MIMM211 real shit

what are the features of the bacterial envelope? how is it different for gram negative, gram positive and mycoplasma?

• gram negative → cytoplasmic membrane, cell wall (thin), outer membrane

• gram positive → cytoplasmic membrane, cell wall (thick)

• mycoplasma → cytoplasmic membrane

what does the periplasmic space include? for gram negative? gram positive?

• gram negative → space between outer membrane and cytoplasmic membrane (includes cell wall)

• gram positive → space between cytoplasmic membrane and cell wall

• enzyme rich

what are the functions of the cytoplasmic membrane?

• contain cytoplasm

• selective transport

what is the cytoplasmic membrane composed of? what model describes its structure?

• phospholipid bilayer

• ~50% protein

• fluid mosaic model → proteins suspended in thin layer of oil

what are phospholipids composed of?

• polar head → phosphate (-), glycerol, R group

• non-polar fatty acid tails

what types of proteins are found in the cytoplasmic membrane?

• transmembrane → transporters

• peripheral → on the surface

what is the function of the cell wall?

• cell structure and rigidity

• prevents swelling and bursting from osmotic pressure

what is the cell wall made of?

peptidoglycan

• glycans → long polysaccharides (alternating NAG/NAM)

• peptides → cross linking NAM units of glycans

how does the peptide cross linking of peptidoglycans differ between gram negatives and positives?

• gram negative → direct bonding of peptides

• gram positive → glycine peptide interbridge between peptide chains

how does penicillin function?

prevents cell wall synthesis

what do gram-positive cells contain in their cell wall to solidify its structure?

• teichoic acid

how is the cell wall anchored in gram-negative cells? what about gram-positives?

• gram negative → lipoproteins → connect cell wall to outer membrane

• gram positive → lipoteichoic acid → connect cell wall too cytoplasmic membrane

what are the functions of the outer membrane?

• protection

• selective transport

what is the outer membrane composed of?

• inner → phospholipids

• outer → lipopolysaccharides (LPS)

what is the structure of LPS?

• O side chain

• core polysaccharide

• fatty acids

what are some structures that occur outside of the cell envelope?

• capsule

• slime layer

• s-layer

what is the main function of structures outside of the cell envelope?

protection

• from phagocytes and protozoa

• environmental changes

• bacteriophage

what are capsules made of? what is its structure?

• polysaccharides

• thick/well organized → visible by microscopy

what are slime layers made of? what is its structure?

• polysaccharides, glycoproteins, glycolipids

• thin/less organized → not easily visible by microscopy

what are s layers made of? what is its structure?

• proteins and glycoproteins

• highly organized → visible by microscopy

what are some surface appendages of bacteria?

• flagella

• pili

what is the function of flagella? what are they made of?

• movement

• protein → flagellin

what is the function of pili?

• adhesion

• sex pili for mating

what are the possible arrangements for flagella?

• monotrichous→ 1

• amphitrichous → 1 at each pole

• lophotrichous → 2 or more at one/both poles

• petrichous→ all over

what happens if flagella rotate clockwise vs counterclockwise?

• counterclockwise→ forward

• clockwise → tumble

what are the different types of bacterial movement?

• chemotaxis

• aerotaxis

• phototaxis

• magnetotaxis

what are some components of the cytoplasm?

• nucleoid region

• ribosomes

• inclusion bodies

• cytoskeleton

what are some inclusion bodies and their functions?

• storage granules → nutrient reserves

• gas vacuoles → helps bacteria float

• magnetosomes → magnetotaxis

what is the most resistant bacterial structure?

endospores

• can survive millions of years in harsh conditions

what is the process of sporulation?

• cell divide into unequal parts

• large part engulfs small part (forespore)

• forespore matures into an endospore

what happens to a forespore as it becomes an endospore?

• gains a thick wall

• dehydrates

• vegatative cell is lysed

what are the components of an endospores wall?

• inner cortex → peptidoglycan

• spore coat → keratin like proteins

• exosporium → proteins, polysaccharides, lipids

what is the name of the process by which endospores become vegetative cells?

germination

what is the process of germination?

• permeability of the wall changes and water enters

• endospore swells and coat ruptures

• germ tube grows out

what are the types of cell division?

• binary fission

• budding

• others: fragmentation, exospore formation

what are the types of exponential population growth?

• random timing/asynchronous→ smooth growth plot

• synchronous → step wise exponential growth plot

what is generation time?

the time for cells to grow and divide

what varies generation time?

• nutrients → creates competition

• toxic metabolic compounds

• all cells in a colony have equal generation time because of equal conditions

what are the phases of cell growth?

• lag phase

• exponential phase

• stationary phase

• death phase

what can lengthen the lag phase?

• inoculum from an old culture

• from nutrient rich to poor medium

• from chemically different medium

• from refrigerated cells

• from cold medium

what conditions are used in a chemostat?

• all nutrients are given at the same rate

• one nutrient limits growth

• growing culture is drained at the same rate

what is the benefit of a chemostat?

• growth can be kept at a known rate

• the natural environment can be replicated

why can bacteria grow at extremely acidic conditions but not basic?

no proton gradient for ATP production

how is oxygen toxic to some species?

• oxygen → superoxide radicals

• superoxide radicals → hydrogen peroxide

• hydrogen peroxide → toxic hydroxyl radicals

what enzymes prevent oxygen toxicity?

• superoxide dosmutase removes superoxide radicals

• catalase and peroxidase remove hydrogen peroxide

what are the contents of an anaerobic jar?

• gas generation envelope creates H2O and CO2

• palladium pellets convert O2 and H2 to water

• O2 indicator

• sealed

what are the growth phases at each point of a petri dish?

• center → stationary/death

• edges → exponential phase

• surface → aerobic

• under the surface → anaerobic

how is cell density measured?

detecting light shined through a culture

how is cell count determined?

serial dilute a sample then count the colonies grown

what is the central dogma of biology?

• DNA → RNA: transcription

• RNA → protein: translation

what is the structure of nucleotides?

• pentose sugar (ribose or deoxyribose)

• phosphate

• nitrogenous base

how are nucleic acids formed?

nucleotides bound at phosphate groups and sugars create a polymer

what is the difference between DNA organization in prokaryotes and eukaryotes?

eukaryotes

• nucleus

• linear chromosomes

• histones form chromatin

prokaryotes

• one circular chromosome

• small basic proteins

• plasmids

what are nucleosomes?

DNA bound to histone H1 proteins resembling beads on a string

what is the process of DNA replication?

helicase unwind the helix and DNA polymerase III uses a strand as a template

what does the semi conservative model of DNA replication mean?

newly synthesized strands have 1 new and 1 parent strand

what does DNA polymerase require to work?

• 5’-3’ direction

• use of dNTPs

how do prokaryotes replicate DNA?

where does DNA replication begin in eukaryotes?

origin of replication

how does DNA unwinding start?

DnaA helicase binds to ORI

DnaB replaces DnaA

what is the purpose of topoisomerases?

release tension ahead of the replication fork

what is the purpose of SSBs?

keep the two DNA strands separate during replication

what is the process of lagging strand DNA synthesis?

• primase synthesizes short RNA primers

• DNA pol III synthesize DNA until the next primer

• DNA pol I replaces RNA and fragments are ligated with ligase

what is a gene?

a nucleotide sequence coding for a mRNA, tRNA or rRNA

what are the regions of a gene?

• promoter

• leader

• coding

• trailer

how many codons are there? how many amino acids?

64 codons for 20 amino acids

which amino acids correspond to only one codon?

trp and met

what is the purpose of transcription?

DNA → RNA

what are the types of RNA?

• mRNA

• tRNA

• rRNA

describe the process of RNA synthesis

• RNA polymerase creates a replication bubble in DNA

• starts at the gene promoter, ends at terminator

• RNA synthesized 5’-3’

describe the structure of RNA

• single strand

• makes base pairings with itself to create loops and stems → clover shape

what are the types of transcription terminators in bacteria?

• Rho independent → hairpin structure in RNA strand followed by 6 U sequence detached RNA strand

• Rho dependent → No Us, sometimes no hairpin → required Rho enzyme to detach

what are the differences between prokaryotic and eukaryotic mRNA?

• eukaryotes: correspond to 1 gene, 5’ cap and poly(a) tail, many introns, transcription in nucleus + translation in cytoplasm

• prokaryotes: corresponds to an operon containing multiple genes, no introns or end modifications, transcription and translation are coupled

describe the process of translation

• occurs in ribosomes

• tRNA anticodon binds to mRNA codon

• amino acid attached to 3’ end of tRNA added to the growing chain

what are the steps of translation?

• initiation

• elongation

• termination

what kind of ribosome is in E. coli? what are its subunits?

70S

• 30S → 16S rRNA

• 50S → 5S and 2 S rRNA

• proteins

where does initiation of translation begin?

shine-dalgarno sequence

what is the process of elongation in translation?

• new tRNAs bind to mRNA at ribosome A site

• growing peptide at P site binds to the amino acid at A site by transpeptidation

• P site tRNA detaches

what are the types of regulation of mRNA synthesis?

• negative control → repressor protein

• positive control → activator protein

• attenuation

what are the types of negative control mRNA gene regulation?

• induction: gene turned on when the substrate is present

• repression: gene turned off when product accumulated

what is the process of induction gene regulation?

• active repressor binds to operator → blocks transcription

• inactivated by inducer → detaches

what is the process of repression gene regulation?

• the gene product → corepressor

• inactive repressor binds when corepressor present

what is an example of positive control gene regulation?

lac operon

• low glucose → high cAMP

• CAP is activated by cAMP

• CAP binds to the promoter to encourage transcription

describe gene regulation attenuation

fine tuning of the rate of gene expression

• after initiation → attenuator sequence

• when less needed the mRNA at this sequence will form a terminator sequence

• when more is needed it will not and transcription continues

what are the functional classifications of mutations?

• morphological

• lethal

• biochemical

• resistant

what are causes of mutations?

• spontaneous→ errors during DNA replication

• mutagen induced → physical (radiation) or chemical

what are point mutations? what types exist?

errors in 1 base pair

• silent → no codon change

• missense → codon changed

• nonsense → creates a stop codon

• frameshift → addition or deletion of a base pair

what are forward and reverse mutations?

• forward → from wild type

• reverse → back to wild type

what are suppressor mutations?

a mutation that suppresses the effects of another

• intragenic → within the same gene

• extragenic → in a different gene

what is a thymine dimer?

cross linking of adjacent thymine units

what is special about 5-bromouracil?

acts as a uracil unit that can bind to A and G

• A → keto form

• G → enol form

what are the main types of DNA repair?

• DNA polymerase proofreading

• mismatch repair

• nucleotide excision repair

• base excision repair

what are secondary DNA repair mechanisms?

• direct removal of lesions (not during replication)

• recombination for double strand breaks and multiple legions

what are the different types of bacterial oxygen tolerance? what enzyme presence corresponds to each?

• SOD and catalase → obligate aerobes and facultative anaerobes (grows faster with less oxygen)

• SOD with no catalase → aerotolerant anaerobe (prefers anaerobic but grows regardless)

• neither SOD or catalase → strict anaerobe

• SOD with low catalase → microaerophile

describe griffith’s transformation experiment

S strain is virulent, R strain is not

• heat killed S does not infect mice

• live R with killed S does → S dna is transforming R dna to make it virulent

what contribution did Avery et al make to griffiths transformation experiment?

proved that DNA was responsible for the transformation of the R strain

what are the classifications of ideal thermal conditions for bacterial growth? rank them increasingly by temperature

• pschrophiles

• psychrotrophs

• mesophiles

• thermophiles

• hyperthermophiles

what are the functions of capsules, slime layers and S-layers?

• protects from phagocytes, bacteriophages and environmental changes

• food reservoir

• waste disposal

• maintain shape and rigidity

label each feature of bacterial morphology

what are the parts of a bacterial gene? which parts are transcribed? which are translated?

• promoter, anti leader, coding region, anti trailer, terminator

• transcribed into mRNA with leader, coding region, trailer

• coding region is translated