Final exam Flashcards
(119 cards)
1
Q
Describe the contributions Hippocrates made to microbiology and when
A
- 400 BC
- first to observe immunity
- bubonic plague survivors could care for plague victims
- realized disease particles are transferred through clothing
2
Q
what myth has resulted in low immunization rates and disease resurgence in the U.S.?
A
- anti-vac movement - Andrew Wakefield (1998)
- vaccinated 12 kids who were already showing signs of autism, then claimed the autism was a result of being vaccinated
- DUMBASS
- no study to support his
- autism develops around age 2, which is about the same age of vaccination
- correlation not causation
3
Q
Describe the contributions Joseph Lister made to microbiology and when
A
- 1865
- came across writings of Semmelweis
- started sterilizing knives with carbonic acid and drastically reduced infection rates
- he was laughed at but shrugged it off
- Father of modern surgery
4
Q
calculate the amount of energy released from a reaction using Gibbs free energies of formation for the products and reactants.
say whether or not the reaction can proceed spontaneously.
A
- Gibbs free energy: amount of “useable” energy (energy available to do work)
- when delta G < 0, energy is given off (exergonic)
- sponanteous
- when delta G > 0, energy is added (endergonic)
- not spontaneous
5
Q
Val
A
Valine
nonpolar (hydrophobic)
6
Q
Describe the chemical structure of peptidoglycan, (including three differences between gram negative and gram positive regarding the chemical composition of the peptidoglycan layer)
A
-
peptidoglycan
- consists of alternating units of N-acetylglucosamine (G) and N-acetylmuramic acid (M)
- glycan strands are connected by peptide bridge (connects G to M)
- keeps the cells together by hydrophobic sources
- PSI = 20 at its softest to hold peptidoglycan together
-
D vs. L amino acids (isomers)
- L amino acids are typically seen in proteins, but we see both in peptide linkage
-
Differences between gram pos. and gram neg:
- length of interbridge is longer from gram pos. (Gly interbridge)
-
DAP (diaminopimelic acid) is in gram neg.
- two amino acid heads
- Teichoic acids are in gram pos.
7
Q
describe three early attempts at immunization
A
-
Edward Jenner
- cowpox vaccine
-
900 AD
- Chinese would scrape off the scabs from recovering smallpox victims, powder it, and use a straw to blow it in the nostrils of children
-
Louis Pasteur
- rabies vaccine
8
Q
describe the three general functions of glycolysis, beta-oxidation, and the TCA cycles (what cell resources do they produce? how much do they produce?)
A
-
beta-oxidation
- produces a lot of reducing power
- if a 16C fatty acid were oxidized, it would produce 8 acetyl CoA, 7 NADH, and 7 FADH2
-
glycolysis
- produces a little bit of reducing power
- produces a little bit of energy
-
net: 2 ATP (4 total but 2 used) + 2 NADH + 2 pyruvates
- 8 ATP total
-
TCA cycle
- produces a lot of reducing power
- produces a little bit of energy
- pre-TCA cycle: 8 ATP total
-
TCA cycle: 8 NADH + 2 FADH2 + 2 GTP
- 30 ATP total
- glycolysis + TCA cycle = 38 ATP/mol of glucose
- remember:
- 1 FADH2 = 2 ATP
- 1 NADH = 3 ATP
9
Q
Describe the importance of protein conformation and what factors influence it
A
- change in protein conformation mediates/facilitates what moves in and out of the cell
-
environment interacting with DNA sequences affects structures
- pH
- ionic concentration
- temperature
-
chaperone proteins (interact with peptide sequence and influence folding of amino acid tails)
- mad cow disease is due to defective chaperone proteins
-
environment interacting with DNA sequences affects structures
10
Q
Glu
A
Glutamate
ionizable; acidic side chain
11
Q
Aromatic side chain amino acids
A
12
Q
Koch’s postulates
A
- steps needed to demonstrate microbial cause of disease
- Association - the microbe must be present in EVERY case of the disease and absent when there is no disease
- Isolation - the microbe must be isolated in pure culture
- Causation - innoculation of healthy animal with pure culture should cause disease
- Reisolation - you should be able to isolate the same microbe from the newly sick animal
13
Q
Define autoclaving and tyndallization
A
-
Autoclaving (sterilize samples) - chamber heated up to 121ºC at 15 PSI for 15-20 min
- endospores will germinate
-
Tyndallization - double autoclaving
- incubate sample for 24 hours
- the 2nd autoclave is used to kill vegetative cells
14
Q
Compare and contrast the structure and movement of prokaryotic and eukaryotic flagella
A
-
eukaryotic flagella:
- membranous sheath with protein tubules embedded
- flexible
-
prokaryotic flagella:
- not flexible - rigid corkscrew protein structure
- works by rotating
- flow of protons past the disc causes rotation (repels)
- lower M ring spins and causes shaft to rotate
- can spin in both directions
- CCW = forward run
- CW = tumbling motion
15
Q
Describe the contributions Alexander Fleming made to microbiology and when
A
- 1929
- microbiologist studying bacteria
- made an accidental discovery by leaving agar plates for a few days when he was on vacation. when he came back, he noticed a green fungal contaminate on one
- where there used to be colonies, there were ghost colonies
- isolated the fungus and found that it could kill bacteria
- identifed the fungus as penicillium
- later on in the early 1940s, other chemists were able to isolate the compound penicillin (1st antibiotic); there was a boom in the discovery of antibiotics and they felt invincible, so they closed TB hospitals (problem - antibiotic resistance)
- STDs are increasing in the U.S. due to antibiotic resistance and a 40% cut in funding by public health
- later on in the early 1940s, other chemists were able to isolate the compound penicillin (1st antibiotic); there was a boom in the discovery of antibiotics and they felt invincible, so they closed TB hospitals (problem - antibiotic resistance)
16
Q
describe the importance of immunization and the role of herd immunity in preventing disease in populations
A
- if you get enough of the population vaccinated, it immunizes the entire population
- 83-94%
- important for those who cannot get vaccinated (immunocompromised)
17
Q
describe the reactions necessary to re-establish the TCA cycle when intermediates are withdrawn to be used for building microbial biomass
A
-
Anaplerotic reaction: different way of recreating oxaloacetate to restart TCA cycle (filling in)
-
pyruvate carboxylase
- CO2 + pyruvate + ATP = oxaloacetate
- used by heterotrophs, but not autotrophs
- this is the reaction we do
-
PEP carboxylase
- PEP + CO2 = oxaloacetate
- this is the reaction many microorganisms do
-
pyruvate carboxylase
18
Q
describe the chemical and physical structure of prokaryotic and eukaryotic membranes
A
- plasma membrane and DNA are not optional
- membrane has a phospholipid bilayer
- the glycerol backbone is the lipid
-
3 carbon chain, phosphate, and 2 fatty acid chains
- long fatty acid chain (non-polar) is hydrophobic and points inward
- charge polar head is hydrophilic and points outward
- proteins in the membrane allow transport
19
Q
Asp
A
Aspartate
ionizable; acidic side chain
20
Q
Describe how the structure and function of the LPS layer differs from the plasma membrane
A
-
outer membrane is less selective than plasma membrane
- no active transport
- Gram positive
- thick peptidoglycan layer embedded with teichoic acids and lipoteichoic acids
- periplasmic space is less defined
- Gram negative
- two layers help to define the periplasmic space (contains a lot of enzymes; solute binding protein)
-
porins:
- transmembrane proteins in membrane that allow material to pass back and forth
- slightly selective - molecular weight and slight charge discrimination
-
Braun’s lipoprotein
- protein inserts into peptidogylcan layer
- hydrophobic interaction keeps it attached
-
LPS (lipopolysaccharide)
- outer portion of outer membrane
-
O-specific side chains
- disguises bacterial cell from immune systems by modifying
- can classify organisms based on their side chains
- changes over time
- example: E.Coli O157-H7
- exotoxin (produced inside of cell and secreted)
- Lipid A and polysaccharide (carbohydrate chain) are endotoxins (part of outer membrane of gram negative cells; causes shock)
- core polysaccharide always stays the same
21
Q
Describe how bacteria behave as they move along a concentration gradient.
Describe the signal transduction that results in this movement.
A
- extend duration of run when there is a higher concentration of attractant
-
signal transduction - biochemical decision making process
- there are sensory proteins on the surface of the cell - MCP (methyl accepting chemotaxis protein)
- transmembrane protein
- lock and key mechanism
- portion outside of the cell binds the substrate
- the portion inside has these chemotaxis proteins:
- CheW (associated with inside of MCP)
- CheA (associated with inside of MCP)
- CheY (floating around inside cell)
- there are sensory proteins on the surface of the cell - MCP (methyl accepting chemotaxis protein)
22
Q
Aliphatic side chain amino acids
A
23
Q
name the genus of one of the two ginormous prokaryotes discovered in the past few years
A
-
Epulopiscium fishelsoni
- from gut of surgeon fish
-
Thiomargarita namibiensis
- found in marine sediments
- largest prokaryote
- most of the cell is covered in a vacuole and storage granules (sulfur and nitrate)
- simple organisms can be large
- large prokaryotes have large vacuoles and cytoplasm pressed against plasma membrane
24
Q
Pro
A
Proline
nonpolar; secondary amino group
25
Define pasteurization
* Treat food products with mild heat to reduce pathogens and increase shelf life
* heated grape juice to 80ºC for 15 min
* killed 98-99% of microorganisms
* inoculated it back with yeast for flavor
26
how were endospores used as a weapon?
* endospores of ***Bacillus anthracis*** in powder form were sent in envelopes to congress
* lesions in lungs
* wiped walls and gassed with chlorine oxide gas, but there were still endospores
* a second gassing made it safe
* biological warfare
27
Gly
Glycine
nonpolar (hydrophobic)
28
Define chemotaxis
* **chemotaxis:** movement in response to chemical repellent or attractant
29
Ser
Serine
polar; aliphatic hydroxyl side chain
30
explain the importance of pure culture techniques in microbiology
* pure culture is a population that contains only a single species or strain of bacteria
* important for studying cultural, morphological, and physiological characteristics
31
define what a high-energy phosphate bond is, and describe the molecular configuration that results in one
* a very low (negative) delta G is a high energy bond; lower than -30 is needed to produce ATP
* a high energy phosphate bond has more stable resonance states
32
Describe the controversy surrounding spontaneous generation.
When and how was it disproved for microorganisms?
What was the alternative hypothesis (which later became a theory)?
* **spontaneous generation** - idea that life comes if you simply get the appropriate elements together
* It was disproved by **Louis Pasteur's swan-necked flask experimen**t in 1861
* alternative hypothesis: germ hypothesis that became the **germ theory**
* bacteria comes from seeds or germs
33
describe **four general mechanisms** by which compounds are transported into cells, which require the expenditure of energy, and identify which are more important in prokaryotes or eukaryotes
* **Facilitated diffusion**
* limited form of diffusion
* gating mechanism that is partially selective
* change of shape is solely dependent on interaction with ion; **no energy involved**
* cannot concentrate things against its concentration gradient; can only equalize concentration
* common in **eukaryotes**
* **Group translocation**
* compound taken up is modified as it enters the cell
* can no longer interact with the membrane proteins once inside, so it cannot get back out of the cell
* work against concentration gradient and accumulate compound inside
* **PEP/PTS**: Phosphoenolpyruvate/Phosphotransferase System
* Series of proteins that help transfer a phosphate to a sugar or other substrate being taken up (intermediate proteins)
* **modification requires energy** (in the form of high energy phosphate bond associated with PEP)
* transmembrane protein is unique for substrate
* example: changing glucose to glucose-6-phosphate
* associated with **prokaryotes**
* **Active transport** (two types)
* **Primary - ABC transporters**
* **ATP binding cassette**
* whole unit: transmembrane protein and outside we have a solute binding protein
* high affinity for substrate
* **Nucleotide-binding protein:** binds and hydrolyzes ATP for energy to change conformation and allow intrusion
* solute changes shape by binding to the substrate
* requires energy (in form of ATP)
* **Secondary**
* requires proton gradient
* protons are pumped outside of the cell as electrons move down the tower "chain"
* can flow back in and cause something else to move out
* sodium gradient is used instead of proton gradient to drive uptake of other compounds like sugars
* oxidative phosphorylation
* **Lipid raft**
* phospholipids are aggregated together only for transport
34
Tyr
Tyrosine
polar; aromatic side chain
35
Describe the contributions **Robert Koch** made to microbiology and when
* **1896**
* **physician** interested in studying disease in animals and later progressed to diseases in humans
* worked with **Anthrax** (disease that affects livestock)
* saw that sick animals had ***Bacillus anthracis*** (produces endospores and used in biological warfare)
* decided to **isolate the bacteria in blood and grow in pure culture**, **then transfer to a healthy animal**. **the problem** with this was lack of technology (they used methods such as **potato** as a host to grow bacteria, innoculating a flask with **broth**, and using a flask with **gelatin** that gives a hard surface to pick bacteria off but **melts at \<37ºC**)
* **solution -** use **agar** (polysaccharide of algae) that is **solid at 37ºC** and a **petri dish** (invented by Richard Petri)
* discovered cause of **cholera**, **TB**, and **20+ other human diseases**
* received nobel prize
* formalized **Koch's postulates**
36
describe the functions of Che A, B, R, W, Y, and Z, and whether the phosphorylated or non-phosphorylated forms are active
* CheR slowly methylates MCP
* affect: changes shape of MCP so it is no longer capable of binding glucose (attractant). As you add more methyl groups, takes higher concentrations of glucose to keep MCP bound to glucose and in the run mode
* when attractant comes off, CheA catalyzes hydrolysis of ATP
* this phosphorylates CheA and produces ADP
* CheA-P phosphorylates CheY
* CheY-P is capable of binding to the flagellar switch and changes the configuration of the switch proteins to change the direction of the flagellum to a CW motion (tumble)
* CheZ dephosphorylates CheY-P
* CheB picks up phosphate from CheA-P
* affect: rapidly demethylates MCP (in phosphorylated state), which allows it to bind glucose again
* CheB and CheY are only active when phosphorylated
37
obligate endosymbionts today
* _Proof that there are obligate endosymbionts today:_
* **Rickettsia** - can exist outside the cell
* only grow and reproduce inside the cell
* Ticks - Rocky mtn spotted fever
* lost ability to retain/generate energy
* **Chlamydia**
* only grow and reproduce inside the cell
* lost ability to generate energy
* **Cyanophora paradoxa** (photosynthetic protozoa)
* remnants of peptidoglycan in primitive chloroplast
* rare and difficult to occur, but is now a **theory** with all the proof
38
describe the cell wall morphologies of gram negative and gram positive bacteria
* **Gram positive**
* plasma membrane with a **thick peptidoglycan** layer
* no outer membrane
* **Gram negative**
* plasma membrane, an **outer membrane (LPS layer),** and a **thin peptidoglycan** layer in the middle
39
describe the glycolysis cycle
* **_Glycolysis:_**
* **+2 ATP (net)**
* **+2 NADH**
* **+2 pyruvate**
* delta G for ATP and ADP = -31 kJ
* **delta G of 1,3-biphosphoglycerate = -52 kJ**
* delta G for glucose-6-P = -14 kJ
* **_substrate level phosphorylation:_**
* high energy bond made using substrate
* can use to convert ADP to ATP using kinase (transfers phosphate)
* **Can also use PEP instead of ATP**
40
Leu
Leucine
nonpolar (hydrophobic)
41
name and describe the process by which fatty acids are converted to acetyl CoA (at the level of detail presented in class - in this case, know the chemical structures of intermediates)
* **structure of fatty acid: carboxyl carbon, alpha carbon, beta carbon**
* **process requires some energy**
* **_steps:_**
* to attach CoA to fatty acid, burn up two high energy phosphate bonds in ATP, producing two inorganic phosphates and AMP
* remember that sulfur is part of CoA; the high energy bond is where the sulfur links to the carbon
* oxidize with FAD, forming FADH2
* hydration (forms hydroxyl bonded to a C)
* oxidation with NAD+ (forms C=O bond where hydroxyl was)
* forms NADH + H+
* thiolysis (another CoA-SH comes in and separates the compound into two)
* **Each round of beta-oxidation clips off two carbons**
* Acetyl CoA is two carbons
* example: **to split an 18 carbon fatty acid**
* **produce 9 acetyl CoA**
* **8 rounds of beta-oxidation**
* **produces 8 FADH2**
* **produces 8 NADH**
* Just **lose two high energy phosphate bonds** one time
42
Secondary amino group amino acid
other amino acid (uncategorized)
43
Sulfur-containing side chains amino acid
44
Explain the functional difference between glycans that have alpha 1,4 glycosidic linkages and those that have beta 1,4 linkages
* **alpha-1,4**
* stores energy
* easy to degrade
* quick access
* starch, glycogen, etc.
* **beta-1,4**
* untouched energy that can last
* cellulose, chitin, hemicellulose, pectin, microbial polysaccharides
* **chitin:** long polymers N-acetylglucosamine in insect exoskeleton and fungal cell walls
* cell wall of plants - cellulose, hemicellulose, pectin, lignin
45
Cys
Cysteine
polar; sulfur-containing side chain
46
Describe the role and structure of endospores
* Endospores: resting structure
* most resistant (heat, chemicals, radiation)
* impermeable coat
* one cell produces one spore
* long-lived (millions of years)
47
Trp
Tryptophan
nonpolar; aromatic side chain
48
Describe the contributions **Martinus Beijerinck** made to microbiology and when
* **1900s**
* described the first virus - **tobacco mosaic virus**
* passed through filter that retains bacterium
* formed **enrichment culture technique**
* altered media and incubation conditions
49
Discuss the differences between the nuclear material of prokaryote and eukaryotes
* **_prokaryotes_**
* **no membrane bound nucleus**
* **single circular dsDNA chromosome**
* **haploid** (one copy)
* chromosome is **4x106 bp**
* **no wasted space**
* **super coiled**
* **0.4 microns** is as small as it can be
* 70s ribosomes
* 16s subunits (rRNA)
* **_eukaryotes_**
* **double membrane bound nucleus**
* **many linear strands of dsDNa**
* **haploid, diploid, polyploid**
* DNA is packaged around histone proteins =\> **nucleosomes**
* nucleosomes aggregate together to form **chromosomes**
* lots of information
* **100 to 10,000x as much info** as prokaryotes
* **lots of wasted space**
* non-coding regions called **introns** that insert in the middle of genes and have to be clipped out
* any cell division has to involve **mitosis** (nuclear division)
* 80s ribosomes
* 18s subunits (rRNA)
50
Lys
Lysine
ionizable; basic side chain
51
explain why the field of microbiology has seen a resurgence in interest during the past two decades
* emerging diseases
* bioterrorism
* antibiotic resistance
* gut microbiology
52
describe the TCA cycle
* Per 2 pyruvates in TCA cycle:
* 8 NADH
* 2 FADH2
* 2 GTP
53
describe at least three locations in these pathways where amino acids enter when they are broken down for energy and reducing power
* (6C) citrate
* (5C) alpha-ketoglutarate
* (4C) succinyl-CoA
* (4C) succinate
54
Describe the contributions **Ignaz Semmelweis** made to microbiology and when
* **1840**
* in charge of Hungarian hospital
* women were dying from puerperal fever (child bed fever)
* deaths were occurring more often with interns that studied corpses then went straight to women giving birth
* when they began washing their hands, rates drastically lowered
* his idea of sanitation to reduce infection was laughed at and he disappeared
55
describe the characteristics that typically distinguish eukaryotic and prokaryotic organisms.
what are the definitive characteristics used to separate the two groups?
* eukaryotic cell:
* **cell membrane**
* **plant or fungus - cell wall**
* **double membrane bound nucleus (contains DNA and chromosomes)**
* golgi apparatus
* mitochondria
* plant - chloroplast
* microtubules/microfilaments
* vacuole
* flagella
* prokaryotic cell:
* **plasma membrane**
* **cell wall**
* **no membrane bound nucleus**
* **storage granules**
* **simple organelles**
* flagellum
* the definitive characteristics used to seperate the two groups are:
* **membrane bound nucleus**
* **compartmentalization**
56
describe the three basic groups (domains) of organisms identified by rRNA sequence analysis and how these differ from the classical five kingdom classification system
* the five kingdom classification is based on morphological characteristics
* plants
* animals
* fungi
* protist
* monera (bacteria)
* three basic domains are based off of DNA sequences
* rRNA - enzyme that produces proteins based on the messenger RNA template
* different groups have different sizes of RNA in two subunits
* prokaryotes (70S)
* 50S and 30S
* 16S rRNA segment in the 30S
* eukaryotes (80S)
* 60S and 40S
* 18S rRNA segment in the 40S
* 3 domains found by Carl Weise:
* bacteria
* archaea
* eukarya
57
Acidic side chains amino acid
58
Asn
Asparagine
polar; amide side chain
59
describe two examples of biological warfare used prior to the 1800's
* mongols attacked a walled city in Ukraine called Caffa
* **catapulted dead plague victims** over the wall
* european settlers knowingly gave Native Americans **blankets contaminated with smallpox**
* 30% mortality
60
provide and use the appropriate equation to calculate the amount of energy released from a reaction based on the change in redox potential and oxidation state
* delta G = -(-24e/mol glucose)(F)(1.25V)
* -2895kJ/mol of glucose
* 1.25 = 0.43+0.82
61
Ala
Alanine
62
Gln
Glutamine
polar; amide side chain
63
Ala
Alanine
nonpolar (hydrophobic)
64
Describe the contributions **Edward Jenner** made to microbiology and when
* **late 1700s**
* worked with **cowpox virus**
* cow maids has a lower incidence of **smallpox**; he hypothesized that they were being exposed to cowpox
* he injected people with cowpox, but discovered that cowpox and smallpox are not that similiar, so it provided little immunity
* he didn't keep good records, so his work had **little impact**
* termed **"vaccination"** (vacca is latin for cow)
65
provide a name for an organism that describes its sources of energy, reducing power, and C
Which combinations are most likely to go together?
* energy
* **phototroph** - energy from light
* **chemotroph** - energy from chemical reactions
* reducing power
* **lithotrophs** - inorganic compounds
* **organotrophs** - organic compounds
* carbon
* **autotrophs** - plants make carbon skeletons for CO2
* **heterotrophs** - carbon backbone from environment
* _combinations:_
* all **organotrophs are heterotrophs**
* all **lithotrophs are autotrophs**
* _common names:_
* humans are **chemoorganoheterotrophs**
* plants are **photolithoautotrophs**
* **chemolithoautotrophs**
66
define the terms uniporter, symporter, and antiporter (classes of transmembrane proteins)
* **uniporters** - tranports one molecule in one direction
* **symporters** - transport two molecules in the same direction
* **antiporters** - transport one compound in the cell and another compound out of the cell
67
describe several common storage compounds found in prokaryotes and what they store (i.e. energy, C, P, S, etc.)
* **_storage granules/inclusion bodies:_**
* **starch** - stores **carbon**
* **glycogen** - stores **carbon**
* **PHB** (poly-beta-hydroxybutyrate) - stores **carbon**
* biodegradable plastic
* **volutin** - stores **phosphate** (phosphorus in bacteria)
* **sulfur granules** - store **sulfur**
* *Thiomargarita namibiensis*
* **carboxysomes** - stores crystalline forms of **rubisco** (ribulose 1,5-biphosphate)
* carbon fixation in plants
68
Ile
Isoleucine
nonpolar (hydrophobic)
69
His
Histidine
ionizable; basic side chain
70
Discuss at least five of the pieces of **evidence** discussed in class indicating that mitochondria and chloroplasts evolved from bacterial **endosymbionts**
* **Endosymbiotic hypothesis**: origination from free-living bacteria now dependent on another organism
* they have their own DNA and are similar to prokaryotes
* circular
* efficient
* double membrane
* 70s ribosomes
* 16s rRNA subunits
* when sequenced, they identified as bacteria (most convincing)
* functionality
* ribosomes: chloramphenicol, kanamycin, tetracycline
* bind to ribosomes and prevent production of protein
71
Describe the contributions **Anton van Leeuwenhoek** made to microbiology and when
* **1680**
* invented the 1st microscope
* referred to organisms as "wee animalcules"
* published pictures
* put into question the hypothesis of spontaneous generation
72
Basic side chain amino acids
73
describe a specific example of group translocation
* Phosphoenolpyruvate (PEP) --\> pyruvate
* adds phosphate to glucose to prevent it from leaving
* phosphate goes from PEP --\> Enzyme I --\> Enzyme III --\> Enzyme II (channel protein; passes phosphate to glucose 6-phosphate)
* In the phosphotransferase system (PTS), energy is used from PEP
* requires energy to modify the compound to keep it from associating with the membrane and exiting the cell
74
describe at least five behaviors or practices that have contributed to increased antibiotic resistance in microbes
* over prescriptions by physicians
* antibiotics given for viruses
* penicillin shots "just in case"
* over the counter availability of antibiotics
* self-diagnosis
* not taking entire dose/treatment
* more sensitive strain is wiped out, but more resistant version is still alive
* inclusion of antibiotics in livestock feed
* 8x as much used
* now can only use if recommended by veterinarian
* antimicrobial/antibacterial soaps
* only effective if left on for 10 min
* new antibiotics discovered
* results in large profit
* cannot be saved for vital cases
* vaccination/immunization
* captured Osama Bin Laden by "vaccinating" children for blood samples
* people in middle east and africa think we use it for mass genocide
* used for politics rather than medical purposes
75
Amide side chains amino acid
76
Phe
Phenylalanine
nonpolar; aromatic side chain
77
identify two inventions by Koch's lab that allowed the development of pure culture techniques
* Agar (polysaccharide of red jelly)
* petri plate
78
provide terms that describe the arrangement of flagella on the prokaryotic cell
* **monotrichous** - single flagellum at one end
* **amphitrichous** - flagella at both ends
* **lophotrichous** - tuft of flagella
* **peritrichous** - all around
79
Describe the contributions **Louis Pasteur** made to microbiology and when
* **mid 1800s**
* **father of microbiology**
* worked with **chicken cholera**
* when chickens were injected with an old culture of cholera, they didn't get sick
* when they were injected with a new culture, some got sick and some did not (the ones who were injected with the old culture)
* came up with the idea of **stimulated immune system**
* took **good notes**
* worked with **rabies virus**
* weakened the virus by heating it up
* injected a kid in Paris who had been bitten with the weakened virus and he survived. hundreds of other people infected went to him
* **developed first effective vaccine**
* **invented swan-necked flask**
* if he left the flask, growth occurred
* if he capped the flask are boiling it, nothing grew
* with the swan-necked flask, he could boil the broth and use no cap and no growth would occur
* **drove final stake through spontaneous generation**
* **made germ hypothesis into the germ theory** (particles in the air were leading to microbial growth)
* **invented pasteurization**
* if you heat up liquids at high temperatures for short periods of time, you can kill off most of the organisms contaminating the solution without significantly affecting the taste
* **original pasteurization - heated grape juice and milk up to 80ºC for 15 minutes**
* **killed 98-99% of organisms**
* could add **yeast** to get the fermentation to produce flavors
* refined today at higher temps for shorter periods of time
80
define "protein conformation"
* Protein conformation: the characteristic 3D shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain
* **Primary structure** - amino acid sequence
* dictated directly by DNA
* codons are transferred to mRNA
* ribosomes link the three letter code to the appropriate amino acid
* **Secondary structure** - folding of sequence
* Two types of structures:
* **alpha helices**
* hydrogen bonds form between nearby amino acids when it spirals (stabilizes)
* **beta sheets**
* hydrogen bond between distant amino acids (stabilizes)
* **Tertiary structure** - higher level of folding
* **Quarternary structure** - association of separate peptide units
81
provide the complete names and recognize the structures of two diffusible carriers of e- and two diffusible carriers of high-energy bonds.
identify the subunits that make up these molecules.
* **_diffusible carriers of reducing powers (e-)_**
* giant molecules that pick up electrons and take them to another location to dump them off
* carry them on the nitrogen base that is associated with the nucleotide
* **NAD (Nicotinamide adenine dinucleotide)**
* **FAD (flavin adenine dinucleotide)**
* ****both are electron carriers and do not have electrons yet
* **NADH and FADH2 have 2 electrons each**
* **Nucleotide = nitrogen base + 5C sugar + phosphate**
* **_diffusible carriers of high-energy bonds_**
* **ATP (adenosine triphosphate)**
* **CoA (coenzyme A)**
* **_subunits:_**
* **NAD:** two ribose sugars, one adenine (nitrogenous base), two phosphates bonded together and nicotinamide
* **FAD:** one ribose, one adenine, one flavin, 2 phosphates, and a ribitol sugar
* **CoA:** one ribose, one adenine, two phosphates, one pantothenate, one acetyl group from cysteine
* **ATP:** one adenine, one ribose, 3 phosphates
82
describe the four basic resources needed by organisms to carry out biological processes
* source of carbon
* reduced carbon backbones on which they can create biomass
* source of energy
* source of reducing power
* source of electrons to reduce compounds
* source of inorganic nutrients
83
Describe the contributions **Sergei Winogradsky** made to microbiology and when
* **1887**
* **Winogradsky column** - model ecosystem used to study a variety of bacteria
* worked with Martinus Beijerinck on environmental microbiology
* enrichment culture technique
* first to demonstrate **nitrogen fixation**
84
name the disease and disease-causing organism that killed more than a quarter of the population of Europe between 1346-1350
* disease: **Bubonic plague ("black death")**
* organism: ***Yersinia pestis***
* flea would bite rat then human
85
Name two genera of organisms that produce endospores.
Steps in spore formation.
* _Genera that form endospores:_
* **Bacillus**
* **Clostridium** - endospore germinates in absence of oxygen
* *C. tetani*
* Botulism (germinates with heat)
* _Steps in formation:_
* 1) signal - running out of nutrients
* 2) DNA divides and membrane partitions it
* 3) the membrane grows back around and encapsulates the cytoplasm and DNA, creating a double membrane
86
Explain how the membranes may be modified during adaptation to different temperatures
* Require a level of fluidity for membranes (except for **lipid rafts**, which are phospholipids covalently bonded with proteins embedded)
* **phospholipids** for the most part are not covalently bonded into place, but kept together by **hydrophobic interactions**. This means that they have to have fluid to function, but not too much
* **Cholesterol**
* found in animal membranes
* function: to manipulate fluidity by extending the range of temperatures in which appropriate fluidity exists
* flat planar compound that **fits in hydrophobic region** (polar -OH region points out)
* **Ergesterol**
* found in fungi membranes
* **Hopanoid**
* function: same as cholesterol
* found in bacterial membranes
* **Double bonds**
* **saturated double bonds**
* push fatty acids out to create a kink, so they cannot get close enough for weak hydrophobic interactions to occur
* increases fluidity due to **more hydrophobic** interactions
* **hot temperatures**
* **Polyunsaturation**
* hydrophobic interactions are minimized
* **cold temperatures**
* **Fatty acid chains**
* **extending the length**
* increases **hydrophobic** interactions
* **higher temperatures**
* more stable
* **shorter tails**
* less hydrophobic interactions
* better for **cold environment**
* **linkage of fatty acids**
* **Archaea** are adapted to extremely high temperatures because they use **ether linkages**
* phospholipid monolayer
* **bacteria and eukaryotes use ester linkages**
87
Describe how the composition of the **cell wall** differs among groups such as bacteria, archaea, plants, animals, diatoms, and fungi
* _cell wall:_
* __**plants**
* ****cellulose
* hemicellulose
* pectin
* lignin (glue)
* **animals**
* none
* **fungi**
* ****chitin (long polymers of N-acetylglucosamine)
* **Diatoms**
* ****silica
* **archaea**
* ****pseudopeptidoglycan (different type of sugar)
88
Thr
Threonine
polar; aliphatic hydroxyl side chain
89
What physical and chemical characteristics make endospores so resistant and long-lived?
* _Structure:_
* **Ex: exosporium**
* fragile protein coat
* **SC: spore coat**
* protein coat is very resistant and impermeable
* **CX: cortex**
* peptidoglycan layer that is loosely cross linked
* **CW: core wall**
* inner most part of spore wall
* **cytoplasm**
* very **dehydrated**
* **normal vegetative cell is 80-90% water**
* **endospore is 10-25% water**
* inactivates enzymes and proteins change shape and become unfunctional to preserve them
* **DNA binding proteins**
* **protect DNA** and absorb hit from **radiation**
* **calcium dipicolinate**
* 25% of weight
* carbon ring with nitrogen and two carboxyls
* DNA binding protein
* **absorbs water**
* **DNA repair enzymes**
* **nonfunctional** in normal state
90
Discuss the differences between the secondary DNA of prokaryotes and eukaryotes
* **secondary DNA:** where DNA is found in cells
* **_prokaryotes:_**
* **viral DNA** (virus can inject its own DNA in a cell)
* **plasmids:** small circular dsDNA that replicates independently of cell
* 5,000 to 10,000 bp (substantially smaller)
* nonessential
* antibiotic resistance gene
* ability to detoxify
* ability to deal with heavy metals
* **eukaryotes**
* **viral DNA**
* **very few plasmids**
* **mitochondria**
* **chloroplasts**
91
Chemical "type structure" of an amino acid
92
determine whether or not a compound could donate or accept an e- from another compound, when you are provided with redox potentials
* **oxidation:** removal of electrons
* looking at H and O can help calculate oxidation state
* H: +1
* O: -2
* oxidation is at the **top of the tower**; these compounds can **donate e-** to the compounds below them
* **largest free energy** at top of tower (**most negative/holds on to e- loosely**)
* **Reduction:** addition of electrons
* reduction is at the bottom of the tower; compounds can **accept e-** from the compounds above them
* highest attraction for e- is at the bottom of the tower; more positive (volts)
* the **lowest free energy** is at the **bottom of the tower** (**most positive/tightly holds e-**)
* **Redox potential:** relative affinity of a compound for electrons; how tightly the electrons are held on (volts)
93
Describe the contributions **Jon Snow** made to microbiology and when
* **1854**
* **father of epidemiology**
* studied cholera outbreaks in London and decided to try to prevent rather than just treat
* made a map of cholera deaths and water pumps
* noticed deaths were occurring around one specific water pump
* took the handle off that pump and disease dwindled
94
Aliphatic hydroxyl side chains amino acids
95
Arg
Arginine
ionizable; basic side chain
96
Describe the contributions **Christian Gram** made to microbiology and when
* **1884**
* **gram stain**
* gram positive - purple
* gram negative - pink
* crystal violet, KI (mordant - keeps stain in bacterial cell), alcohol (wash), safranin (counter stain)
97
provide a list of macro- and micronutrients required by most microorganisms
* plant macronutrients - C HOPKNS CaFe Mighty good
* carbon
* hydrogen
* oxygen
* phosphorus
* potassium
* nitrogen
* sulfur
* calcium
* iron
* magnesium
* plant micronutrients - Mn CuZn MoCloB
* manganese
* copper
* zinc
* molybdenum
* chlorine (needed by plants, but not microorganisms)
* boron
98
explain what is meant by "substrate-level phosphorylation."
explain why some texts identify different steps in pathways as the exact location of s.l.p.
* substrate level phosphorylation is how high energy bonds are made using a substrate
* can convert ADP to ATP using kinase (transfers phosphate)
* some texts think s.l.p. takes place when ATP is created while others think the most important step is when **high energy phosphate bonds are created**
99
provide names of at least three membrane bound e- carriers, and explain how these function to create a proton gradient
* **_membrane bound e- carriers:_**
* **flavoprotein**
* **quinone**
* **cytochrome bc1**
* **cytochrome c**
* **cytochrome a**
* redox potentials rise (becomes more positive) as we go from carrier to carrier
* **drop in redox** is used to move protons across the membrane
* **outside of the membrane is more protons and inside of the membrane is more hydroxyl** which creates a **concentration gradient** that is a form of energy **(ATP synthase or ATPase)**
100
explain how reducing power and energy can be converted from one to another
* a series of oxidation/reductions that dump electrons down the tower
* **NADH oxidizes to NAD**. electrons get dumped down tower on flavoprotein which gets reduced.
* flavoprotein gets oxidized and dumps electrons onto something down the tower which gets reduced
* so on and so on
* **energy is released** every time electrons reach a step because **compounds change shape** (positive to negative charge) when they go from oxidized to reduced
* as electrons get passed down, it **grabs a proton and moves it out of membrane** (pumping or shuttle mechanism caused by change in shape)
* since protons come from water, **protons are outside of the membrane and hydroxyl is inside of the membrane.** the **concentration gradient forms energy** (drive flagellum, active transport, production of ATP using ATPase)
* electrons are eventually passed to oxygen (terminal electron acceptor), forming water. the **energy of electrons is completely dissipated**
* * **_to convert energy to reducing power:_**
* reduce concentration of one side of the reaction to drive it in the opposite direction
* **change concentration** = change position on tower (able to **reduce NAD to NADH)**
* higher concentrations of NAD relative to NADH = drops down the tower
* **lower redox potential -\> more likely to give up electron and be oxidized**
* high proton concentration = reduced state = less likely to give up electrons = increasing redox potential
* **use high ATP to pump protons out and electrons are transferred back onto NAD forming NADH**
101
explain why oxidation of FADH2 produces less energy than oxidation of NADH
* FADH2 comes in lower on the tower, so it only pumps 6-8 protons -\> 2 ATP
* NADH pumps 8-10 protons, so when protons flow back into the cell, it can produce a maximum of 3 ATP
102
describe in detail two examples of glucose fermentation, and identify the key characteristics of all fermentation
* **_two types of glucose fermentation:_**
* **lactic acid fermentation**
* dump electrons stripped off carbon skeleton onto **pyruvate** -\> **reduce lactate** and produce NAD
* **decarboxylate pyruvate**
* **reduce acetaldehyde** and use the electrons from NADH to produce **ethanol** and more NAD
* **_key characteristics of all fermentations:_**
* **no net oxidation or reduction** of substrate (carbon skeleton)
* **ATP is generated by s.l.p.** not oxidative phosphorylation
* **not much energy i**s harvested (2 ATP versus the 38 ATP from respiration)
* **organic acids and alcohols** are produced and secreted from the cell (waste products)
103
explain the differences between aerobic respiration, anaerobic respiration, and fermentation, including differences in the amount of energy harvested during each process
* **_aerobic respiration_**
* oxygen is terminal electron acceptor
* 38 ATP
* **_anaerobic respiration_**
* something other than oxygen is used as a terminal electron acceptor (i.e. ferric iron or nitrate)
* will eventually shift to **methanogens** when all other resources are used
* **cytochrome will stay in reduced state** (no place for electrons to go)
* can't carry out steps in TCA cycle (NAD will be reduced to NADH and FAD would be FADH2)
* **not as much energy yielded**
104
describe noticeable changes in the environment when anaerobic respiration occurs and either FeOOH, MnO2, or SO2-2 are used as terminal electron acceptors.
describe the environmental impacts that can occur when chemolithotrophs use H2S or FeS2 as a source of reducing power
* **flooded soils**
* FeOOH, MnO2, or SO4-2 becomes more soluble
* **swamps**
* H2S or FeS2 cause odor
* reduced species are more toxic than oxidized species
* example of **methane**: compost, dairy, waste
* cows burp because microorganisms are in its rumen, producing methane
105
describe three mechanisms by which the specific activity of an enzyme molecule can be controlled
* **_product inhibition_** (fastest)
* **A→B** (changing concentrations will change direction)
* if it's a negative delta G, it can go to the right
* if it's a positive delta G, it can't go to the right
* **delta G (*real nonstandard*) = delta G (*standard*) + *rT log(q)***
* **q = product concentration / reactant concentration
* works well with **delta G around -3 to 0**
* **instantaneous** - as soon as product increases it shuts down
* **_allosteric regulation_**
* enzymes act as **lock and key** with an **active site** to fix substrate
* **end product must accumulate** before enzyme activity is shut down
* **weak bonds**
* allosteric site binds allosteric effectors (have effect of shape of active site)
* **allosteric activator - improves shape; positive**
* **allosteric inhibitor (feedback inhibition) - make shape worse so substrate can't bind; negative**
* when it operates:
* **immediately following branch points**; enough product shuts down enzyme early on
* good for reaction with **very low delta G values**
* **_covalent modification_** (longest)
* **small molecules** are attached to the enzyme
* **phosphate, methyl groups, ADP** (example: CheB)
* acts as a switch to turn on and off (like chemotaxis)
* **long term** to shut down enzyme activity
* **more negative delta G**
106
give an example of an enzyme found in glycolysis that is controlled by allosteric regulation, and name the allosteric activator and inhibitor for this enzyme in bacteria
* phosphofructokinase (third enzyme of glycolysis)
* activator - ADP
* inhibitor - PEP
107
identify two types of reactions (or points along a pathway) that are typically regulated by feedback inhibition
* immediately at a branch point within the pathway
* when the change in G of a reaction is too negative to be controlled by concentration of the products
108
describe two ways that the **quantity of enzyme** in a cell may be negatively controlled.
describe when you would expect one mechanism to be used as opposed to another.
* **_repression_**
* **corepressor** (i.e. arginine) **+ repressor** bind to operator to **block transcription**
* used when you have lots of the compound and don't need enzymes to produce more **(biosynthesis reactions)**
* **negative control**
* **_induction_**
* operon is normally blocked by repressor
* **inducer binds to the repressor and pulls it away to allow transcription**
* used when you need the energy from the substrate **(catabolic reactions)**
* i.e. lactose
* **negative control**
109
describe in detail one positive control mechanism.
describe an operon that is regulated by both positive and negative control mechanisms.
* **Cababolite "repression"** - presence of glucose prevents transcription in lac operon
* **CAP (catabolite activator protein) = CRP (cyclic AMP receptor protein)**
* ****stimulates binding of RNA polymerase
110
describe the three major steps in the process of binary fission
* **_cell elongation_** (elongates cell to 2x original size)
* **autolysins** - enzymes that break peptide bonds in peptidogylcan layer of cell wall
* clips and lays down new material
* penicillin prevents the new material from being laid down (only effective with growing cell)
* **_chromosome replication_** (circular chromosome)
* origin of replication - 300 bp region
* series of enzymes come in:
* **DNA helicase** - splits apart double helix
* one for each replication fork
* **single stranded DNA binding proteins**
* ****keep base pairs from reattaching
* keep ssDNA from degradation
* **DNA gyrase** - ahead of helicase to untie supercoiling caused by helicase
* breaks knots and reattaches
* **primase** - RNA polymerase that creates a 10 bp long RNA primer
* **DNA polymerase III**
* ****3' to 5' exonuclease activity
* leading strand (continuous)
* new nucleotides are only added to the 3' carbon of the growing strand
* lagging strand (okazaki fragments)
* can only grow away from replication fork so primase jumps ahead and new forms backwards
* proofreading capability
* **DNA polymerase I**
* ****5' to 3' exonuclease activity (degrades RNA primer and makes new DNA; starts at 5' end of chain)
* proofreading capability
* **ligase** - seals the nick made by DNA polymerase I to link okazaki fragments together
* **_cross wall/septum formation_**
* ingrowth of cell wall -\> ingrowths meet -\> break apart due to brownian motion -\> two daughter cells are formed
111
calculate changes in bacterial population size during exponential growth when provided information on initial population size and µ
*Nt = Noeµt*
µ = instantaneous growth rate constant per unit time
112
distinguish between microbial growth rate and the growth rate constant, and provide an equation that shows the relationship between the two
dN/dt = µN
dN/dt = instantaneous rate of increase = "cells per hour"
113
primary impact of pH on microbial growth
* nutrient solubility
* element toxicity
114
provide an equation that describes the effect of substrate concentration on the growth rate constant.
be able to provide appropriate units for the monod constants, µmax and Ks
describe, using a graph, what the constants in the equation refer to
describe how these constants would differ between copitrophs and oligotrophs
* **monod equation** - microbial growth rate constant relating substrate concentration
* ***µ = (µmax[s]) / (ks + [s])***
* ks = substrate concentration that produces 0.5µmax (mg x L-1)
* µmax = plateau of the graph; maximum specific growth rate (h-1)
* **copiotroph -** adaptation to high substrate concentration
* faster growing
* higher growth rate
* **oligotroph** - adapted to low [s]
* slow growing
115
describe the free radical forms of oxygen that are toxic to some microorganisms and how particular enzymes deal with these free radicals
* **superoxide**
* most common
* more reactive than hydrogen peroxide but not as reactive as the hydroxyl radical
* **peroxide**
* weakest oxidizing species and most stable
* **hydroxyl radical**
* ****strongest oxidizing species and most dangerous
116
describe the typical size of a virus and compare it to a typical bacterium
* virus is 20-400 nm
* bacterium is 0.2-10 micrometers
117
difference between influenza and norovirus (structure)
* influenza is an enveloped helical structure
* norovirus is a naked icosahedral virus
118
name and describe the different phases of a "growth curve" for a virulent bacterial virus and what technique is needed to measure the length of those phases
* **_phases:_**
* **__latent period**
* ****includes the **eclipse** (virus inside bacteria) and **early maturation** phases
* **viral nucleic acid replicates and protein synthesis occurs**
* **maturation period**
* ****assemble virions and release
* number of infectious virions inside host cell rises dramatically
* **burst size** - number of virion release per cell
119
