FINAL EXAM MICROBIOLOGY

As an energy source, chemoorganotrophs can use

Carbon compounds

As an energy source, phototrophs can use

light

what is an eukaryotic microbe?

fungi

The movement of water through a membrane (osmosis) is caused by

Unequal solute concentrations

A microorganism that causes disease is referred to as a

pathogen

This man invented the compound microscope and coined the word “cell” as the basic unit of life

Robert hooke

This man was the first to have a germ-theory of disease, and also coined the word “syphillis”

Giancarlo fracastoro

This man is the grandfather of microbiology

Louis pasteur

Bacteria are essential for the function of which element?

nitrogen

Sulfur is formed in which biomolecule?

proteins

major components of the cell membrane

phospholipids

LPS & Flagella are

PAMPS

The periplasmic space is

between the cytoplasmic and outer membrane

pili are located

on the cell surface

which of the following is NOT a feature of most prokaryotic DNA?

code with AUG like eukaryotic RNA

a biofilm is

a protective habitat for microorganisms

requires oxygen

obligate aerobe

requires between 2-10% O2

microaerophile

grows the best with O2, but doesn't require it

facultative anaerobe

does not need O2

aerotolerant anaerobe

does not need O2, and oxygen is toxic to it

obligate anaerobe

bacteria produce new cells in

binary fision

bacteria menaquinone is your

vitamin K

Cow, rice paddies, swamps have in common?

methane production

bacteria are essential

clouds

describe 3 positive contributions of bacteria in the world we live in

Gut
- Fermentation
- Decomposition
- Bioremediation
- Digestion

what are PAMPs? 2 examples

Pathogen associated molecular patterns
LPS & flagella

osmosis is

passive transport

penicillin & lysosome antibacterial properties

Both penicillin & lysozyme work on bacteria cell walls. Penicillin weakens the cell walls of dividing bacteria, so that they burst and die due to osmotic pressure. Lysozyme is a small enzyme that attacks the same protective cell wall of a bacterium, causing it to degrade.

main cellular metabolism pathway

Glycolysis
- Inputs of glycolysis: glucose, outputs: 2 molecules pyruvate, 2 molecules of ATP, NADH

Why do organisms undergo fermentation? Name 2 molecules used in fermentation that accept electrons? 2 molecules products of fermentation?

Ferment in the absence of oxygen
- Majority of organisms need oxygen for respiration, fermentation energy is too low for them. They die within minutes total of oxygen. Fermentation can supply the aerobic energy in them.
- GAPDH requires NAD
- Products of glycolsis: pyruvate, atp, nadh
- Oxidize pyruvate, shove electrons on alcohol
- Ferment to regenerate NAD for glycolysis to function
- 2 molecules used in fermentation that accept electrons: pyruvate & acetate
- 2 molecules products of fermentation? Lactate, ethanol, propanol, organic alcohols

Why are alkaline environments more hostile to life than acidic environments?

Acidic environments have more protons, basic have more hydroxyl ions, interfere with protons and generate more water
- Basic environment destroys proton gradients
- Point of electron transport chain? Generate proton gradient

compare prokaryotes & eukaryotes

Eukayotes have membrane bound organelles
- Prokaryotes have ribosomes and nucleiods but just floating around
- Eukaryotes have a nucleus
- Transcription and translation occur at the same place in prokaryotes
- Ribosomes are completely different
- Prokaryotes have circular chromosomes and eukaryotes are linear chromosomes

compare gram positive & gram negative

- They both have peptidoglycan but gram positive has more
- Outer membrane present in gram negative, absent in gram positive
- Positive is purple, negative is pink
- Gram negative outer membrane made of LPS
- Gram positives have teichoic acids uphold the glycan together
- Secretion systems 1-6 gram negative, 7 gram positive
- Gram positive is more sensitive because the peptidoglycan is exposed and doesn’t have outer membrane
- Similarities: flagellated, similar genetics

Glucose-6-phosphate goes into 2 metabolic pathways, what are they? General functions of the pathways? Common intermediates? Major products?

Pentose phosphate pathway
o General function: nucleotides, anabolic
- Glycolysis
o General function: catabolic , atp
- Common intermediates?
o G3p – glyceralderhydrolide 3 phosphate
o F6P- fructose 6 phosphate
- Major products?
o PPP- nucleotides
o Glycolysis- ATP

Process of chemotaxis detailing both cellular and local control regulation of it

Moving with the concentration gradient,
- Run, tumble, run
- Counterclockwise= run
- Clockwise= tumble
- Once sensor becomes demethylated you run again

How is glucose made? What is the pathway? Name 3 other pathways other than glycolysis that helps make this happen

- Calvin benson cycle
- Input: CO2
- 3 other cycles that use CO2: TCA cycle, transition step, pentose phosphate pathway
- Direct production of g3p
- Ribisco grabs co2 and shove, 3 carbon molecules

If you were to design a drug that interferes with prokaryotic protein synthesis, what would you target? Possible side effect?

Bacterial ribosomes because they are different from ours. Prokaryotes have a 70s and we have an 80s.
- Possible side effect? Disrupt gut biomes- nonpathogenic biomes, potential mitochondrial interference (antibiotic doesn’t get into mitochondria membrane—too much traveling)

The two strands of the DNA double helix are held together with what bonds?

hydrogen

The word virus actually means

poison

Tropism refers to the ability of a virion to

Infect a specific cell type`

Chloroplasts and mitochondria have

70s ribosome

For the TAC what is complementary RNA?

AUG

a silent mutation

Changes nucleotide sequence but not the amino acid codon

a missense mutation

Changes the amino acid codon but does not necessarily affect protein function

a nonsense mutation

Results in premature stop codon

which of the following is true for prokaryotic translation?

which of the following is true for prokaryotic translation?

phenotype refers to

Physical characteristics

genotype refers to

genetic signature

the first virus discovered was

tobacco mosaic

unlike cell based life, viruses laxk

shared gene homologues

this man discovered reverse transcriptase (the primary enzyme needed by HIV for its replication cycle), unlocking a new era in understanding viral infection

David baltimore

a lytic cycle

destroys host cell

add amino acid to what

TRNA

small, circular DNA molecules contain nonessential genes in bacteria are called?

plasmids

briefly describe two ways that viruses are phylogenetically classified

viroplasm is

A rearrangement of internal host membranes

an unmutated genotype is called:

Wild type

which of the following is never found in virions?

Small nucleotides

The major structural differences between DNA and RNA

RNA has extra oxygen

what is AMEs test?

Carcinogen screening : AMES test… looking for mutation that goes back to wild type, reversion
o Rat liver extract + salmonella (mutant require histidine)—dies if doesn’t have histidine
§ Expose it to mutant and put it on plates that do not have histidine – control
§ If it causes mutation then it grows
Why rat liver extract?
- Same reason you should not drink antifreeze….its metabolite, preserves , overwhelm enzymes by drinking alcohol
- The mutagen isn’t a mutagen on its own, possible that the enzymes in your liver can turn it into one, check to see if it is metabolites

How does CRISPR protect bacteria from phage infection? How might you take advantage of CRISPR to harm bacteria?

Many bacteria use a system known as CRISPR-Cas to defend themselves against infection by viruses called phages. This system protects the bacterial cell by taking a short length of DNA from the phage and inserting this 'spacer' into its own genome.
They could use CRISPR to edit the gene by changing the DNA from the harmful variant to a healthy variant. This could potentially prevent or cure a genetic disease.

describe 3 methods of horizontal gene transfer and explain why HGT mutation matter for human health

Transformation
Transformation is a form of genetic recombination in which a DNA fragment from a dead, degraded bacterium enters a competent recipient bacterium and is exchanged for a piece of DNA of the recipient. Transformation usually involves only homologous recombination, a recombination of homologous DNA regions having nearly the same nucleotide sequences. Typically this involves similar bacterial strains or strains of the same bacterial species.
Transduction
Transduction involves the transfer of a DNA fragment from one bacterium to another by a bacteriophage. There are two forms of transduction: generalized transduction and specialized transduction.
Conjugation.
Genetic recombination in which there is a transfer of DNA from a living donor bacterium to a living recipient bacterium by cell-to-cell contact. In Gram-negative bacteria it typically involves a conjugation or sex pilus.

when certain bacteria are placed into media with glucose and lactose they peripherally use glucose before ing lactose. Draw the expected growth curve, and explain the molecular mechanism that causes the curve. Also draw the expected curve if the bacteria had a mutation in EIIA where it could not phosphorylate EIIB

What essential element is particularly important for immune system?

iron

Which of the following is not a epithelial surface?

liver

Which of the following is a mechanical means of removing harmful microbes?

tears

Epithelial surfaces, mucous, microbes?

serve as physical barriers to infection

Macrophages and dendritic cells are

monocytes

neutrophils & basophils are

granulocytes

T cells and B cells are

lymphyocytes

all are

leukocytes

which antibodies primarily circulating

igG

which antibodies primary mucous surfaces

igA

Which of these cells does not directly kill pathogens or cells?

Cd4+Tcells

Cytotoxic CD8+T cells can

All the above– destroy foreign cells, destroy virus infected host cells, destroy cancerous host cells

CD4+T helper cells can

Any and all the above Promote B cell maturation, activate CD8+T cells, augment macrophage function

PAMPS are typically recognized by

TLRs and NLRs

primary immune organ

thymus

the APR is a function of which organ?

liver

MHC I vs II

MHC I - self antigen
MHC II- foreign antigen

Activate vs passive immunity vs artificial vs natural

Passive- you are protected by immunologic responses that aren’t yours
o Children born with mothers antibodies
o Natural: mother breastfeeding
§ igG and igA in breast milk
§ monocytes in breast milk—immune cells
o artificial: Ab therapy
§ plasma donation
o Artificial - antisera
§ Hyperimmune globulin
§ Plasma from high-expressors
o Immune globulin
§ Enriched from multiple sources
§ Measles
§ CVID
o Artificial – antitoxin
§ Plasma from animals

FUNCTION OF ADJUVANTS

Attract dendritic cells & activate them because vaccines are not capable of driving an inflammation without a adjuvant and attracts the immune cells

HOW DOES A SUPERANTIGEN WORK?

. Activate T cells (CD4) lots of antigen specific T cells, drive immune response & inflammation

What is NF-Kb? Would it make a logical target for interfering with immune activation?

It is a transcription factor. No, because if you shut off immune cells you shut off inflammation. It is nonspecific and you need a immune response, it shuts off everything leading to immunodeficiency and they die of opportunistic infections.

What are two strategies pathogens use to invade elements of the immune system?

Complement receptors have proteases that can chew up bound complements, antibodies, c receptors
b. Capsules—adhere to host cells, phagocytose

What is the concept of herd immunity?

Population as a whole are vaccinated so the one immunocompromised person is also protected until in contact with other people who are also unvaxxed

How is complement activated and how Is it function?

Classical, alternative, mannose lectin pathway
i. Classical start with c1, c2& c4 get cleaved
ii. Alternative c3 binds itself

Other than complement, what are the 5 others?

Neutralization, immobilization, agglutination, opsonization, ADCC

How are B cells activated? Describe consequence of producing IgE instead of IgA

Needs to see what it is specific for and bound to T Cell that recognize same antigen
b. Basophils & eosinophils, granulocytes, you get allergies

How do natural killer cells recognize their targets? How does this cause organ rejection?

Stress markers & antibodies they get target to
b. Inhibit by presence of MHC, NKC cannot do its job

3 separate ways infection can lead to autoimmunity and pathogens

Molecular mimicry
i. Very similar recognize another, and cause destruction, mistaken antigens
1. EBV & MS
b. Bystander activation
i. Immune response, self-reactive T cells which turn into Tregs, one function does something else
1. HPV
c. Epitope spreading
i. React to multiple things, inflammation, damage
1. Type 1 diabetes & beta cells attack insulin

Ignaz Semmelweis

- WASH YO HANDDSSSSS
- Alzheimer’s & nose picking? Introducing foreign bacteria
- Puerperal fever (S. Pyogenes) (delivered babies after messing with corpse – did not wash hands)
- Noticed differences in death rate
- Got fired & put in mental institute cz no one wanna wash their hands

John Snow

- London 1854
- Cholera from wastewater
- Geographically mapped cases of diarrhea
- [GHOST MAP}
o People on left side of street were getting sick while right was not. They were drinking water that has waste in it, so it was in the water pumps.
o Causes major dehydration through diarrhea.

epidemic

- One location or population
- Ex- ebola

pandemic

- Multiple continents, population
- Ex- covid

endemic

- Specific to a location
- Baseline rate of disease
- Ex- plague, EBV

reservoirs

- Places where pathogen hang out
- Ex- concerts, packed places, chickens, soil

transmission

- Vector- alive
- Fomites- nonliving
- Transmits diseases
- Fomites, people, animals, food, water, air
- Point of source
- Virulence—LPS, toxins, ability to bind, dose, incubation time

things that depend on you

- Immunity
o Herd
o Immunization
- Health
o Smoke, obese
- Age
o Very young or old
- Gender
o Males are at higher risk
o Stress levels, testosterones cause stress
- Culture
- Genetics
o MHC/HLA type