Lecture 2: Cell structure and function Flashcards

Question

Resolution explained

Answer 1

* The ability of a lens to distinguish small objects that are close together * Ex) resolving power of 0.2μm * Two points can be distinguished if they are at least 0.2 μm apart * Light must pass between two points for them to be viewed as separate objects (providing clarity)

Answer 2

resolution improves

Answer 3

↓ ENERGY ↓ RESOLUTION

Answer 4

↑ ENERGY ↑ RESOLUTION

Answer 5

DANGEROUS b/c energy it carries can be transferred all the way to DNA for ex & can result in damage/mutation that can lead to cancer - ↑ energy radiation is dangerous b/c energy it carries will then be transferred to other objects its in contact with

Answer 6

NO - bc as you magnify, it doesn't mean the resolution maintains clarity - ex: zooming on phone doesn't mean it will still be clear

Answer 7

DOESN'T mean/guarantee resolution will also increase; dependent on microscope you chose

Answer 8

1. Cannot fit between arms, poor resolution 2. Fit between arms, resolution improves 3 and 4. As diameter of objects thrown decreases, greater numbers pass between the arms & the resolution increases

Answer 9

Improving contrast results in a better final image | • Staining improves contrast

Answer 10

Dyes are organic compounds (carbon containing CH2-COO-) that bind to specific cellular materials (inside the cell)

Answer 11

energy source

Answer 12

methylene blue, safranin, and crystal violet

Answer 13

One dye used to color specimen - just shows if something is THERE or NOT "one size fits all"

Answer 14

colored portion of a dye | - colour your cell will appear as a conseq. of that dye adhering to portions of the cell or cellular structures

Answer 15

basic= + | cell is negatively charged so they attract and cell will be blue

Answer 16

positively charged chromophore • Binds to negatively charged molecules on cell surface - (+) at pH=7 ex- crystal violet

Answer 17

1. Basic dye | 2. Acidic dye

Answer 18

ALWAYS HAVE A NET (-) CHARGE - if you apply a basic stain it will adhere - if you apply an acidic stain it will repel

Answer 19

``` negatively charged chromophore • Repelled by cell surface • Used to stain background • Negative stain (-) at pH=7 ``` ex- nigrosin

Answer 20

1. Preparing a smear Spread culture in thin film over slide Dry in air 2. Heat fixing and staining (dehydrating sample so it is stuck on slide, therefore it doesn't get rinsed off in next step) - Pass slide through flame to heat fix - Flood slide with stain; rinse and dry 3. Microscopy - Place drop of oil on slide; examine with 100 objective lens * NO DIFFERENTIATION, just can see that there's pink circles - details on cell shape size arrangement

Answer 21

be negatively charged on their external surface

Answer 22

architecture of their cell wall is different

Answer 23

a differential stain | Separates bacteria into 2 groups based on cell wall structure

Answer 24

It is useful to know if organism is gram + or - bc some antibiotics target only certain + or - so its useful to know

Answer 25

you take antibiotics that target gram + bacteria you leave the gram - bugs alone - better toxicity

Answer 26

cells that retain a primary stain | • Purple

Answer 27

cells that lose the primary stain • Take color of counterstain • Red or pink

Answer 28

- plasma membrane | - THICK peptidoglycan

Answer 29

- plasma membrane - THIN peptidoglycan layer - outer membrane

Answer 30

1. Apply CRYSTAL VIOLET stain purple & basic: Gram + = purple Gram - = purple Human cell = purple 2. Apply IODINE = a mordant - intensifies bound stain -> bulkens up the stain molecules so they will stay trapped Gram + = purple Gram - = purple Human cell = purple 3. Apply ALCOHOL = a decolourizer Gram + = purple (trapped in cage like structure - alcohol bulked them up so they can't get mordant & crystal violet out) Gram - = colourless Human cell = colourless (bc no cell wall) 4. Apply SAFRANIN (pink & basic) - sticks to any living cell Gram + = purple (pink will stick but will stay purple b/c it never came off & its darker) Gram - = pink Human cell = pink

Answer 31

everything will be BLACK bc the darker one was added after alcohol so it will trump yellow bc darker

Answer 32

gram negative have outer membrane so when you douce in crystal violet it will stick bc the cell has a net negative charges but when alcohol is added it will remove colour

Answer 33

differential stains Detects mycolic acid in the cell wall of the genus Mycobacterium - Mycobacterium – retains primary stain • Fuchsia (pink)- carbol fusion sticks to mycolic acid Anything else on slide – color of counterstain • Blue

Answer 34

has plasma membrane, gram +, & MYCOLIC ACID (hydrophobic) as the outside of their peptidoglycan

Answer 35

- hydrophobic - outside of their peptidoglycan - unique to members of mycobacterium genus - can engage with things ALSO hydrophobic

Answer 36

undergo a gram stain | - so has to do AFS

Answer 37

No bc like dissolves like so they will engage with hydrophobic things acidic and basic stains are charged meaning they are hydrophilic so these stains won't work

Answer 38

pink | - which shows mycobacterium everything else, all other cell types are blue

Answer 39

basic= positive charges so it'll stick to cells that aren't acid fast -> stick to other gram +/- , human cells, anything that has a net negative charge on outermost surface

Answer 40

EVERYTHING is blue nothing is pink so you can perform a gram stain for further analysis

Answer 41

they want to collect enough of a sample for 2 tests 1) to do acid fast stain 2) gram stain

Answer 42

the stain to remain purple b/c it's trapped in peptidoglycan, it won't come out (not outer membrane)

Answer 43

``` Endospores retain primary • Green • Cells counterstained • Pink- safranin • Ex. Bacillus anthracis spores. ```

Answer 44

*PRODUCED BY ONLY SOME BACTERIA AND ALWAYS PRODUCED BY GRAM POSITIVE BACTERIUM resilient structures ex: if a bacterium finds themselves in a situation where water/nutrients are limited, they can enter in spore state (metabolically inactive) where he hides out until conditions become more favourable for survival, then he comes out & wakes up & starts metabolism & being normal again ex: rice - when they fuel replication from those conditions, the microbial count goes up! - & if you take it & put it on fridge, it will grow slowly - can destroy with an autoclave- combines temp & pressure for ex

Answer 45

Everything would be pink

Answer 46

NO- b/c you'll have bugs there that the pink is sticking too but you don't know if its gram + or - (it can be either) - it's only when you know it produces endospores, that you know it must be gram + & therefore will produce a purple stain

Answer 47

purple - because it's an endospore forming & gram + are the only kind of bug that'll form an endospore

Answer 48

Phase ring amplifies differences in the refractive index of cell and surroundings • Improves the contrast of a sample without the use of a stain • Allows for the visualization of live samples • Resulting image is dark cells on a light background (similar to general microscope but not pretty colours)

Answer 49

Specimen is illuminated with a hollow cone of light • Only refracted light enters the objective • Specimen appears as a bright object on a dark background • Used to observe bacteria that don’t stain well • Ex) Treponema pallidum – the causative agent of syphilis opposite of phase contrast

Answer 50

• Used to visualize specimens that fluoresce • Emit light of one color when illuminated with another color of light • Cells may fluoresce naturally • Ex. Photosynthetic Cyanobacteria (origin of eukaryotic chloroplast) have chlorophyll • Absorbs light at 430 nm (blue-violet) • Emits at 670 nm (red) • Or after staining with Fluorescent dye • Ex) DAPI specifically binds to DNA

Answer 51

characteristic of the chemical properties of a fluorescent particle - have to know what this is so it can be absorbed - have to strike this with light of a particular wavelength

Answer 52

what's given off to provide the fluorescents that you see

Answer 53

LARGER wavelength - because of the energy that was absorbed, some of it was converted to heat - so not all of it will be there - b/c there is a loss of heat, when this gets absorbed you're gonna have less that'll come out which means that wavelength must be larger b/c larger wavelength is lower energy which counts for amount spent in absorption activity

Answer 54

take antibody and couple it with fluorescent particle then put it into cell and treat the cell with absorptions wavelength

Answer 55

* Uses a polarizer to create two distinct beams of polarized light * Gives structures such as endospores, vacuoles, and granules a three- dimensional appearance * Structures not visible by bright-field microscopy are sometimes visible by DIC * still using light microscope but structures not visualized by brightfield can be seen by this

Answer 56

* Uses a computerized microscope coupled with a laser source to generate a three- dimensional image * Computer can focus the laser on single layers of the specimen * Different layers can then be compiled for a three-dimensional image * Resolution is 0.1 μm for CSLM three dimensional layering

Answer 57

use electrons instead of photons to image cells and structures • Wavelength of electrons is much shorter than light --> higher resolution nm ranges in resolution reverse direction of light microscope

Answer 58

• Transmission electron microscopes (TEM) • Scanning electron microscopes (SEM)

Answer 59

Electron beam focused on specimen by a condenser • Magnets used as lenses • Electrons that pass through the specimen are focused by two sets of lenses • Compound microscope • Electrons strike a fluorescent viewing screen High magnification and resolution (0.2 nm) Specimen must be very thin (20 – 60 nm) (Inject it with resonance so that cell hardens, creating a solid structure) use microtome= diamond knife to do thin sectioning *USED TO SEE OUTSIDE OF THE CELL

Answer 60

Must be stained with metalsa=> lead or uranium => metal is heavy means subatomic particle number will be high= e- number is high => heavy metal stain will be electron dense will stick differently that to ribosome or DNA • Bind to cell structures to make them more electron dense • Enables visualization of structures at molecular level

Answer 61

magnification is constant but EM provides way better resolution - EM has much smaller resolving power

Answer 62

• Specimen is coated with a thin film of heavy metal (e.g., gold) • An electron beam scans the object (rather than going thru thin section • Scattered electrons are collected by a detector, and an image is produced • Allows an accurate 3D image of specimen’s surface. *SEE OUTSIDE OF THE CELL

Answer 63

(before nucleus) • No membrane bound nucleus or organelles (genetic material is floating around cell) • Generally smaller than eukaryotes (bc they pack alot less) • Simple internal structure • Divide by binary fission (get whole new organism rather than in us where we increase total concentration of cells) • Most are unicellular

Answer 64

Mitosis bc resulting in genetically identical daughter cells no genetic variation just a means of increasing cell number when we do mitosis we increase in cell number binary fission is ur getting a whole new organism

Answer 65

* Diverse metabolism (allows them to live in diff environments) * Live in a broad range of ecosystems * Pathogens and non-pathogens

Answer 66

* Diverse metabolism * Live in extreme environments * Non-pathogens - only thing they share with bacteria is prokaryotic structure

Answer 67

``` • Roughly spherical • Ex) Streptococcus pyogenes - causes strep throat - flesh eating bacteria *same species but different strains ```

Answer 68

• Rod shaped • Ex) E. coli - bladder infection, fecal contamination - asymmetrical shape

Answer 69

* Spiral shaped * Ex) Spirillum volutans - helical morphology - shorter length, rigid causes restricted flexibility

Answer 70

• Spirochete • Ex) Treponema pallidum - helical confirmation but longer so more flexible - STI Budding & appendaged bacteria (allows it the ability to make contact with the surface) • Ex) Caulobacter crescentus Filamentous bacteria • Ex) Streptomyces griseus - long and thin so good SA for absorption

Answer 71

physiology, ecology, phylogeny, etc. of a prokaryotic cell has nothing to do with genetics either

Answer 72

• Optimization for nutrient uptake (small cells and those with high surface-to- volume ratio) - sa; v ratio- better membrane to interact with enviroment • Swimming motility in viscous environments or near surfaces (helical or spiral-shaped cells) - if cell has particular shape it can cut thru and move one • Gliding motility (filamentous bacteria) - maximize contact with environment

Answer 73

diplococcus diplobacillius streptococci staphylococci

Answer 74

* E.coli~1.0x3.0μm * Staphylococcus aureus ~ 1.0 μm diameter Very small: • Mycoplasma genitalium ~ 0.3 μm (STI) -> anmaly bc it doesn't have a cell wall -> outer most component is the plasma membrane similar to a animal cell which doesn't have a cell wall so you would not put into a gram stain bc it would look pink bc alchol would destain the membrane so gram stain is not an effective way to identify Very large: • Epulopiscium fishelsonii ~ 80 x 600 μm.

Answer 75

Surface-to-volume ratios, growth rates, and evolution • Advantages to being small • Small cells have more surface area relative to cell volume than large cells (i.e., higher S/V) • Support Greater Nutrient Exchange Per unit cell volume • Tend to grow faster than larger cells

Answer 76

• Cellular organisms <0.15 μm in diameter are unlikely • Open oceans tend to contain small cells (0.2–0.4 μm in diameter) • Many pathogenic bacteria are also small (missing many genes whose functions are supplied to them by host) - makes things more efficient * you have to fit ribosomes etc in so they can only be so small

Answer 77

• Thin structure that surrounds the cell ->makes it easier for nutrients to come in and waste to leave * Vital barrier that separates cytoplasm from environment * Highly selective permeable barrier; enables concentration of specific metabolites and excretion of waste products - > chooses what gets in - > cell has the ability to let glc and lactose in - > wastes can be toxic if they accumulate so its imp part of membrane function to let wastes out *BOTH PROKARYOTES AND EUKARYOTES HAVE THIS

Answer 78

* General structure is phospholipid bilayer (2 layers) * Contain both hydrophobic (fatty acid) and hydrophilic (glycerol-phosphate) components * Can exist in many different chemical forms as a result of variation in the groups attached to the glycerol backbone * Fatty acids point inward to form hydrophobic environment; hydrophilic portions remain exposed to external environment or the cytoplasm

Answer 79

membrane is amphipathic because it has both polar and non polar components - polar heads non polar tails

Answer 80

- 3 carbon back bone c1; has x group which determine identity c2 and c3; have fA tails which determine characteristics depending on length or saturation vs unsaturation

Answer 81

According to the hydrophobic effect if you put a phospholipids into water they naturally form a bilayer in order to form favorable interactions

Answer 82

The hydrophobic tails will interact favourably with the oil (nonpolar with nonpolar) and the heads will face inward

Answer 83

they come together and naturally circulize | -> ends come together so they aren't touching water

Answer 84

Unsaturation=> lower boiling point, more fluidity, less vdws so less what required saturation=> higher boiling point, melting point, solid at room temp, more vdws so more heat to break

Answer 85

glycerol ( 3 carbon backbone with 3 OH groups) • 2 Fatty acids • Phosphate • Side chain (optional)

Answer 86

molecule carries full or partial charge | • Hydrophilic

Answer 87

molecule is uncharged • Hydrophobic electrons are held in the middle- non polar covalent bond

Answer 88

the electrons are held on N more closely bc polar covalent bond

Answer 89

The membrane has a net negative charge - look at picture in notes - the x group charge can make it have net negative charge

Answer 90

* 8–10 nm wide * Embedded proteins * Stabilized by hydrogen bonds and hydrophobic interactions * Mg2+ and Ca2+ help stabilize membrane by forming ionic bonds with negative charges on the phospholipids * Somewhat fluid

Answer 91

Length of FA tails - > which determines how far the head will be from one another - > if you adjusted length to much the protein wouldn't insert properly into membrane

Answer 92

membrane has a net negative charge

Answer 93

Mg2+ and Ca2+ help stabilize membrane by forming ionic bonds with negative charges on the phospholipids - > membrane has net negative charge which means the phospholipids repel each other - > divalent cations help with this

Answer 94

semi fluid - > if fully fluid like puddle of oil it wont work and if hard like rock that won't work - > The tails are far apart so you can't get vdws interactions so it creates fluidity bc the tails are not locked in position

Answer 95

Non polar amino acids | -> uncharged hydrophobic

Answer 96

vdws interactions | -> weak interaction between non polar

Answer 97

* Outer surface of cytoplasmic membrane faces the environment * In gram-negative bacteria, interacts with a variety of proteins (periplasmic proteins) that bind substrates or process large molecules for transport * Inner surface of cytoplasmic membrane interacts with proteins involved in energy-yielding reactions and other important cellular functions * Integral membrane proteins * Peripheral membrane proteins

Answer 98

Firmly embedded in the membrane | -> analogous to inner mitochondrial membrane and will have ETC

Answer 99

- intergral membrane proteins | - go all the way thru membrane

Answer 100

``` One portion anchored in the membrane - are attached to extracellular face or intracellular - attache dto hydrophilic regions - using H bonds or ionic interactions (electrostatic interactions) ```

Answer 101

Ether linkages in phospholipids of Archaea | -. provides better thermal stability

Answer 102

Bacteria and Eukarya that have ester linkages in phospholipids

Answer 103

Archaeal lipids lack fatty acids (REQUIRE CARBOXYLIC GROUP FOR FA THAT WOULD BE ESTER SO THEY DON'T HAVE); have isoprenes instead • Major lipids are glycerol diethers and tetraethers • Can exist as lipid monolayers, bilayers, or mixture

Answer 104

C5 Tails- hydrophobic | - come together; c5+ c5= c10

Answer 105

2 ethers - 1 glycerol neck bilayer

Answer 106

2 glycerlo necks 4 ether linkages - monolayer; no gaps meaning you get more vdws interactions so you have more to melt

Answer 107

membrane will hold better at higher temps

Answer 108

The bilayer- bc membrane will want to solidfy so you would want more of this to prevent bc these impart fluidity

Answer 109

- monolayer; no gaps meaning you get more vdws interactions so you have more to melt - bilayer- gaps so less thermal stability

Answer 110

Lipid monolayer | - impart a lot of stability

Answer 111

extremely heat resistant - bc more vdws Commonly found in hyperthermophilic Archaea (grow best at temperatures above 80oC)

Answer 112

small non polar material can move freely along concentration gradient

Answer 113

No - are more controlled need transporters/ channels - ex- pores for polar material which are very specific to a certain material

Answer 114

Permeability barrier • Polar and charged molecules must be transported • Transport proteins accumulate solutes against the concentration gradient (ACTIVE TRANSPORT, moving things from areas of low to high bc they can't freely pass thru membrane allowing it to accumulate) Protein anchor • Holds transport proteins in place Energy conservation • Generation of proton motive force

Answer 115

they have to stay in that position bc its essential the ETC stays like this or you would lose function

Answer 116

The gradient would disappear and energy could not be harvested so you want protons to move from high to low and stay so that ATP synathse can allow them to move thru and make ATP

Answer 117

toxins like cyanide make the membrane leaky to protons which means that the protons can mover wherever and don't need to use ATP synthase so you lose the ability to harvest energy to make ATP and lose the ability to make gradients this is lethal bc your energy production stops and brain run out of gas

Answer 118

* Show saturation effect | * Highly specific (bringing in one particular material)

Answer 119

molecule is moving directly thru the PM (no transmembrane protein is required) - very limited, inefficient bc molecule might be polar to large

Answer 120

physically binding to and guiding molecule into cell rather than following the gradient

Answer 121

transmembrane protein (polar) - dramatic increase in solute entry and then levels off bc once all the binding sites are saturated it can't go any faster - > similar to enzyme activity; vmax cooks in the kitchen

Answer 122

* Simple transport * Group translocation * ABC system All require energy in some form, usually proton motive force or ATP (ALL ACTIVE TRANSPORT)

Answer 123

All require energy in some form, usually proton motive force or ATP

Answer 124

Driven by the energy in the proton motive force - ex of secondary active transport - > energy released from proton movement from high to low funds energy needed to move another solute from low to high

Answer 125

Chemical modification of the transported substance driven by phosphoenolpyruvate For a cell that has an abundance of nutrients all around it, it will want to take in all these extra nutrients, so the cell responds by taking in much as possible and exceed equ' and keep bringing in more by bringing it in and phosphorylating it your changing the molecule when you do this its now a different molecule, so you wont reach equ' between molecule and molecule phosphorylated outcome is solute inside the cell is consistently staying low meaning you can bring lots in maximizing intake potential, a lot more can come in

Answer 126

Periplasmic binding proteins are involved and energy comes from ATP. _ take ATP hydrolyze is and releases energy which is used to pay -> type of active transport bc ATP is directly being spent

Answer 127

uniport, symport, and antiport

Answer 128

transport in one direction across the membrane

Answer 129

``` function as co-transporters - move in same direction ```

Answer 130

transport a molecule across the membrane while simultaneously transporting another molecule in the opposite direction

Answer 131

moving 2 things at once using one transporter

Answer 132

Simple transport Lactose is transported into E.coli by the simple transporter lac permease - a symporter- 2 molecules being moved in the same direction - activity is energy driven - transports H+ and lactose into the cell simultaneously - proton releases energy which is used to pay for lactose movement - lactose is going against concentration gradient, moving from low to high

Answer 133

Group Translocation Sugar is phosphorylated during transport across the membrane Moves glucose, fructose, and mannose Phosphoenolpyruvate (PEP, is the most energy rich molecule used for substrate level phosphorylation) donates a P to a phosphorelay system P is transferred through a series of carrier proteins and deposited onto the sugar as it is brought into the cell *motivation is to try and establish equ but once equ is reached you can't have more in so instead you phosphorylate it so its no longer glc no longer part of glc gradient so glc can keep coming in

Answer 134

• Involved in uptake of organic compounds (e.g., sugars, amino acids), inorganic nutrients (e.g., sulfate, phosphate), and trace metals • Typically display high substrate specificity • Gram-negatives employ periplasmic-binding proteins and ATP-driven transport proteins • Gram-positives employ substrate-binding lipoproteins (anchored to external surface of cell membrane) and ATP-driven transport proteins

Answer 135

you need many ABC in cell bc 1 is specific to one molecule; so a substantial amount of the bacterial genome is dedicated to providing instructions to make ABC bc you need a seperate one for each nutrient

Answer 136

non-specific transmembrane protein found in gram negative organisms - is in outer membrane and is non specific as long as size and polarity is met

Answer 137

found in gram negative organisms binds to nutrient and delivers it to ABC allowing the nutrient to be taken up by the cell - you have these for nutrients stuff you want to come in not for toxins

Answer 138

porins in outer membrane (transmembrane protein) -> nonspecific as long as polar and size is met then it can pass thru > outer membrane is like a fence things can freely pass into the yard (periplasmic space) but to enter the house cytoplasm they need to go thru PM which is specific enters periplasmic space where the nutrient float around - periplasmic binding proteins are also floating around find nutrient they are specific to and bring to ABC transporter

Answer 139

substrate binding lipoproteins - lipoproteins are attached to PM, swimming around in extracellular fluid find nutrients for what its specific and guide it to ABC

Answer 140

``` Solute binding protein • Periplasm • Binds specific substrate Integral membrane proteins (transporter) ATP-hydrolyzing proteins • Supply energy for the transport event ```

Lecture 2: Cell structure and function Flashcards

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