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bacteria Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

state the cellular structures in bacteria.

A
  1. cell wall
  2. cell surface membrane
  3. 70s ribosomes
  4. pill
  5. flagellum
  6. capsule
  7. chromosome
  8. plasmid
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2
Q

describe the structure of the cell wall.

A

peptidoglycan, which is made of a network of modified-sugar polymers cross-linked with short polypeptides,
causing it to be hard and rigid

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3
Q

state 3 functions of the bacterial cell wall.

A
  1. give cell shape and structural integrity
  2. prevent osmotic rupture
  3. serve as anchorage point for flagellum
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4
Q

describe the structure of the cell surface membrane.

A

phospholipid bilayer

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5
Q

state 3 functions of the cell surface membrane.

A
  1. separate the cell contents from the external environment
  2. control the movement of substance in and out of the cell
  3. form specific infolding that carry out specialised functions (eg. ATP production, photosynthesis)
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6
Q

describe the structure of 70s ribosomes

A

made of 30s and 50s ribosomes

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7
Q

state the function of the 70s ribosomes

A

site of polypeptide synthesis (translation)

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8
Q

describe the structure of pili

A

made of protein
hair-like appendages

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9
Q

state the function of pili.

A

enable bacteria to adhere to
1. their substrates or
2. to each other (eg. during conjugation)

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10
Q

describe the structure of flagellum.

A

made of protein
hollow cylinder that is rigid and waveshaped
rotates at the base via a corkscrew motion
one or many present

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11
Q

state the function for the flagellum.

A

motility

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12
Q

describe the structure of the capsule.

A

made of polysaccharide, protein, or protein-carbohydrate complex
(like a shell around the bacteria)

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13
Q

state 2 functions of the capsule.

A
  1. enable the bacteria to adhere to their substrates or to each other to form a colony
  2. offer protection against dehydration and attack host immunity system
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14
Q

describe the structure of the chromosome.

A

single,
circular,
double-stranded DNA
associated with only a small amount of DNA-binding non-histone proteins
folds into a supercoil

small genome
most are coding sequences
no introns
few repetitive DNA sequences
compact genetic organisation with little intergenic spaces (non-coding DNA)

located in the nucleoid region
undergoes semi-conservative DNA replication during binary fission

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15
Q

state the function of a chromosome.

A

contain large number of essential genes which
code for the synthesis of proteins and enzymes
required for cell metabolism

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16
Q

describe the structure of the plasmid.

A

small, circular, double-stranded DNA
located in the cytoplasm
extra-chromosomal DNA
replicate independently of the bacterial chromosome

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17
Q

state 2 functions of the plasmid.

A
  1. contain fewer genes
  2. contain non-essential genes
    genes code for synthesis of proteins and enzymes
    which confer for evolutionary advantage (eg. resistance to antibiotics)
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18
Q

state the 2 main processes in binary fission.

A
  1. bidirectional semi-conservative DNA replication
  2. division of parental cell to daughter cell (asexual reproduction)
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19
Q

describe the process of binary fission.

A
  1. origin of replication attaches to the cell surface membrane
  2. DNA starts to replicate via bidirectional semi-conservative DNA replication
    - double-stranded DNA separates at the ori, producing 2 copies of the origin
    - each separated DNA strand acts as a template for replication
    - at each replication fork, the leading strand is made continuously towards the fork and the lagging strand is made discontinuously away from the fork via the formation of Okazaki fragments
    - enzymes cut, twirl, reseal the double helix to prevent the DNA from tangling
  3. the newly synthesised DNA ori moves and attaches to the plasma membrane at the other pole of the cell
    - 2 bacteria chromosomes ori end up at opposite poles of the cell
    - bacterial cell elongates at the same time
  4. cell surface membrane invaginates into half & new cell wall synthesised = 2 genetically identical daughter cells
    - DNA replication is complete
    - cell is twice the original size
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20
Q

state 2 sources of genetic variation in bacteria.

A
  1. spontaneous mutation
  2. horizontal gene transfer (transformation, transduction, conjugation) - unidirectional transfer of DNA
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21
Q

state the 2 potential benefits of horizontal gene transfer for recipient bacteria.

A
  1. formation of new bacterial strains
    which may produce proteins and enzymes involved in antibiotics resistance/
    result in recipient bacteria able to use a new metabolite for survival
  2. increase in virulence
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22
Q

describe what transformation is.

A

mechanism of gene transfer in which foreign naked DNA is taken up by a competent recipient bacteria through its cell wall and cell surface membrane from external environment
- bacteria that have been killed release their naked DNA into the extracellular environment

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23
Q

explain the transformation stage of horizontal gene transfer.

A
  1. double-stranded foreign naked DNA binds to cell-surface proteins/ DNA binding proteins found on the competent recipient bacteria
  2. one of the 2 strands is degraded as it passes into the cells by a nuclease
  3. the single strand aligns with the homologous segment of the DNA (high degree of similarity in nucleotide sequence) on the bacterial chromosome
    - undergoes homologous recombination an exchange of genetic material between 2 similar DNA sequences
    - foreign DNA may also be inserted into the chromosomes by specific enzymes
  4. recipient cell is now called recombinant/ transformed cell as it contains DNA from 2 different cells
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24
Q

state the 2 factors affecting transformation.

A
  1. DNA size
  2. competence of recipient cell
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25
Q

explain how DNA size affects transformation.

A

double-stranded DNA is sensitive to nucleases in the environment and so success of transformation is limited to DNA size
transformation efficiency decreases with increasing DNA size

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26
Q

explain how the competence of recipient cell affects transformation.

A

naturally competent bacteria cells express
1. competence-associated genes that encodes for DNA uptake apparatus
- not expressed continuously
- switched on during certain phase of growth cycle or by other factors (eg. high cell density, antibiotic stress, DNA damage)
2. proteins that protect naked DNA for exonucleases in cytoplasm can undergo transformation

other bacteria that are not able to take up DNA naturally can be artificially permeated in vitro by treatment with chemicals (eg. Ca2+ ions)

to make the bacterial cell membrane permeable for DNA uptake, the cells are normally treated with a brief period of heat or electricity.

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27
Q

describe what is transduction.

A

mechanism of gene transfer between bacteria in which fragments of donor DNA are introduced into recipient bacteria with help of bacteriophage
this occurs due to errors that occur during the life cycle of the bacteriophage, where bacteria DNA are accidentally packaged into phage capsid.
the resultant phage infects other bacterial cells and the bacterial DNA of the host bacteria is then transferred to recipient cells
the transduced donor DNA may be incorporated into the recipient bacterial chromosome by genetic recombination

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28
Q

state the 2 types of transduction and the phages that meditated them.

A
  1. generalised transduction - mediated by lytic phage
  2. specialised transduction - mediated by lysogenic phage
29
Q

describe the process of generalised transduction.

A

in generalised transduction, donor bacterial genes are randomly transferred to a recipient bacterial cell by lytic bacteriophage during the lytic cycle

  1. adsorption and penetration
    - lytic phage recognises and binds to specific receptors on the bacterial cell wall and injects viral DNA into the bacterial cell
    - lytic phage breaks down the donor DNA into smaller pieces
  2. replication and maturation
    - accidental random packaging of donor bacterial genes, together with viral DNA into capsid of newly assembled phages
  3. release
    - host cell lysed, releasing transduced phages along with other phages
  4. reinfection
    - transducing phages containing bacterial donor DNA fragments recognising and binding to another bacteria and injecting donor DNA into a new host
    - donor DNA is then incorporated into bacterium DNA by homologous recombination into recipient DNA of new host
30
Q

describe the process of specialised transduction.

A

in specialised transduction, specific donor bacterial genes adjacent to the prophage site are transferred to a recipient bacterial cell with lysogenic bacteriophage during the lysogenic cycle

  1. adsorption & penetration
    - lysogenic phage recognises and binds to specific receptors on the bacteria cell wall and injects viral DNA into bacterial cell
  2. lysogenic cycle
    - viral DNA integrates into host bacterial chromosome at insertion sites to form a prophage
  3. replication and maturation
    - under stress, prophage is excised from host chromosome
    - donor bacterial genes adjacent to either side of prophage insertion sites may be excised together with prophage due error
    - during viral assembly, phage DNA with bacterial DNA replicated and packaged into phage capsids
  4. release
    - host cell is lysed, releasing transducing phage progenies
  5. reinfection
    - newly released phages containing bacterial donor genes along with phage genomes recognises and binds to specific receptor on another bacterium, and inject foreign DNA into new host
    - donor DNA incorporated into bacterium DNA via genetic recombination in 2 ways
  6. site-specific integration: whole prophage (viral and adjacent bacterial DNA) inserted into recipient cell chromosome
  7. homologous recombination: between similar sequences of bacterial DNA in donor and recipient chromosome
31
Q

explain what is the significance of transduction.

A

allow lysogenic conversion to occur (lysogenic phage induce change in phenotype of infected bacteria, due to genes carried on lysogenic phage that may enhance the virulence of bacterial host)
bacteria which was previously harmless becomes virulent strain, providing source of virulent strains

32
Q

describe what conjugation is.

A

mechanism of gene transfer between bacteria that involves physical contact between the 2 bacterial cells
physical contact achieved by formation of cytoplasmic channel (sex pilus) through the transfer of DNA from donor to recipient cell

33
Q

describe what the donor cell is in conjugation.

A

donor cell is F+ cell, containing specific plasmid (F plasmid), carrying F factor
F factor contains genes that code for proteins involved in
1. replication of plasmid
2. formation of sex pilus that extends to recipient cell, facilitating plasmid transfer
F factor may also carry other genes that confer growth advantage for bacterium

34
Q

describe what a recipient cell is in conjugation.

A

recipient cell is F- cell which lacks the F factor
after conjugation is completed, the F- has a copy of the F plasmid and converted to a F+ cell

35
Q

describe the process of conjugation.

A
  1. F+ cell initiates conjugation through the formation of sex pilus which extends towards the F- cell
  2. sex pilus recognises and binds to the specific receptor site on the cell wall of F- cell and provides physical contact between the cells.
    - retracts pulling the donor and recipient cells close together
    - a temporary conjugation tube is formed between 2 cells
  3. one strand of F plasmid is cut by endonuclease at ori
    - move into recipient cell via conjugation tube
  4. each original strand in donor and recipient cell used as template to synthesise a complementary strand, forming double-stranded F plasmid in both cells by rolling circle mechanism
  5. sex pilus is then broken and plasmid in F- cell circulises with DNA ligaments, producing new F plasmid in F- cells
    - both cells now contain F plasmid and are F+ cell
36
Q

explain the significance of conjugation.

A

allow for the transfer of F factor and other genes on the F plasmid from donor to recipient cells to occur
F factor may exist as segment of bacterial chromosome, allowing transfer for whole chromosome into recipient cell

37
Q

state what are operons.

A

operons are clusters of structural genes found in the main bacterial chromosome that are involved in a single biochemical pathway, where their gene products perform related functions

38
Q

state the 4 gene sequences included in the operon.

A

POST
1. promoter
2. operator
3. structural genes
4. terminal sequence

39
Q

state how structural genes are transcribed and its advantage.

A

structural genes are under the control of the same promoter and operator, so the gene expression turned on and off as a single transcriptional unit to form polycistronic mRNA (mRNA that code for more than 1 protein) - punctuated with start and stop codons for translation of individual proteins

grouping functionally-related genes under common transcriptional control allows bacteria to rapidly adapt to environmental changes

40
Q

describe what promoter is.

A

transcription occurs under single promoter where RNA polymerase binds to for transcription

41
Q

describe what a operator is and how it works.

A

operator lies close to promoter, allowing repressor to bind to it
operator regulates the expression of gene when a repressor is bound to it, by blocking transcription of structural genes by RNA polymerase

42
Q

describe what the termination sequence is and how it works.

A

DNA sequence that signals the end of transcription
transcribed region on mRNA complementary to termination sequence on DNA template forms a hairpin loop, causing RNA polymerase to detach from DNA and release RNA transcript

43
Q

state what regulatory genes are and how they work.

A

regulatory genes code for specific protein products (transcriptional regulatory proteins) that regulate the expression of structural genes
regulatory genes have their own promoters and expressed constituitively

44
Q

describe the 2 types of transcriptional regulatory proteins and how they work.

A

transcriptional regulatory proteins bind to specific DNA-binding sites upstream of operon to regulate transcription initiation

  1. repressor proteins
    - negative regulatory proteins that inhibit transcription when bound to operator
    - some repressor required co-repressor
    - other repressor can inactivated when bound to inducer
  2. activator proteins
    - positive regulatory proteins stimulate transcription when bound to specific DNA elements
45
Q

state the 2 types of operons.

A
  1. repressible
  2. inducible
46
Q

describe expression for repressible operons.

A

repressible operon code for repressible enzymes that are part of anabolic pathways
repressible enzymes can be switched off by co-repressors, which are usually products in the pathway being regulated (end product inhibition)
expression of repressible operons normally switched on and needs to be repressed

47
Q

explain the action of repressor protein with repressible operons.

A

repressor protein encoded by regulatory genes are usually inactive
upon binding to co-repressor, repressor became activated and bind to operator
this blocks RNA polymerase from binding to promoter and prevent transcription initiation of structural genes

48
Q

describe expression of inducible operon.

A

inducible operon usually code for inducible enzymes part of catabolic pathways
synthesis of inducible enzymes only stimulated in presence of inducers which is substrate in pathway that is regulated
expression of inducible operons normally switched off and need to be induced

49
Q

explain action of repressor protein with inducible operon.

A

repressor protein encoded by regulatory gene normally active
upon binding to inducer, repressor inactivated and does not bind to operator
RNA polymerase can then access and bind to promoter, initiating transcription of structural genes.

50
Q

explain advantage of regulatory systems of inducible and repressible operon.

A

inducible operon: let cell save energy cost of making enzymes when no substrate available on which they can act
repressible operon: let cell conserve resources

51
Q

explain advantage of regulatory systems of inducible and repressible operon.

A

inducible operon: let cell save energy cost of making enzymes when no substrate available on which they can act
repressible operon: let cell conserve resources

52
Q

explain advantage of regulatory systems of inducible and repressible operon.

A

inducible operon: let cell save energy cost of making enzymes when no substrate available on which they can act
repressible operon: let cell conserve resources by not making proteins coded by structural genes when too much of products already present

53
Q

state example of repressible operon and its function.

A

trp operon
encode for proteins and enzymes involved in regulation of biosynthesis of amino acid, tryptophan, when growth medium lacks it, which is needed for polypeptide synthesis (anabolic pathway)

54
Q

state the 4 parts of trp operon.

A
  1. promoter
  2. operator
  3. 5 structural genes - trpE, trpD, trpC, trpB, trpA
  4. termination sequence
55
Q

state the regulatory gene of the trp operon.

A

trpR gene
encode for inactive trp repressor protein (thus expression of trp operon usually switched on)

56
Q

describe what happens to the trp operon in the absence of tryptophan.

A

when the tryptophan concentration in the cell is low, more tryptophan needs to be synthesised.
the trpR regulatory gene is constituitively expressed and thus the trp repressor is continuously synthesised.
trp repressor is inactive and does not bind to the operator.
RNA polymerase recognises and binds to the promoter of the trp operon.
this initiates the transcription of the 5 structural genes.
the transcription of the trp operon is switched on.
repressible enzymes are synthesised for tryptophan synthesis.

57
Q

describe what happens to the trp operon in the presence of tryptophan.

A

when the tryptophan is present at high concentration, the biosynthesis of tryptophan is not needed.
thus the cell needs to stop synthesising proteins involved in tryptophan biosynthesis to conserve resources.
the trpR regulatory gene is constituitively expressed and thus the trp repressor is continuously synthesised.
the trp repressor is inactive.
tryptophan, the co-repressor, binds to the allosteric sites of the trp repressor, altering its 3D conformation at the DNA-binding site.
this activates the trp repressor, which then binds to the operator.
this reduces the accessibility of the promoter to RNA polymerase, and does not allow the RNA polymerase to bind to the promoter.
thus there is no transcription initiation of structural genes, and transcription is switched off.
repressible enzymes are thus not synthesised.

58
Q

state example of inducible operon and its function.

A

lac operon encode for proteins and enzymes required for transport and digestion of disaccharide lactose for use as a carbon source for bacteria

59
Q

state 5 parts for the lac operon.

A
  1. CAP-binding site (catabolic activator protein)
  2. promoter
  3. operator
  4. structural genes (lacZ, lacY, lacA)
  5. termination sequence
60
Q

state the regulatory gene of the lac operon.

A

lacI gene encodes for active lac repressor protein

61
Q

state the protein products and its functions of the 3 lac structural genes.

A
  1. lacZ - encode for enzyme beta-galactosidase
    - catalyse hydrolysis of lactose into galactose and glucose
    - convert lactose into allolactose
  2. lacY - encode for channel protein
    - allow lactose entry into bacteria
  3. lacA - encode for enzyme lactose transacetylase
    - adds acetyl groups to lactose
62
Q

describe the CAP binding site and its function.

A

catabolite activator protein (CAP) binds to CAP-binding site, located directly upstream of promoter
this stimulates a higher rate of transcription of structural genes through more efficient positioning of RNA polymerase at promoter

63
Q

describe what happens to the lac operon in absence of lactose.

A

lac enzymes are not synthesis because no lactose is present, helping to conserve resources.
lacI gene is constituitively expressed and thus the lac repressor is continuously expressed in its active form.
lac repressor recognises and binds to the operator
this causes RNA polymerase to be unable to access and bind to the promoter
thus no transcription initiation of structural genes
thus transcription is switched off
beta-galactosidase, lactose permease, lactose transacetylase is not synthesised

64
Q

describe what happens to the lac operon in presence of lactose.

A

presence of lactose provides alternative source of carbon and lac enzymes need to be synthesised quickly to take in lactose to cell and break it down to glucose and galactose for respiration.
lacI regulatory gene is constitutively expressed and thus the lac repressor will be synthesised continuously in its active form.

because there is always low levels of permease and beta-galactosidase synthesis.
- some lactose from the surrounding can enter the cell by lactose permease
- beta-galactosidase isomerises lactose to allolactose

allolactose functions as inducer to bind to allosteric site of repressor, altering the 3D conformation of DNA-binding site of repressor, causing the lac repressor to be inactive
the inactive lac repressor is unable to bind to the operator and thus the RNA polymerase can access and bind to the promoter, initiating the transcription of structural genes.
the transcription of lac operon is switched on and thus beta-galactosidase, lactose permease, and lactose transacetylase is synthesised and used in metabolism of lactose sugars

65
Q

describe and explain how the lac operon is influenced by both positive and negative control.

A

operon negatively controlled by repressor when repressor represses expression of operon
- when lac repressor bind to operator, resulting in lac operon switched off and no expression of lac structural genes

operon positively controlled by catabolite activator protein when CAP increases expression of specific operon
- when CAP binds to CAP-binding site, CAP facilitate more efficient positioning of RNA polymerase to promoter, resulting in high expression of lac structural genes.

66
Q

describe the metabolic preference of sugars in E. coli bacterium and how that affects the regulation of lac operon.

A

glucose: preferred energy source because easiest sugar to metabolise but not all of host food contain abundant supply of glucose
if glucose present in environment, glucose will be used first

lactose: if present as only energy source, need to be hydrolysed to galactose and glucose
glucose can be used immediately while galactose has to be converted to glucose for use in respiration

and thus lac operon is regulated by the availability of lactose and glucose in the environment, such that the cell conserves resources by making enzymes only when needed

67
Q

describe what happens to the lac operon when there is presence of lactose, absence of glucose.

A

lactose is the only carbon source and thus the bacteria must utilise the lactose quickly by inducing high rate of transcription of lac operon
beta-galactosidase isomerises lactose to allolactose, which then binds to allosteric site of lac repressor and alters 3D conformation of DNA binding-site of repressor, inactivating the lac repressor, causing it unable to bind to the operator
adenylate cyclase is active when glucose concentration is low, resulting in increase conversation of ATP to cAMP, increasing intracellular concentration of cAMP
cAMP binds to allosteric site of CAP, altering its conformation at the DNA-binding site, activating the CAP.
the active CAP then binds to the CAP-binding site, this binding facilitates more efficient positioning of RNA polymerase at the promoter.
the RNA polymerase binds to the promoter and initiates transcription of structural genes
transcription of operon is then switched on with high rates of transcription by RNA polymerase
beta-galactosidase, lactose permease and lactose transacetylase is then synthesised at high levels

68
Q

describe what happens to the lac operon in the presence of lactose and presence of glucose.

A

in the presence of glucose, bacteria utilises glucose preferentially. lac operon transcription is not needed, until the glucose is used up.
beta-galactosidase isomerises lactose to allolactose, which binds to allosteric site of lac repressor, altering the 3D conformation of DNA binding site of repressor, causing the lac repressor to be inactivated
the inactive lac repressor is unable to bind to operator
when glucose concentration is high, there is decrease in concentration of ATP to cAMP, leading to decrease in intracellular concentration of cAMP
CAP is not bound to cAMP, and thus CAP is inactive and does not bind to CAP-binding site
RNA polymerase binds to promoter inefficiently and initiate transcription of structural genes
thus the transcription of operon is switched on but at low rates by RNA polymerase
beta-galactosidase, lactose permease and lactose transacetylase is synthesised at low levels

h2 biology (3 decks)

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