Nabi Handout 6 panopto

start codon (AUG) Amino acid

Methionine

AA's with sulfur

cystiene, methionine

does the STOP codon code for an amino acid?

no; it signals for release factors

silent mutation

mutation in a nucleotide that does not cause a change in the AA coded

valine is

hyrophobic

glutamate, aspartate are both

hydrophillic

aspartate and glutamate would probably be on the ____ surface of the cell since they are hyrophillic

outer

missense mutation

results in a different AA being added into the protein

nonsense mutation

results in a premature stop codon

an example of how powerful a point mutation can be is _____. _____ may be rendered useless by a point mutation that causes it to no longer recognize the the cell wall to be able to ____

vancomycin, inhibit the cell wall synthesis

capsular polysaccharides and efflux pumps aid in creating

antibiotic resistant bacteria

blocking of an efflux pump may

kill bacteria (gram -)

UV radiation can cause

adjacent thymine dimers

UV light (can/can not penetrate biofilms)

can not

photolyase enzyme

Absorbs light in visible range and uses this energy to cleave thymine dimer

Nucleotide Excision Repair (NER)

a DNA repair system in which several nucleotides in the damaged strand are removed from the DNA and the undamaged strand is used as a template to resynthesize a normal strand.

3' and 5' nucleases cleave these out!!

xeroderma pigmentosa

A disease that confers increased susceptibility to skin cancers of all types due to the lack of an endonuclease necessary for thymidine dimer repair.... people with this are very sensitive to light

UV light (did/did not) effect the proteins in milk, and it did kill the bacteria in it

did not

do humans have photolyase?

no

anti sigma factors...

block transcription by binding to sigma factors and preventing them from associating with RNA polymerase

the DNA polymerase needs _______ exonuclease activity for proofreading

3'--->5'

mutations can be

harmful, beneficial, and neutral

most bacteria have a ____ mutation rate than eukaryotes

higher... genome size negatively coorelates with mutation rate. (they replicate more often and have bad proofreading)

RNA virsuses usually

lack proofreading

base excision repair

DNA repair that first excises modified bases and then replaces the entire nucleotide. starts with glycosylase

base excision repair vs nucleotide excision repair

Base excision repair: corrects deamination aka converting C to U or A to hypoxanthine usually that happened by accident

Nucleotide excision repair: correcting pyrimidine dimers. Defect in this causes xeroderma pigmentosa.

the cell membrane of a thermophile will be more ____ and contain more _____. They need more stability

rigid, contain more saturated fats.

mesophile cell membranes are a

balanced ratio of saturated and unsaturated fatty acids

psychrophiles have a membrane composed of more ____, giving a more ____ cell membrane to adapt for the cold temperatures

unsaturated and polyunsaturated fatty acids, giving a more fluid cell membrane

Listeria monocytogenes

a mesophile that is a re

thermophiles are likely to have much less ____ residues in their cell wall and many more _____ and ___ residues to maximize rigidity

less glycine, more charged and hydrophobic residues. (lysine, glutamate, aspartate)

also have more non-covalent interactions like salt bridges

mesophiles have a ___ amino acid composition

standard... even mix

psychrophiles have a ______ membrane structure with more ____ residues and less ___ and ___ residues.

flexible,

more glycine resiudes

less charged and aromatic residues

Heat shock proteins (HSPs)

help thermophiles refold denatured proteins

cryoprotectants

produced by psychrophiles to prevent ice formation and maintain cellular processes

chaperone proteins

assist in folding other proteins

helicobacter pylori can sense ____ via its channel called ____

low pH, Ure I

Helicobacter pylori employs ___ to break urea down into _____ in order to raise the pH of the stomach linine

urease, ammonia

bacteria use the ____ to balance their cytoplasmic pH

PMF- proton motive force

amino acid decarboxylase systems

salmonella, listeria have this. they take the carboxylic acid groups off of the AA's and release them as CO2. forms amines in the process

arginine deiminase system

listeria has this. catabolizes arginine to ammonia which will become ammonium. raises pH

F1F2 ATPase pumps

expel protons from the cytoplasm, are coupled with ATP hydrolysis to increase interal pH of the cell.

upregulation of heat shock proteins

indirect strategy to survive in acidic environments. an increase in chaperone expression (ClpB, DnaK, GroEL) to refold and repair proteins

induction of cross-protective mechanisms

indirect pH defnese mechanism: an increase in stress response mechanisms that act against reactive oxygen species.... allows bacteria to build tolerance

modification of cell surface

indirect pH defense mechanism: production of a capsular polysaccharide, countering or slowing the influx of protons

OR: production of flagella

alteration of cellular metabolism

another indirect defense mechanism to acidic environments in which the bacteria downregulates its genes and metabolism (VBNC cells?)

acidithobacillus ferrooxidans

acidophillic bacteria that uses the pH as a "battery system". will oxidate iron, sulfur, and hydrogen.

how alkaliphiles survive?

specialized Na+/H+ antiporter systems to maintain neutral pH's. many alkaliphiles require sodium ions for growth.

the Sodium motive force may also be used to power Na+/H+ antiporters

Sodium carbonate NaCO3 is also used to maintain a high pH

_____ are used for sustained survival in osmotic stress

organic osmolytes

E.coli glycine betaine pathway

Choline ---> betaine aldehyde ---> glycine

accumulation of glycine betaine protects cell from osmotic stress

TrkG and TrkH transporters

TrkG does Na+ dependent K+ uptake (symporter)

TrkH does Na+ independent K+ uptake (uniporter)

H-NS. Histone-like Nucleoid Structuring Protein may repress expression of

TrkG

______ will transport K+ in the absence of osmotic pressure

TrkH