads and can then be eluted by passing a salt gradient through the column. At low salt concentrations, protein molecules and beads are attracted by their opposite charges. At higher salt concentrations, negatively charged saw ions bind to the positively charged beads, displacing the negatively charged proteins. Affinity chromatography the ability of proteins to bind specifically to other molecules. This well used technique is also known as antibody affinity where a specific antibody which will bind a particular protein are bound to the beads. Then, when the mixed solution is added to the column, only the protein that binds the antibody coating the beads is retained, whereas everything else passes through. The protein of interest can then be eluted by adding a solution that disrupts the antigen-antibody complexes. The ability of this technique to separate particular proteins depends on the selection of appropriate binding partners that bind more tightly to the protein of interest than to other proteins.

How do genetic mutations arise?

Genetic mutations can arise through a number of either internal or environmental causes. One example of an internal process which can lead to mutations is DNA replication when replication errors occur from the transcriptional machinery. In these rare instances, the wrong nucleotide can be inserted into a position due to wobbling in the DNA helix which can cause transitions or transversions. Alternatively, deletions or insertions can occur when strand slippage occurs or when there are errors during crossing over. In any case, these errors can be propagated during later replication cycles when each parent strand separates, unless the error is caught and fixed beforehand. Mutations caused by environmental factors are often called mutagens because they induce changes in the DNA sequence at a much faster rate than most internal causes. Usually, exposure to these environmental mutagens causes damage to the DNA structure which makes it difficult or impossible to repair. Certain chemical agents can induce changes in nitrogenous base structure through alkylation, deamination, oxidation, intercalation, etc. which ultimately directly lead to a change in the base or promote mismatching of bases. Alternatively, exposure to high energy molecules such as radiation and UV light can induce breaks in the DNA strands or cross linking between pyrimidine bases.

16. How are myeloma cells similar to hybridoma cells? How are they different?

Hybridoma technology is a method for producing large numbers of identical antibodies (also called monoclonal antibodies). ... The myeloma cell line that is used in this process is selected for its ability to grow in tissue culture and for an absence of antibody synthesis.

13. In certain electron microscopy methods, the specimen is not directly imaged. How do these methods provide information about cellular structure, and what types of structures do they visualize?

In one type of transmission electron microscopy, the sample is coated in a heavy metal (frequently evaporated platinum) and subsequently covered in a carbon film. The specimen is then dissolved, forming a replica "shell" with the same shape as the original specimen. This replica is then placed under the transmission electron microscope and imaged. This can provide information on the shape, size and conformation of the sample imaged. This method is not without its shortcomings. It is only usable for relatively large, static samples- it cannot be used to image, say, an individual cholesterol molecule. This method is most useful for visualizing structures such as organelles, DNA and virus particles. It can additionally be utilized to assess cell membrane shape and morphology. One alternative preparation method is to slowly turn the sample while depositing the metal layer, which can provide more information than simply working with a static sample (Hendricks, 2014).

14. Do you think that drugs targeting proteins involved in mitosis would be effective in cancer treatment?

Inhibiting mitosis as a whole would rapidly result in death- cell replication is required for organism level processes (digestion, oxygen transport, etc.). It may be possible to use mitosis protein inhibitors in a combination therapy. Antibody Drug Conjugates (ADCs) are a class of therapies currently being evaluated for oncological indications, with some commercially available products such as Adcetris (FDA Website, 2018). These therapeutics are made of several parts- a surface receptor targeting monoclonal antibody highly expressed on tumor cells, a payload, and a linker binding the two pieces together. It is theoretically possible to couple a monoclonal antibody with a mitosis-inhibiting small molecule payload using an endocytosed linker. This method would help to circumvent the general toxicity of the mitosis-inhibiting payload. Inhibiting or modulating mitosis is a dangerous game, but with proper safeguards and molecular design I believe it is possible to utilize this pathway to treat cancer

26. Why is it important to study cells and organelles?

It is important to study cells and organelles for many reasons. I believe that the most important reason is because every living being is made up of cells and every cell is made up of organelles. In order to understand how a living being works we must understand every part of that living being. Once we understand every part of the living being then we can study it, to improve the living being's life, animals or humans. For example, once we understand how cells and organelles work we can understand how to treat and prevent illness and injury.

12. Why are tissue samples commonly cut into thin sections (less than 80 micrometers thick), as opposed to labeling and imaging through a large tissue sample (e.g., an entire organ or organism)?

Live tissues and cells are known to not absorb light and are difficult to see under a light microscope. As a result, in order to visualize small details in the tissue, or sample, it is necessary to "fix," or stabilize/freeze the sample with chemicals that cross-link proteins and amino acids (Lodish, H. et al, 2016). Formaldehyde is a common fixative chemical that cross-links amino acids to adjacent molecules, which stabilize the sample for further processing, such as staining that will facilitate visualization (Lodish, H. et al, 2016). Whole tissues, or cells, have very low permeability, even after treatment to increase permeability and it would be difficult to stain for visualization. Additionally, light has a much more difficult time passing through a thick, whole sample, than a thinly sliced sample.

. Explain why research on protostomes (such as the fruit fly Drosophila melanogaster) can be extrapolated and applied to deuterostomes (such as humans)?

Many traits and characteristics are preserved through evolutionary history in humans, and research done on other less complex eukaryotes can suggest important trends within humans. For example, as a model for humans, the fruit fly was initially integral to understanding genes and how chromosomal differences affect embryonic development. From this discovery, humans have been able to utilize fruit fly models for detailing cell differentiation and lineage, how a genome influences phenotypical expression, and so much more. As we understand the scope of how research models can simplify otherwise complicated inner workings, it is important to understand the implications of every scaling difference when it comes to larger eukaryotes.

Mass spectrometry is a powerful tool in proteomics. What are the key features of a mass spectrometer? Describe how mass spectrometry and two-dimensional polyacrylamide gel electrophoresis could be used to identify a protein expressed in cancer cells but not in normal healthy cells.

Mass spectrometers have four key features An ion source where charge usually in the form of protons is transferred to the peptide or protein of interest. This is called ionization. The conversion to ions happens in the presence of a high electrical field. This directs the charged ion to the mass analyzer Mass analyzer. This is always in a high vacuum chamber and separates the ion by there mass to charge ratios. The charged ions strike a detector. Detector. The detector gives a relative measurement of the amount or abundance of each ion in the sample. The fourth component is the computer system that is used to calibrate the instrument, store, receive and process the data generated by each component. Protein samples from healthy and cancerous would be collected the healthy cells would be used as a control sample for comparison. Both samples would be prepped for two-dimensional polyacrylamide gel electrophoresis. After electrophoresis both gels would be dyed, and each compared. If a protein was identified in the cancer sample and not the healthy one it could be isolated from the gel. That sample then could be run on the mass spectrometer. Through each of the components described above the each of the ion's mass could be calculated. This data will be converted through the computer system and be compared to known peptides and could deduce the best match to the peptide of interest.

What are primary cells and transformed cells? Do they have infinite lifespans?

Primary cells are isolated directly from tissue, for example from human liver or mouse kidney. These cells will only survive and divide a finite number of times before they cannot divide anymore and the cells stop growing (called senescence). For primary cells this is usually around 50 generations, which is still a lot of cultured cells, but not an infinite number. Transformed cells, typically cancer cells derived from tumors, can grow and divide indefinitely. These cell lines are extremely useful for research. One of the most famous examples of this is HeLa cells, derived from a cervical cancer tumor.

Various methods have been developed for detecting proteins. Describe how radioisotopes and autoradiography can be used for labeling and detecting proteins. How does Western blotting detect proteins?

Radioisotopes are radioactive versions of common elements, such as carbon-14. These radioisotopes can be swapped for the non-radioactive versions and given to cells to incorporate newly made, amino acids. These amino acids are now labeled with a radioactive tag and are incorporated to proteins. Autoradiography is the detection method for these new radiolabeled amino acids and proteins. After a given incubation time so the radiolabel can bond, the sample is washed to remove any non-bonded radiolabels. This sample can now be imaged via exposure to a photographic emulsion or electronic detector. This can give us the location of the proteins of interest as well as where they may move to over time. Western Blotting detects proteins by their affinity to bind to antibodies. After protein samples have been ran on a gel, by gel electrophoresis, the proteins are then transferred onto a nitrocellulose membrane. This membrane is subjected to various blocking and washing steps, but is eventually incubated with 2 antibodies. The first antibody specifically binds to the protein of interest. The second antibody binds to the first, but additionally has a luminescence property. Using chemiluminescence, it can produce a light that can be recorded on a film or a sensitive detector. The presence and intensity of the band can give you an indication of whether a protein is present, and relatively how much.

22. What are the functions of the nuclear envelope?

The nuclear envelope is a double membrane structure comprised of an inner and outer phospholipid bilayer connected by intermediate filaments. Travel through the nuclear envelope is regulated by a system referred to as the nuclear pore complex (NPC). The nuclear envelope, with the NPC, acts similar to the primary function of the cellular membrane. It allows the free flow of ions and smaller molecules to pass through unhindered. Larger molecules such as proteins and tRNA are selectively regulated and moved in or out with the assistance of transport proteins.

19. Are genetic mutations always detrimental/harmful? Justify your answer.

The theory of Evolution is based upon the idea that some mutations/ phenotypes have been advantageous and are carried on through to the next generation at a higher rate than those that are less advantageous through the process of natural selection Mutations also may not be advantageous but not harmful depending upon where and how they occur. Missense mutations replace one single nucleotide, resulting in a single amino acid substitution. Where this substation occurs is the determining factor if it will be detrimental. If the substitution occurs in a sequence the determines protein folding or binding the function of the protein may be inhibited

14. What limitation applies to most forms of electron microscopy?

There are several limitations that apply to most forms of electron microscopy. An important limitation is that cannot analyze live specimens because they are places in a vacuum; electrons are scattered easily by air molecules. One other limitation of electron microscopy includes it only being able to produce black and white images under the microscope as opposed to colored images via other microscopes. Another limitation of electron microscopy includes it being costly and expensive. This form of microscope is very sensitive to external magnetic fields and vibration. Special training is necessary to use the electron microscope to examine and prepare specimens appropriately. This device is also large and bulky.

1. A number of techniques can separate proteins on the basis of their differences in mass. Describe the use of two of these techniques, centrifugation and gel electrophoresis. The blood proteins transferrin (MW 76 kDa) and lysozyme (MW 15 kDa) can be separated by rate-zonal centrifugation or SDS-polyacrylamide gel electrophoresis. Which of the two proteins will sediment faster during centrifugation? Which will migrate faster during electrophoresis?

Therefore, longer proteins will flow more slowly through the gel than smaller ones. Therefore using the same example above, the lysozyme proteins will move more quickly through the SDS-polyacrylamide gel because they will be able to more easily fit through the pores of the gel than the larger, longer blood proteins Centrifugation is one of the more commonly used techniques to separate a collection of proteins of different masses or densities and primarily works using rapidly spinning a solution of materials to create centrifugal force. The centrifugal force applied to the tube has a differential effect on proteins that is proportional to their mass, meaning that compounds with a higher mass will settle towards the bottom of the tube faster than those with a lower mass. If the centrifugation process lasts long enough, some of the less soluble proteins in solution will migrate to the very bottom of the tube and precipitate into a pellet, in a process known as sedimentation, which can be separated from the remainder of the solution. This is the primary basis for differential centrifugation and is best used as a first step in conjunction with other purification techniques. The rate at which a compound in solution will settle to the bottom of the tube is known as the sedimentation rate. Rate-zonal centrifugation is another technique which can be used for separating soluble proteins into different regions of the solution. When the tubes are spun, proteins of different weight created a gradient in the solution and by separating the solution into fractions, you can isolate proteins of different mass. In the example provided above, the blood proteins will sediment faster than the lysozyme proteins because they will have a greater density and will be more affected by the centrifugal force. Gel electrophoresis is another common technique for separating proteins of different mass and can be a little more useful when working with proteins that have a more similar size. While all types of electrophoresis operate by introducing an electrical gradient to a porous gel for separation by differences by net charge, SDS-PAGE or sodium dodecylsulfate - polyacrylamide gel electrophoresis, is used to help separate via mass when two items have a similar net charge. SDS acts to denature proteins by disrupting hydrophobic interactions within the core and confers negative charge to the portions of the protein it is bound to. Since proteins of a similar size are in a denatured state and are bound to relatively the same amount of SDS, then the separation of the materials will be more influenced by how easily they can flow through the porous gel rather than by their other properties.

21. Suppose you design a custom antibody to label Protein F, which has a mass of 48 kDa. What methods might you use to verify that your custom antibody labels proteins with a mass of 48 kDa? In other words, what would you do if you were given a large piece of tissue and asked to confirm that the custom antibody labeled 48 kDa proteins?

To confirm that this antibody labeled proteins with mass of 48kDa I would do a Western blot. Taking the tissue, I would homogenize it, then lyse the cells. These lysates should contain the entire protein content of the cells in the tissue. Next, denature the proteins with SDS so that they separate based on size, rather than shape/charge/etc. Run this lysate on a polyacrylamide gel along with a molecular weight ladder. Once the samples have run across the gel, transfer the proteins from the gel to a membrane. Block the membrane with a blocking buffer, then use your custom antibody as the primary antibody, it should bind to your protein of interest. Use a secondary antibody that binds to your custom antibody and can also be detected easily with fluorescence. Now, you should have a Western blot with a ladder in one lane and a single band at 48kDa in the sample lane. If so, then you can conclude that your antibody binds to a protein with molecular weight of 48kDa. Your imaged Western blot might look something like this, if the bands were at 48kDa

Physical methods are often used to determine protein conformation. Describe how x-ray crystallography, cryoelectron microscopy, and NMR spectroscopy can be used to determine the shapes of proteins. What are the advantages and disadvantages of each method?

X-ray crystallography: A protein crystal (comprised of millions of proteins in a lattice structure) is analyzed by beams of x-rays passing through. The electrons cause the rays to refract onto photographic film or an electron probe and the resulting pattern is interpreted. Advantages: Cheaper/simple to operate, possible to determine the three-dimensional structure (shape), useful for larger molecules Disadvantages: Elaborate diffraction patterns, requires advanced calculations, usually require 'fixing' or staining of proteins, not all proteins are crystallizable Cryoelectron Microscopy: a diluted protein sample is applied to a slide and rapidly frozen in liquid helium/nitrogen and then is viewed under an electron microscope. Hundreds of protein images are then recorded and computer assembled to recreate a three-dimensional model. Advantages: Does not require fixing or staining, computer analysis/modeling, can view protein unhindered, small sample required Disadvantages: Relatively expensive, very low signal-to-noise ratio with H, O, N, and C NMR Spectroscopy: a concentrated protein solution is analyzed when placed in a magnetic field and the effects on the nuclear spin of the molecules are measured. Used to determine the distance between atoms. Advantages: Does not require crystallization of proteins, can show protein dynamics, high 3-D resolution on an extremely small scale Disadvantages: limited on the size of protein (<5 kDa), highly expensive (equipment), requires large pure sample

5. __________ is the most common molecule used by cells to capture, store, and transfer energy. a. ATP b. ADP c. L-glucose d. D-glucose e. water

a. ATP

RNA is made from a DNA template in a process called: a. transcription b. translation c. complementary base pairing (G=C, A=T) d. genetic coding e. catalyzation

a. transcription

9. Which structure degrades aged organelles through a process of autophagocytosis? a. nucleus b. lysosome c. rough ER d. smooth ER

b. lysosome

10. What type of gene mutation causes a change in only one DNA base pair (see below), resulting in the substitution of a single amino acid? a. nonsense mutation b. missense mutation c. frameshift mutation d. insertion e. deletion

b. missense mutation

. Protein is made from an RNA template in a process called: a. transcription b. translation c. complementary base pairing (G=C, A=T) d. genetic coding e. catalyzation

b. translation

17. Explain why the process of cell fusion is necessary to produce monoclonal antibodies used for research.

cell fusion is necessary for monoclonal antibody production because it is capable of selectively producing a monoclonal antibody to a specific protein of interest. The mechanics of making the fused cells (hybridomas) allows the user to selectively target the fused cells that have the antigen and immortality line to grow, while the unfused cells die off. This allows the user to easily pick out the fused cells that produce the pure, monoclonal antibodies.

12. Briefly describe the endosymbiont hypothesis.

endosymbiotic hypothesis states that eukaryotic cells evolved when certain prokaryotic cells were taken up (via endosymbiosis) within other prokaryotic cells. These engulfed prokaryotic cells became organelles, such as mitochondria and chloroplasts. One of the most convincing pieces of evidence for this theory is the existence of mitochondrial DNA and chloroplast DNA which are separate from nuclear DNA. This theory has been around since the 19th century, however it was re-popularized and legitimized via a 1967 article by Lynn Sagan titled 'On the origin of mitosing cells'.

24. What are the functions of the Golgi complex?

fter proteins synthesized in the rough endoplasmic reticulum are transported to the Golgi complex via transport vesicles, they undergo a series of enzyme catalyzed chemical modifications that enable these proteins to function normally. These chemically modified proteins are then sorted and delivered via a secondary set of transport vesicles to their respective destinations within the cell.

What are the functions of the plasma membrane?

mechanical barrier, selective permeability, electrochemical gradient, communication, cell signaling 1. define the shape and boundaries of the cell, 2. facilitate transport of materials into and out of the cell and serve as the first point of contact for signaling molecules, 3. maintain the 3D structure of the cell with cholesterol, and 4. engage in intercellular recognition.

8. What are the types of cytoskeletal filaments, and which type is composed of actin subunits?

microfilament Cells also have cytoskeletal components. These components include tubulin-based microtubules, actin-based microfilaments, and lamin- or keratin-based intermediate filaments. These cytoskeletal components are important for a number of functions, including cell structure, cell motility, and intracellular motility. These cytoskeletal components commonly work together to carry out cellular processes

23. What are the functions of the rough endoplasmic reticulum?

rough endoplasmic reticulum is an organelle found in Eukaryotic cells. The rough ER is full of ribosomes and is continuous with the outer membrane of the nucleus. As the meeting place for mRNA, Amino acids, and the previously mentioned ribosomes, it is also the hosting site of protein production. Afterwards, protein-laden vesicles bud off and travel to the Golgi complex for folding and other completion steps that lead to a fully functioning protein.

1. All of the following are macromolecules EXCEPT: a. polysaccharides b. proteins c. nucleic acids d. sugars e. all of the above are macromolecules

sugars The large macromolecules of life are made up of units of smaller molecules. These smaller molecules are called monomers, and chains or groups of monomers come together to form polymers. The polymers above, polysaccharides, proteins, and nucleic acids, are made up of these smaller monomer units: Polymer = polysaccharide, monomer = sugar (sometimes called monosaccharide) polymer = protein, monomer = amino acid polymer = nucleic acid, monomer = nucleotide

What type of gene mutation (see below) is defined by its premature stop codon and shortening of the protein?

the image, the fourth amino acid has a nonsense mutation of the first base pair in the codon which turns it into a stop codon. According to the lecture, a nonsense mutation will likely change a protein's function, especially if it is early in the amino acid sequence since the entire protein could end up truncated. I'm also relatively sure that cystic fibrosis is the result of a nonsense mutation.

11. Define fluorescence. How does the wavelength of light used to illuminate a specimen affect the ability to resolve objects within the specimen?

tissue is illuminated by a specific wavelength of light, like 488nm light. Then, the light emitted is of a lower energy, longer wavelength, like 507nm. One potential problem with fluorescence microscopy is that you damage your fluorescently labeled sample with the light you're illuminating it with, especially if you are taking many images over a long period of time. One way around this is to excite the fluorochrome with two photons with half the energy of a single excitation photon like is depicted on the right. Two photons of light of double the wavelength - 960nm wavelength - will excite the fluorochrome the same as a single photon of 488nm light assuming that they arrive to the same point in space at the same time. This limits the damage from high energy, short wavelengths of light, because only the imaged focal plane is illuminated.

7. Is it thought that all living organisms descended from a common ancestral cell? Why or why not?

yes the first living cells from a long long time ago, accumulated differences through mutations, which ultimately gave rise to the variety of forms we see today over those evolutionary timescales. That makes it possible to understand cellular processes common to most, if not all, cells by studying those processes in model organisms. Model organisms are species for which there has been a combined effort from many labs to characterize its anatomy and physiology, as well as developing a molecular toolbox for manipulating cellular processes.