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H2 Biology > Genetics of Bacteria > Flashcards

Genetics of Bacteria Flashcards

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1
Q

what do all bacterial cells lack, given that they are prokaryotic?

A

a true nucleus and membrane-bound organelles

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2
Q

what are the features of the peptidoglycan that make up bacterial cell walls? (peptide and carbo)

A

“peptido”: short string of amino acids that cross-link adjacent polysaccharide strands, forming network w high tensile strength
“glycan”: linear polymer of alternating monosaccharide subunits, linked by beta (1,4) glycosidic bonds

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3
Q

describe the cell wall of gram-positive bacteria, and what polymer is commonly found on it?

A

thick, multi-layered
outside the cell membrane
covalently linked to teichoic acid

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4
Q

what is teichoic acid (found on cell wall of gram + bacteria)?

A

major cell surface antigens
polymer of substituted glycerol units linked by phosphodiester bonds

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5
Q

how many cell membranes do gram-negative bacteria have, and where is the peptidoglycan cell wall located?

A

one outer, one inner (cytoplasmic) membrane
peptidoglycan layer between two membranes, in the periplasmic space

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6
Q

what is the difference between gram-positive and gram-negative cell walls, and their susceptibility to physical damage?

A

gram-negative has thinner cell wall, more vulnerable

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7
Q

what is the distinguishing factor of the outer membrane of gram-negative cell wall?

A

presence of various embedded outer lipopolysaccharides

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8
Q

what are the characteristics of lipopolysaccharides on gram-negative bacteria’s outer membrane?

A

polysaccharide portion (O-polysaccharide) is antigenic, used to distinguish different bacteria
lipid portion (lipid A) is toxic to humans and animals: endotoxin bc it’s not secreted

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9
Q

describe the gram-staining procedure used to differentiate gram-positive and negative bacteria

A

crystal violet dye: taken up by all bacteria
iodine as a mordant (to make colour permanent)
alcohol added
counterstained with red dye safranin

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10
Q

what are the results of the gram-staining procedure for both types of bacteria?

A

gram-negative cells lose their colour and counterstained with safranin, gram-positive cells retain violet dye

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11
Q

why do gram-negative and -positive bacteria have different colours upon gram-staining?

A

gram-positive bacteria have dehydrated walls with closed pores, violet dye cannot escape
gram-negative bacteria lets alcohol readily penetrate lipid-rich, thin peptide layer does not prevent passage, dye easily removed

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12
Q

what does the endosymbiont theory state?

A

mitochondria and plasmids of eukaryotes originated from symbiosis between separate single-celled organisms

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13
Q

what is the argument of serial endosymbiosis?

A

early ancestor of eukaryotic cell engulfed an oxygen-using non-photosynthetic prokaryotic cell
engulfed cell became the endosymbiont of host cell
over time, merged into a single organism: eukaryotic cell with mitochondrion

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14
Q

what is the evidence available to support the endosymbiont theory? (organelles being mitochondria and chloroplasts)

A

inner membranes of organelles have enzymes and transport systems are similar to prokaryotes
organelles contain circular DNA (plasmids), not chromosomes
organelles replicate similarly to certain prokaryotes
ribosomes of organelles more similar to prokaryotic ribosomes than eukaryotic

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15
Q

what is the structure of a bacteria chromosome, and how is it compacted?

A

single, circular, double-stranded DNA, containing essential genes (non-essential are plasmids)
DNA associated with histone-like proteins that compact into looped domains, then supercoiling

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16
Q

how are genes grouped in bacteria?

A

grouped into operons, multiple genes under the control of the same promoter and regulatory elements
prokaryotic genes lack introns (no need RNA splicing)

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17
Q

what is the structure of and function of bacterial plasmids?

A

small, circular, double-stranded extrachromosomal DNA
beneficial (non-essential) genes that confer protective traits like antibiotic resistance, toxin synthesis, enzyme production
selective advantage

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18
Q

name the three roles of genetic material in bacteria

A

replication
gene transfer
gene expression

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19
Q

what is the process in which genetic material is transmitted from parent to offspring in bacteria, and define the process

A

binary fission (vertical gene transfer)
asexual reproduction in which two genetically identical daughter cells are produced from a single parent cell
- involves replication of bacterial chromosome

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20
Q

what is the downside of binary fission, and what other processes address it?

A

inability to cause genetic variation
transformation, conjugation, transduction can address that

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21
Q

describe the process of binary fission, in detail

A
  1. the bacterial chromosome is attached to the plasma membrane
  2. at the only origin of replication, double-stranded DNA chromosome separates, forming replication bubble
  3. semi-conservative DNA replication occurs, where each parental strand of DNA is used as a template for DNA replication
  4. replication bubble expands bidirectionally until two identical double-stranded circular DNA chromosome forms (each with its own site of attachment to the plasma membrane)
  5. cell elongates, membrane growth moves two chromosomes apart
  6. septal ring controls creation of septum, which invaginates (grows inwards) along with the cell membrane, cleaving daughter cells via cytokinesis
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22
Q

what are the three processes in which bacterial genetic material is exchanged, and what are the two cells required for these mechanisms?

A

transformation, transduction, conjugation
donor cell (provides DNA) and recipient cell (accepts DNA)

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23
Q

what are the effects of genetic recombination and homologous recombination?

A

genetic recombination generates genetic variation
homologous recombination involves in the integration of donor’s DNA into the recipient cell’s chromosome

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24
Q

briefly describe the process of transformation in bacteria

A

recipient cell takes up small fragments of naked DNA from surrounding environment

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25
Q

what are the two sources of DNA for transformation?

A

donor bacteria cell which lyses (ruptures) and releases DNA into environment, degraded by exonuclease enzymes, no histone proteins OR artificially constructed plasmids

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26
Q

only what type of bacterial cells can undergo transformation, and how is that determined?

A

competent cells
depends on presence of competence factors produced by bacterial cells, which are cell surface proteins that bind to DNA fragments and aid in their uptake

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27
Q

describe the process of transformation, in detail

A
  1. donor bacterial cell lyses and releases naked DNA fragments
  2. competent recipient cell takes up fragment via competence factor
  3. homologous recombination of donor DNA into recipient cell’s chromosome
  4. excision and degradation of host’s original DNA
  5. recombinant recipient cell created
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28
Q

what are the two ways to artificially induce transformation by increasing competency in bacteria?

A

CaCl buffer and heat shock
electroporation

utilisation of plasmid DNA (self-replicating and more stable), no need for homologous recombination, just uptake

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29
Q

briefly describe the process of transduction in bacteria, and name the two types of transduction

A

bacteriophages (agents of transfer) carry bacterial genes from first host cell (donor) to second host cell (recipient) due to errors in phage reproductive system

generalised and specialised

30
Q

how are defective phages used in generalised transduction created?

A
  1. virulent phage (eg. T4) injects its DNA into donor bacterial cell, degrading its chromosome (lytic cycle)
  2. phage hijacks donor’s DNA replication machinery to synthesis more phage DNA; gene expression machinery to synthesis more phage proteins
  3. maybe, small piece of donor’s degraded DNA accidentally packaged in new phage capsid during assembly stage of lytic cycle: defective phage
31
Q

describe the process of generalised transduction (aft defective phage production), in detail

A

donor cell lysed, new phages (including defective) released into the environment
defective phage infects recipient bacteria, injecting DNA fragment into it
homologous recombination: donor DNA incorporated into recipient cell’s genome, forming recombinant cell

32
Q

describe the process of specialised transduction, in detail

A
  • temperate phages (eg. lambda phage) integrates their DNA into donor cell at prophage insertion site (PIS)
  • upon induction, phage genome is excised. imprecise excision causes phage DNA to take with it a small region of bacterial DNA adjacent to PIS
  • hijacking donor cell’s replication and expression machinery, each phage now has part of donor’s DNA
  • donor lysed, releasing phages that infect recipient and inject donor DNA into it
  • donor DNA incorporated into recipient
33
Q

how is donor DNA incorporated into recipient genome to form a recombinant cell in specialised transduction?

A

prophage integration (if segment of phage DNA transferred contains genes required to enter lysogenic cycle)
OR
homologous recombination (if segment of phage DNA transferred does not contain genes required to enter lysogenic cycle)

34
Q

state the differences in type of phage, phage reproductive cycle, and type of donor DNA in generalised VS specialised transduction

A

generalised: virulent, lytic, any donor gene
specialised: temperate, lysogenic converting to lytic upon induction, only genes near prophage insertion site transferred due to imprecise excision

35
Q

briefly explain the process of conjugation in bacterial cells

A

direct contact between donor (F+) and recipient (F-) bacteria causes establishment of cytoplasmic bridge / sex pilus, both donor and recipient cells contain F factor at the end

36
Q

what are F+ and F- bacterial cells?

A

F+: extrachromosomal F factor (F plasmid)
F-: no F factor (will gain it after conjugation)

37
Q

describe the process of conjugation for bacterial cells, in detail

A

F+ donor cell uses sex pilus to attach to F- recipient cell, forming temporary cytoplasmic mating bridge
sugar-phosphate backbone of one strand of F plasmid is nicked by endonuclease, separating from its complementary strand
nicked single-stranded DNA moves to F- recipient cell through bridge
each parental strand becomes a template for DNA replication of a complementary daughter strand (semi-conservative replication)

38
Q

upon the completion of DNA replication in conjugation, what happens?

A

DNA ligase catalyses synthesis of phosphodiester bond to close gap in each F plasmid
cells move apart and sex pilus broke, forming 2 bacterial cells that are both F+

39
Q

what processes found in eukaryotes do not occur in prokaryotes due to simultaneous transcription and translation being possible?

A

post-transcriptional modifications like 5’methylguanosine cap, RNA splicing, 3’poly(A) tail

40
Q

what are the three main differences between prokaryotic and eukaryotic cells? (chromosome compaction, gene contents, membranes)

A

prokaryotic chromosomes less compact than eukaryotic ones
prokaryotic genes are grouped into operons, each controlled by one promoter; eukaryotic genes have one promoter per gene
prokaryotes do not have membrane bound organelles, but eukaryotes do

41
Q

what two regions does a prokaryotic gene’s promoter consist of?

A
  1. RNA polymerase recognition site (5’-TTGACA-3’)
  2. Pribnow box / RNA polymerase binding site (5’-TATAAT-3’)
    - non template strands
42
Q

what does a prokaryotic gene’s coding region consist of?

A

start codon 5’-AUG-3’, ends with stop codon (not interrupted by introns)

43
Q

what does a prokaryotic gene’s UTRs consist of?

A

5’ UTR: sequences between transcription start site to start codon, including sequence transcribed to form Shine-Dalgarno sequence required for ribosome binding during translation
3’ UTR: sequences aft stop codon

44
Q

what does a prokaryotic gene’s terminator gene consist of?

A

dislodges RNA polymerase from template DNA strand

45
Q

what are the four components of a prokaryotic operon

A
  1. promoter (RNA polymerase recognition site and Pribnow box / RNA polymerase binding site)
  2. coding region (no introns)
  3. 5’-UTR (gives Shine-Dalgarno for ribosome binding) and 3’ UTR (aft stop)
  4. terminator sequence (dislodge RNA polymerase)
46
Q

state the three stages of transcription in prokaryotes

A
  1. initiation
  2. elongation
  3. termination
47
Q

what occurs during initiation of transcription in prokaryotes?

A

sigma factor on RNA polymerase recognises and binds at -35 bp recognition sequence and -10 bp Pribnow box (AT rich) in promoter

RNA polymerase transiently unwinds DNA to form transcription bubble, one strand used as transcription template

48
Q

what occurs during elongation of transcription in prokaryotes?

A

RNA polymerase reads DNA template strand in 3’ to 5’ direction, ribonucleoside triphosphates added 5’ to 3’ by RNA polymerase, single-stranded mRNA trails out of transcription bubble and is reannealed

49
Q

what occurs during (each of the two types of) termination of transcription in prokaryotes?

A
  • intrinsic termination (rho-independent)
    (GC rich, palindromic) terminator sequence within RNA forms hairpin loop structure via complementary BP, so RNA polymerase dissociates
  • rho-dependent
    termination factor called rho factor that binds at rho recognition site on mRNA, moves towards RNA polymerase and destabilises mRNA-DNA hybrid, releasing newly synthesised mRNA
50
Q

what are the three stages of translation in prokaryotes, and what precedes these steps?

A

initiation, elongation, termination

tRNA activation by aminoacyl-tRNA synthase

51
Q

what occurs during initiation of translation in prokaryotes?

A

30S small ribosomal subunit recognises and binds to Shine-Dalgarno sequence in 5’ UTR of mRNA
ribosome is positioned so AUG is in P site
initiator tRNA (methionine) bonds at P site
large subunit binds to small
translation-initiation complex is formed

52
Q

what does it mean that prokaryotic mRNAs are polycistronic?

A

multiple Shine-Dalgarno sequences found along mRNA’s length, different segments are translated to give rise to diff proteins

53
Q

what occurs during elongation of translation in prokaryotes?

A

binding of aminoacyl-tRNA to A site, translocation, empty tRNA yeet from P site, next tRNA enters at A (similar to eukaryotes)

54
Q

what occurs during termination of translation in prokaryotes?

A

binding of release factors that enter the A site causes release of plp chain and dissociation of ribosomal subunits

55
Q

what are the two major modes of regulation in a prokaryotic cell?

A

transcriptional control: amt or presence of mRNA produced
post-translational control: influences activity of preexisting proteins, adding functional groups or cleavage

56
Q

what does a prokaryotic operon consist of?

A

promoter: for RNA polymerase to bind to and initiate transcription
operator: regulates rate of transcription of structural genes by interacting with specific repressor protein
structural genes: exons no introns

57
Q

what are inducible operons in prokaryotes?

A

normally not transcribed
turned on (induced) by substrate of enzyme which acts as inducer
enzymes only produced when substrate is present
(enzymes r prolly for catabolic pathways breaking stuff down)

eg. lac

58
Q

what are repressible operons in prokaryotes?

A

normally transcribed, turned off upon accumulation of product of metabolic pathway (functions as corepressor)
(enzymes r prolly for anabolic pathways synthesising stuff)

eg. trp operon

59
Q

compare the type of metabolic pathway of inducible and repressible operons

A

inducible: catabolic
repressible: anabolic

60
Q

compare the usual state of repressor protein of inducible and repressible operons

A

inducible: active conformation, binds to operator, prevents RNA polymerase from binding to promoter
repressible: inactive conformation, does not bind to operator, allows RNA polymerase to bind

61
Q

compare the conditions under which transcription occurs, and its significance for inducible and repressible operons

A

inducible: availability of substrate, enzymes only made when needed, conserve energy
repressible: availability of end product in sufficient quantity, resources not used to make stuff when there’s enough

62
Q

what do the trp and lac operons code for?

A

trp: enzymes involved in synthesis of tryptophan
lac: Z beta-galactosidase that breaks down lactose; Y galactoside permease, allows bacteria to intake lactose; A transacetylase, unclear lol

63
Q

how does the trp operon function in the absence of tryptophan?

A

trp is repressible
- trp repressor in inactive conf, cannot bind to operator, RNA polymerase can bind to promoter, operon on and genes expressed, tryptophan synthesised

64
Q

how does the trp operon function in the presence of tryptophan?

A

tryptophan corepressor, activating trp repressor, it binds to operator, RNA polymerase cannot bind, operon off and genes not expressed, tryptophan not synthesised

65
Q

what are the dual controls the lac operon is under?

A

lac repressor: negative control (presence / absence of lactose)
catabolite activator protein (CAP): positive control (presence / absence of glucose)

66
Q

how does the lac operon function in the absence of lactose?

A

lac repressor in active, binds to operator sequence of operon, RNA polymerase cannot bind, operon off no expression, hydrolysis of lactose does not occur

67
Q

how does the lac operon function in the presence of lactose?

A

allolactose (lactose isomer) formed in small amounts
inducer, binds to lac repressor and inactivates it
inactive repressor cannot bind to operon, RNA polymerase can bind to promoter, transcription occurs, operon on and hydrolysis of lactose occurs

68
Q

why do bacterial cells only require the enzymes for lactose breakdown in the absence of glucose and presence of lactose?

A

bacteria’s POV: glucose > lactose

69
Q

how does the lac operon function in presence of glucose?

A

cAMP signal molecule concentration falls
no binding between cAMP and catabolite activator protein
CAP is inactive, does not bind to CAP binding site
very slow transcription, even if lactose is presence

70
Q

describe the mode of action of antibiotics

A

H2 Biology (24 decks)

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