Lecture Exam 3

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 

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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 

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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

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binary fission

* Most common method of cell division 

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snapping division

* Elongates and older outer cell wall snaps to reveal new cell wall 

arrangements of prokaryotes

diplo

* two

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strepto

* chain

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tetrads

* clusters of 4 arranged in same plane (cocci)

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sarcinae

* large brick like arrangements

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staphylo

* big clumps of cells

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palisade

* only bacilli
* fence like structure

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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
* **E**ager **L**eprechauns **M**unched **S**aucy **S**andwiches **B**efore **C**hrist
* 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

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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

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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 

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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 

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Treponema pallidum 

* Causes syphilis 

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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

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Toxoplasmosis

* Parasite that is carried by cats
* Tell pregnant women to not empty cat litter
* Parasite can get across the placenta

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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

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Acanthamoeba 

* Can also cause meningitis and encephalitis 

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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

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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

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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

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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

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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

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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

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Entry

* Viral DNA remains silent as a prophage

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Prophage entry

* Prophage incorporates itself in the host cell’s DNA

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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

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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

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Steps 6-8 are Synthesis

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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