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Microorganisms > Exam 2 - Part 2 > Flashcards

Exam 2 - Part 2 Flashcards

1
Q

RNA synthesis is under the direction of DNA

A
  • RNA produced has complementary sequence to the template DNA
    three types of RNA are produced
  • mRNA carries the message for protein synthesis
  • tRNA carries amino acids during protein synthesis
  • rRNA molecules are components of ribosomes
  • a single RNA polymerase catalyzes
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2
Q

components of bacteria RNA polymerases

A
  1. core enzyme = catalyzes RNA synthesis
  2. sigma factor = no catalytic activity, helps the core enzyme recognize the start of genes
  3. holoenzyme = 1 + 2
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3
Q

transcription

A
  • initiation, elongation, and termination

- only a short segment of DNA is transcribed

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4
Q

promoter

A

site where RNA polymerase binds to initiate transcription (is not transcribed)

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5
Q

transcription termination

A

occurs when core RNA polymerase dissociates from template DNA
- two types: intrinsic and rho-dependent

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6
Q

transcription in bacteria

A
  • Polycistronic mRNA often found in bacteria and archaea
  • Contains directions for >1 polypeptide catalyzed by a single RNA polymerase–reaction similar to that catalyzed by DNA polymerase
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7
Q

transcription eukaryotes

A
  • differs from bacterial transcription in a few ways
    eukaryotes have 3 major RNA polymerases
  • promoters differ from those in bacteria by having combinations of many elements
  • RNA polymerase II is a large aggregate, containing 10 or more subunits
  • catalyzes production of heterogeneous nuclear RNA (hnRNA) which undergoes posttranscriptional modification to generate mRNA
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8
Q

eukaryotic genes

A

initially made up of exons (expressed sequence) and introns (intervening sequence)

  • spliceosome splits out introns
  • alternative splicing gives variety
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9
Q

what is considered genes?

A
  • DNA sequences that code for tRNA and rRNA are considered genes
  • genes coding for tRNA may code for more than a single tRNA molecule or type of tRNA
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10
Q

ribozymes

A

spacers between the coding regions are removed after transcription, some by the use of special ribonucleases

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11
Q

the genetic code

A 
Universal
Remained unchanged
First two letters of each codon
Initiation codon
Termination codons (non-sense)
Code degeneracy
Wobble hypothesis
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12
Q

prokaryotic ribosome

A

70S ribosome, split into 30S and 50S subunits

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13
Q

eukaryotic ribsosome

A

80S ribosome, split into 40S and 60S

- in mitochondria or chloroplasts

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14
Q

translation

A
  • synthesis of polypeptide directed by sequence of nucleotides in mRNA
  • It is coupled with transcription
  • Ribosome: site of translation–polyribosome (polysome)
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15
Q

polyribosome

A

complex of mRNA with several ribosomes

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16
Q

amino acid activation

A

-tRNA has to be charged with an amino acid before it goes to the ribosome
aminoacyl-tRNA synthetase proofreads and adds on the correct amino acid

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17
Q

elongation

A
  • sequential addition of amino acids to a growing polypeptide
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18
Q

peptidyl (donor-P) site

A

binds initiator tRNA or tRNA attached to growing polypeptide (peptidyl-tRNA)

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19
Q

aminoacyl (acceptor-A) site

A

binds incoming aminoacyl-tRNA

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20
Q

exit (E) site

A

briefly binds empty tRNA before it leaves ribosome

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21
Q

what are the three stop codons?

A

UAA, UAG, UGA

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22
Q

what are the purposes of release factors?

A
  • aid in recognition of stop codons
  • 3 RFs function in prokaryotes
  • only 1 RF active in eukaryotes
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23
Q

molecular chaperones

A
  • proteins that aid the folding of nascent polypeptides
  • protect cells from thermal damage - e.g., heat-shock proteins
  • aid in transport of proteins across membranes
  • examples: DNAj and DNA k
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24
Q

overview of gram positive and gram negative protein secretion

A
  • gram-positive and gram-negative bacteria have different problems secreting proteins based on the differences between the structure of their walls
  • Both G+ and G- use the Sec-dependent pathway for transporting proteins across the membrane
  • Other secretion pathways also exist, but all systems require energy
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25
Q

SEC dependent pathway

A
  • general pathway
  • translocate proteins from cytoplasm across or into plasma membrane
  • Attached to pre-protein is signal peptide which: delays the folding, chaperone proteins keep preproteins unfolded, and removed once pre-protein emerges from plasma membrane
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26
Q

protein secretion in gram negative

A
  • Type I, II, II, IV, and V–- Transport across the OM

–Transport across Periplasmic space

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27
Q

Type 1 (ABC) protein secretion pathway

A
  • ubiquitous in prokaryotes

- transports proteins from cytoplasm across both plasma membrane and outer membrane

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28
Q

Type 3 protein secretion pathway

A

secretes virulence factors of Gram-negative bacteria from cytoplasm, across both plasma membrane and outer membrane, and into host cell

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29
Q

Type 4 protein secretion pathway

A

are unique because they secrete proteins and transfer DNA during conjugation

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30
Q

where does the regulation of gene expression occur?

A
  • transcription initiation
    –transcription elongation
    –translation
    –posttranslation
31
Q

operons

A

the sequence of bases coding for one or more polypeptides along with the promoter and operator or activator binding sites

  • unique to bacteria
  • normally controls sugar metabolism
32
Q

lac operon is an example of what type of control and types of genes?

A

negative transcriptional control of inducible genes

33
Q

the lac operon

A

contains genes needed to catabolize lactose

  • negative control with the lac repressor to the operator
  • positive control with the CAP
34
Q

global regulatory systems

A
  • regulatory systems that affect many genes and pathways simultaneously
  • important for bacteria since they must respond rapidly to a wide variety of changing environmental conditions
  • controls multiple operons that can be related or unrelated
35
Q

regulon

A

genes or operons controlled by a common regulatory protein

36
Q

modulon

A

operon network under control of a common global regulatory protein but individual operons are controlled separately by their own regulators

37
Q

what are some examples of global regulatory systems?

A
  • regulatory proteins
    –alternate sigma factors
    –two component signal transduction (regulatory) systems
    –phosphorelay systems
38
Q

diauxic growth

A

biphasic growth pattern in which there is preferential use of one carbon source over another when both are available in environment
–lag occurs after preferred substrate is exhausted followed by the resumption of growth using the second source
- catabolite repression plays a role in this pattern of growth

39
Q

mutations

A

stable, heritable changes in sequence of bases in DNA

  • in prokaryotes usually produce phenotypic changes
  • can occur spontaneously or be induced by chemical mutagens or radiation
  • mistakes are usually made and fixed before it moves onto the next generation
  • is only considered a mutation when it is passed on from a parent cell to a daughter cell
40
Q

point mutation

A

silent mutation – change nucleoside sequence of codon – but not the encoded amino acid

41
Q

missense mutation

A

a single base substitution that changes codon for one amino acid into codon for another amino acid

42
Q

nonsense mutation

A

converts a sense codon to a stop codon

43
Q

frameshift mutation

A

results from insertion or deletion of one or two bases pairs in the coding region of the gene

44
Q

induced mutations

A

caused by agents that directly damage DNA

45
Q

base analogs

A
  • structurally similar to normal bases

- mistakes occur when they are incorporated into growing polynucleotide chain

46
Q

DNA modifying agents

A

alter a base causing it to mispair

47
Q

intercalating agents

A

distort DNA to induce single nucleotide insertions and deletions

48
Q

Ames test

A
  • based on observation that most carcinogens are also mutagens
  • tests for mutagenicity are used as screen for carcinogenic potential
  • Reversion rate in presence of suspected carcinogen reversion rate in absence of suspected carcinogen
49
Q

proofreading

A
  • correction of errors in base pairing made during replication
    –errors corrected by DNA polymerases
50
Q

direct repair

A
  • used to directly repair thymine dimers
    –thymines separated by photochemical reaction using visible light catalyzed by photolyase
  • called photoreactivation
  • can break the bond with a photo reaction from light, can be repaired with enzymes
51
Q

mismatch repair

A

-type of excision repair
–mismatch correction enzyme scans newly synthesized DNA for mismatched pairs
–mismatched pairs removed and replaced by DNA polymerase and DNA ligase

52
Q

DNA methylation

A
  • to distinguish old DNA strands from new DNA strands
    –old DNA (template strand) methylated; new DNA not methylated
    –the repair system cuts out the mismatch from the unmethylated strand
  • catalyzed by DNA methyltransferases
53
Q

SOS response

A
  • inducible repair system
  • a global control network
  • used to repair excessive damage that halts replication, leaving many gaps
    –RecA protein initiates recombination repair
    –RecA protein also acts as protease, destroying a repressor protein and thereby increasing production of excision repair enzymes
  • a highly error-prone repair used in a life-or-death situation
  • used a response to the environment
54
Q

Horizontal gene transfer

A
  • occurs via three mechanisms (conjugation, transformation, and transduction) evolved by bacteria to create recombinants
  • all three mechanisms depend on some type of recombination
  • genes can be transferred to the same or different species
55
Q

bacterial conjugation

A
  • the transfer of genes between bacteria that depends on: direct cell to cell contact mediated by the F pilus, a type IV secretion system, and rolling circle replication of plasmid
  • direct contact of 2 bacteria via a pili
56
Q

vertical gene transfer

A

transfer of genes from a parent cell to a daughter cell

57
Q

mutations can be induced by physical mediums

A
  • x-ray and gamma = penetrating, very harmful, will break up DNA into pieces
    UV = not penetrating, effects the surface, can cause a thymine dimer
58
Q

DNA binding domain: helix turn helix

A
  • alpha helix with a turn and another alpha helix
  • can hold the DNA
  • structure dictates function
  • CAP is a type of helix turn helix
59
Q

what is the role of CAP proteins in catabolic repression?

A
  • used in dioxic growth
  • CAP is activated by cAMP, which acts as a hunger signal
  • when there is low glucose, there is more cAMP
  • cAMP is used to activate CAP, and to make it bind to the CAP binding site
60
Q

sigma 24

A

make more flagella for movement away from chemotaxis

61
Q

sigma 60

A

metabolize nitrogen

62
Q

sigma 70

A

exponential growth

63
Q

sigma 32

A

heat shock proteins

64
Q

what are some DNA binding domains?

A
  • leucine zipper

- zinc finger

65
Q

CAP binding

A
  • effect RNA polymerase binding
66
Q

what is the purpose of sigma factors?

A
  • prelude the RNA polymerase complex to find the promoter region
  • each sigma factor controls a group of genes
67
Q

small RNA

A
  • 50-100 base pairs
  • regulatory mechanisms
  • makes RNA from the complementary strand
68
Q

antisense RNA

A
  • if a copy of DNA is made from the coding strand instead of the complementary strand
  • opposite of the complementary strand, and it can find to mRNA
  • can prevent ribosomes and complexes from binding and synthesizing the mRNA
69
Q

attenuation of trp operon

A
  • slows down from a stem-loop formation
  • if a loop forms in the 1:2 region it pauses or if it forms in the 3:4 region it stops
  • the 2:3 region loop allows it to continue
70
Q

allolactose

A
  • binds to the lac repressor and inhibits it, prevents lac operon from binding
  • acts as a corepressor
71
Q

negative transcription control

A

proteins bind to DNA and inhibit expression

72
Q

regulatory proteins

A
  • regulate transcription
  • inducers and repressors
  • compete in the promoter region and can determine if RNA pol will bind
73
Q

inducible genes

A
  • genes that are normally off but will get turned on when needed
  • lac operon
  • catabolic
74
Q

repressible genes

A
  • genes that are normally on unless turned off deliberately
  • synthetic
  • trp operon

Microorganisms (11 decks)

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