lab exam

Question 1

what are grey sources

Answer 1

have content that is ‘accessible’ but may not be cited, may not be vetted and may be potentially incorrect. they could be websites, videos. or other informal ‘publications’. they are useful to orient yourself

Question 2

what is primary literature

Answer 2

a paper or journal article. they write about the results of their research.
- will have a materials and methods or results section, it is likely primary literature

Question 3

what are secondary literature

Answer 3

when an expert in the field writes a comprehensive summary of the current and historical primary literature, all cited. it usually is clearly marked as ‘review’

Question 4

what are tertiary literature

Answer 4

summarizes primary and secondary literature sources for a broader audience. ex. textbooks

Question 5

how do you paraphrase

Answer 5

1. reword: different words to describe the material or explaining content in a different way
2. rework: restructuring of the information that you are paraphrasing
3. cite (twice): in text citation (briefly cite w/i sentence - author 1 et al. year) and literature cited section: full citation (every author, year, article title, journal, volume:pages)

Question 6

what are 3 ways to communicate results

Answer 6

articles in peer-reviewed journals, conference presentations, and research posters

Question 7

what are features of scientific articles, posters, and presentations

Answer 7

title, abstract, introduction, materials and methods, results, discussion, conclusion, and literature cited

Question 8

what is scientific style

Answer 8

gives abstract truths that can be used to predict outcomes of individual situations. uses deductive reasoning (general ideas to develop specific conclusions or predictions). is context free - the facts are stand-alone units, can be stated independently without losing meaning. accuracy of claims is crucial

Question 9

what is narrative style

Answer 9

describes an individual case, case is used to create generalization. uses inductive reasoning (specific observations are used to to make generalization). it cant easily be broken into parts. if sentences are moved often they lose their impact because the context has changed. is based on the depiction of an individuals experience, on believability of the situations and the narrative

Question 10

what do these definitions mean: variable, constant, group, assumption, experimental group, control group, +/- control group, manipulated variable, responding variable, and controlled variable

Answer 10

variable: condition that change
constant: condition that stays unchanged
group: an individual or replicate set that all have the same treatment
assumption: this is a base belief
experimental group: treatment that is exposed to the manipulated variable
control group: treatment that is not exposed to the manipulated variable
+/- control group: treatments are designed to test fundamental assumptions in the experiment; they give expected positive or negative results
manipulated variable: variable that is changed in an experiment
responding variable: variable that is being measured
controlled: a variable that you change in both the control group and experimental group

Question 11

what is the differences between continuous and discrete data

Answer 11

continuous: collected over a steady continuum, at consistent increments
discrete: allows you to show data that falls into categories

Question 12

what are the minimum lab ppe requirements

Answer 12

lab coat, full length pants, full coverage shoes, tall socks, UV-resistant safety glasses, nitrile gloves (when req’d)

Question 13

what are the parts of a brightfield microscope

Answer 13

ocular lens: eyepiece
objective lenses: gather the light from the specimen, magnify the image, and project the magnified image towards the ocular lens
stage: where the slide is placed
condenser lens: focuses the light onto the specimen
aperture iris diaphragm: increases and decreases the amount of light that improves the contrast
light source: light bulb
field iris diaphragm: controls the amount of light in the field of view
coarse focus knob: moves the stage up and down
fine focus knob: brings the image into sharp focus

Question 14

what is magnification

Answer 14

an object increases its its apparent size. the total magnification of the microscope refers to how much an object appears to be magnified using that combination of lenses (of 40/.65 - it is the 40 (# of magnification)

Question 15

what is resolution

Answer 15

is the capacity to distinguish two adjacent points as being distinct. the resolution value (R) is the minimum distance required between two points for them to remain visible identifiable (of 40/.65 - it is the .65 (# of micrometer)). it tends to be that the best microscopes have the smallest resolution values. the r value is a function of the optical properties of the lens and the wavelength of light used

Question 16

how do you calculate the total magnification of a microscope

Answer 16

total magnification = magnification of ocular lens x magnification of objective lens

Question 17

what are two ways of determining the actual size of a specimen

Answer 17

method 1: proportion of field of view occupied by the specimen (estimate the proportion that the specimen occupies, you can determine the size of the specimen)
method 2: ocular micrometer (the miniature ruler set in one of the ocular lenses of you microscope | to determine cell size: measure the cell using the ocular micrometer and multiply by the length of each ocular division at that magnification)

Question 18

how do you calculated the magnification of an image or drawing

Answer 18

magnification of drawing = size of the drawing/actual size of the specimen

Question 19

what do membranes do

Answer 19

separate, organize, and regulate
cell membranes consist of a phospholipid bilayer with embedded proteins and sometimes other molecules. in optimal conditions membranes are fluid

Question 20

which of the following would improve magnification, resolution, or contrast
i. reducing the amount of light
ii. switching from a 40X objective lens (40/.65) to a 100X lens (100/1.25)
iii. using immersion oil
iv. switching 10X ocular lenses with 15X ocular lenses
v. staining the specimen
vi. changing the light source from a 400nm light to a 500nm light
vii. changing the light source from a 500nm light to a 400nm light

Answer 20

i. contrast
ii. magnification and resolution
iii. resolution
iv. magnification
v. contrast
vi. resolution
vii. reduces resolution

Question 21

what are pure cultures

Answer 21

an isolated group of genetically identical cells (can be easily contaminated)

Question 22

what is a colony

Answer 22

a small mass of genetically identical cells

Question 23

what is a medium

Answer 23

a solution or solid that contains nutrients that cells can use to grow and divide

Question 24

what are lawns

Answer 24

a dense, even, layer of bacteria on the plate

Question 25

what are microtubules

Answer 25

have multiple functions in cells. they are generally responsible for organelle movement

Question 26

what are microfilaments

Answer 26

they are responsible for amoeboid movement of a cell to move by assembling and disassembling networks of microfilaments to create viscous and liquid regions of the cytoplasm. they are also responsible for organelle movement

Question 27

what are intermediate filaments

Answer 27

they have structural roles in the cell

Question 28

what is contrast

Answer 28

the difference in light intensity between an object and its surround medium

Question 29

what are stains

Answer 29

they are coloured compounds that react with particular components of cells and increase contrast. by using different types of stains, the cellular location of certain classes of macromolecules can be ascertained

Question 30

what are different ways that you can compensate for a lack of contrast

Answer 30

1. stains 2. decreasing the amount of light, you eyes will differentiate any difference better with less intense light 3. special types of microscopes to manipulate light - dark field allows the light to enter the specimen indirectly and focuses the light so that any un-scattered light does not shine into the objective lens - a phase contrast microscope slows the light that passes through them to different extents. (does not alter the intensity of light) - fluorescence microscopes allows you to observe specimens and structures that are able to fluoresce when exposed to light

Question 31

what is empty magnification

Answer 31

if you increase the magnification without increasing the resolution, the insufficient resolution of details does not improve the quality of the image

Question 32

what are 2 ways resolution values can be decreased

Answer 32

1. using an illumination source with a smaller wavelength 2. increase the numerical aperture of the objective lens. can effectively be increased by placing oil between the lens and the specimen being viewed. (deflected the light rays leaving the specimen away from the objective lens)

Question 33

how can you calculate the resolution of a microscope

Answer 33

R=0.61λ/N.A. 0.61 is a constant specific to our microscope λ is wavelength of light N.A. is the numerical aperture of the lens (relationship between the refractive index of the medium and the size and working distance of the lens

Question 34

how do you draw a specimen

Answer 34

- all diagrams w/ a sharp pencil - diagrams are large - do not shade or sketch - label identifiable structures (horizontal line from structure to the label) - dont show all observable detail - include the magnificaiton of the drawing in the lower right corner of your drawing

Question 35

what are the ways that paramecium, rotifers, euglena, and amoeba move

Answer 35

paramecium (single-celled motile protist) move through cilia (swimming) rotifers (small multicellular organisms) use cilia and 'toes' to crawl in water euglena (single-celled photosynthetic protist) moves using flagella amoeba changes it's shape to move

Question 36

what are specs

Answer 36

spectrophotometers can be used to determine the concentration of pigments or cells in a liquid solution. by using the absorbance value that it gives you (at a certain wavelength) you can determine the concentration of the chromophore

Question 37

how do specs work (4)

Answer 37

1. the spectrophotometer has a light source that emits white light 2. the light passes through a prism that separates the light beam into different wavelengths 3. a narrow slit is used to select the wavelength that passes through the sample 4. the photoelectric tube reads and compares the amount of light striking the sample (the ratio of transmitted light to incident light is called transmittance (the amount of light that passes through) and the negative log of transmittance is called absorbance (measures the amount of light that is absorbed))

Question 38

what can you use a spec for

Answer 38

1. to characterize absorbance patterns of solutions of solutions or pigments 2. to measure concentration (particles in suspension reduce transmittance by scattering light (turbidity) rather than absorbing it

Question 39

how do you calculate dilution and use dilution to calculate concentration of the diluted solution

Answer 39

dilution = (volume of original solution)/(volume of original solution + volume of solvent) concentration of diluted solution = (concentration of undiluted solution)(dilution)

Question 40

how do you make a standard curve

Answer 40

1. use stock solution to plan a dilution series 2. pipette set volumes of the stock solution and its solvent into each tube 3. mix the liquid with a vortex and use a spectrophotometer to measure the absorbance at a set wavelength 4. graph a standard curve 5. use the standard curve to determine the concentration of a sample

Question 41

what is mutualistic, commensal, and parasitic

Answer 41

m: when 2 organisms of different species work together, each benefiting from the relationship c: living in a relationship where 1 organism obtains food or benefits from another without damaging or benefiting it p: an organism that lives on a host, taking what it needs to stay alive while often injuring the host

Question 42

what is the point of following an aseptic technique

Answer 42

it will help you prevent bacteria in the environment from contamination your work and prevent bacteria in your work from contaminating you and the environment

Question 43

what is a lawn and a zone of inhibition

Answer 43

l: a dense layer of bacteria z: an area of clearing around the disc where sensitive organisms are unable to grow (if the organism is antibiotic resistant, no zone will exist)

Question 44

what are the mechanisms of resistance

Answer 44

1. the cells can modify the antibiotic itself via degradation or alteration 2. can block influx 3. can also have a 'global adaptation', an alteration that prevents the antibiotic from attacking

Question 45

what are enzymes

Answer 45

they are proteins that catalyze metabolic reactions. most of the metabolism required for life would not occur without the catalytic actions of enzymes. they lower the reactions activation energy

Question 46

what happens during an enzymatic reaction

Answer 46

the molecule to be metabolize (substrate or reactant) fits into a uniquely shaped pocked of the enzyme called the active site. the substrate transiently binds with the enzyme as it is converted into an end product.

Question 47

what is amylase and why is it essential

Answer 47

it is an enzyme that is found in many different types of organisms. it is essential for plants because it allows the plant to use starch that it has stored after photosynthesis. it takes starch that is too large to pass through the cell membrane and breaks it down into smaller molecules that are able to pass through

Question 48

how does amylase work

Answer 48

it hydrolyses the alpha (1->4) bonds in amylose, resulting in glucose molecules, dimers of glucose molecules called maltose.

Question 49

what are the 3 phases of cellular respiration

Answer 49

glycolysis (glucose makes pyruvate, atp and nadh), citric acid cycle (pyruvate oxidized to make atp, nadh, fadh2, and co2), and oxidative phosphorylation (electron transfer chain to make atp)

Question 50

what are the two phases of photosynthesis

Answer 50

z-scheme and calvin cycle

Question 51

how does glucose metabolize in eukaryotes

Answer 51

w/ O -> goes through the citric acid cycle to produce a lot of ATP w/o O -> goes through alcohol or lactic acid fermentation (which regenerated NAD+) not much ATP produce

Question 52

what are the 4 phases of physiological curve

Answer 52

- the lag phase (period of time required for reactions to begin) - the log phase (reactions proceed at maximum rate) - stationary phase (time where the rate of reaction plateaus) - death phase (the quantity of the responding variable that is produced is outnumbered by the quantity consumed or degraded)

Question 53

what is bacterial genomic dna

Answer 53

it encodes all the essential functions of a bacterial cell

Question 54

what is bacterial plasmid dna

Answer 54

it is present in some, but not all, bacterial cells. they are usually in a supercoiled conformation where the circular double helix molecule becomes twisted upon itself. the genes located on a plasmid are not required for survival of the cell when it is in optimal living conditions. plasmid genes can confer extra attributes that allow the cell to survive in conditions it could not survive.

Question 55

what is an overview of the plasmid purification protocol

Answer 55

1. transfer liquid culture to tubes, pellet cells out of liquid medium, remove medium 2. rinse residual medium off of cells using STE. remove STE 3. resuspend cells in solution I 4. lyse cells with solution II, denature DNA and proteins 5. precipitate genomic DNA and proteins with solution III, remove genomic DNA and proteins 6. precipitate plasmid DNA using 95% ethanol 7. wash DNA pellet with 70% ethanol 8. remove 70% ethanol from plasmid DNA 9. resuspend/dissolve plasmid DNA in tris buffer

Question 56

what is the point of the step "close the lids of the microfuge tubes and vortex the pellets for a few seconds"

Answer 56

vortexing disrupts the pellet of cells and facilitates ell resuspension in the next step

Question 57

what is the point of solution I, solution II, and solution III in a plasmid prep

Answer 57

- solution I is a buffered, isotonic solution used to resuspend the bacterial cells - solution II contains SDS and NaOH. SDS is a detergent that denatures proteins and disrupts the plasma membrane, causing the cells to lyse. NaCl denatures the DNA - solution III is an acidic potassium acetate solution that neutralizes the pH and allows DNA to re-form however it produces an insoluble mass of DNA (allows for removal of it) at this point, you remove the supernatant and get rid of the DNA

Question 58

what is the point of adding 95% and 70% ethanol?

Answer 58

95% ethanol removes the water molecules from DNA which therefore which causes the plasmid DNA and RNA to come out of solution and precipitate 70% ethanol will remove the remainder of the salts so that the pellet is easier to dissolve in aqueous solutions

Question 59

what are the 3 ways that antibiotic resistant can be transferred between cells (horizontal transfer)

Answer 59

1. transformation - plasmid is picked up from the environment 2. conjugation - genetic material is transferred via a pilus 3. transduction - a virus infects a bacterium and injects its genetic material

Question 60

what are the 4 types of DNA mutation

Answer 60

1. silent mutation (no effect, codon will encode the same amino acid) 2. missense mutation (changes the amino acid, severity of effect will depend on the similarity of amino acid) 3. nonsense mutation (changes the codon to a stop codon) 4. no mutation (nucleotide is replaced with the same nucleotide)

Question 61

what are the 3 techniques to enumerate cells

Answer 61

1. plate count method, counts living cells only (viable cell count) *30-300 rule 2. petroff-hausser counting chambers obtains a direct count of living and dead cells. a thin layer of cell suspension is spread on the slide and the number of cells in this volume is directly counted using a microscope (uses a etched grid) 3. spectrophotometers (using turbidity and standard curves)

Question 62

how do you calculate percent of competent cells that are transformed

Answer 62

% transformed = (number of competent cells that were transformed)/(number of competent cells that could be transformed) x100%