Midterm 1 Flashcards

(183 cards)

1
Q

Microbiology

A

the study of microbes

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2
Q

microbes

A

forms of life too small to be seen with the naked eye

ex:
Bacteria
Viruses
Protists
Fungi (two kinds, yeast & mold)
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3
Q

t or f: 10^14 bacteria in body 10^13 human cells in body

A

TRUE there are 10x more bacteria in the human body than human cells

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4
Q

amniotic fluid has ______

A

antimicrobial properties

cleanses birth canal but doesn’t get rid of bacteria completely

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5
Q

babies born _______ are healthier

A

through birth canal

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6
Q

bacteria help plants take up ______

A

nitrogen

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7
Q

what are the characteristics of a living object?

A
  • metabolism, growth, reproduction
  • genetic variation/evolution
  • response/adaptation to external environment
  • homeostasis

-a self organizing, self-replicating, non-equilibrium system

EMPHASIZE REPRODUCTION

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8
Q

key difference between bacteria and virus?

A

viruses ARE NOT MADE OF CELLS!!!!!!

viruses are have genetic material covered in capsid. cannot reproduce themselves don’t have enzymes. need a host.

OUTSIDE OF CELLS VIRUSES ARE NON-LIVING

INSIDE CELLS VIRUSES ARE LIVING

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9
Q

outside of host viruses are _______

inside host viruses are ________

A

non-living

living

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10
Q

life needs _____

A

genetic material

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11
Q

definition of life

A

self-organizing, self replicating, non-equilibrium system

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12
Q

life is made up of 4 macromolecules?

A

polypeptides, nucleic acids, lipids, polysaccharides

all are organic molecules

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13
Q

why do we have more RNA than DNA?

A

we need to continuously make protein whereas we only need one copy of DNA

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14
Q

RNA polymerase

A

uses DNA as template to make RNA

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15
Q

Glycogen phosphorylase

A

converts glycogen into glucose monomers

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16
Q

Glycogen phosphorylase

A

converts glycogen into glucose monomers

important because brain runs on glucose

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17
Q

flagellin

A

protein that are apart of flagella that help the movement of bacteria

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18
Q

FtsZ

A

key component of cell division machinery in bacteria

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19
Q

Most important role of cell membrane?

A

separate outside from inside of cell.

also in prokaryotes the etc to make atp is on the plasma membrane

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20
Q

up until 1970s, organisms were placed into two categories:

A

prokaryotes and eukaryotes

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21
Q

eukaryote v prokaryote

A

eukaryote: has membrane bound organelle structures (mitochondria, nucleus)
prokaryote: no membrane bound organelles. circular dna

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22
Q

how did scientists discover/define the three domains of life?

A

RIBOSOMAL SEQUENCING
ribosomal RNA. the amount of it varies significantly in the three domains

DNA sequencing was used to compare sequences of ribosomal RNA genes in different organisms

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23
Q

three domains:

A

bacteria, archaea, eukarya

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24
Q

what is the first branch between bacteria and archaea?

A

HISTONES!!!!!!

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25
``` bacteria: nuclear membrane? membrane-bound organelles? plasma membrane? cell wall? RNA polymerases? Histones? ```
nuclear membrane = no membrane bound organelles = rare only a few types found in a few species plasma membrane = similar to eukarya cell wall = found in nearly all species constructed of peptidoglycan RNA polymerase: single polymerase Histones = histone like proteins
26
``` archaea: nuclear membrane? membrane-bound organelles? plasma membrane? cell wall? RNA polymerases? Histones? ```
nuclear membrane = no membrane bound organelles = rare only a few types found in a few species plasma membrane = different from bacteria and eukarya cell wall = found in nearly all species constructed of various materials RNA polymerase: single polymerase. eukaryal-like RNA pol II Histones = yes
27
``` eukarya: nuclear membrane? membrane-bound organelles? plasma membrane? cell wall? RNA polymerases? Histones? ```
nuclear membrane = yes membrane bound organelles = multiple distinct types found in all species plasma membrane = similar to bacteria cell wall = found in somespecies constructed of various materials RNA polymerase: three main (RNA pol 1,2,3) Histones = yes
28
why do we study microbes?
they are very fast and easy to grow they can produce enzymes and other molecules for industrial medical uses most of them have small numbers of genes, making them simple to study genetic manipulation of single celled bacteria is usually much easier than multicellular eukarya
29
early environment of earth:
very little oxygen the surface of planet was a soup of chemicals in liquid form initial synthesis led to the first forms of macromoleculues (and their use in primitive single-celled organisms)
30
early environment of earth:
very little oxygen the surface of planet was a soup of chemicals in liquid form initial synthesis led to the first forms of macromolecules (and their use in primitive single-celled organisms)
31
endosymbiotic theory:
symbiosis: interaction between two orgs one living inside the other primitive prokaryotic microbes ingested other microbes starting a symbiotic relationship forming the first basic eukaryotes. (mitochondria, chloroplasts)
32
commensalism
one org is benefited the other is neutral type of symbiotic relationship
33
parasitism
one benefits other hurts type of symbiotic relationship
34
mutualistic
both benefit type of symbiotic relationship
35
how did the first microbial life arise? | STANLEY MILLER
used electric spark to simulate the spark that might have started forming organic molecules in the primordial soup. spark needed to start forming organic molecules however molecules alone aren't life
36
how did early organic molecules change into the four macromolecules in cells today?
early iron containing surfaces may have helped turn the early organic molecules into the larger ones we know how can they replicate? ribozymes (a combination of ribonucleic acid and enzymes) can serve dual purpose. RNA could serve dual purpose as a genetic storage AND an enzyme. micelles may have been an early form of the plasma membrane
37
t or f: micelles do NOT exist in nature
t
38
why is the bilayer required instead of a monolayer?
plasma membrane is semi permeable!!! would not be possible by monolayer. size of micelle is more limited (much smaller) than bilayer so many things wouldn't fit. polar molecules that can kill cells easily cannot get into or out of the cell easily because of the nonpolar tails in the middle of the bilayer.
39
how did early microbial life form?
early conditions formed RNA + micelles. these came together into primitive cell using RNA for storing genetic info and coding
40
WHY DID CELLS CHANGE FROM USING RNA TO DNA FOR STORING GENETIC INFO?
double stranded DNA provides better backup copy of genetic information and is more stable
41
t or f: rna is less stable than dna
t
42
why is rna less stable than dna?
While DNA contains deoxyribose, RNA contains ribose, characterised by the presence of the 2'-hydroxyl group on the pentose ring (Figure 5). This hydroxyl group make RNA less stable than DNA because it is more susceptible to hydrolysis
43
how are microbes associated with diseases?
people used to believe that disease was associated with angry gods or bad air. the first microbes were observed from 1623-1673 by Anton van Leeuwenhoek 1665: Robert Hooke invented cell theory: all living things are composed of cells
44
Robert Hooke
INVENTED CELL THEORY THAT ALL LIVING THINGS ARE MADE FROM CELLS
45
spontaneous generation
the hypothesis that life arises from nonliving matter; a "vital force is necessary for life John Needham- boiled chicken broth and saw growth (but it was contaminated) NOT TRUE
46
biogenesis:
hypothesis that living cells arise only from preexisting cells LAzzaro Spallanzani did the boiled chicken broth and covered the flask and sawno growth. people critiqued saying closing it prevented from opening
47
PASTEUR
S shaped flask experiment. made neck long but didn't close it and no contamination happened. microorganisms are present in the air but air itself does not giv e birth to microorganisms pasteurization: application of high heat for a brief period of time!
48
pasteurization:
application of high heat for a brief period of time!
49
Robert Koch
discovered tuberculosis and anthrax bacteria as causes. CREATED GERM THEORY "a specific microorganism causes a specific disease"
50
methods to prevent infection caused ______
a dramatic drop in us deaths from infectious diseases. used antiseptics, sanitation improvements like sewage treatment, food/water safety (pasteurization), personal hygiene improvements, vaccination also antibiotics
51
size of bacteria
0.5 to 5 micrometers bigger than viruses, smaller than eukaryotic cells
52
mycoplasma gallicepticum
the smallest known organism capable of independent growth and reproduction parasite in gut of primates
53
thiomargarita nambiensis
largest bacteria ever discovered a gram negative proteobacterium found in the ocean sediments of the continental shelf of Namibia
54
cocci
spherical
55
bacilli
rod-shaped
56
vibrios
curved rod
57
spirilla
spiral | syphillis example
58
pleiomorphic
varied shapes | h pylori example
59
barrelia burgedorferi
cause lyme disease
60
possible shapes of bacteria
``` cocci bacilli vibrios spirilla pleiomorphic ```
61
single arrangement
do not touch each other
62
diplo/tetra arrangement
bacteria go in twos or fours
63
strepto arrangement
bacteria make a chain
64
staphylo arrangement
bacteria cluster! there may be some singles or diplos around but it couldn't be all singles
65
"multicellular" organizations of bacteria
are single but look multicellular hyphae (branching filaments of cells) mycelia (tufts of hyphae) trichomes (smooth unbranched chains of cells)
66
hyphae
branching filaments of cells
67
mycelia
tufts of hyphae
68
trichomes
smooth unbranched chains of cells
69
examples of bacteria with multicellular organizations
cyanobacteria- the cells adhere to each other through common cell wall forming long multicellular filaments myxobacteria are dramatic example of multicellular bacteria
70
nucleiod
nuclear area where the DNA in bacteria chill
71
breakdown of cytoplasm
80% water, 20% protein
72
plasmid
small dna molecule in cell that is physically separated from chromosomal dna and can replicate independently. usually small circular double stranded DNA
73
why are plasmids considered a genetic advantage for bacteria?
can have antibiotic resistance genes
74
bacteria contain ______ chromosome
one circular
75
inclusion bodies
(also called elementary bodies) sites of wild multiplication consist of wild capsid proteins
76
carboxysomes
have rubisco. used for carbon fixation in the calvin cycle. they do carbon fixation rxns
77
magnetosomes
store magnetic material. composed of lipid membrane and magnetic materials. organelle associated with DIRECTION FINDING. organisms that have these look for a specific environment of microaerophilic environment
78
FtsZ and MreB
cytoskeletal proteins in bacteria
79
MreB
homologue of actin helps shape bacteria because MreB polymerizes to form actin-like helical bands next to plasma membrane
80
FtsZ
homologue of tubulin FtsZ aids in cell division by helping the formation of the Z ring
81
ParM and ParR
ParM ParR and ParC come together to form a complex and help in the segregation of plasmid when a cell replicates. Plasmids replicate when the cell divides and whenever they want to just have many copies of it ParM polymerizes and depolymerizes to help with segreation and direction of plasmid movement
82
hopanoids
sterol-like molecules in plasma membrane that helps with stability across a range of temperatures
83
__ and __ are small and can diffuse across the pm readily
O2 and CO2
84
_____ is helped across the pm by _____
water; aquaporins
85
osmosis
the movement of water across pm toward the side with a higher solute (particle) concentration osmosis can cause a cell to swell with water or shrivel as water leaves but a strong cell wall can help keep bacterial cell alive during these hardships
86
facilitated diffusion
using protein channel to move particles with concentration gradient
87
active transport
using energy to move particles against a concentration gradient ex. amino acids, glucose, na k pump
88
primary active transport
uses ATP P-type ATPase: sodium potassium pump, calcium pump, proton pump ABC (ATP binding cassette) transporter: MDR, CFTR, etc.
89
secondary active transport
uses other sources of energy such as co-transport or coupled transport one molecule goes with its gradient to allow something else to go against its gradient
90
ABC transporter
substrate binds protein interacts with solute. complex interacts with channel. channel undergoes conformation change. atp hydrolysis provides energy for opening channel and moving solute
91
antiport
na k pump cotransport in opposite directions
92
symport
go in same direction. cotransport of sodium and glucose
93
plasma membrane methods for capturing energy. what is that energy used for?
embedded electron transport chains can help create proton motive force can be used for respiration/photosynthesis can be used to derive motion (flagella)
94
how does the plasma membrane hold sensory systems?
proteins in the pm can be used to detect environment changes the cell can use the detected changes to alter gene expression to respond
95
protein secretion in the pm SecG,SecE etc.
making proteins and shipping them outside the cell SecG, SecE, SecY act as a transport system. SecA functions like a doorman deciding when things can cross the membrane. A signal peptide tells the protein where to go and SecB binds it so that it won't fold and atp hydrolysis occurs. SecE, SecG, and Sec Y form the channel that lets the protein out and then the signal peptide is removed by a peptidase
96
cell wall
not all bacteria have but 90% do. composed of cross linked strands of peptidoglycan subunits forming a matrix. increases structural strength. provides protection from osmotic lysis/mechanical forces involved in binary fission
97
peptidoglycan makeup
disaccharide NAG and NAM connected by beta 1 4 glycosidic bond. arranged nag nam nag nam. a peptide chain with a few amino acids are attached. the amino acids are attached only to NAM and vary from species to species. all are d amino acids. can crosslink in various ways.
98
amino acids only attach to ______
NAM
99
how does the cell wall form?
outside of plasma membrane. bactoprenol is a lipid that is amphipathic. It spans entire plasma membrane. it serves as a conduit to transport new peptidoglycans from the plasma membrane to the periplasmic space step 1: f6p and glutamine at step 5 nag and nam are synthesized, the nag reacts with utp --> udp + nag. some of this is converted to udp-nam. this combines with a peptide. this attacks bactoprenol. udp-nag comes back and and attaches to nam causing a flip
100
transglycosylation
hydroxyl group of nag will attack
101
___ and ___ can degrade cell wall
lysozyme (attacks beta 1,4) and lysostaphin secretions (acts on the crossbridge)
102
b-lactam antibiotics
break cell wall. prevent peptidoglycan crosslinking which | weakens the cell wall structure
103
antibiotic resistance & b-lactam antibiotics
some bacteria can produce an enzyme (beta lactamase) that destroys the b-lactam ring structure addition of a second drug to inhibit that enzyme restores the drugs efficiency tldr the bacteria can't inactivate the antibiotic because we are distracting the enzyme it uses to do so
104
what happens when you weaken the cell wall?
the cell cant resist osmotic pressure changes and will likely rupture (hypotonic conditions)
105
protoplast v spheroplast
protoplast have two membranes and come from gram - bacteria | spheroplasts have one membrane and come from gram + bacteria
106
Hans Christian Gram
bacteria are stained crystal violet, iodine stabilizes the crystal violet in the cell material, alcohol can extract crystal violet from the cell and the stain complex gets removed from gram negative and remains in gram positive so gram negative cells stain pink and gram positive cells appear purple
107
gram negative cells stain _____ gram positive cells stain ______
pink purple
108
gram positive cells have
thicker outer layer of peptidoglycan a very narrow periplasmic space teichoic acids in the peptidoglycan (that are negatively charged)
109
gram negative cells have
a varying width periplasmic space containing a very thin layer of peptidoglycan an outer membrane composed of lipopolysaccharide
110
why did professor graham see a different staining for + and -?
gram positive retained stain because alcohol reacts with sugar thick layer in peptidoglycan and it shrunk the layer and it held the violet
111
how does techoic acid make the cell wall stronger?
the negative acids interact with positive ions
112
LPS from gram-negative cells can be ____________
harmful.
113
LPS structure
lipid a (endotoxin) portion induces a strong inflammatory response o outer side chain of polysaccharides can vary dramatically and even be changed by the microbe to evade host immune response
114
t or f gram - infections are harder to treat than gram +
true
115
how can nutrients get through gram positive cell walls?
the gram positive peptidoglycan layer has large pores throughout its matrix
116
how can nutrients get through gram negative cell walls?
the gram negative cell has porin and TonB proteins in its outer membrane to transfer molecules to the periplasmic space
117
S layer (surface layer)
part of cell envelope found in many types of bacteria composed of identical proteins and glycoproteins bound to rigid peptidoglycan containing layer via secondary cell wall polymers of gram positive bacteria closely associated with the lipopolysaccharide of the outer membrane of gram negative bacteria
118
flagellum
motility from flagella: spiral, hollow, rigid filaments extending from cell surface -locations and number vary from species to species locomotion and sensory!!!!! 15-20nm function rather than structure
119
structure of flagella
filament of multiple flagellin proteins 5-10 micro meter long hook protein portion that connects filament to basal body basal body = disk like structure that produces torque on the filament to turn it like a propeller -gets energy from plasma membrane (proton motive force)
120
energy to spin flagella is derived from _____
proton motive force
121
_____ give flagella direction
basal body
122
when flagella change direction, their movement changes from _____ to ______
directional to nondirectional (tumble)
123
axial flagella
attached in periplasmic space. when it moves inside it creates a corkscrew and we can seethe entire cell body rotate
124
pili
adherence molecules to stick to surface fibers of pilin protein possess other proteins on their tips for sticking a sex pilus is a different structure used for conjugation
125
conjugation
sex pilus
126
pili v fimbriae
``` pili = conjugation fimbraie = adherence (thinner and shorter than flagella) ```
127
capsules
have k antigen made up of polysaccharides surrounding some cells provide defense against host immunity, protection against drying out (dessication) MAJOR VIRULENCE FACTOR because body can't recognize the capsule as foreign help make biofilms
128
biofilms
provide protection and enhanced survivability in harsh environments example of biofilms include dental plaque and mold on bathroom surfaces
129
t or f most microbes cant be cultured
true
130
archaea
prokaryotes that have distinct properties. look like bacteria but are different. some live in inhospitable places.
131
extremophiles
can live in inhospitable environment first archaea discovered fit this bill
132
how do we know archaea is distinct?
comparison of rRNA gene sequences helped to establish phylogenic trees
133
methanogens
a poorly characterized group of microbes capable of producing methane as a byproduct
134
t or f: ch4 traps more radiation than co2
t
135
halobacterium salinarium growth req
3.0-5.0 M NaCl
136
pyrococcus furiosus growth req
100 degrees C
137
picrophilus ashimae growth req
0.7 pH
138
methanogenium frigidum growth req
15 degrees C
139
genetic sequence analyses indicate that the branching point occurs when ____________
occurs when archaea and eukarya branch off from bacteria.
140
WHAT IS THE BRANCHING POINT?
development of histones !!!
141
Size of archaeal cells
0.5-5 micrometers can vary greatly
142
shapes of archaeal cells
vary similar to bacteria
143
genetic material of archaea
usually a singular circular chromosome and lack a membrane bound nucleus however many of the DNA replication enzymes of archaea look like those of eukarya
144
archaeal histones
archaeal dna is complexed with histones (like eukarya) in the nucleoid histones form structures that dna wraps around HISTONE STRUCTURE IS DIFFERENT IN ARCHAEA AND EUKARYA
145
histones can allow DNA to be ______
stabilized
146
archaea histone structure
contain h3 and h4 types histones in a tetramer of histone proteins eukaryotic histones make octamer of h2a h2b h3 and h4
147
archaeal cytoskeleton
cytoskeleton homologues are found in both bacteria and archaea Ta0583 is an actin homolog that resembles eukaryal actin (equivalent to MreB)
148
what is ta0583 equivalent to in bacteria and eukarya?
MreB in bacteria | actin in eukarya
149
cytoskeletal proteins from M.thermoautotrophicum and M. kandleri more closely resemble ________ cytsokeletal proteins
bacterial
150
archaea have ____ and _____ but these structures are different than their equivalents in bacteria and eukarya
plasma membrane and (sometimes) cell wall
151
how does the archaeal plasma membrane differ from bacteria/eukarya?
different bilayers construction instead of glycerol 3 phosphate with fatty acid and a ester linkage we have glycerol 1 phosphate and phytanyl and the linkage is an ether ALSO THE PLASMA MEMBRANE CAN BE A MONOLAYER INSTEAD OF A BILAYER
152
why can the archaeal plasma membrane be a monolayer?
it has glycerol 1 phosphate on both sides which make it like a bilayer monolayer is likely more stable at higher temperature because of this.
153
ignicoccus membrane
have an outer membrane and periplasm the atp synthase enzymes are housed in this main outer membrane rather than the main plasma membrane of the cell WE CAN EXPLOIT THIS FOR DRUG DELIVERY
154
cell wall functions
physical and osmotic protection
155
in archaea the cell wall is composed of mostly __________
pseudomurein (slightly different peptidoglycan structure) NAG-NAT instead of NAG-NAM
156
t or f: some archaea lack a cell wall
true
157
pseudomurein is different in three ways from peptidoglycan, what are they?
beta 1,3 linkage instead of beta 1,4 NAG-NAT instead of NAG-NAM THEY ARE L AMINO ACIDS INSTEAD OF D
158
thermoplasma acidophilum
DO NOT HAVE A CELL WALL AND CANT MAINTAIN SHAPE
159
how are flagella similar and different in bacteria versus flagella
similar: rotate to move cell different: they are much thinner in archaea and in archaea it attaches at the based of the cell membrane rather than the tip like bacteria
160
archaeonics
use chemicals in the archae for antibiotics haloarchae and sulfolobus are used archaeonics
161
pfu DNA polymerase
PCR: heat DNA, separate the strands. problem was heating killed the enzyme dna polymerase so youd have to add more became tedious SOOOOOOO we used dna polymerase from archaea that are stable at 95 deg celsius -- taq dna polymerase pfu - heat stable moreso than taq dna polymerase. it has 3' to 5' exonuclease activity
162
exonuclease activity in pfu
makes pfu better than taq polymerase because the 3' to 5' exonuclease activity proof reads the DNA polymerase that works in the 5' to 3' direction
163
are archaea pathogenic?
NO KNOWN EXAMPLES. however some methanogens are associated with infection in mice.
164
two major phyla of archaeons:
- euryarchaeota | - crenarcheota
165
two less major phyla of archaeons that have been proposed:
nanoarchaeota (only one current member the symbiotic archaeon nanoarchaem equitans) korarchaeota (thermophilic ones that don't fit well in the two major)
166
recently detected species of archaea
ARMAN | archaeal richmond mine acidophilic nanoorganisms
167
crenarcheota
most abundant marine archaea could be important to biogeochemical cycling of carbon and nitrogen thermophiles/hyperthermophiles (growing at temps greater than 55-80 deg respectively) many are acidophiles, some are barophiles ex. sulfolobus solfataricus
168
sulfolobus solfataricus
a type of crenarcheote opt temp 80 opt ph 2-4
169
adaptations for crenarcheota to survive in extreme environment
- tetraether lipids/lipid monolayers - more alpha helical regions in proteins - more salt bridges/side chain interactions in proteins - more arginine/tyrosine less cysteine/serine - strong chaperone protein complexes - thermostable dna-binding proteins - reverse dna gyrase enzyme to increase dna supercoiling
170
mesophile temperature range
15-40 degress celsius
171
psychrophiles temperature range
< 15 degrees celsius
172
euryachaeota: methanogens
methanogens they reduce co2 with h2 to produce methane ch4 and water h2o in an unusual reaction energy released can be used to fix carbon all identified methanogens are strict anaerobes ex. m smithii
173
m smithii
predominant archaeon in our gut. plays role in digestion of polysaccharides by reducing co2 with h2 to produce methane and water in animals free from bacteria and then we give them a lot of m smithii they become very fat
174
euryarchaeota: halophiles
require NaCl concentration greater than 1.5 M high salt environments are fairly rare--these areas vary between 5 to 34% salinity the ocean is typically 3.5% salinity
175
how do halophiles deal with osmotic shock and loss of water?
they maintain high intracellular potassium concentration to offset high Na concentration in the envrionment however this solution can cause its own problems denaturing proteins and splitting dsDNA
176
what are the problems that arise from halophiles maintaining high intracellular potassium levels and how do cells overcome these problems?
DNA denaturing --> higher GC content (stronger bonds) Protein denaturing -->highly acidic proteins that remain more stable in high salt environment
177
halobacterium
type of halophile. A TYPE OF ARCHAEA NOT BACTERIA THE NAMING IS UNFORTUNATE produce energy through odd form of phototrophy do not use chlorophyll or etc use bacteriorhodopsin to harness light energy and produce a proton motive force that is used to make atp bacteriorhodopsin gives off a reddish hue
178
anton van leeuwenhoek
father of microbio observed first microbes by making microscope
179
robert hooke
invents cell theory
180
john needham
spontaneous generation theory (proven wrong) put boiled nutrient broth into covered flasks (contamination allowed for growth inside because flasks weren't sealed)
181
lazzarro spallazani
biogenesis he did same experiment has needham but sealed the flasks and nothing grew. critics said that cutting off the flasks from the environment might preclude growth though
182
louis pasteur
fixed the chicken brother scenario with his s shaped flasks that allowed the broth to be open to the environment
183
robert koch
GERM THEORY' specific org causes specific disease