Midterm 1 Flashcards
Microbiology
the study of microbes
microbes
forms of life too small to be seen with the naked eye
ex: Bacteria Viruses Protists Fungi (two kinds, yeast & mold)
t or f: 10^14 bacteria in body 10^13 human cells in body
TRUE there are 10x more bacteria in the human body than human cells
amniotic fluid has ______
antimicrobial properties
cleanses birth canal but doesn’t get rid of bacteria completely
babies born _______ are healthier
through birth canal
bacteria help plants take up ______
nitrogen
what are the characteristics of a living object?
- metabolism, growth, reproduction
- genetic variation/evolution
- response/adaptation to external environment
- homeostasis
-a self organizing, self-replicating, non-equilibrium system
EMPHASIZE REPRODUCTION
key difference between bacteria and virus?
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
outside of host viruses are _______
inside host viruses are ________
non-living
living
life needs _____
genetic material
definition of life
self-organizing, self replicating, non-equilibrium system
life is made up of 4 macromolecules?
polypeptides, nucleic acids, lipids, polysaccharides
all are organic molecules
why do we have more RNA than DNA?
we need to continuously make protein whereas we only need one copy of DNA
RNA polymerase
uses DNA as template to make RNA
Glycogen phosphorylase
converts glycogen into glucose monomers
Glycogen phosphorylase
converts glycogen into glucose monomers
important because brain runs on glucose
flagellin
protein that are apart of flagella that help the movement of bacteria
FtsZ
key component of cell division machinery in bacteria
Most important role of cell membrane?
separate outside from inside of cell.
also in prokaryotes the etc to make atp is on the plasma membrane
up until 1970s, organisms were placed into two categories:
prokaryotes and eukaryotes
eukaryote v prokaryote
eukaryote: has membrane bound organelle structures (mitochondria, nucleus)
prokaryote: no membrane bound organelles. circular dna
how did scientists discover/define the three domains of life?
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
three domains:
bacteria, archaea, eukarya
what is the first branch between bacteria and archaea?
HISTONES!!!!!!
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
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
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
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
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)
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)
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)
commensalism
one org is benefited the other is neutral
type of symbiotic relationship
parasitism
one benefits other hurts
type of symbiotic relationship
mutualistic
both benefit
type of symbiotic relationship
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
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
t or f: micelles do NOT exist in nature
t
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.
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
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
t or f: rna is less stable than dna
t
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
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
Robert Hooke
INVENTED CELL THEORY THAT ALL LIVING THINGS ARE MADE FROM CELLS
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
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
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!
pasteurization:
application of high heat for a brief period of time!
Robert Koch
discovered tuberculosis and anthrax bacteria as causes.
CREATED GERM THEORY “a specific microorganism causes a specific disease”
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
size of bacteria
0.5 to 5 micrometers
bigger than viruses, smaller than eukaryotic cells
mycoplasma gallicepticum
the smallest known organism capable of independent growth and reproduction
parasite in gut of primates
thiomargarita nambiensis
largest bacteria ever discovered
a gram negative proteobacterium
found in the ocean sediments of the continental shelf of Namibia
cocci
spherical
bacilli
rod-shaped
vibrios
curved rod
spirilla
spiral
syphillis example
pleiomorphic
varied shapes
h pylori example
barrelia burgedorferi
cause lyme disease
possible shapes of bacteria
cocci bacilli vibrios spirilla pleiomorphic
single arrangement
do not touch each other
diplo/tetra arrangement
bacteria go in twos or fours
strepto arrangement
bacteria make a chain
staphylo arrangement
bacteria cluster!
there may be some singles or diplos around but it couldn’t be all singles
“multicellular” organizations of bacteria
are single but look multicellular
hyphae (branching filaments of cells)
mycelia (tufts of hyphae)
trichomes (smooth unbranched chains of cells)
hyphae
branching filaments of cells
mycelia
tufts of hyphae
trichomes
smooth unbranched chains of cells
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
nucleiod
nuclear area where the DNA in bacteria chill
breakdown of cytoplasm
80% water, 20% protein
plasmid
small dna molecule in cell that is physically separated from chromosomal dna and can replicate independently.
usually small circular double stranded DNA
why are plasmids considered a genetic advantage for bacteria?
can have antibiotic resistance genes
bacteria contain ______ chromosome
one circular
inclusion bodies
(also called elementary bodies)
sites of wild multiplication
consist of wild capsid proteins
carboxysomes
have rubisco. used for carbon fixation in the calvin cycle. they do carbon fixation rxns
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
FtsZ and MreB
cytoskeletal proteins in bacteria
MreB
homologue of actin
helps shape bacteria because MreB polymerizes to form actin-like helical bands next to plasma membrane
FtsZ
homologue of tubulin
FtsZ aids in cell division by helping the formation of the Z ring
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
hopanoids
sterol-like molecules in plasma membrane that helps with stability across a range of temperatures
__ and __ are small and can diffuse across the pm readily
O2 and CO2
_____ is helped across the pm by _____
water; aquaporins
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
facilitated diffusion
using protein channel to move particles with concentration gradient
active transport
using energy to move particles against a concentration gradient
ex. amino acids, glucose, na k pump
primary active transport
uses ATP
P-type ATPase: sodium potassium pump, calcium pump, proton pump
ABC (ATP binding cassette) transporter: MDR, CFTR, etc.
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
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
antiport
na k pump
cotransport in opposite directions
symport
go in same direction.
cotransport of sodium and glucose
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)
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
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
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
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.
amino acids only attach to ______
NAM
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
transglycosylation
hydroxyl group of nag will attack
___ and ___ can degrade cell wall
lysozyme (attacks beta 1,4) and lysostaphin secretions (acts on the crossbridge)
b-lactam antibiotics
break cell wall. prevent peptidoglycan crosslinking which
weakens the cell wall structure
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
what happens when you weaken the cell wall?
the cell cant resist osmotic pressure changes and will likely rupture (hypotonic conditions)
protoplast v spheroplast
protoplast have two membranes and come from gram - bacteria
spheroplasts have one membrane and come from gram + bacteria
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
gram negative cells stain _____
gram positive cells stain ______
pink
purple
gram positive cells have
thicker outer layer of peptidoglycan
a very narrow periplasmic space
teichoic acids in the peptidoglycan (that are negatively charged)
gram negative cells have
a varying width periplasmic space containing a very thin layer of peptidoglycan
an outer membrane composed of lipopolysaccharide
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
how does techoic acid make the cell wall stronger?
the negative acids interact with positive ions
LPS from gram-negative cells can be ____________
harmful.
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
t or f gram - infections are harder to treat than gram +
true
how can nutrients get through gram positive cell walls?
the gram positive peptidoglycan layer has large pores throughout its matrix
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
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
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
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)
energy to spin flagella is derived from _____
proton motive force
_____ give flagella direction
basal body
when flagella change direction, their movement changes from _____ to ______
directional to nondirectional (tumble)
axial flagella
attached in periplasmic space. when it moves inside it creates a corkscrew and we can seethe entire cell body rotate
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
conjugation
sex pilus
pili v fimbriae
pili = conjugation fimbraie = adherence (thinner and shorter than flagella)
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
biofilms
provide protection and enhanced survivability in harsh environments
example of biofilms include dental plaque and mold on bathroom surfaces
t or f most microbes cant be cultured
true
archaea
prokaryotes that have distinct properties. look like bacteria but are different. some live in inhospitable places.
extremophiles
can live in inhospitable environment
first archaea discovered fit this bill
how do we know archaea is distinct?
comparison of rRNA gene sequences helped to establish phylogenic trees
methanogens
a poorly characterized group of microbes capable of producing methane as a byproduct
t or f: ch4 traps more radiation than co2
t
halobacterium salinarium growth req
3.0-5.0 M NaCl
pyrococcus furiosus growth req
100 degrees C
picrophilus ashimae growth req
0.7 pH
methanogenium frigidum growth req
15 degrees C
genetic sequence analyses indicate that the branching point occurs when ____________
occurs when archaea and eukarya branch off from bacteria.
WHAT IS THE BRANCHING POINT?
development of histones !!!
Size of archaeal cells
0.5-5 micrometers
can vary greatly
shapes of archaeal cells
vary similar to bacteria
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
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
histones can allow DNA to be ______
stabilized
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
archaeal cytoskeleton
cytoskeleton homologues are found in both bacteria and archaea
Ta0583 is an actin homolog that resembles eukaryal actin (equivalent to MreB)
what is ta0583 equivalent to in bacteria and eukarya?
MreB in bacteria
actin in eukarya
cytoskeletal proteins from M.thermoautotrophicum and M. kandleri more closely resemble ________ cytsokeletal proteins
bacterial
archaea have ____ and _____ but these structures are different than their equivalents in bacteria and eukarya
plasma membrane and (sometimes) cell wall
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
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.
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
cell wall functions
physical and osmotic protection
in archaea the cell wall is composed of mostly __________
pseudomurein
(slightly different peptidoglycan structure)
NAG-NAT instead of NAG-NAM
t or f: some archaea lack a cell wall
true
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
thermoplasma acidophilum
DO NOT HAVE A CELL WALL AND CANT MAINTAIN SHAPE
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
archaeonics
use chemicals in the archae for antibiotics
haloarchae and sulfolobus are used archaeonics
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
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
are archaea pathogenic?
NO KNOWN EXAMPLES.
however some methanogens are associated with infection in mice.
two major phyla of archaeons:
- euryarchaeota
- crenarcheota
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)
recently detected species of archaea
ARMAN
archaeal richmond mine acidophilic nanoorganisms
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
sulfolobus solfataricus
a type of crenarcheote
opt temp 80 opt ph 2-4
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
mesophile temperature range
15-40 degress celsius
psychrophiles temperature range
< 15 degrees celsius
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
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
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
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
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
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
anton van leeuwenhoek
father of microbio observed first microbes by making microscope
robert hooke
invents cell theory
john needham
spontaneous generation theory (proven wrong) put boiled nutrient broth into covered flasks (contamination allowed for growth inside because flasks weren’t sealed)
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
louis pasteur
fixed the chicken brother scenario with his s shaped flasks that allowed the broth to be open to the environment
robert koch
GERM THEORY’
specific org causes specific disease
