mutation
any change in nucleotide sequence
insertions/deletions and substitution
major kinds of mutations
point mutation
when a single base pair is added, deleted or changed
kinds of point mutations
Silent mutations, missense mutations and nonsense mutations
silent mutation
no change in amino acid sequence of polypeptide
missense mutation
Slightly different amino acid sequence
Sickle cell
1 single base pair to be substituted in hemoglobin chain
nonsense mutation
Codes for stop codon
Polypeptide synthesis ceases
Usually result in loss of fitness (reproduction)
frameshift insertion/deletion
Major difference in amino acid sequence
physical mutagens
Ionizing radiation
penetrates deeply
Destabilizes it
Destroys DNA of cells
Nonionizing radiation
UV light
Thymine dimers
Double thymine's stick together and then gets cut out causing frameshift mutations
chemical mutagens
Nucleotide analogs - Disrupt DNA and RNA replication
Bromouracil can replace thymine
Nucleotide-altering chemicals - Result in base-pair substitutions and missense mutations
Frameshift mutagens - Result in nonsense mutations
base excision repair
Can remove incorrect nucleotides
light repair
Can produce photolyase to repair and get rid of thymine dimers by using natural light to produce photolyase
nucleotide excision repair
Can cut out multiple nucleotides to repair thymine dimers and repair the strand
mismatch repair
Can remove large parts of a single strand to repair incorrect nucleotide repair
error-prone repair
an inefficient mechanism for repairing DNA damage that often results in mutations
cocci
circular bacteria
bacillus
rod shaped bacteria
vibrio
comma shaped bacteria
spirochete
corkscrew like bacteria
spirilium
wavy like bacteria
star
pleomorphic
can change shape
endospores
formation
when there is a severe lack of nutrients
function
allows the bacterium to produce a dormant and highly resistant cell to preserve the cell's genetic material in times of extreme stress.
types of reproduction
budding
cell elongates to form a bud that eventually breaks off mother cell
binary fission
Most common method of cell division
snapping division
Elongates and older outer cell wall snaps to reveal new cell wall
arrangements of prokaryotes
diplo
two
strepto
chain
tetrads
clusters of 4 arranged in same plane (cocci)
sarcinae
large brick like arrangements
staphylo
big clumps of cells
palisade
only bacilli
fence like structure
v shape
form a v
mycoplasma
live in osmotically protected environments
lack of cell wall makes them naturally more antibiotic-resistant
antibiotics that act by degrading cell walls cannot kill mycoplasma
Clostridium
detrimental
Form endospores
Vegetative cells produce toxins
Medically relevant members
C. tetani – causes tetanus
C. perfrigens – causes gas gangrene
C. botulinum – causes botulism & and is used in botox
C. dificile (C. diff)– causes severe diarrhea and is resistant to most antibiotics
Make hydrogen sulfide gas – smells like rotten eggs
Bacillus
B. cereus – causes food poisoning
B. anthracis – causes anthrax by producing toxins that kill surrounding tissues
Was used in bioterrorism attack in 2001
Cutaneous, inhalation
If untreated, ~20% & 100% fatal (inhalation), respectively
Inhalation anthrax needs to be picked up within 24 hours of inhalation
Listeria
Can contaminate milk & meat
Causes food poisoning
Able to reproduce when refrigerated
Evades host immune response
Streptococcus
Strep pyogenes common cause of strep throat
Gram-positive catalase negative
Strep pneumonae
Can cause middle ear infections
Strep mutans
Takes hold and can overpopulate and lead to cavities
Ferments sugar to produce acids
These acids destroy tooth enamel
Can cause diseases including pharyngitis, impetigo (more common manifestation of strep in young children; cutaneous), pneumonia, necrotizing fasciitis, etc.
Staphylococccus
S. aureus can cause diseases such as toxic shock, pneumonia, etc.
MRSA is a serious problem
MRSA - Methicillin resistant staph. aureus
medically important firmicutes
low G+C content
classifys gram positive bacteria
Eager Leprechauns Munched Saucy Sandwiches Before Christ
E - enterococcus
L - Listeria
M - mycoplasma
S - streptococcus
S - staphylococcus
B - bacillus (spore former)
C - clostridium (spore former)
Enterococcus
found in GI track
Causes nosocomial UTI in immunocompromised patients
Increase in vancomycin resistant enterococci (VRE)
low vs high G+C content
low G+C
less than 50% guanine and cytosine nucleotides in their DNA
similar 16s rRNA sequence
high G+C
more than 50% of guanine and cytosine nucleotides in their DNA
Gram-positive bacteria
Identified by a fast acid stain
Their rRNA is similar
mycobacterium
slow growth
M. tuberculosis & M. leprae are pathogenic
need long term antibiotic treatment because of slow generation time
Corynebacterium
Corynebacterium are aerobes & facultative anaerobes
C. diphtheriae causes diphtheria
Pleomorphic (have different shape)
Cell wall does not invaginate it snaps
Actinomyces
Actinomyces form branching filaments
A. israelii can destroy tissue
Nocardia
cause pneumonia in hospitalized patients
proteobacteria classes
Alphaproteobacteria
Betaproteobacteria
Gammaproteobacteria
Deltaproteobacteria
Epsilonproteobacteria
diseases caused by alphaproteobacteria
Rickettsia rickettsii causes Rocky Mountain Spotted Fever
Brucella causes brucellosis
pathogenic betaproteobacteria
Neisseria gonorrhoeae & N. meningitidis
Inhabits mucous membranes of mammals
Causes gonorrhea, meningitis, pelvic inflammatory disease
Bordetella pertussis
Causes pertussis (whooping cough), usually in children < age 5 years
gammapreoteobacteria
Gram negative rods
most abundant class of pathogenic proteobacteria
common pathogens are
Escherichia coli
Commensal
May or may not benefit the host
GI infections
Gastroenteritis (stomach flu), UTIs, sepsis, renal failure (hemolytic uremia syndrome)
Klebsiella pneumoniae
Nosocomial & community acquired infections
Pseudomonas aeruginosa
Wound infections or pneumonia
sepsis, UTIs (Urinary Tract Infection), ear & lung infections
1/10 nosocomial infections
Biofilms are common in cystic fibrosis
Yersinia pestis
Causes the plague
Most common/well known is bubonic plague
People would get infection from a flea bite
Causes buboes (collection of blood, pus, bacteria)
Also causes gangrene (end stages)
Mortality rate of 20-50%
pathogenic epsilonproteobacteria
Campylobacter jejuni causes acute gastroenteritis (stomach flu)
Is in the jejunum in small intestine
Helicobacter pylori causes gastric ulcers
Creates bubble around itself that neutralizes acidity
chlamydia
are very small cocci that reproduce only within the cells of mammals
Obligate intracellular parasites
Chlamydia trachomatis causes STDs & neonatal blindness
Common complication is pelvic inflammatory disease
Inflammation of the fallopian tubes – can cause infertility
bacteroides
Not a spore former
Obligate anaerobes that normally inhabit the GI tract
Digest cellulose & other complex carbohydrates that are indigestible by humans
Bacteroides fragilis can cause abdominal, pelvic, blood & other infections
spirochetes
Motile by axial filaments
Treponema pallidum
Causes syphilis
Borrelia burgdorferi
Causes Lyme disease
eukaryotic classification
Earliest schemes based groups based upon structural similarities
Linnaeus – Plants and Animals
20th century – Fungi, Protista, Plants, Animals, (bacteria were Monerans)
21st century – Fungi, Parabasalids, Diplomonads, Euglenazoa, Avleolata, Rhizaria, Amoebozoa, \n Plants and Animals
problems with protist classification
included both large, photosynthetic, multicellular algae and nonphotosynthetic, unicellular protozoa
abandoned classifying schemes that are so strongly grounded in large-scale structural similarities in favor of schemes based on similarities in nucleotide sequences and cellular ultrastructure
protozoa characteristics
eukaryotic
unicellular
lack a cell wall
why there are many different taxonomic schemes for protozoa
they classify them based on 18S rRNA nucleotide sequencing and features made visible by microscope
very diverse phylum of organisms
euglenid
Characteristics of both plants and animals
Have both mitochondria and chloroplasts
Chloroplasts almost identical to those in green plants
Flagella contain a crystalline rod of unknown function
Mitochondria have disk-shaped cristae
Photoautotrophic plant like
alveolates
Apicomplexans
The most pathogenic
Non motile protozoa
Special organelles that allow them to attach and enter host cells
Do not have cilia, flagella
Through bite of insect vector
Plasmodium
Responsible for causing malaria
3 major types
All transmitted by mosquitos
Toxoplasmosis
Parasite that is carried by cats
Tell pregnant women to not empty cat litter
Parasite can get across the placenta
Dinoflagellates
Hard outer shells made of silica
Photosynthetic and chemoheterotrophs
Few species that are highly toxic to humans
Known to cause red tides
Usually where agricultural runoff goes into the ocean
Massive bloom from all the fertilizer and extra nutrients
Produce potent neurotoxin
Can impact shellfish
amoebas
Naegleria
Brain eating amoeba
Usually found in the south
Can burrow through cribriform plate
100% fatal
From people swimming and water sports in bodies of water w muddy bottoms
Acanthamoeba
Can also cause meningitis and encephalitis
Entamoeba
Live in digestive tract of animals
Can cause amoebic dysentery
Can cause severe dehydration until it results in death
Can live in water
parabasalids
One of the simplest types
Lack mitochondria
Mitosomes perform similar functions to mitochondria
Have a single nucleus
Contain Golgi body–like structure called a parabasal body
Helps to package proteins
Important parabasalids – Trichomonas vaginalis
STI
Lives in vaginal canal
When pH becomes more alkaline it proliferates
diplomonads
Lack mitochondria
Have mitosomes in the cytoplasm
Mitochondrial genes found in the nuclear chromosomes
Also lack Golgi bodies and peroxisomes
Have two equal-sized nuclei and multiple flagella
Whip side to side like a fin
Do not spin like bacteria flagella
Important diplomonad: Giardia intestinalis
Parasite found in water
Extremely hard to get rid of it
Causes diarrhea (can last a month)
rhizaria
Amoebae exhibit little uniformity
Do not make blob-like extensions of their membrane
Rhizaria are amoebae with threadlike pseudopods
Foraminifera - Often live attached to the ocean floor
Most are fossil species
Radiolaria -Have ornate shells of silica, Live as part of the marine plankton
amoebozoa
Amoebae with lobe-shaped pseudopods and no shells
Can form cysts (like endospores – increase resistance)
Includes some human pathogens
Found in almost every wet environment
Most in fresh water
what distinguishes fungi from other eukarya
chemoheterotrophs
Lack chlorophyll
Fungal walls contain chitin
Most are not truly multicellular
Most famous are penicillin and saccharomyces (brewer's yeast)
Most are aerobes
Others are facultative anaerobes
Heterotrophic as saprophytes (decomposers)
major shapes of fungi
Molds—composed of long filaments called hyphae
Yeasts—small, globular, and composed of a single cell
dimorphic
Produce both yeastlike and moldlike shapes
Change in response to environmental conditions
fungi nutrition
Saprophytic Nutrition: The absorption of food from dead or decaying organic matter
Parasitic Nutrition: The absorption of food from living organisms
mold nutrition
secretes digestive juices (enzymes) directly on the food
enzymes cause the food to become soluble, which it is then absorbed by the mold
asexual fungi reproduction
Spores
Asexual
Can bud
sexual fungi reproduction
Gametophytes
Contain half the chromosomes
Come together to form sporocysts
algae
Simple, photosynthetic organisms that photosynthesize similarly to plants
Different from plants in that every cell can become a gamete (a sex cell)
Can be unicellular or colonial
All aquatic
why microbiologist study parasitic worms
Larvae are microscopic and are usually the diagnostic features of many parasitic worms.
vectors
a living organism that transmits an infectious agent from an infected animal to a human or another animal
arachnids
Can be mechanical or biological vectors of disease
Ticks and mites are the most common biological vectors
Adult stages have eight legs, two body parts and mouthparts made to burrow
tick and mite diseases
Lyme disease, Rocky mountain spotted fever, tularemia, tick-borne encephalitis
fleas disease
Plague
lice diseases
Vectors for typhus
flies diseases
Leishmaniasis, Sleeping sickness
mosquito diseases
Most important arthropod vectors of disease
Malaria, Yellow fever, Dengue fever, Viral encephalitis, Rift valley fever, West nile, Zika
kissing bug diseases
Chagas disease
mechanical vector
insect or arachnid tracks through something and it is transmitted to us through touch
biological vector
involves getting bitten by insect or arachnid
virus
when a virion enters a host cell
virion
When a virus is not inside a host cell
nucleic acid (single- or double-stranded RNA or DNA) and a protein coat, the capsid
viral genetic material
Either DNA or RNA, never both
dsDNA
Double stranded
ssDNA
Single stranded
ssRNA
DsRNA
virus specificity
depends on capsid or envelope structure
Many viruses infect certain cell or tissue types within the host (tissue tropism)
The virus needs a specific receptor to invade the host cell
all organisms are susceptible to viruses
viral envelope
Have a cell membrane around the outside of them
Cell membrane from the host cell
Phospholipid bilayer
Obtain it through budding
Pushed out of the cell and gain a membrane through it
Does not do transport, diffusion, osmosis
Typically, it's easier to get rid of enveloped viruses
More susceptible to lysol, bleach, disinfectants
Proteins that stick out
Can be part of the cells glycocalyces
Can be hard to detect because it has host characteristics
viral capsids
Protein case that encloses genetic material
Protects it when outside of a host
Helical
Screw
Icosahedral/polyhedral
Anywhere from 10-20 sides
Complex viruses have both helical and icosahedral symmetry
viral classification
based on
Type of nucleic acid
Presence of an envelope
Shape
Size
Viral genera have only been organized into families
Relationships among viruses are not well understood by taxonomists
lytic cycle
only in bacteriophages
Attachment
Nonmotile
Contact with host cell is random
Dependent upon chemical attraction between tail fibers and receptors on host membrane
Will only attach to pili, cell wall, or flagella for E. coli
Entry
To break through cell wall, it releases lysozyme to dissolve outer part of cell wall
Helical part contracts and squirts nucleic acid into bacteria
After entry viral enzymes begin to degrade bacterial DNA
Synthesis
Begins to create viral genome for new viruses
For dsDNA viruses, the viral genome directs the synthesis of new capsid proteins, tail, viral polymerase, and lysozyme
Assembly
Capsid proteins begin to assemble inside the host cell
Tails and tail fibers begin to assemble and attach to head
Capsids form around viral genomes, or the genomes are pumped into the newly formed capsid
Release
As lysozymes weakens the cell wall of the bacterium the new virions can burst free from the cell
lysogenic cycle
Attachment
Same as in lytic cycle, but the host cell’s DNA is not destroyed
Entry
Viral DNA remains silent as a prophage
Prophage entry
Prophage incorporates itself in the host cell’s DNA
Lysogeny
Every time the bacterial chromosome replicates, the viral DNA is copied along with it
All daughter cells will now carry the prophage
Lysogenic phages can cause the phenotype of the bacterium to change from harmless into pathogenic
Induction
At some point the prophage may be excised from the host DNA
At this point it reenters the lytic phase
Inductive agents include physical and chemical agents that damage bacterial DNA
Steps 6-8 are Synthesis
Assembly and Release
occurs just as in lytic cycle
animal viruses
Can be enveloped or non-enveloped
Replication of animal viruses within a host share the same 5 stages as lytic cycle
Few changes