Exam 1 Flashcards
Cellular organisms include
- fungi
- protists
- bacteria
- archaea
Acellular organisms include
- viruses
- viroids
- satellites
- prions
Viruses are composed of
protein and nucleic acid
Viroids are composed of
RNA
Satellites are composed of
nucleic acid, often RNA
Prions are composed of
protein
Prokaryotic cells lack what?
a true membrane
T / F: prokaryotic cells always lack a true membrane
F
What is true of eukaryotic cells?
eukaryotic cells have a membrane enclosed nucleus, are morphologically complex, and are usually larger than prokaryotic cells
The three domain system is based on a comparison of what?
ribosomal RNA genes
The 3 domains
- bacteria
- archaea
- eukaryotes
Cyanobacteria produce significant amounts of
oxygen
Archaea are distinguished from bacteria by what?
unique rRNA gene sequences
Some Archaea have unique __________ and _________
metabolic characteristics, membrane lipids
Many Archaea live where?
in extreme conditions
Protists are generally _____ than Bacteria and Archaea
larger
Algae + cyanobacteria produce ____% of oxygen
75
Yeast are a ___cellular fungi
uni
Mold are _____cellular fungi
multi
What yeast is often used in labs?
Sacchromyces cervesiae
_____ are the smallest of all microbes
viruses
Viruses require ________ to replicate
host cell
T / F: some viruses can cause cancer
T
T / F: oldest fossils on earth are microbial fossils
T
How old is the oldest fossil?
3.5 billions years old
_______ were the first life forms on earth
bacteria
For how long were bacteria the only life form on earth?
4.6 bya
What was the earliest molecule?
RNA
Ribozymes
RNA molecules that perform cellular work
Ribozymes are functional as what?
RNA
Earliest cells may have been RNA surrounded by _____
liposomes
______ is the precursor to double stranded DNA
RNA
The endosymbiotic hypothesis
the theory that some of the organelles in eukaryotic cells were once highly efficient prokaryotic cells
Which organelles are thought to originate from endosymbiont?
mitochondria and chloroplasts
Why are mitochondria and chloroplasts thought to uphold the endosymbiont theory?
mitochondria and chloroplasts contain DNA/RNA
rRNA genes show bacterial ______
lineage
16S rRNA (length, role)
- 1,500 nt RNA molecule
- structural role in the ribosome
- acts as a scaffold defining the positions of the ribosomal protein
Two regions of 16S rRNA
- highly conserved regions
- hyper variable regions
16S rRNA is ideal for what?
phylogenetic analysis due to the slow rate of evolution of the gene
Few differences in 16S rRNA indicates
close relation between species
Evolutionary distance
aligned rRNA sequences from diverse organisms are compared and differences counted to derive a value
T / F: time of divergence is determined by evolutionary distance
F
Archaea and Eukarya evolved ________ of Bacteria
independently
Archaea and Eukarya diverged from ________ ancestry
common
_________ of genetic material led to selected traits
mutation
Bacteria and Archaea increase genetic pool by _______ within the same generation
horizontal gene transfer
Who was the first person to observe and describe microorganisms accurately?
Antony van Leeuwenhoek
The idea that micro-organisms are the result of the process of decay is what theory
spontaneous generation
Who disproved spontaneous generation theory?
Louis Pasteur
Miasma theory
disease caused by foul air and bad smells
Louis Pasteur demonstrated that microorganisms carry out what process?
fermentations
Louis Pasteur developed what process to avoid wine spoilage by microbes?
pasteurization
Who provided indirect evidence that microorganisms were the causal agents of disease?
Joseph Lister
Joseph Lister developed what system and what did it result in?
aseptic surgery techniques, fewer postoperative infections
Who established the relationship between Bacillus anthracis and anthrax?
Robert Koch
Koch’s (4) Postulates
- the microorganism must be present in every case of the disease but absent from healthy organisms
- the suspected microorganisms must be isolated and grown in a pure culture
- the same disease must result when the isolated microorganism is inoculated into a healthy host
- the same microorganisms must be isolated again from the diseased host
What disease did Koch experiment on to test his postulates?
TB
Limitations of Koch’s Postulates
- some organisms cannot be grown in pure culture
- using humans in completing the postulates is unethical
- asymptomatic carriage
- co-infections
- dysbiosis
Koch’s work led to discovery of development of
- agar
- petri dishes
- nutrient broth and nutrient agar
- methods for isolating microorganisms
Taxonomy
science of biological classification
Taxonomy consists of what 3 separate but interrelated parts
- classification
- nomenclature
- identification
Highest taxonomic rank is ______
domain
Within domain
phylum, class, order, family, genus, species
Binomial system used 2 names, the first name is the ____ and the second is the ____
genus, species
Species
population of cells with similar characteristics
Genus name
italicized and capitalized
Species name
italicized but not capitalized
Gene nomencltaure
- three lowercase letters followed by an uppercase fourth letter
- italicized
- / abcD /
Protein nomenclature
- same four letters as gene name
- not italicized
- first and last letter capitalized
- AbcD
Prokaryotes differ from eukaryotes in _____ and _____
size, simplicity
Most prokaryotes lack
internal membrane systems (nuclear membrane, r and s ER, mitochondria)
Prokaryotes = what two domains?
bacteria and archaea
Overarching characteristics of prokaryotic cells
- no nucleus
- one chromosome
- usually unicellular
- no organelles
- 70S rRNA
- plasma membrane
- cell wall
- 80-90% genome density CDS
- cell size: 1-10 micro m
Most common bacterial shapes
cocci and rod
Arrangement of bacterial cells is determined by
plane of division
Diplococci
pairs
Streptococci
chains
Staphylococci
grape-like clusters (dividing in alternating planes)
Tetrads
4 cocci in a square
Sarcina
cubic configuration of 8 cocci
Coccobacilli
very short rods
Streptobacilli
chain of rods
Vibrios
resemble curved rods, comma shaped
Spirilla
rigid helices
Spirochetes
flexible helices
Mycelium
network of long, multinucleate filaments
Pleomorphic
organisms that are variable in shape
Smallest bacteria (name and size)
0.3 micro m, Mycoplasma
Average rod size
1.1-1.5 micro m wide x 2-6 micro m long
______ is one of the biggest viruses that infects humans
Pox virus
Bacterial genome size (range)
500,000 bp to 10 million bp
What increases S/V ratio?
corkscrew shape
_____ cell size increases S/V ratio
small
Bacterial cell organization (3) common features
- cell envelope
- cytoplasm
- external structures
Layers of cell envelope
- cell membrane
- wall
- S-layer
All bacteria must have
cell membrane, cell wall, cytoplasm
_____ and ______ are variable to bacteria
S-layer, external structures
Typical bacterial cell structure (describe)
plasma membrane is further in than cell wall which is further in than capsule
Layers outside cell wall
S-layer, capsule
__________ is an absolute requirement for all living organisms
plasma membrane
Plasma membrane functions
- encompasses the cytoplasm
- selectively permeable barrier
- interaction with external environment
- metabolic processes
Hydrophobic regions associate with each other (_____), hydrophilic regions exposed (______)
inside, outside
Peripheral = ________% total membrane protein
20-30
Peripheral protein characteristics
- loosely attached to membrane
Integral protein = ____% of total membrane protein
70-80
Integral protein characteristics
- amphipathic (embedded within membrane)
- carry out important functions
- may exist in microdomains
Saturated bacterial lipids = ___ fluid
less
Hopanoids
sterol-like molecules, stabilize membrane
Macronutrients
- C, O, H, N, S, P
- found in organic molecules such as proteins,
lipids, carbohydrates, and nucleic acids - K, Ca, Mg and Fe
- cations and serve in variety of roles including
enzymes, biosynthesis - required in relatively large amounts
- mostly needed as cofactors for enzymes
Micronutrients
- trace elements
- Mn, Zn, Co, Mo, Ni and Cu
- often supplied in water or in media components
- ubiquitous in nature
- serve as enzymes and cofactors
- passively enter the cell
Growth factors
- organic compounds
- essential cell components (or their precursors) that the cell cannot synthesize
- must be supplied by environment if cell is to survive
- any organic compound that a cell must take up
Amino acids are needed for _____ synthesis
protein
Purines and pyrimidines are needed for ______ synthesis and are the basic building blocks for ____
nucleic acid, DNA
Vitamins function as _______
enzyme cofactors
Heme
iron
An example of nutritional immunity
body keeps iron in a form that is inaccessible to bacteria
What two transport mechanisms do all microorganisms use?
facilitated diffusion, active transport
Group translocation is used by
bacteria and archaea
Endocytosis is used by
Eukarya only
H2o, O2 and CO2 often move across membrane by
passive diffusion
Facilitated diffusion typically involves
carrier proteins
In facilitated diffusion, direction of movement is from ______ to _____ and, ____ require energy
high concentration to low concentration, does not
How does facilitated diffusion differ from passive diffusion?
- uses permeases (membrane bound carrier molecules)
- smaller concentration gradient is required for significant uptake of molecules
- effectively transports glycerol, sugars, and amino acids
Facilitated diffusion is more prominent in ____ than in
eukaryotic cells, bacteria or archaea
Passive diffusion is
linear
Active transport is a(n) ______-dependent process
energy
Active transport movement
- moves molecules against the concentration gradient
- concentrates molecules inside cell
3 types of active transport
- primary active transport
- secondary active transport
- group translocation
Primary active transport (characteristics, what microorganisms it is observed in)
- ABC transporters
- use ATP
- observed in bacteria, archaea and eukaryotes
- consists of 2 hydrophobic membrane spanning domains, 2 cytoplasmic associated ATP-binding domains, substrate binding domains
Secondary active transport
- use ion gradients to cotransport substances (instead of ATP!)
- symport
- antiport
Symport
two substances both move in the same direction
Antiport
two substances move in opposite directions
Group translocation
- energy dependent transport that chemically modifies molecule as it is brought into cell
- a variety of sugars can be transported by PTS systems
- Enzyme I and Hpr are the same in all PTS systems
- specificity lies with Enzyme II
Siderophore
secreted by microorganisms to aid in iron uptake
Cell wall functions
- maintains shape of the bacterium
- helps protect cell from osmotic lysis
- helps protect from toxic materials
- may contribute to pathogenicity
T / F: a lot of bacteria can survive without cell wall (no osmotic pressure) but not without cell membrane
T
Gram-positive bacteria stain
purple
Gram-negative bacteria stain
pink
T / F: peptidoglycan is found in bacterial cell wall and nowhere else
T
Area between peptidoglycan and plasma membrane
periplasm
Peptidoglycan (murein)
rigid polymer structure that lies just outside the cell plasma membrane
Gram (+) peptidoglycan: _____ nm thick
20-80
Gram (-) peptidoglycan: ______ nm thick
2-7
Peptidoglycan structure
- two alternating sugars: NAM and NAG
- peptide strand (alternating D- and L- amino acids)
L amino acid is connected to NAM or NAG?
NAM
Chains in peptidoglycan are crosslinked to other chains via
peptides
Crosslinking can be direct or
by a peptide inter-bridge
Most common #3 amino acid is
DAP
Most common type of linkage is
3 - 4 linkage
Amino acid at #3 position can be
- DAP
- L-Lys
- L-Hsr
Linkage types
3 - 4
2 - 4
Composition of linkage
- direct
- bridged
Protein translation by ribosomes exclusively utilizes
L-amino acids
T / F: D-amino acids are common
F
The most common place in nature to find D-amino acids
bacterial cell wall
Peptidoglycan backbone
- alternating NAM-NAG sugars
- beta-(1,4) linked
- beta-(1,4) glyosidic bond
Gram (+) cell walls
- 20-80 nm thick peptidoglycan
- may also contain teichoic acids
Teichoic acids
- polymer consisting of alternating phosphate/sugar groups
- (-) charged
- help maintain cell envelope
- protect from environmental substances
- may bind to host cells
- covalently connected to peptidoglycan
- may also be covalently connected to lipids in plasma membrane (LTA)
TA: anchored to ____
cell wall
LTA: anchored to/in _____
plasma membrane
Sortase
- periplasmic protein
- anchors other proteins to cell wall
Periplasmic space of Gram (+) bacteria is ____ than that of Gram (-)
smaller
Gram (+) cell walls
- important for virulence
- covalently linked to peptidoglycan
- proteins have protein sequence LPXTG
- covalently linked to peptidoglycan through T residue by enzyme sortase
Gram (-) cell walls are _____ complex than Gram (+) cell walls
more
Gram (-) cell walls
- consist of a thin layer of peptidoglycan surrounded by an outer membrane (OM)
- outer membrane composed of lipids, lipoproteins and LPS
- no teichoic acids
- plasma membrane sometimes called inner membrane (IM)
Important differences between Gram (-) and (+) cell walls
- Gram (+) cell walls have no OM
- Gram (+) cell walls have thicker peptidoglycan/cell wall
- Gram (-) has LPS, no TA
Periplasmic space of Gram (-) cell
- 20-40% of cell volume
- many enzymes present (hydrolytic enzymes, transport proteins, etc.)
In Gram (-) cell walls, the OM lies
outside thin peptidoglycan layer
OM is _____ bonded to peptidoglycan by
covalently, Braun’s lipoprotein
Outer surface of OM consists of
LPS
Inner layer of OM composed of
phospholipids
T / F: LPS is only found in Gram (-) bacteria
T
LPS structure
- O side chain (O antigen) (extended out from cell)
- core polysaccharide
- lipid A (embedded in OM)
Importance of LPS
- core polysaccharide contributes to (-) charge on cell surface
- lipid A helps stabilize OM structure
- creates a permeability barrier
- O antigen protects from host defenses
- lipid A can act as a toxin (endotoxin)
Gram (-) OM permeability
- more permeable than IM due to presence of porin proteins
- porin proteins form channels to let small molecules pass
One major function of the cell wall is to protect the bacterial cell from
osmotic stress
Hypotonic environments
- solute concentration is higher inside the cell
- water moves into cell and cell swells
- cell wall protects from lysis
Hypertonic environments
- solute concentration is higher outside the cell
- water leaves the cell
- plasmolysis occurs (shrinking of cytoplasm)
If peptidoglycan cell wall is removed…
- cells will lyse if they are in a hypotonic solution
- survive in isotonic solution
Gram (+) bacteria without peptidoglycan
protoplasts
Gram (-) bacteria without peptidoglycan
spheroplasts
3 most common types of components outside the cell wall
- capsules
- slime layers
- S-layers
Capsules
- usually composed of polysaccharides
- resistant to phagocytosis
- protect from desiccation
- exclude viruses and detergents
- well organized, not easily removed from cell
Slime layers
- may aid in motility
- similar to capsules except diffuse, unorganized and easily removed
S-layers
- regularly structured layers of protein or glycoprotein that self-assemble
- Gram (-): S-layer adheres to OM
- Gram (+): S-layer is associated with the peptidoglycan surface
Cytoplasm
material bounded by the plasmid membrane
Bacterial cytoplasmic structures (5)
- cytoskeleton
- intracytoplasmic membranes
- ribosomes
- nucleoid and plasmids
- inclusions
Cytoskeleton (3 eukaryotic cytoskeletal elements, role, homologs)
- 3 eukaryotic cytoskeletal elements: actin, tubulin, intermediate filaments
- plays role in cell shape and structure, internal organization, localization of components within the cell
- homologs of all three have been identified in bacteria
FtsZ
- tubulin homolog
- found in many bacteria
- forms ring during septum formation in cell division
MreB
- actin homolog
- maintains shape by positioning peptidoglycan synthesis machinery
- found in rods
CreS
- IF homolog
- rare
- maintains shape in curved bacteria (prevents peptidoglycan synthesis on one side)
Intracytoplasmic membranes
- extension of the plasma membrane into cytoplasm
- many metabolic reactions can only happen in/at a membrane, provides more surface area that can then provide space for reactions
- observed in many photosynthetic bacteria and bacteria with high respiratory activity
Ribosomes
- complex protein/RNA structures
- sites of protein synthesis
Bacterial and archaeal ribosome
70S
Eukaryotic ribosome
80S
Bacterial rRNA
- 16S small subunit
- 23S and 5S in large subunit
Ribosomes are found where in bacteria?
free floating in cytoplasm
The nucleoid
- genetic material of the cell
- usually not membrane bound
- consists of chromosome and associated proteins
- usually 1 closed circular, DS DNA molecules
______ condenses nucleoid
Supercoiling
Plasmids
- extrachromosomal DNA
- exist and replicate independently of chromosome
- contain non-essential genes
Episomes
when plasmids integrate onto chromosomes
Inclusions
- granules or organic or inorganic material that are stockpiled by the cell for future use
- general term for anything random found in cytoplasm
External structures (functions)
- attachment to surfaces
- cell movement
- protection
- horizontal gene transfer
3 best known examples of external structures
- pili
- fimbriae
- flagella
Pili and fimbriae
- short, thin, hair-like appendages (up to 1,000 per cell)
- proteinaceous
- helical tubes
- functions include attachment to surfaces, motility and DNA uptake
- attachment to surfaces is main function
Sex pilus
- longer, thicker, less numerous
- genes for formation found on plasmids
- required for conjugation
- forms between bacterial cells
Flagella
- long thread-like appendages extending outward from plasma membrane and cell wall
- up to 20 micro m in length
- functions include motility, attachment to surfaces, virulence factors
- motility is main function, acts as a propeller
- can be 4-5x larger than the cell
- corkscrew shape
Monotrichous
one flagellum
Polar (flagella distribution)
flagellum at end of cell
Amphitrichous
one flagellum at each end of cell
Lophotrichous
cluster of flagella at one or both ends
Peritrichous
spread over entire surface of cell
3 parts of flagella
- filament
- extends from cell surface to the tip
- hollow, rigid cylinder of flagellin protein - hook
- links filament to basal body - basal body
- series of rings that drive flagellar motor
Filament subunits self-assemble with help of filament cap at
tip, not base
Chemotaxis
move toward chemical attractants such as nutrients, away from harmful substances
4 common types of motility
- flagellar movement
- spirochete motility
- twitching motility
- gliding motility
Flagellar movement
- flagellum rotates like a propeller (very rapid rotation)
- CCW: forward motion (run)
- CW: cell spins around (tumble)
Spirochete motility
- flagella remain in periplasmic space inside OM (periplasmic flagella)
- multiple flagella form axial fibril which winds around the cell
- corkscrew shape exhibits flexing and spinning movements
Twitching motility
- pili at ends of cell
- extend and contact surface
- retract, pulling the cell forward
- short, intermittent, jerky motions
Gliding motility
- not well-defined process
- various proposed mechanisms
- smooth movements
- smile layers?
In a graph of flagellar mediated chemotaxis:
- each corner indicates a _______
- in absence of attractant, flagella rotate CCW and CW with ______ frequency
- when concentration of attractant increases, the frequency of CW is _____, runs in direction of attractant are ______
- when concentration of attractant decreases, frequency of CW is ______, cell redirects until _______
- tumble
- equal
- reduced, longer
- increased, moving towards attractant
The bacterial endospore
- complex, dormant structure formed by some bacteria
- various locations within the cell
- resistant to numerous environmental conditions (heat, radiation, chemicals, desiccation)
Sporulation
- process of endospore formation
- occurs in hours (up to 10)
- normally commences when growth ceases because of lack of nutrients
- complex, multistage process
Purpose of sporulation
survival and preservation of the genetic matieral
Formation of vegetative cell
- activation (prepares spores for germination, often results from treatments like heating)
- germination (environmental nutrients are detected, spore swelling and rupture of spore coat, increased metabolic activity)
- outgrowth (emergence of actively growing cell)
One thing Archaea are not known to do
cause disease in humans
Archaeal size, shape, arrangement
- cocci and rods are common shapes (others can exist)
- no spirochetes or mycelial forms yet
- branched/flat shapes
- sizes vary (typically 1-2 x 1-5 micro m for rods, 1-5 micro m diameter for cocci)
- smallest observed is 0.2 micro m in diameter
Properties that bacteria and archaea have in common
- inclusions
- ribosomal size
- chromosomal structure
- plasmids
- external strucutres
Archaeal cell envelopes
cell envelope consists of
- plasma membrane
- no peptidoglycan
- cell wall (some lack one, however)
- additional external layers (S-layer may be only component outside plasma membrane, capsules and slime layers are rare)
Archaeal envelopes differ from bacterial envelopes in
the molecular makeup and organization
Archaeal membrane lipids (building block, composition)
- composition is very different than that of bacteria
- building block is 5 carbon branched molecule isoprene
- lipid chains of isoprene are branched, unlike the chains of bacterial phospholipids
Branching of membrane lipids affects
fluidity of membrane
Archaeal lipids are attached to glyercol by
ether linkages
Bacterial lipids are attached to glycerol by
ester linkages
Some archaeal lipids and membranes have…
- diglycerol tetraethers
- pentacyclic rings (increases membrane rigidity)
Archaeal lipid and membrane composition supports what idea?
that archaea evolved independently of bacteria
Most common type of archaeal cell envelope is
S-layer outside plasma membrane
Additional layer outside of the S layer may be composed of
polysaccharide
Some archaeal cell walls contain a peptidoglycan-like polymer called
pseudomurein
Differences between pseudomurein and peptidoglycan
- beta,1-3 linkage
- no D amino acids
- NAT and NAG
Protein translation by ribosomes exclusively utilizes
L-amino acids
Archaeal cell walls have a thick _______ layer, and often stain
polysaccharide, Gram (+)
Archaeal cells use what mechanisms for nutrient uptake
- primary active transport
- secondary active transport
T / F : archaea have more proteins than bacteria
T
5.8S suggests relationship between
eukaryotes and archaea
_____ may be involved in archaeal adhesion mechanisms
pili
Cannulae
- hollow, tube-like structures on the surface of thermophilic archaea in the genus Pyrodictium
- function is unknown
- connects cells together, helps them adhere to each other and the surface around them
Hami
- not well understood
- looks like a grappling hook
- involvement in cell adhesion mechanisms (?)
Archaeal flagella: growth occurs where?
at the base
Differences of archaeal flagella
- thinner than bacterial flagella
- more than one type of flagellin protein
- flagellum are not hollow
- hook and basal body are difficult to distinguish
- add subunits to base, not tip
Two groups of eukaryotes commonly possess microbial members
- protists
- fungi
T / F: protist is a taxonomic group
F
Eukaryotic cell envelopes
- plasma membrane is lipid bilayer
- consists of plasma membrane and all coverings attached to it
- usually don’t have cell wall (protists and fungi do)
- sphingolipids and cholesterol contribute to strength of membrane
Cell walls of photosynthetic algae commonly composed of
cellulose, pectin, and silica
Cell walls of fungi consist of
cellulose, chitin or glucan
T / F: cell wall of a eukaryotic cell is typically complex
F
Cytoplasm of eukaryotes
- consists of the cytosol and many organelles
- cytoskeleton plays a role in cell shape and movement (microfilaments, microtubules, intermediate filaments)
_____ cytoskeletal component is involved in cell motion and shape changes
actin filaments
Intermediate filaments
- heterogeneous elements of the cytoskeleton
- role in cell is unclear
- play a structural role
- some shown to form nuclear lamina, others help link cells together to form tissues
Microtubules
- think cylinders
- help maintain cell shape
- involved with actin filaments in cell movements
- participate in intracellular transport processes
Lysosomes
- intracellular digestion (important for clearing microbes from eukaryotic cells)
- contain hydrolases (enzymes that hydrolyze molecules and function best under slightly acidic conditions)
- maintain an acidic environment by pumping protons into their interior
Endosytosis
- used to bring materials into the cell
- solutes or particles taken up and enclosed in vesicles pinched from plasma membrane
Phagocytosis
- cell surface protrusions surround and engulf particles
- particles are taken up inside a membrane bound vesicle
Receptor mediated endocytosis
- external receptors on cell surface
- specifically bind macromolecules
- binding triggers endocytosis
- receptor and bound molecule are taken up
Eukaryotic ribosomes
- may be attached to ER or free in cytoplasmic matrix
- when present in ER: bound via 60S subunit
ER ribosomes
secreted and membrane proteins
Free ribosomes
cytoplasmic proteins
External cell covering (eukaryotic cells) and what they are associated with
- cilia, movement
- flagella, movement
______ may have lateral hair-like projections
flagella
_______ move in an undulating fashion
- wave from base to tip, pushes cell
- wave from tip to base, pulls cell
flagella
_______ beat with two phases, working like oars, and have highly coordinated movements
cilia
In what type of cell are introns rare in?
archaeal and bacterial
Describe the plasma membrane lipids of
- bacterial cells
- archaeal cells
- eukaryotic cells
- bacterial cells: ester-linked phospholipids and hopanoids; some have sterols
- archaeal cells: glycerol di-ethers and diglycerol tetraethers
- eukaryotic cells: ester-linked phospholipids and sterols
