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Lecture exam 1 Flashcards

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1
Q

Give an example of a solute

A

Sodium chloride

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2
Q

Define halophile and osmotolerance

A

Halophile: loves salts
Osmotolerance: has a salt limit

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3
Q

Define acidophile, neutrophil, and alkaliphile

A

Acidophile: Likes acidic environments
Neutrophil: Likes neutral environments
Alkaliphile: Likes basic environments

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4
Q

Define psychrophile, mesophile, thermophile

A

Psychrophile: Likes extreme cold
Mesophile: Likes moderate temperatures
Thermophile: Likes extreme heat

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5
Q

Define piezophile (barophile)

A

Likes high-pressure environments

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6
Q

Define obligate aerobe, obligate anaerobe, and microaerophile

A

Obligate aerobe: Needs lots of air/ oxygen
Obligate anaerobe: Needs no air/ oxygen
Microaerophile: Likes a little air/ oxygen, but not a lot

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7
Q

Define metabolism

A

The total of all chemical reactions occurring in the cell

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8
Q

Define anabolism and catabolism

A

Anabolism: the biosynthesis of new organic molecules from smaller organic and inorganic compounds
Catabolism: breaking down of molecules into smaller units while releasing energy, ‘fueling reactions’

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9
Q

Microbes are big producers of what two elements?

A

Oxygen and nitrogen

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10
Q

Define and give examples of the 3 types of cellular work

A

1) Chemical: synthesis of complex biological molecules
2) Transport: taking up nutrients, eliminating wastes, and maintaining ion balances
3) Mechanical: movement of structures that are part of the cell (motility, rotation of flagella, partitioning of chromosomes)

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11
Q

Define chemoorganotroph, chemolithotroph, and phototroph

A

Chemoorganotroph: energy source is organic molecules
Chemolithotroph: energy source is inorganic molecules
Phototroph: energy source is light

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12
Q

Define autotroph and heterotroph

A

Autotroph: Carbon source is CO2
Heterotroph: Carbon source is organic molecules

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13
Q

Define organotroph and lithotroph

A

Organotroph: electron source is organic molecules
Lithotroph: electron source is inorganic molecules

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14
Q

The most commonly used practical form of energy is?

A

ATP

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15
Q

Give 3 examples of altered ATP, and briefly describe how altering ATP works

A

-Guanosine, cytidine, uridine
-Enzymes hydrolyze bonds and alter original triphosphate molecule of ATP to make different energy sources

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16
Q

Name the basic purposes of GTP, CTP, and UTP (guanosine, cytidine, uridine)

A

GTP: protein synthesis
CTP: lipid synthesis
UTP: peptidoglycan, and polysaccharide synthesis

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17
Q

Give 5 examples of cellular processes that are exergonic reactions.

A

Aerobic respiration
Anaerobic respiration
Fermentation
Phototrophy
Chemolithotrophy

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18
Q

Give 3 examples of cellular processes that are endergonic reactions

A

Chemical work
Transport work
Mechanical work

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19
Q

Give 4 examples of carbon sources

A

CO2, sugars, amino acids, and fatty acids

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20
Q

Define substrate level phosphorylation

A

The generation of ATP (or GTP/UTP, etc)) from ADP (or GDP/ UPT, etc) by chemical reaction

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21
Q

Define oxidative phosphorylation

A

An alternative way to create ATP generated by a proton gradient

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22
Q

Define oxidation-reduction (redox) reactions

A

Electrons move from an electron donor to an electron acceptor

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23
Q

The ETC (electron transport chain) of bacteria is very similar to that of what?

A

Mitochondria

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24
Q

Describe the chemiosmotic hypothesis and how it relates to the ETC

A

As electrons move through the chain, energy is generated; this energy allows protons to be pumped across the membrane to create electrochemical gradient. This gradient (charge separation) is the energized state called Proton Motive Force

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25
Q

Give a quick 5 bullet-point synopsis of what happens during the ETC

A

1) NADH is an electron donor
2) A series of redox reactions pump protons through the membrane
3) Until the electrochemical gradient is established
4) Oxygen is the final electron acceptor
5) ATP synthase accepts protons to generate ATP

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26
Q

What are the three pathways of glucose catabolism, and which is the most common?

A

1) Embden-Meyerhof pathway: most common
2) Entner-Doudoroff pathway: only in prokaryotes
3) Pentose Phosphate Pathway

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27
Q

Describe the Embden-Meyerhof pathway of glucose catabolism

A

-Amphibolic (both catabolic and anabolic)
-Generates NADH as its electron donor
-Starts with glucose, 2 ATP are used to generate 3 Glyceraldehyde 3-phosphate
-End product is pyruvate
-Uses a redox active coenzyme

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28
Q

Describe the Entner-Doudoroff pathway of glucose catabolism (what is it found in, what is its electron donor, what does it make)

A

1) Only found in prokaryotes
2) NADPH is generated, which an electron donor
3) Produces:
-KDPG
-Part 1 end products are pyruvate and glyceraldehyde 3-phosphate
-Part 2 end product is pyruvate
-Creates 2 pyruvates, doesn’t create 2 extra ATPs like the embden-meyerhof pathway (but does still generate ATP)

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29
Q

Describe the Pentose Phosphate Pathway of glucose catabolism (what makes it unique, what does it start with, what’s a part of the pathway, what is the electron acceptor)

A

-May be older than the other pathways. It’s carried out by enzymes in the cells, but can be done without them.
-Starts with 3 glucose-6, changes the chemistry of it until you end up with pyruvate
-Glyceraldehyde-3-p and 6-phosphogluconate are a part of the pathway
-NADP is electron acceptor

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30
Q

Describe the TCA Cycle (Aka Krebs Cycle, Aka Citric Acid Cycle)
What is made right away, what plays a large role, what is broken down, what are the electron donors, and what gets oxidized?

A

-NADH is made right when it enters the cycle
-Acetyl-coenzyme A plays a large role
-GDP is broken down into GTP, which are the high-energy molecules
-FAD and FADH2 and NAD and NADH are electron donors; there are 5 electron donors in the cycle
-The process oxides pyruvate into 3 carbon dioxides
-Generates GTP

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31
Q

Describe what happens to the ETC if we grow bacteria with low aeration in the stationary phase

A

Then there’s only a certain amount of oxygen to help the ETC run, so they generate less hydrogen and have to conserve

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32
Q

What two things is proton motive force driven by?

A

The proton gradient and active transport

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33
Q

What is the ATP yield from aerobic respiration, and what kind of phosphorylation do these ATP come from?

A

-Yields 32 ATP
-Primarily from oxidative phosphorylation, but also uses some substrate-level phosphorylation.

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34
Q

Give an example of chemorganotropy

A

Anaerobic glucose metabolism

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35
Q

What is anaerobic glucose metabolism called?

A

Chemorganotrophy

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36
Q

Describe the diversity of electron acceptors and why it’s important

A

-There’s a huge diversity of electron acceptors, which is important for the diversity of microbes in general.
-Diversity is impacted by nitrate waste that leaks from farms, factories, etc into the environment; nitrate occurs in oxygen depleted sediments and soils.

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37
Q

What type of reaction is chemorganotrophy

A

A dissimilatory nitrate reduction (denitrification)

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38
Q

What does chemorganotrophy break down, and what does three things does it then break down into?

A

Nitrate > nitrite > nitric oxide > nitrogen gas

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39
Q

Nitrites oxidate iron atoms in hemoglobin, which means _____ nitrite consumption can lead to poor oxygen

A

high

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40
Q

What are the four unifying themes of fermentation?

A

1) NADH is oxidized to NAD+
2) Oxygen is not needed
3) Electron acceptor is pyruvate
4) ETC cannot operate, which leads to reduced ATP production

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41
Q

What happens to pyruvate during fermentation, and why do people find this valuable?

A

Pyruvate is converted to lactate and/or X (which is then turned into Y); X & Y can be used in weapons production

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42
Q

True or false: A lot of fermenters can be explosive, so they’re often used to manufacture weapons

A

True

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43
Q

List 4 types of fermentation

A

1) Lactic acid fermentation (has two types)
2) Alcohol (ethanol) fermentation
3) Complex fermentation
4) Other fermentation substrates: variety of sugars, amino acids, and organic acids

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44
Q

List and describe the two different types of lactic acid fementers

A

1) Homolactic fermenters: use the Embden-Meyerhof pathway to reduce pyruvate to lactate (lactate dehydrogenase). (tldr: only make lactate)
2) Heterolactic fermenters: also produce ethanol and CO2

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45
Q

Briefly describe reactants, products, and enzyme of alcohol (ethanol) fermentation

A

Sugars > ethanol + CO2 (enzyme: alcohol dehydrogenase)

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46
Q

Briefly describe the components of complex fermentation

A

Mixed acid (#1, 5, 6, 8, 9)
Butanediol (#1, 4, 5, 6, 9)

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47
Q

Give examples of monosaccharides and disaccharides, and describe what monosaccharides do

A

Monosaccharides such as: galactose, mannose, fructose are modified by enzymes to make the sugar the enzyme wants to carry down the pathway
Disaccharides such as: maltose, sucrose, lactose, cellobiose

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48
Q

List 4 other types of catabolism not otherwise talked about

A

Lipid catabolism, protein catabolism, fatty acid beta oxidation, and transamination

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49
Q

Describe what happens in lipid catabolism and protein catabolism (ex: X is broken down using Y into Z)

A

1) Lipids: Tricylglycerols and other lipids are broken down with lipases into fatty acids
2) Proteins: Polypeptides are broken down by proteases into amino acids

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50
Q

Describe what happens in fatty acid beta oxidation and transamination

A

1) Fatty Acid Beta Oxidation: 2 carbons are broken down for every fatty acid broken down because they’re good electron donors, as well as acetyl-Coa.
-The fatty acid carbon sources can be extremely beneficial to the cell.
2) Transamination: If the cell is starving and needs pyruvate, they can take an amino acid and a-Ketoglutarate to make pyruvate and glutamate
-Intermediates of the krebs cycle are produced

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51
Q

What are the energy and carbon sources in phototrophy?

A

Light is a source of energy; the pigments in the cell (chlorophyll b and bacteriochlorophyll a) trap light energy
Carbon source is often CO2

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52
Q

Describe how pigments are important to phototrophy

A

-The alternating/ conjugated double bonds of the pigments allow for the generation of electron resonance (meaning they bounce from double bond to double bond)
-The types of chlorophyll have a great versatility in wavelength absorption

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53
Q

In what types of organisms does oxygenic photosynthesis occur, and briefly describe its two stages

A

1) Occurs in plants, eukaryotic algae, and cyanobacteria
2) Photons initiate the transfer of electrons, then:
-Photosystem 1 traps light at longer wavelengths
-Photosystem 2 traps light at shorter wavelengths

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54
Q

Photosystem 1 traps light at _____ wavelengths, and photosystem 2 traps light at ______ wavelengths

A

longer; shorter

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55
Q

Describe what happens during the light reactions of oxygenic photosynthesis (what does it generate and need; what does it initiate; where do electrons flow; what’s made to be used in the dark reactions?)

A

-Generates O2 and NADPH; needs H2O to initiate photolysis and needs NADP.
-Initiate the two photosystems
-Electrons flow from H2O to NADP with aid of energy from photosystems; ATP is synthesized by noncyclic photophosphorylation
-ATP and NADPH are then used to generate CO2 in the dark reactions

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56
Q

What are the reactants and products of oxygenic photosynthesis?

A

ATP and NADPH are used to generate CO2 in the dark reactions

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57
Q

What is cyclic photophosphorylation? What does it produce, what doesn’t it produce, and what organisms use it?

A

-Cyclic photophosphorylation is used to generate ATP by organisms who have only developed one photosystem
-Produces no oxygen and no NADPH is made
-Used by all phototrophic bacteria, but plants can shift to this when their ATP runs low

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58
Q

____________ are the type of bacteria that evolved the second photosystem

A

Cyanobacteria

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59
Q

Cyanobacteria are Gram-____________

A

negative

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60
Q

Describe the ecological and evolutionary contributions of cyanobacteria

A

-They’re the organisms that evolved photosystem II
-They’ve had a large impact on how we’ve estimated how long life has been around (4.5 billion years/ as old as the universe)
-Big impacts in the astrobiology field (Richard Hoover claims he found cyanobacteria inside a meteorite

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61
Q

Name the 3 structures unique to cyanobacteria

A

1) Gas vesicles
2) Phycobilisomes
2) Thylakoid

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62
Q

Describe phycobilisomes

A

Found only in cyanobacteria, they’re antenna on the thylakoids that are loaded with photopigments to take in light; >95% energy efficiency. Are recycled when the cell is starving.

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63
Q

Describe the morphology diversity, colony formation, and motility of cyanobacteria

A

-Very diverse shapes (rod-structures, spiral strands, balls of cells, etc)
-Usually form a colony with a gelatinous sheath around it
-No flagella, but can move together as a colony

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64
Q

What does bacterial photosynthesis resemble, what does it have for efficiency, and what is the most important thing they produce?

A

-Resembles plant system
-Has an on/ off switch for efficiency
-Produce oxygen (among other things) and are used in the generation of ‘clean and green energy’

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65
Q

Describe the problem of algal blooms

A

-The organisms can excrete toxins during algal blooms when there are to too many bacteria in one area
-Implicated in causing ALS

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66
Q

Describe anoxygenic (or anaerobic) phototrophy; what is it, what type of bacteria use it, and how fast is it compared to oxygenic phototrophy

A

1) Defined as photosynthesis without the use of oxygen
-There’s a cyclic electron flow during anoxygenic phototrophy due to only having 1 photosystem
2) Carried out by purple sulfur bacteria and nonsulfur bacteria
3) Much slower than oxygenic phototrophy and generates less ATP
>Green sulfur bacteria have chlorosomes (store chlorophyll) and a baseplate to make up for only having 1 photosystem

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67
Q

What is unique about green sulfur bacteria?

A

They have chlorosomes that store chlorophyll and a baseplate to make up for only having 1 photosystem (because they’re anaerobic phototrophs)

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68
Q

Name two light-processing structures

A

Phycobilisomes and chlorosomes

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69
Q

Name the 3 types of phototrophy

A

1) Anoxygenic phototrophy
2) Oxygenic phototrophy
3) Rhodopsin-based phototrophy

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70
Q

Describe rhodopsin-based phototrophy

A

A light-driven proton pump; conformation changes relocate protons to the periplasm and generates a pH gradient for chemiosmosis (No ETC!)

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71
Q

What are the 3 major groups of chemolithotrophs?

A

Hydrogen-oxidizing
Nitrifying
Sulfur-oxidizing

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72
Q

Define and describe chemolithotrophy; what is its definition, and what is its major disadvantage?

A

-Defined as the breaking down of inorganic substances for energy
-These substrates have a much higher reduction potential than organic substrates; so if less energy is obtained, the bacteria need to eat more to grow

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73
Q

What can be directly oxidized to provide electrons for ETC and PMF, and what is this called?

A

Sulfite; sulfite oxidation

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74
Q

Describe the two methods of sulfur oxidation

A

-Sulfite can be directly oxidized to provide electrons for ETC and PMF
-Can also be oxidized and converted to APS; this process yields electrons + ATP (substrate level phosphorylation)

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75
Q

Describe the unusual electron flow in the ETC of Nitrobacter

A

-Nitrate can go with forward electron flow to make ATP and PMF, or reverse electron flow to make NADH for biosynthesis
-Can’t generate a ton of ATP
-When nitrites are converted to nitrates, nitrates are readily absorbed by the plants

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76
Q

Define anabolism; give an example of catabolism, and when does anabolism go backwards?

A

1) “Building reactions”
2) Catabolism: Heterotrophs degrade their carbon sources into one or more intermediates of the central metabolic pathway
3) Anabolism only goes backwards if the cell is eating itself

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77
Q

List the 6 principles governing biosynthesis

A

1) Large molecules are made from small molecules
2) Many enzymes are bifunctional
3) Some enzymes function in one direction only
4) Anabolic pathways are irreversible
5) Catabolism and anabolism are physically separated
6) Catabolism and anabolism use different cofactors

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78
Q

What are the 3 phases of the Calvin cycle?

A

1) Carboxylation
2) Reduction
3) Regeneration

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79
Q

In what two places does the Calvin Cycle occur?

A

Occurs in:
1) The stroma of chloroplasts
2) The carboxysomes of bacteria

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80
Q

Describe the Calvin cycle (what is it, what is its goal, where does it occur, and what are its 3 phases?)

A

-Defined as the reductive pentose phosphate pathway; aka carbon fixation.
-Its goal is to convert carbon dioxide and water into organic compounds to be used by the cell
-Its 3 phases are carboxylation, reduction, and regeneration
-Occurs in stroma of chloroplasts and in carboxysomes of bacteria
-There is also a reductive TCA cycle

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81
Q

Describe the difference between enzymes and ribozymes

A

Proteins called enzymes
RNA called ribozymes

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82
Q

What do enzymes do?

A

Speed up chemical reactions (catalysts)

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83
Q

Bacteria are ________, whereas fungi, protozoa, parasites are _________.

A

prokaryotes; eukaryotes

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84
Q

What structures and organelles do bacteria have?

A

-Bacteria do not have internal membrane-bound organelles
-Bacteria have no sophisticated internal structures: no nuclear membrane, no mitochondria, no Golgi, no endoplasmic reticulum

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85
Q

List and describe the 6 common shapes of bacteria

A

Cocci: round
Coccobacilli: two cocci attached to each other
Curved: horseshoe shaped
Diplococci: two cocci next to each other
Bacilli: rod-shaped
Spiral: wavy-shaped

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86
Q

Define morphology

A

The form and structure of an organism or group of identical organisms

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87
Q

What do you need to know about a bacteria cell to identify its morphology?

A

What stage of growth a bacteria is in

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88
Q

Patterns of groups of identical bacteria are reflective of what?

A

cell division/ binary fission

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89
Q

Define pleomorphic

A

Each cell of a species has a slightly different shape when it divides

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90
Q

Describe aggregation properties (how are they determined and how can they be important)

A

-Determined by the orientation of the cell division plane to the axis of the cell and the tendency of progeny cells to adhere to one another
-Can be characteristic of a species

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91
Q

What functions do structures from the cytoplasmic (inner) membrane and outward perform?

A

1) Protection from the external environment (includes host defense)
2) Permeability barrier for selective transport of nutrients and information
3) Control over physical location (ex: through flagella)

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92
Q

What does an environment primarily see first about a bacteria? Why?

A

Structures, because they are both external and unique (or foreign)

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93
Q

How does medicine exploit bacterial structures?

A

Structures are often important antigens, so they can be used as vaccine targets and in diagnostics and epidemiology

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94
Q

Bacterial structures and their composition often reflect what?

A

Adaptations to the environment

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95
Q

Cell surface _______ can be targets for antibiotics
Cell surface _______ can be a barrier to antibiotics

A

structures; properties

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96
Q

What do bacterial cells use external structures for?

A

1) Cell surface structures often used to attach to and invade host cells and “sense” their environment to appropriately express virulence factors
2) Certain structures are not necessarily essential for viability, but are often important in pathogenesis as virulence factors

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97
Q

True or false: Structures are not expressed at all times and may be lost during continuous culture in laboratory media

A

True

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98
Q

What does peptidoglycan (murein) do in a cell?

A

One of the key components of bacteria that makes up cell wall and is the basis for a Gram stain reaction

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99
Q

The cell membrane of a bacteria is called the _______ membrane

A

cytosolic

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100
Q

List the 4 uses of peptidoglycan

A

1) Key contributor in overall shape of bacteria
2) Crucial for osmotic stability
3) Unique structure found only in bacteria
4) Makes a good target for antimicrobial agents (since it’s unique to bacteria and crucial to their survival)

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101
Q

Define lipopolysaccharide

A

An endotoxic structure found in the outer membrane (of the cytosolic membrane) of gram-negative bacteria.

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102
Q

How can you tell lipoteichoic acid and teichoic acid apart?

A

Lipoteichoic acid has a connection down to the cell membrane, whereas teichoic acid is only on the surface of the cell wall.

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103
Q

Lipoteichoic acids and teichoic acids are only found in gram-_______ bacteria

A

positive

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104
Q

Describe the characteristics of a gram-negative cell envelope (4)

A

1) Inner membrane: symmetrical bilayer of phospholipids
2) Periplasm: sandwiched between IM and OM / gel-like matrix
3) Outer membrane: asymmetrical bilayer of lipids
-Phospholipids in the inner leaflet and LPS in outer leaflet
4) Outer membrane serves serves as a selective permeability barrier that is virtually impermeable to hydrophilic solutes

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105
Q

How does the difference between gram-positive and gram-negative bacteria affect treatment plans for patients?

A

Since gram-negative bacteria’s outer membranes are virtually impenetrable to hydrophilic solutes, it affects which antibiotics are used in treatment

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106
Q

Define porins

A

Channel-forming proteins for the purpose of allowing
influx of nutrients and extrusion of waste products

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107
Q

True or false: The fluid mosaic model applies to the lipid bilayer of bacteria

A

True

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108
Q

What is a phospholipid made of?

A

Has a head group and long hydrophobic fatty acid chains

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109
Q

Describe the importance of phospholipids to bacteria

A

-There’s a lot of diversity in just phospholipids; there are numerous fatty acids that can make up the fatty acid chains.
-Can vary in saturation (triple bonds, double bonds, single bonds, etc), length, cis/trans bond confirmations, isomerase, branched fatty acids, anteiso, and modification with OH groups
-Aids in membrane homeostasis (particularly with environmental changes like pH, salinity, oxygen, pressure, temperature, etc)

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110
Q

If a bacteria needed to change an element of itself to avoid lyseing due to environmental changes, what element would that be?

A

The fatty acids of phospholipids

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111
Q

Define a cell wall and describe where they can and can’t be found

A

-Defined as a semirigid structure surrounding the cytoplasmic membrane enabling the cell to resist bursting from osmotic pressure
-Found only in true Eubacteria, not found in Mycoplasmas

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112
Q

True or false: the cell membranes of bacteria are porous

A

True, so nutrients/ metabolites can actively diffuse to the plasma membrane

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113
Q

What is the main component of a bacteria’s cell wall?

A

Peptidoglycan (murein)

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114
Q

Describe what peptidoglycan (murein) is composed of

A

-Consist of a polymer of sugars and amino acids that forms a mesh-like layer located outside the cytoplasmic membrane
-Carbohydrate portion consists of alternating residues of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
-A peptide chain (3-5 amino acids) is attached to N-acetylmuramic acid (NAM)
-Contains cross-linking bridges

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115
Q

How does the peptidoglycan of bacterial cell walls undergo degradation and remodelling? (what initiates it?)

A

Through autolysins that introduce controlled breaks for growth/division

116
Q

Describe the importance of peptidoglycans for immune response (what specific things trigger immune response)

A

-Peptidoglycan is conserved microbial structure that is immunogenic; recognized by the Nod proteins (innate immune response)
-Bacteria incorporate D-amino acids (unlike humans’ L-amino acids), so we know to attack it

117
Q

Peptidases only recognize the ______ of amino acid residues

A

L-isomers

118
Q

Are the peptides found in peptidoglycan produced ribosomally or enzymatically?

A

Enzymatically

119
Q

There are _______ layers of peptidoglycan in Gram-positive organisms and _______ layers of peptidoglycan in Gram-negatives

A

20-40; 1-2

120
Q

What increases the structural integrity of bacterial cell walls?

A

Peptidoglycan subunits are cross-linked between the peptides

121
Q

Describe the difference in the cross-linkage of peptidoglycan subunits in Gram-positive and Gram-negative cells

A

Gram negative: DAP to D-Ala via direct attachment
Gram positive: Glycine linker (D-Ala to L-Lys)

122
Q

Describe how lysozymes damage bacterial cells, and where lysozymes are found

A

-They’re an enzyme that damages the cell wall of bacteria by catalyzing hydrolysis of the 1,4-beta-linkages between NAG and NAM residues in peptidoglycan
-Defense of the innate immune response: lysozyme is present in various secretions including tears, saliva, and mucus.

123
Q

Describe Transpeptidation/ Carboxypeptidase reactions (how do they work and how does the bacteria die)

A

-Penicillin-binding proteins (PBPs) are the targets for penicillin and other β-lactam antibiotics
-Penicillin and related β-lactam antibiotics resembles the ‘transition state’ conformation of the D-Ala-D-Ala substrate when bound to these enzymes.
-Basically they make bacteria divert their resources so they can’t make peptidoglycan (as fast), so our body can catch up and kill the bacteria

124
Q

Describe how the rigid cell wall of bacteria grows

A

-Peptidoglycan is constantly being synthesized and degraded.
-Autolysins (murein hydrolases) are used to aid in cell wall growth
-A group of enzymes that exist in all bacteria contains peptidoglycan and can break down the peptidoglycan chains in small sections to allow for growth and cell divisions
-Like lysozymes, they cleave the β-1,4 linkages in the glycan chain
-The process must be regulated as to not allow osmotic rupture of the cell

125
Q

Describe teichoic and lipoteichoic acids

A

-Defined as polymers of chemically modified ribose or glycerol
-Only found in Gram-positive bacteria and are connected by phosphate groups (ester linkage)
-May be covalently modified with sugars, choline, or D-alanine groups that serve as antigenic determinants

126
Q

Teichoic and lipoteichoic acids are only found in Gram-________ bacteria

A

positive

127
Q

Teichoic acids may be covalently attached to the ________ _______, whereas lipoteichoic acid contains a lipid moiety that anchors the polymer in the _________ ________.

A

peptidoglycan layer; cytoplasmic membrane

128
Q

LTA (lipoteichoic acids) are recognized by the innate immune system as what?

A

One of the conserved microbial structures (Pathogen Associated Molecular Pattern, aka PAMPs)

129
Q

Describe the characteristics of gram-positive bacteria

A

-Thicker cell wall, no outer membrane, no LPS, no endotoxin, sensitive to lysozymes, more susceptible to penicillin
-Often have teichoic acid, some strains do sporulation, capsule is sometimes present, and some strains produce exotoxins.

130
Q

Describe the characteristics of gram-negative bacteria

A

-Thinner cell wall, has an outer membrane, has LPS, has endotoxins, no teichoic acid, no sporulation, resistant to lysozymes.
-More resistant to penicillin, sometimes has a capsule, and some strains produce endotoxins

131
Q

Describe the discovery of Hans Christian Joachim Gram (1853-1938)

A

Discovery of Gram stains was made while attempting to distinguish between two pneumonia causing organisms: Streptococcus pneumoniae (Gram-positive) and Klebsiella pneumoniae (Gram-negative)

132
Q

-Bacteria are primarily colorless (transparent) and exhibit a variety of shapes.
-Some bacteria have a thick “cell wall” (peptidoglycan), which stains _____ and is gram-positive.
-Some bacteria have only small amounts of peptidoglycan, which stains _____ and is gram-negative.

A

purple; red

133
Q

Describe the 6 steps of a Gram stain

A

1) Spread bacteria out on a microscope slide using a drop of water or saline if needed, then bacteria are fixed onto the slide (and dead) using heat.
2) Primary stain: Then the slide is flooded with crystal violet, rinsed with water (by now all bacteria are purple).
3) Mordant: Then the slide is flooded with iodine and rinsed with water.
-Iodide exchanges with chloride ions in dye; iodide is bigger and causes dye to precipitate.
4) Decolorize: with alcohol for 2-5 seconds (easy step to mess up), then rinse with water.
5) Alcohol permeabilizes the envelope of gram-negatives, so the precipitated purple dye comes out. The thick cell wall prevents dye from coming out in gram-positives.
6) Secondary stain: Safranin for 1 min, rinse with water

134
Q

Give 2 examples of bacterium that are exceptions to the Gram stain

A

1) Intracellular bacteria (i.e. bacteria that grow inside a eukaryotic cell)
2) Mycobacterium tuberculosis

135
Q

Why doesn’t the Gram stain work on some bacteria?

A

The organisms produce a waxy coat [long-chain hydrocarbons, sugars, additional components], and waxy coats are resistant to acids

136
Q

Describe an Acid-Fast stain

A

-Dye is introduced into tubercule bacteria using heat
-Washing in acid will not remove the dye [i.e., “acid-fast”]

137
Q

What are the 3 ways to classify bacterial colony morphology?

A

Form, elevation, and margin

138
Q

Describe the use of agar in the lab

A

-Agar has a semi-solid matrix and porous nature which allows for infusion of nutrients
-Bacteria-containing samples are either streaked or spread on plates to isolate individual bacterial cells
-Each colony grows from a single viable bacterium (a ‘colony-forming unit’ or CFU)

139
Q

Define simple, complex, enriched, selective, and differential mediums

A

1) Simple medium: defined, minimal nutrients
2) Complex medium: nutrients not precisely defined
3) Enriched medium: specific components added for “difficult to grow” bacteria
4) Selective medium: contains chemicals, antibiotics that inhibit some bacteria and allow growth of other bacteria
5) Differential medium: contains substates for biochemical reactions and indicators to illustrate the byproducts of reactions

140
Q

What 3 characteristics of bacteria are important to know when studying colonies?

A

1) Some bacteria produce natural colors
2) Some bacteria secrete enzymes such as hemolysins (lyse RBCs)
3) Some bacteria ferment specific sugars

141
Q

List 8 external bacterial structures

A

Flagella
Pili
Fimbriae
Sex Pilus
Type III Secretion Apparatus
Capsule
Glycocalyx (slime layer)
Polysaccharides

142
Q

Describe flagella and their importance

A

-Highly specialized, complex organelles for locomotion/ motility
->50 genes involved in assembly and function
-Very long proteinaceous filaments that have an a-helical arrangement [corkscrew-like]
-Apparatus spans the entire envelope of bacteria
-Within the host, flagella are critical for reaching mucosal surfaces (especially areas with fast flow)

143
Q

Define monotrichous, lophotrichous, amphitrichous, and peritrichous flagellum

A

1) Monotrichous flagella: one flagella
2) Lophotrichous: multiple flagella (6-8) from one pole
3) Amphitrichous: one flagella on each of the two poles
4) Peritrichous: has flagella all over its body

144
Q

List the 3 components of flagella

A

1) Basal body: anchored into the membrane
2) Hook region: extends just beyond the outer membrane
3) Helical filament: extends to the external environment

145
Q

How are flagella assembled?

A

In a step-by-step manner using a specialized protein secretion pathway called type 3 secretion

146
Q

How fast can flagella go?

A

Up to 100mph

147
Q

Describe the use of flagella in H. Pylori

A

H. Pylori will create a “sheath” of flagella using synthesized sugar; the most vulnerable point of a flagella is its very tip, so they have extra proteins that create a “terminal bulb” at the ends of the flagella.

148
Q

Coordinated counterclockwise motion of flagella leads to swimming, and is a(n) __________
Clockwise motion of flagella leads to tumbling, and is a(n) _________.

A

Counterclockwise swimming is an attractant; clockwise tumbling is a repellent

149
Q

Define chemotaxis

A

Swimming motility; movement toward or away

150
Q

Describe the structure of flagella

A

1) There’s a protein structure across the envelope, called the basal body or rotor.
2) Just above the basal body there’s a hook, called a universal joint
3) The filament acts as a propeller

151
Q

What are flagella driven by?

A

Ionic potential/ proton motive force

152
Q

The motor that turns the flagella rotates on average _____ rpm.
E. coli = ______rpm
Vibrio = ______rpm

A

500; E. coli is 5,000rpm; Vibrio is 100,000rpm

153
Q

How does flagella motion activate for chemotaxis?

A

Chemoreceptors in envelope relay information to flagellar apparati, so the flagella turn on when the bacteria senses food

154
Q

Why is adherence so important to bacteria?

A

Provides an advantage, prevents removal by fluids

155
Q

True or false: Virtually all pathogenic bacteria having ways of attaching themselves firmly to host cells

A

True

156
Q

Define pili (fimbriae) and what they do

A

Defined as filamentous appendages composed of “pilin” protein that are anchored to the outer membrane of Gram negative bacteria
-Mediate attachment to eukaryotic host cells

157
Q

Pili are primarily found in Gram-________ bacteria

A

negative

158
Q

Pili are peritrichou; define peritrichou

A

Hairy all over

159
Q

Give an example of a specialized pili

A

Sex or F pilus for bacterial conjugation

160
Q

What can be described as “rod-shaped protein structures extend from the bacterial surface and bind to host cell surface molecules (typically carbohydrates.)”?

A

Pili

161
Q

True or false: Pili can be evenly distributed or located preferentially to one part of the bacterial cell.

A

True

162
Q

Define afimbrial adhesins. What kind of bacteria are they found in?

A

Defined as bacterial surface proteins that are not organized in a rodlike structure and mediate tight binding between bacteria and host cell.
-All bacteria have these

163
Q

Bacteria may produce both pili and afimbrial adhesins. Why?

A

To lock into the surface if it’s in an area of fast flow

164
Q

Define capsules

A

Capsules are an enormous layer of polysaccharides

(With the exception of Bacillus anthracis poly-D glutamic acid, a polypeptide capsule)

165
Q

What does the capsule of bacteria do?

A

It’s anti-phagocytic; it’s also called the K-antigen and has thousands of serotypes

166
Q

What is the K antigen?

A

Capsules

167
Q

Define glycocalyx and what it does

A

-Also known as the slime layer, it’s a “loose” layer of polysaccharides
-It functions in attachment/adherence/motility and is a key feature of biofilm formation

168
Q

What is a key feature of biofilm formation?

A

Glycocalyx

169
Q

Define the S-layer (surface layer) and what it does

A

-A layer on the outside of the cell wall composed of a single protein species [sometimes glycosylated] that forms a crystalline array
-This layer is small; you’d need electron microscopy to observe it
-Aids in protection against environmental stress (osmotic, pH, enzymatic) and in phagocytosis

170
Q

Lipopolysaccharide (LPS) is found on the surface of Gram-________ bacteria; it is not present on the other type of Gram bacteria

A

negative

171
Q

Name and describe the 3 components of lipopolysaccharides (LPS)

A

1) Lipid A domain: phosphorylated lipid with sugar backbone
2) Core region: oligosaccharide chain
3) O-antigen: polysaccharide chain

172
Q

Describe the role of the lipid A domain (region I) of lipopolysaccharides (LPS)

A

-Hydrophobic anchor, holds LPS in the outer membrane.
-The portion of LPS responsible for endotoxicity
-Activates Toll-receptor (innate immune response)
–Changing the lengths of the acyl chains, changing the number of acyl chains, adding ethanolamine/phosphate/etc to the phosphate groups to alter its surface charge, or adding amino acids to Lipid A can prevent Lipid A from activating the Toll-receptor
-Important: Some bacteria synthesize a non-inflammatory lipid A to evade immune recognition

173
Q

What is the portion of LPS responsible for endotoxicity?

A

The lipid A domain (region I)

174
Q

What activates the Toll-receptor?

A

Lipid A domain

175
Q

Describe the role of the core oligosaccharide region (region II) of lipopolysaccharides (LPS)
(what is it made of, is it required, what’s its clinical relevance?)

A

-Consists of short chain of sugars attached directly to lipid A
-Not required for growth in laboratory
-Clinical Relevance: During infection thought to be required for maintaining permeability properties of the outer membrane

176
Q

Describe the role of the O-antigen/ O-polysaccharide region (region III) of lipopolysaccharides (LPS)

A

-Repeating unit of oligosaccharide subunits made up of 3-5 sugars attached directly to the outer core region (up to 40 units long)
-Major antigenic determinant with great variation between species and even strains
-Used as basis for determining serogroup of a bacterial strain
-Clinical Relevance: Loss of O-antigen results in loss of virulence; O-antigen provides protection from host defenses

177
Q

The loss of what part of a lipopolysaccharide leads to loss of virulence?

A

The O-antigen; it provides protection from host defenses

178
Q

Give 5 examples of internal structures found in bacteria

A

Gas vacuole, ribosomes, inclusions, nucleoid, endospore

179
Q

What is the purpose of a gas vacuole?

A

Buoyancy for floating in aquatic environments

180
Q

What is the purpose of ribosomes?

A

Protein synthesis

181
Q

What is the purpose of inclusions?

A

Storage of carbon, phosphate, and other substances

182
Q

What is the purpose of the nucleiod?

A

Localization of genetic material (DNA)

183
Q

What is the purpose of an endospore, and in what type of bacteria are they found?

A

-Survival under harsh environmental conditions; only observed in bacteria
-Specifically only some gram-positive bacteria

184
Q

What are the 3 main components of the bacterial cytoskeleton, and what do they do?

A

1) FtsZ: A division protein widely observed in bacteria; forms a disc shape in the center of the cell
2) MreB: maintains cell (rod) shape, localizes proteins
3) Crescentin: introduces crescent-shaped morphology

185
Q

Name and briefly describe the density of 3 storage inclusions found in bacteria

A

1) Glycogen (sugar)
2) Polyhydroxyalkanoate granules: Very light
3) Polyphosphate granules: Very dense; store phosphate

186
Q

What is the purpose of vacuoles?

A

To store gas for buoyancy in an aquatic environment

187
Q

What do magnetosomes do?

A

Aid in orientation to seek nutrients; based on earth’s magnetic poles

188
Q

What is the purpose of carboxysomes?

A

A specialized site for CO2 fixation (a protein coat with an enzyme inside)

189
Q

There are as many as ________ ribosomes growing in a bacterial cell, whereas eukaryotes have up to ________

A

70K; 10 million

190
Q

Why is the difference in size and composition between a prokaryote and eukaryote important?

A

It’s important for antibiotics; they can pick out bacterial ribosomes and keep them from synthesizing proteins

191
Q

Describe bacterial nucleiods

A

-Most are circular
-No membrane
-Have proteins and histone-like proteins that interact and organize things

192
Q

Name 3 types of bacterial plasmids and briefly describe what they do

A

1) Conjugative plasmids: the F factor; transfers copies of themselves into another bacteria
2) R (resistance) plasmids: can be conjugative (transfered through bacterial “sex”); delivers antibiotic resistance genes
3) Virulence plasmids: encode genes for pathogenicity

193
Q

Some Gram-_________ bacteria are spore-formers

A

positive

194
Q

What is the purpose of sporulation, and what do spores contain?

A

1) Spores represent a dormant state for long-term survival; formation (sporulation) is induced by harsh environmental conditions
2) Spores contain the entire chromosome enveloped by a membrane, peptidoglycan and an outer protein coat (keratin-like)

195
Q

Certain conditions will cause spores to become activated; this is called _____________

A

germination

196
Q

What aspect of sporulation is useful in diagnosis?

A

The location of endospores

197
Q

Name 4 locations of endospores

A

1) Central
2) Swollen sporangium (makes cell somewhat sperm-shaped)
3) Terminal (at the end of a rod-cell)
4) Subterminal (almost at the end of a rod-cell)

198
Q

Why do we typically set autoclaves to 121 degrees celcius?

A

That’s the temperature that can kill endospores

199
Q

Briefly describe the unique
morphology of protozoa, amoeba, and algae

A

Protozoa: motile due to cilia that cover their surface, heterotrophs
Amoeba: has a pseudopod and a contractile vacuole to control movement; prevents excess water inside the cell
Algae: have stored starch grains so they have carbon on-demand, use sunlight’s energy or can use organic compounds, extreme diversity, extremely abundant

200
Q

Describe the differences between passive and facilitated diffusion (what substances and how)

A

1) Passive diffusion: Non-polar lipid-soluble substances diffuse passively from high to low concentration
2) Facilitated diffusion: can control specific (sugars, ions, charged polar molecules, ATP, etc) or nonspecific transport (water, glycerol, urea, etc), allows nutrients in and out.

201
Q

What are the two types of facilitated diffusion?

A

Specific and nonspecific transport

202
Q

Describe the rates of diffusion in passive and facilitated diffusion

A

The rate of transport is rather linear in passive diffusion, whereas the rate of transport in facilitated diffusion is very quick, but plateaus due to the saturation effect.

203
Q

Define active transport

A

Transport of a substance against a concentration gradient

204
Q

Define primary and secondary active transport

A

Primary active transporters: use ATP for energy
Secondary transporters: use gradient for potential energy

205
Q

What does primary active transport utilize to move substances?

A

Uniport transport: The one-way transport of a single molecule

206
Q

Uniport transport is an example of __________ _______ transport, whereas antiport and symport transport are examples of _________ ________ transport.

A

Primary active transport; secondary active transport

207
Q

List and describe the two types of secondary active transports

A

1) Antiport: 2 molecules are transported in different directions
2) Symport: 2 molecules are transported in the same direction
(Can be very complicated and involve multiple subunits or phosphate transfer)

208
Q

What do phosphotransfer systems (group translocations) require?

A

Has to have a series of phosphate handoffs, which generates energy and the ability to phosphorylate the sugar.

209
Q

Define siderophore and what it allows bacteria to do

A

-A molecule that binds to various forms of iron and makes it available to the cell
-This allows bacteria living in an animal to steal that creature’s iron

210
Q

Define microbiology

A

The branch of biology dealing with the structure, function, uses, and modes of existence of microscopic organisms.

211
Q

True or false: Microbiology usually includes immunology, as well as the methods and technology used to study microbes

A

True

212
Q

What 4 fields of study fall under the broad term ‘microbiology’?

A

Virology, mycology, parasitology, bacteriology

213
Q

What did Jainism (600bc) and Mahavira believe about microbiology?

A

Mahavira asserted the existence of unseen microbiological creatures living in earth, water, air, and fire

214
Q

The ancients called microbes “________ _______” and the Greeks called them “________ _______”

A

Ancients: ‘invisible spirits’
Greeks: anthropomorphic gods

215
Q

What did the Roman Marcus Terentius Varro say about microbiology?

A

“there are certain minute creatures which cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and thereby cause serious diseases”

216
Q

What was the prevailing theory of illness through the end of the 1800s?

A

The Miasma theory of bad air/ poisonous vapor

217
Q

Girolamo Fracstoro (1546) asserted that disease is caused by invisible creatures placed in 3 categories; what were those 3 categories?

A

1) Those that infect by contact
2) Those that infect by fomites (any surface an “invisible creature” could be on)
3) Those that infect by distance

218
Q

A lot of people denied the existence of microbes until we could see and study them, which happened during what century?

A

17th century (1600s)

219
Q

What was the theory of spontaneous generation?

A

the theory that living organisms could develop from nonliving matter

220
Q

What were the 3 pieces of evidence those who supported spontaneous generation used?

A

The ‘spontaneous generation of’:
1) Maggots on meat
2) Frogs on mud
3) Mice from grain

221
Q

What was John Needham (1748)’s experiment in support of spontaneous generation, and why was the experiment flawed?

A

He applied heat to a broth and put a stopper on it; over time the broth became turbid. He asserted that it was sterile broth and that the creatures creating the turbidity spontaneously generated.
However, it was not sterile because the bottle of broth was open briefly after heating, and it may not have been boiled (unsure because Needham took terrible notes).

222
Q

Who were the people who conducted the first two experiments that challenged spontaneous generation?

A

1) Francesco Redi (1665)
2) Lazzaro Spallanzani (1765)

223
Q

What was Francesco Redi (1665)’s experiment?

A

He put one piece of meat in an unsealed flask, one in a flask sealed by a cork, and one flask covered by gauze. The unsealed flask had flies, maggots, ands eggs on it; the sealed flask had nothing on it; the flask covered with gauze had flies and fly eggs on the gauze because the flies could smell the meat.

224
Q

What was Lazzaro Spallanzani (1765)’s experiment?

A

He heated broth and air in an open flask, and the flask became turbid. Then the did the same thing in a sealed flask, and the flask remained clear.

225
Q

What was the experiment of Schwann and von Dusch (19th century)?

A

They found that if air was filtered through a cotton filter and attached to an otherwise sealed, previously heated flask, the flask would remain clear as long as the cotton filter was there.

226
Q

What experiment did Louis Pasteur (late 19th century) conduct that helped disprove the theory of spontaneous genration?

A

He applied heat to two containers of unsterile broth, sterilizing them, and broke the neck of the first sterile flask, but kept the neck of the second sterile flask intact. He found that the microbes were trapped at the base of the second flask and it remained clear, but that the first flask became turbid.

227
Q

What were Pasteur’s 4 major contributions to science?

A

1) Pasteurization: a technique invented by Louis Pasteur to sterilize liquid.
2) Vaccines: Pasteur helped create a couple vaccines.
3) Crystals: studied crystals and organic chemistry.
4) Microbial fermentation; certain microorganisms are able to take sugars and convert them into something different.

228
Q

In 1836 and 1845 the fungal origin of what two diseases was discovered?

A

Silkworm disease and potato blight

229
Q

Describe the effects of potato blight in the 1800s

A

-By 1800, the potato became the staple of life for Irish peasants
-In 1845, a “queer mist” came over the Irish Sea
Potato stalks turned black; potatoes began to putrify (smell bad)
-40% of the crop was destroyed
-Desperate for food, people ate anything they could scavenge (‘The Great Hunger’)
-Malnutrition leads to susceptibility to disease
-Began the process of migration (only ⅕ made it, so their ships were called ‘coffin ships’)
-Cause of the Great Hunger: having a single-crop economy
-Role of Potato Blight in World War I

230
Q

Who is known as the “Father of modern infection control”?

A

Ignaz Simmelweis

231
Q

Describe the discovery of Ignaz Simmelweis

A

In 1847 his midwives found that adequate hand hygiene can prevent transmission of puerperal fever

232
Q

In 1867 _______ ________ created a method for the sterilization of operating instruments and antiseptic practice

A

Joseph Lister

233
Q

What was Friedrich Henle’s major contribution towards microbiology?

A

In 1840, Friedrich Henle’s work began the “germ theory” of disease; wrote a famous essay called “On Miasma and Contagia”

234
Q

Between 1860-4, _________ ________ demonstrated that fermentation and the growth of microorganisms in nutrient broths did not proceed by spontaneous generation

A

Louis Pasteur

235
Q

In 1876, Robert Koch provided convincing evidence “germ theory” of disease with his work on what two things?

A

Bacillus anthracis and anthrax

236
Q

What was the intent of Koch’s postulates?

A

To act as a set of criteria to establish the cause of an infectious disease

237
Q

List Koch’s 4 postulates

A

1) Association of the microbe with the lesions of the disease
2) Isolation of the bacteria in pure culture
3) Showing that the isolated bacterium causes disease in humans or animals
4) Re-isolation of the bacterium from the intentionally infected animal

238
Q

What were the problems with Koch’s postulates?

A

Multiple microbes can be responsible for different sickness symptoms at the same time, some microbes can’t be isolated in a pure culture, there might not be a suitable animal model, some infections don’t necessarily show lesions, and we can’t ethically infect humans with something deliberately.

239
Q

What were the problems with Koch’s postulates?

A

Multiple microbes can be responsible for different sickness symptoms at the same time, some microbes can’t be isolated in a pure culture, there might not be a suitable animal model, some infections don’t necessarily show lesions, and we can’t ethically infect humans with something deliberately.

240
Q

List the Molecular Koch’s Postulates proposed by Stanley Falkow (4 postulates)

A

1) Phenotype or property under investigation should be associated with pathogenic members of a genus or pathogenic strains of a species. The gene in question should be found in all pathogenic strains of the genus or species but be absent from nonpathogenic strains
2) Specific inactivation of the gene(s) associated with the suspected virulence trait should lead to a measurable loss in pathogenicity or virulence (animal model)
3) Reversion or allelic replacement of the mutated gene should lead
to restoration of pathogenicity.
4) The gene, which causes virulence, must be expressed during infection

241
Q

What are the two main drawbacks to the Molecular Koch’s Postulates?

A

1) Not all pathogens have suitable animal models
2) Gene intractability: we have no idea how to manipulate the genes of some bacteria (ex: obligate intracellular bacteria).

242
Q

If you have an infection and your doctor decides to use Koch’s postulates to help find the cause, what would be the 4 steps they would take?

A

1) Associate the lesion with disease
2) Swab the lesion to get the bacteria into a pure culture
3) Infect an animal with the bacteria culprit
4) Swab the animal’s lesion to reisolate the bacteria

243
Q

If you have an infection and your doctor decides to use the Molecular Koch’s Postulates to help find the cause, what would be the 5 steps they would take?

A

1) Observe virulence in an infection causing strain of bacteria but not in other strains.
2) Measure the phenotype
3) Inactivate the virulent gene; virulence decreases
4) Reintroduce the virulent gene; virulence returns to normal
5) Virulent gene must be expressed during infection

244
Q

What were the 4 main advances of the Golden Age of Microbiology?

A

Advances in cultivation techniques, immunology, identification of causative agents, and microbial ecology

245
Q

What were the advances in cultivation techniques that came about during the Golden Age of Microbiology?

A

1) Gelatin to agar
-Gelatin melts at 25 degrees celsius and some bacteria degrade gelatin, whereas agar doesn’t melt until 100 degrees celsius
2) Richard Petri (dish)

246
Q

What were the advances in immunology that came about during the Golden Age of Microbiology?

A

1) Bacterial attenuation
2) Vaccine success

247
Q

What were the advances in microbial ecology that came about during the Golden Age of Microbiology? (2 things)

A

1) Understanding contributions of soil bacteria (Winogradsky)
2) Public health measures were devised and implemented
-Health departments were created, diseases were monitored locally, and diseases were monitored internationally

248
Q

The causative agents of what two illnesses were identified during the Golden Age of Microbiology?

A

Anthrax and tuberculosis

249
Q

Microbes generate _____ of the oxygen we breathe

A

1/2

250
Q

Only ___% of the cells that make up your body are mammalian

A

10%

251
Q

Define basic microbiology

A

Studying microbes and defining their characteristics, typically in a lab.

252
Q

Define applied microbiology

A

Exploiting microorganisms for a specific product or purpose (ex: wine and beer production, some food production, agricultural applications, cleaning oil spills applications, and renewable energy applications)

253
Q

Define medical microbiology and name its subcategories

A

Defined as the study of diseases of humans and animals
1) Clinical microbiology
2) Public health microbiology
3) Epidemiology
4) Immunology

254
Q

Define microbial ecology and name its subcategories

A

Defined as how microbes interact with organisms and components of their habitats
1) Plant microbiology
2) Geomicrobiology
3) Biodegradation and bioremediation
4) Evolutionary/ archeological microbiology

255
Q

Define agricultural microbiology and name its subcategories

A

Defined as the impact of microorganisms on agriculture
1) Soil microbiology
2) Food and dairy microbiology

256
Q

Define industrial microbiology and name its subcategories

A

Defined as exploiting microbes for practical and technological use
1) R&D (Research and Development)
2) Biotechnology / Pharmaceutical

257
Q

Describe the concept of feedback inhibition in cellular chemical reactions

A

-A method of matching supply with demand
-Each pathway branch is independently controlled
-This is because enzymes have a pH and temperature optima

258
Q

Define chemolithotropy and what organisms do it

A

-Energy source is inorganic molecules
-Exclusive to microbes

259
Q

Describe the scientific method in the context of microbiology

A

-Most microbiological studies can fulfill the requirements of testing
-However, evolutionary studies cannot provide any frame of reference because these studies are very difficult to do.

260
Q

What are the 3 main pieces of evidence that support the current history of life on earth?

A

1) Macro and microfossils
2) Carbon dating (of rocks and life)
3) Physicochemical environment of earth

261
Q

Who wrote The Origin of Life? What does it describe?

A

-Oparin in the 1920s
-Describes a ‘primeval soup’ of organic molecules that could be created in an oxygenless atmosphere because of sunlight

262
Q

What did Haldane say about the origins of life in the 1920s?

A

Said oceans were a ‘hot dilute soup’ from which the organic compounds formed

263
Q

Describe the Primordial Soup Theory from 1952 (who did it, what 4 things did they combine, and what were their results?)

A

-Miller and Urey
-They combined H2O, H2, CH4, NH4 in a glass chamber and applied electrical shocks
-1 week later, 15% of carbon was organic molecules (i.e. amino acids)

264
Q

What does the theory of thermal proteinoids say, and who wrote it?

A

-Says heating amino acid mixtures leads to polymer formation and catalysis
-Sidney Fox

265
Q

Define abiogenesis

A

The study of how organic biological life can naturally arise from inorganic matter

266
Q

What did the 1986 World Hypothesis argue?

A

That RNA is the original, most primitive molecule (i.e. it came first) because it:
-Has a capacity for storing, copying, and replicated genetic information
-Can have enzymatic properties (regulate gene expression and synthesize proteins)
-Is linked to protein, DNA, and cellular energy

267
Q

What are the 3 pieces of evidence that support RNA as the original, most primitive molecule?

A

-Has a capacity for storing, copying, and replicating genetic information
-Can have enzymatic properties (regulate gene expression and synthesize proteins)
-Is linked to protein, DNA, and cellular energy

268
Q

Describe the conditions of prebiotic earth

A

Low oxygen, high UV, temperature extremes

269
Q

Analyzing stromatolites (rock layers) told us what about the history of life?

A

The appearance of cyanobacteria signifies the introduction of oxygen into the atmosphere

270
Q

In what year was the first direct evidence for primitive cellular life found? How old was the evidence?

A

-In 1977 the first direct evidence of primitive cellular life was 3.5 billion year old fossils from Australia.
-Have since found Stromatolites in Greenland from 3.7bya

271
Q

What is the first step of cellular organization? Who demonstrated this?

A

Oparin described ‘coacervates’, which are microspheres of phospholipids.
It showed the self-organizing capacity of polymeric molecules, which is the first step toward cellular organization

272
Q

The ______ (the primitive version of a prokaryotic cell) evolved into Archaea and Bacteria

A

pogenote

273
Q

Describe the extremophiles of archaea

A

-Lithotrophic, anaerobic
-Chemically distinct membranes
-Tolerate high temps, high salinity, and high acidity

274
Q

Define endosymbiosis

A

The interaction between two organisms in which one organisms lives within the other

275
Q

Describe the endosymbiotic hypothesis (who wrote it, what does it mean, and what 3 things is it the origin of?)

A

-Lynn Margulis, 1980
-Endosymbiosis: The interaction between two organisms in which one organisms lives within the other
-Generally accepted as the origin of 3 eukaryotic organelles: mitochondria, chloroplasts, and hydrogenosomes

276
Q

True or false: In endosymbiosis, the bacteria eventually lose the ability to live independently

A

True

277
Q

List the 3 pieces of evidence for the Endosymbiotic Hypothesis

A

1) Mitochondria and chloroplasts have bacteria-like DNA and ribosomes; mitochondria also performs binary fission
2) Rickettsia species (obligate intracellular bacteria) has a genome that is mores similar to mitochondria than any other bacteria
3) Cyanobacterial genus lives inside marine invertebrates; it’s thought to be an ancestry of chloroplasts and plants and algae

278
Q

Describe the Hydrogen Hypothesis

A

Anaerobic bacterium produce H2 and CO2 as end products of metabolism, which leads to either:
1) The endosymbiont developing the ability to perform aerobic respiration (mitochondria)
2) The endosymbiont saying the same (hydrogenosome: small organelles in organic protists)

279
Q

It was about ___________ years ago when cyanobacteria began to synthesize oxygen on the surface; before that, oxygen was absorbed in the water and land for ______________ until it accumulated in the environment

A

2.4 billion; 1.3 billion years

280
Q

Describe The Great Oxygenation Event

A

-About 2.4 billion years ago when cyanobacteria began to synthesize oxygen on the surface
-Oxidized methane into carbon dioxide
-Potentially a ‘snowball earth’ episode that threw a bunch of water on earth and drastically increased oxygen levels

281
Q

Define the Gaia Hypothesis

A

A self-regulating Earth is controlled by the community of living organisms

282
Q

Define panspermia and give an alternative name for it

A

-The theory that life exists throughout the universe and is distributed by meteoroids, asteroids, and SSSBs (small solar system bodies)
-Also called exogenesis

283
Q

Describe the composition of the membranes of gram-positive and gram-negative bacteria

A

1) Gram positive: Thick outer membrane of peptidoglycan, small periplasmic space with lipoteichoic acids, inner cytosolic membrane
2) Gram negative: Thin outer membrane of peptidoglycan, large periplasmic space, inner cytosolic membrane

284
Q

If the cell is starving and needs pyruvate, it can take an ______ and ______________ to make pyruvate and ___________.
What is this concept called?

A

amino acid and a-Ketoglutarate; glutamate.
This is transamination

285
Q

Describe the order of building things in a bacterial cell (5 steps)

A

1) Heterotrophy or autotrophy
2) Fueling to make fueling products
3) Biosynthesis to make building blocks
4) Polymerization to make macromolecules
5) Assembly of structures

Microbiology (42 decks)

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