Microbiology 3050 Exam 4 Clemson University Krista Rudolph

Fermentation in chocolate

1. pulp fermented by yeast and lactic acid

2. high temperature and ethanol kill the beans

3. contributes to flavor and color

Fermentation in food

- used for food preservation

- may involve a succession of microbes

- a self-limiting process

- changes the flavor, texture, and odor of the food

Lactic Acid Bacteria (LAB)

gram-positives that tolerate acidic conditions, non-spore forming, aerotolerant with a strictly fermentative metabolism

used for fermented dariy products

Probiotics

live microorganisms which when administered in adequate amounts confer a health benefit to the host

Pros of probiotics

- improve lactose intolerance

- control diarrhea

- anticancer (colin)

- coloniation resistance *

- May lower blood presure and cholesterol

- improve oral health

- immunomodulation

cons of probiotics

-difficult to accurately assess effectiveness

-not regulated by FDA

•misleading advertising

•most yogurts have relatively low CFU counts

•voluntary "Live Active Culture" seal

-may cause

•mild side effects

•systemic infection in severely immunocompromised individuals

Prebiotics

substances (like food) that promote the growth of probiotics

immunomodulation

inducing an immune response

Production of alc beverages

produced by yest from the fermentation of sugar to ethyl alcohol and CO2

Wine production (enology)

Fermented grapes

1. Must preparation: grapes crushed to yiled must

2. fermentation: prim=3-5days at 20-28 C

secondary (malolactic) =1-3weeks at 20C

3. aging

4. Racking

Beer procuction

fermented malted (germinated grains)

Beer and Ale production

1. mash: mashing process sed to release fermentable sugars from graisn

2. wort: mash heated with hops in brew kettle (provide flavor and assist in clarification (antimicrobial)

3. fermentation

4. storage

must

crushed grapes that release sugar

mash

crushed grains that release sugar

wort

clear liquid containing fermentable sugars

distilled spirits

Whiskey and bvourbon begun with sour mash (mash inoculated with homolactc bacteria)

- following ferm, distilled to concentrate alcohol

- fresh distillate is colorless, color comes from aging in barrels

Bottom yeast used for production of

Lager beers

Top yeast used for production of

Ale

virus structure

10-2300 nm diameter

- nucleic acid surrounded by a capsid (naked)

- nucleocapsid surrounded by envelope and glycoprotien

Nucelocapsid

capsid + nucleic acid

Virus symetry

Helicle (rod)

Icosahedral (cube looking)

complex/binal

positive sense ssRNA

genome and mRNA are same sequence

RNA Genome (-) -> MRNA (+) -> Protein

negative sense ssRNA

genome and mRNA are compliments

1. RNA genome (+) used as MRNA (+)

2. RNA genome (+) -> DNA (-) -> mRNA (+) -> Protein

viral envelopes

outer, flexible, membranous layer

lipids and carbohydrates of the envelope are host derived

Protein spikes protect envelope

- viral host attachment

- enzymatoc activity

- role in nucleic acid replication

- identification of virus

Viral replication process

1. attachment

2. entry

3. uncoating of genome

4. synthesis

5. assembly

6. release

Latent period

time before virus is released

eclipse period

enzymes, nucleic acid, and protein coats form

Maturation period

structural formation of virus

bacteriohages

viruses that infect bacteria

- most contain dsDNA

- most are naked

virulent (lytic) phage

- begins multiplying immediately after entry

-lyses bacterial host cell

Ex. T4 (only lytic) (gram -)

Temperate (Lysogenic) phage

reproduce as virulent phages (lytic) or remain within host cell without destroying it

ex. Lambda

Lysogeny

uses integrase enzyme to integreate into host chromosome

- always integreates between galactose and biotin operons (attachemnt spot for Lambda)

- phase may switch from lysogenic to lytic cycle upon INDUCTION

prophage

integrated bacteriophage genome

integrase

enzymes that integrate viral genome to bacteria

Attachment site for viral integration

between galactose and biotin operons

Lysogenic conversion

change in host phenotype induced by lysogeny

Lytic cycle

triggered by drop in levels of lambda repressor

excisionase

"SOS response enzymes", binds to integrate and enables it to reverse integration process

Animal Viruses

Use endocytosis, fusion with the host cell membrane or inject to enter cell

- many replicate in the nucleus of the animal cell

- many are enveloped

effects of animal viruses

Virulent: death of the cell and release of the viruses

Latent: Virus is present but not replicating

Persistent: slow release of virus without cell death

Cancer: tumor cell division

Latent viral infection ex

HSV: in children the cold sores as adult

Varcilla zoster: chicken pox then shingles

Persistant viral infection ex

Hepititis B

HIV

Oncoviruses

viruses that cause cancer

Retrovirus

enveloped RNA virus that replicate through a DNA intermediate

- uses reverse transcriptase

- RNA to DNA

Provirus stage

integrated HIV DNA onto host chromosome

SARS-Cov-2

Enveloped with club shaped spikes

- positive sense ssRNA genome

SARS-Cov-2 Infection

Spike glycoprotein attaches to host receptor

- enters host cell via fusion with host cell membrane or endocytosis

SARS-Cov-2 transmission

jumped from bats to civets to humans (zoonotic)

- person to person via direct contact or droplets

- asymptomatic carriers

- incubation period: 5.2 days

- Common symptoms: fever, cough, fatigue

Nucleoid

Location of chromosome and associated proteins

- not usually membrane bound

- ussually one circular, double strandded DNA molecule

Plasmids

extra-chromosomal DNA

- exist and replicate independently pf chromosome

- contain few genes (non-essential)

forward mutation

wild type to mutant form

- ex. prototroph (nonnutritional mutant) -> auxotroph (nutritional mutant)

reverse mutation

mutant form to wild type

same-site revertant

mutation reverted at same exact base pair site

Second-site revertant

suppressor mutations, original mutation turned off

Screening

detecting mutations via observation

Selection

Confer some type of advantage to the organisms that possess them (ex. drug resistance)

Selectable mutations

placing organisms under conditions where growth of a particular genotype will be favored

Transformation

uptake of naked DNA by a competent cell followed by integration of the DNA into the recipient cell's genome

Transduction

virus injection, chromosome disruption, host cell lyses releasing viruses containing its own host DNA

generalized transduction: DNA from any portion of host genome is packaged (lytic pathway)

specialized transduction: specific region of DNA packaged (lysogeny)

- occures when prophage is incorrectly exercised

Conjugation

plasmid transfer or chromosome transfer

4 fates of donor DNA during HGT

1. integration of donor DNA -> population of stable recombinants

2. Donor DNA selt replicates (plasmid) -> population of stable recombinants

3. Donar DNA cannot replicate -> No stable recombinats

4. Host resitriction (cuts up foreign DNA) -> No stable recombinants

homologous recombination

a reciprocal exchange between a pair of DNA molecules with same/similar nucleotide sequence

- cross over

40 base pairs or less = low level recombination

100 base pairs or more = high level recombination

Homologous recombination process

1. DNA is nicked

2. SSB and RecA form protein complex

3. crossover(strand inversion)

RecA

protein that is required for homologous recombination

F+/-

sex fertility gene

tra

conjugative "transfer" gene

Ori

origin of replication

tnp

transposase gene

PCR

polymerase chain reaction

- synthesises large quantities of DNA fragment

PCR requirements

1. target DNA

2. primers

3. DNA polymerase (taq)

4. dNTP's

PCR steps

1. Denaturation

2. Annealing

3. Extension

molecular cloning

isolation and incorporation of a piece of DNA into a vector so it can be replicated and manipulated

molecular cloning steps

1. isolate DNA

2. insert DNA to vector

3. Introduce cloned DNA to host

characteristics of plasmids that make them useful cloning vectors.

easy to purify

small size

independent origin of replication (ori)

multiple copy number

presense of selectable markers

DNA ligase

binds DNA to vector

microbiota

- bacteria regularly found at anatomical site

- associated with healthy body tissue

- found on surfaces of body and mucous membranes

- relationship begins at birth

Bacteria on skin

propiondacterium acnes

Bacteria in mouth

Streptococcus spp.

Bacteria in stomach

helicobacter pylori (stomach ulcers)

Bacteria in small intestine

Enterococcus faecalis, lactobacilli

increasing number of bact as move down

bacteria in large intestine

bactericides and clostridium

largest microbial population

makeup 1/3 weight of fecal matter

bacteria in upper respiratory tract

staphylococci and streptococci

Bacteria in lower respiratory tract

no normal microbiota

Bacteria in Urogenital Tract

E. coli (UTI) and lactobacillus acidophilus (Vagina, maintains acidic conditions)

Relationship between noraml microbiota and host

- colonization resistance

- produce vitamins, amino acids, organic acids

- developement of immune system

Infection

situation in which a microorganism is established and growing in a host, whether or not the host is harmed

Disease

damage or injury to the host that impairs host function

Incubation period

time between pathogen entry and the development of signs and symptoms - not contagious

Prodromal period

onset of signs and symptoms that are not yet specificities enough to make a diagnosis - contagious

Illness period

the disease is most severe and displays characteristic signs and symptoms - immune response triggered

Convalescent period

signs and symptoms begin to disappear

Innate immune response

- Phagocytes are primary effector cells

- acts as 1st line of defense

- bodys ability to recognize and destroy pathogens or their products

- lacks immune memory

includes: physical barriers, chemical meidators, phagocytes (cells that ingest, kill pathogens)

Phagocytes

- nonspecific reponse

- results in inflammation

- Some act as antigen preseting cells (APC)

Adaptive immune response

- Lymphocytes are primary effector cells

- 2nd line of defense

- reconize antigens from pathogens

- have memory

B-cells: attack invaders outside cell

T-cells: attack invaders inside cell

Antibodies: produces by activated plasma B cells

Adaptive specific immunity

Cells mediated

- T Cells

- mobile

- diff into helper and cytotoxic cells

Antibody mediated

- B Cells

- not very mobile

- mature in bone marrow

- require TH helper

- diff into plasma cells (produce antibodies) and memory B cells

Natural Active immunity

infection, developing own immune response

Natural passive immunity

maternal antibodies (from mom)

Artifical active immunity

vaccination

Artifical passive immunity

immune globulin therapy