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BM211: Introduction to Microbiology > Block A Lecture 2 - Microbial Genes and Genomes > Flashcards

Block A Lecture 2 - Microbial Genes and Genomes Flashcards

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Biology 101 flashcards
1
Q

What is the biological “information flow” of transcription and translation?

A

Transcription - DNA -> RNA
Translation RNA -> Protein
(Slide 6)

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2
Q

What does the biological “information flow” begin with?

A

DNA replication
(Slide 6)

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3
Q

What is the proteome?

A

The collection of all proteins present in the cells
(Slide 7)

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4
Q

What is the nucleoid?

A

The DNA containing instruction for making the proteome and RNA machinery
(Slide 7)

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5
Q

What was the result of the experiment performed by Lartigue and colleagues in 2007, where they transplanted complete genomic DNA from mycoplasma mycoides into cells of Mycoplasma capricolum?

A

The resulting organism containing only the donor genome (M. Mycoides) and by all phenotypic tests was M. Mycoides, proving the genome contains the information which defines an organism
(Slide 10)

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6
Q

What is the half-life of mRNA?

A

Minutes
(Slide 12)

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7
Q

What is contained in a prokaryotic gene?

A

START codon followed by the coding region followed by a STOP codon
(Slide 14)

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8
Q

What are the 2 possibilities that a eukaryotic gene can contain?

A

Either Exon (coding region) OR
Exon followed by an intron (non-coding region) followed by an exon x n
(Slide 14)

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9
Q

Genes can be compared by aligning and examining their sequences. What are the functions of the nucleotide and amino acid levels of comparison?

A

Nucleotide level comparison is used to compare evolutionary history whereas amino acid level is used to compare protein function
(Slide 15)

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10
Q

What does the sequence alignment of proteins look like?

A

One row per protein and 1 column per amino acid. With differences between sequences highlighted and insertions/deletions shown with gaps.
Amino acids are coloured by similar chemistry
(Slide 16)

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11
Q

What does the sequence alignment of nucleotides look like?

A

One row per sequence and one column per nucleotide with bases being coloured by identity
(Slide 17)

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12
Q

What are the 3 types of “function” that a gene can have?

A

Molecular Function
Cellular component
Biological process
(Slide 19)

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13
Q

What is the “Molecular” function of a gene?

A

The proximate biochemical activity that it performs e.g an enzyme degrading a substrate
(Slide 19)

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14
Q

What is the “Cellular Component” function of a gene?

A

The location - relative to cellular structures - that the molecular function is performed
(Slide 19)

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15
Q

What is the “Biological Process” function of a gene?

A

The process, at a cellular or organism level to which it contributes to
(Slide 19)

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16
Q

What is the gene ontology knowledgebase?

A

A widely-used resource maintained by the GO Consortium, which is a computer database which contains traceable evidence based statements of functions for specific gene products.
(Slide 20)

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17
Q

What is an ontology?

A

A logical structure defining relationships between functions
(Slide 20)

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18
Q

In transcription in bacteria, what are the starts of genes (called promoter regions) recognised by?

A

Sigma factors
(Slide 23)

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19
Q

In transcription in bacteria, what 2 things come together to form a holoenzyme?

A

RNA polymerase and sigma factors
(Slide 23)

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20
Q

What are sigma factors denoted by?

A

Their molecular wait in kDa
E.g σ 70 = 70kDa
(Slide 24)

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21
Q

Are sigma factors unique to a promoter sequence?

A

Yes, different distinct sigma factors recognise different promoter regions
(Slide 24)

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22
Q

What does the number of sigma factors a bacteria contains vary by?

A

Taxa (A scientifically classed group or entity)
(Slide 24)

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23
Q

What 4 subunits (not including the sigma factor) does the RNA polymerase holoenzyme contain?

A

α, ß, ß’ and ω (omega) subunits
(Slide 26)

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24
Q

How does RNA polymerase enable RNA nucleotides to assemble along the template DNA strand?

A

RNA polymerase opens up and unwinds DNA, which creates a transcription bubble where RNA nucleotides can assemble along the template DNA strand
(Slide 27)

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25
Q

What happens in bacterial transcription after the RNA polymerase sigma factor holoenzyme recognises the promotor region and binds to the DNA?

A

The sigma factor is released and RNA polymerase moves along the template strand, generating the primary transcript
(Slide 28)

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26
Q

What happens in bacterial transcription after RNA polymerase reaches the termination site?

A

The mRNA transcript and RNA polymerase are released
(Slide 28)

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27
Q

What is the termination signal to stop transcription?

A

An inverted repeat in the stand followed by a poly-T/U
(Slide 29)

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28
Q

What is an “inverted repeat”?

A

A single stranded sequence of nucleotides followed downstream by its reverse complement
(Slide 29)

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29
Q

How is a “Stem-Loop” structure formed in transcribed RNA?

A

By inverted repeats interacting
(Slide 29)

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30
Q

How does a “stem-loop” structured transcribed RNA cause mRNA and RNA polymerase dissociation?

A

The step-loop structure makes RNA polymerase pause, then the run of week A-U bonds are not strong enough to maintain attachment resulting in dissociation
(Slide 29)

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31
Q

Other than using “stem-loop” structured transcribed RNA, what is another way that RNA polymerase can be dissociated from the mRNA transcript in bacterial transcription?

A

A rho protein binding to the RNA chain and moving down the chain towards the RNA polymerase-DNA complex, RNA polymerase then stalls at a transcription stop point. When the rho protein catches up with RNA polymerase, dissociation occurs
(Slide 30)

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32
Q

Where does the Rho protein bind to the extending RNA chain in bacterial transcription?

A

At a cytosine rich rho utilization site
(Slide 30)

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33
Q

How many RNA polymerases do Archaea and Eukaryotes have?

A

Archaea have only a single RNA polymerase whereas eukaryotes have 3
(Slide 30)

34
Q

What 2 things are sufficient for transcription to start in archaea?

A

The “TATA box” promoter region being recognised by the TATA binding protein (Tbp) and the B recognition element (BRE) being recognised by archaeal transcription factor B (Tfb)
(Side 32)

35
Q

What are 2 ways in which gene products can be regulated?

A

Modification of the gene product directly
Make the product more / less potent
(Slide 35)

36
Q

What are 4 ways in which a gene product can be modified directly to regulate it?

A

Degradation
Covalent modification
Modification by protein interaction
Feedback inhibition
(Slide 35)

37
Q

What are 2 ways a gene product can be made more or less potent to regulate it?

A

Inhibit /enhance translation
Inhibit / enhance transcription
(Slide 35)

38
Q

What are genes organised into in prokaryotes?

A

Operons
(Slide 36)

39
Q

What are operons?

A

Multiple genes between a promotor and a terminator
(Slide 36)

40
Q

Why are operons useful?

A

As it allows co-ordinated expression of multiple related genes in prokaryotes
(Slide 36)

41
Q

Operons are transcribed together, what does this mean?

A

That they are translated into protein at roughly the same time and frequently encode gene products that act together
(Slide 36)

42
Q

Are DNA-binding proteins usually homodimeric or heterodimeric?

A

Homodimeric
(Slide 37)

43
Q

What does homodimeric mean?

A

That the protein dimer is comprised of 2 identical proteins rather than 2 different proteins
(Slide 37)

44
Q

What 2 domains does each protein in the DNA-binding protein dimer have?

A

A binding domain and a recognition domain
(Slide 37)

45
Q

What is the function of the binding domain of a DNA-binding protein?

A

So that they interact with each other (though sometimes this can be triggered by a cofactor)
(Slide 37)

46
Q

What is the function of the recognition domain of DNA-binding proteins?

A

So both proteins in the DNA-binding protein dimer can recognise the same DNA sequence in the major groove (but in opposite directions)
(Slide 37)

47
Q

What are the 2 main effects that DNA-binding proteins have on transcription?

A

Binding may block / repress transcription (negative regulation)
Binding may enhance or activate transcription (positive regulation)
(Slide 39)

48
Q

What is the arg operon?

A

The genes contained in E.coli which enable it to make it’s own arginine
(Slide 40)

49
Q

How can we make E.coli express the arg operon?

A

By growing it in a medium containing no arginine
(Slide 40)

50
Q

What 3 enzymes do genes contained in the arg operon encode?

A

ArgB ArgC and ArgH
(Slide 40)

51
Q

What is an operator and where are they usually located?

A

A region of DNA that acts as a regulatory element in controlling the transcription of adjacent genes. It is typically located adjacent to the promoter region of a gene
(Slide 40)

52
Q

How can arginine synthesis in E.coli be inhibited via feedback inhibition?

A

Arginine binds to a DNA-binding protein (ArgR) that binds the arg operator blocking transcription and repressing the arg operon
(Slide 41)

53
Q

What is the lac operon?

A

Genes in E.coli which encode for 3 gene products which process lactose
(Slide 43)

54
Q

What control is the lac operon an example of and what does it require?

A

It is an example of a negative control in which an inducer is required for transcription to occur
(Slide 43)

55
Q

What 2 scientists won the Nobel prize for discovering the lac operon?

A

Jacob and Monod
(Slide 43)

56
Q

What 3 enzymes which help process lactose are encoded for by the lac operon?

A

LacA, LacY and LacZ
(Slide 43)

57
Q

What are the functions of LacA, LacZ and LacY?

A

LacZ (ß-galactosidase) breaks down lactose
LacY (ß-galactoside permease) transports lactose across the membrane
LacA (ß-galactoside transacetylase) acetylates lactose
(Slide 43)

58
Q

In E.coli, what binds to the lac operator when no lactose is present?

A

Lacl
(Slide 43)

59
Q

In E.coli, how does lactose lead to LacA, LacY and LacZ being produced?

A

It binds to the Lacl protein, inducing conformational changes. This causes Lacl to dissociate from the lac operator, enabling RNA polymerase to be able to bind to the lac promoter and transcribe the operon eventually resulting in LacZ, Y and A being produced once the operon is transcribed and the resulting mRNA transcript translated
(Slide 44)

60
Q

What is the mal operon?

A

Genes in bacteria such as E.coli which encode enzymes to help process maltose
(Slide 46)

61
Q

Does the mal operon have a strong or weak promotor region?

A

Weak
(Slide 46)

62
Q

What does the mal operon contain upstream of the promoter region?

A

An activator binding site
(Slide 46)

63
Q

What happens when an activator protein (MalT) binds to the activator binding site?

A

RNA polymerase binding is strengthened and transcription can occur
(Side 46)

64
Q

What needs to happen before MalT can bind to DNA?

A

A maltose inducer molecule must bind to MalT first
(Slide 46)

65
Q

What are some operons controlled by?

A

A regulatory protein / proteins
(Slide 47)

66
Q

What are multiple operons called by the same regulatory protein(s) called and what does this mean?

A

A regulon, and it means that the operons are expected to be expressed at about the same time
(Slide 47)

67
Q

What is global regulatory control?

A

Simultaneous regulation of multiple operons
(Slide 48)

68
Q

On top of regulatory proteins, what do many operons also respond to?

A

Global controls
(Slide 48)

69
Q

What is “catabolite repression”?

A

It is a global control which affects transcription of multiple catabolic operons
(Slide 48)

70
Q

If E.coli is grown in a culture with glucose and lactose in it, what is used first?

A

The glucose is used up, and lactose is only used up after all the glucose has been exhausted
(Slide 48)

71
Q

What 2 regulatory sites does the lac operon, and many other bacterial operons have?

A

A local/specific operator and an upstream activator-binding site (C)
(Slide 49)

72
Q

How can the upstream activator-binding site (C) be used to enable transcription of an operon?

A

The activator site is bound by CRP (cAMP receiving protein) which enables transcription
(Slide 49)

73
Q

What needs to occur first, before CRP can bind to the upstream activator-binding site?

A

cAMP needs to bind to CRP
(Slide 49)

74
Q

What are the 2 reasons that lactose is not used in the presence of glucose?

A

Glucose represses synthesis of cAMP
Glucose stimulates transport of cAMP out of the cell
^ These lower the level of cAMP, shutting down cAMP-dependant transcription which prevents cAMP from binding CRP and therefore preventing the lac operon being activated and lactose being processed
(Slide 50)

75
Q

What enzyme catalyses DNA supercoiling?

A

DNA gyrase
(Slide 54)

76
Q

What enzyme unwinds the DNA double helix?

A

DNA helicase

77
Q

What is the pentose-phosphate pathway?

A

A metabolic pathway which occurs in the cytoplasm of cells and is used to generate NADPH and pentoses (5-carbon sugars)

78
Q

What does the pentose-phosphate pathway play important roles in?

A

Cellular processes such as biosynthesis, antioxidant defence and and production of ribose-5-phosphate

79
Q

What are 5 membered sugars used in?

A

The biosynthesis of DNA and RNA

80
Q

What is the difference between plasmids and chromosomes?

A

Plasmids contain genes which are not essential for cellular growth and replication

BM211: Introduction to Microbiology (21 decks)

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